RiceWiki - User contributions [en]

MADS

2014-06-07T11:11:13Z

Kathy: /* The Flower Induction and Flower Organ Formation Subnetworks */

==Brief Introduction==
===Background===
MADS-box family member are known to be involved in many important processes during plant growth and development<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The word MADS finds its origin from the first letters of its founding members, Mini Chromosome Maintenance 1 (MCM1) of yeast (Saccharomyces cerevisiae), Agamous (AG) of Arabidopsis (Arabidopsis thaliana), Deficiens (DEF) of snapdragon (Antirrhinum majus) and Serum Response Factor (SRF) of humans (Homo sapiens)<ref name="ref1" />.

They are characterized by the presence of a conserved domain of approximately 60 amino acids located in the N-terminal region; this domain is named the MADS-box domain and is involved in DNA binding and dimerization<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The MADS-box family has been divided into two main groups. The type I consists of ARG80/SRF-like genes of animals and fungi, also designated as M-type genes in plants, and type II contains MEF2-like genes of animals and yeast as well as MIKC-type genes of plants<ref name="ref1" /><ref name="ref3" />.The plant-specific MIKC-type MADS-box proteins include three additional domains followed by the MADS domain, viz. a less-conserved Intervening region of ~30 amino acids, a moderately conserved Keratin-like domain of ~70 amino acids mainly involved in heterodimerization, and a highly variable C-terminal region of variable length implicated in transcriptional activation and higher-order complex formation<ref name="ref4" /><ref name="ref5" /<ref name="ref6" />.
[[File:mads_box1.jpg|center|thumb|1000px|'''Figure 1.''' ''Protein Structure of '''BGIOSGA004940''' '']]
[[File:Gene_tree_1.jpg]]'''Figure 2.Gene tree'''

===Evolutionary relationships between rice and Arabidopsis MADS-box family genes===
A separate phylogenetic tree was also generated from complete protein sequences of all the MADS-box genes in rice and Arabidopsis (Figure 3). Of the 75 rice MADS-box genes, 38 grouped with MIKCc, six with MIKC*, nine with Mβ, 13 with Mα and 10 grouped with Mγ-type Arabidopsis genes<ref name="ref7" />.

[[File:Gene_tree_2.jpg]]'''Figure 3.Phylogenetic analysis of rice and Arabidopsis MADS-box proteins'''

===MADS-box transcription factors ===
The best studied plant MADS-box transcription factors are those involved in floral organ identity determination. Combinations of A-, B-, and C-function genes determine the development of the four whorls of an Arabidopsis flower: A-function genes determine sepal development; A- and B-function genes determine petal development; B- and C function genes determine the stamen development, and C-function genes are necessary for carpel development<ref name="ref2" /><ref name="ref3" />.

== Organization and structure of MADS-box genes==
===Location of genes===
The individual genes were localized on chromosomes based on the 5' and 3' coordinates for respective gene models in TIGR database.Out of five types of MADS-box genes, the Mγ genes were confined to chromosome 1, 3 and 4, while Mβ genes were present only on chromosome 1. No chromosomal bias was observed in the distribution of MIKCc,MIKC* and Mα genes.<ref name="ref7" />
[[File:Gene_location.jpg]]
'''Figure 4.''' Chromosomal location of rice MADS-box '''

===Distribution of conserved motifs===
The MEME motif search tool was employed to identify the conserved motifs present in MADS-box proteins (Figure 5). Motifs 1, 6 or 2 specifying the MADS domain were found in all the members of the MADS-box family. All proteins belonging to MIKCc and MIKC* groups had motif 1-type MADS domain..Most Mα proteins also had the motif 1-type MADS domain except OsMADS72 and 77 which contained motif 6. Motif 6 was found to be the most common type of MADS domain in Mβ-type proteins.Distinctively, in case of Mγ proteins a larger MADS domain of 83 amino acids was detected, followed by a coiled coil region and a region of unknown complexity as indicated by Simple Modular Architecture Research Tool (SMART) version 3.4<ref name="ref7" />.
[[File:Conserved_motifs.jpg]]'''Figure 5.Distribution of Conserved motifs in rice MADS-box proteins'''

===Expression profiling of MADS-box genes===
Expression profiles have been generated using avadis™ software version 4.2. X-axis represents the developmental stages. Y-axis represents average log2 expression values.Genes exhibiting these expression patterns have been represented by numbers. Dotted lines have been drawn to demarcate vegetative organs, panicle and seed developmental stages（Figure 6）.
[[File:Expression_patterns.jpg]]'''Figure 6.Expression patterns of MADS-box genes in rice in vegetative as well as panicle and seed development.'''
[[File:Differential_expressions.jpg]]'''Figure 7.'''

Differential expressions shown by seven MADS-box genes in response to various abiotic stress conditions.Left panel shows four genes up regulated and right panel shows down regulated genes more than 2 folds with p value less than 0.05 in response to three abiotic stress conditions. X-axis represents seedling followed by stress samples (CS, cold stress; DS, dehydration stress; SS, salt stress). Y-axis represents average expression values obtained using microarrays. Error bars represent standard error for data obtained in three biological replicates(Figure 7).

==''Japonica'' Group==
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'''[[Os07g0108900]]'''
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'''[[Os05g0203800]]'''
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'''[[Os12g0207000]]'''
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'''[[Os03g0752800]]'''
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'''[[Os03g0122600]]'''
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'''[[Os10g0536100]]'''
||
'''[[Os06g0162800]]'''
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'''[[Os01g0883100]]'''
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'''[[Os01g0886200]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os04g0461300]]'''
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'''[[Os06g0712700]]'''
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'''[[Os02g0731200]]'''
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'''[[Os03g0215400]]'''
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'''[[Os02g0579600]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os12g0206800]]'''
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'''[[Os08g0531900]]'''
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'''[[Os03g0753100]]'''
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'''[[Os05g0203600]]'''
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'''[[Os02g0170300]]'''
|-style="background:white; color:black" align="center"
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'''[[Os02g0761000]]'''
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'''[[Os04g0614100]]'''
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'''[[Os05g0423400]]'''
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'''[[Os08g0431900]]'''
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'''[[Os04g0304400]]'''
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!
'''[[Os06g0223300]]'''
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'''[[Os06g0667200]]'''
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'''[[Os06g0217300]]'''
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'''[[Os03g0186600]]'''
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'''[[Os01g0922800]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os12g0501700]]'''
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'''[[Os08g0112700]]'''
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'''[[Os01g0726400]]'''
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'''[[Os12g0407400]]'''
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'''[[Os11g0658700]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os04g0387400]]'''
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'''[[Os03g0253400]]'''
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||

||

|}
==''Indica'' Group==
{| style="background:#A1A3A6; width:85%;" border="0"
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA002178]]'''
||
'''[[BGIOSGA008820]]'''
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'''[[BGIOSGA004940]]'''
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'''[[BGIOSGA020546]]'''
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'''[[BGIOSGA007336]]'''
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'''[[BGIOSGA011213]]'''
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'''[[BGIOSGA008494]]'''
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'''[[BGIOSGA022872]]'''
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'''[[BGIOSGA036463]]'''
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'''[[BGIOSGA009797]]'''
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'''[[BGIOSGA008983]]'''
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'''[[BGIOSGA018624]]''
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'''[[BGIOSGA029053]]'''
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'''[[BGIOSGA017110]]'''
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'''[[BGIOSGA003731]]'''
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'''[[BGIOSGA016105]]'''
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'''[[BGIOSGA005076]]'''
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'''[[BGIOSGA015021]]'''
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|}

==MADS Box Protein Interactions==
===Comprehensive Analysis of MADS Box Transcription Factor Dimerization===
Remarkably, the MIKC proteins that contain the K-box, a domain specific for type II plant MADS box proteins that is presumed to fold into an amphipathic a-helical structure<ref name="ref8" /><ref name="ref9" /><ref name="ref10" />,interact preferably with other type II proteins and hardly form dimers with the type I MADS box proteins. However, there are some exceptions. In particular, there is a preference for interactions with type I proteins from the Ma subclade. Among the type I proteins, most heterodimers are found between members of different subclades. Interactions among Ma proteins are rare, but they dimerize preferentially with many proteins of the Mb and Mg clades. Similarly, only a few interactions among members of the Mb and Mg clades were observed, and Mb-Mg heterodimers are rare. This suggests that the participation of a Ma protein is a prerequisite for a stable dimer consisting of only type I proteins. Although many interactions were observed, a relatively large number of MADS domain proteins appeared to have no interactions at all. Possibly these proteins interact only with non-MADS box proteins, or alternatively,particular interactions are not formed in a yeast two-hybrid assay. For example, the interaction between the B-type proteins APETALA3 (AP3) and PISTILLATA (PI) was not found in this screen. Previously, these proteins appeared to interact exclusively in a higher-order complex, with either SEPALLATA3 (SEP3) or AP1<ref name="ref11" /> ,suggesting that the additional factors stabilize the AP3-PI dimer. This requirement for stabilizing factors to maintain specific dimers could be more general.Homodimerization is another form of MADS domain transcription factor interaction that is difficult to detect by yeast two-hybrid analysis <ref name="ref12" />,and hence, many homodimers have probably been missed in this screening.

Subsequently, the proteins were clustered based on the obtained interaction patterns, which allows the identification of proteins with similar interactions and groups of proteins that are highly connected (Figure 8). This analysis gives clues about the involvement of proteins in certain developmental programs. It reveals groups of proteins with common known functions, but more informatively, also shows clusters containing uncharacterized proteins, for which a function can now be predicted, based on their presence in a particular interaction cluster.
[[File:ABC_8.jpg]]'''Figure 8.'''

Interactome Map of the Arabidopsis MADS Box Transcription Factor Family.Proteins are organized based on hierarchical clustering of their protein–protein interaction patterns. Proteins that do not interact in the screen are omitted from this figure. Protein–protein interactions are indicated with red blocks and no interactions with green blocks. Presence of clustered proteins with a putative similar function is indicated with a colored bar on the left and bottom side of the figure: red for embryo, green for root, blue for flowering,and yellow for floral organs.
===The Flower Induction and Flower Organ Formation Subnetworks===
The regulation of flowering time is a complex process in which many environmental and internal signals are integrated, finally giving rise to a switch from vegetative to generative development at the appropriate time. MADS box transcription factors have shown to play pivotal roles in the flowering program and occupy many important positions in the hierarchical network <ref name="ref13" /><ref name="ref14" />.Based on the interaction data obtained in this study, we tried to unravel two subnetworks composed of interactions between known MADS box proteins involved in flower induction and flower organ formation (Figure 9). The proteins AP1 and FRUITFULL (FUL) are present in both subnetworks, which would refer to their early and late function in flowering <ref name="ref15" /><ref name="ref16" />.However, the most striking observation is that many of the floral organ identity proteins, such as AGAMOUS (AG), SEP1/2/3, and SHP1/2 proteins, interact not only with positive regulators of flowering, such as SUPPRESSOR OF CONSTANS 1 (SOC1) and AGAMOUS-LIKE 24(AGL24), but also with a negative regulator, SVP, implying that there is both positive and negative crosstalk between the two pathways via protein interactions, as pointed out above.

[[File:ABC_9..jpg]]'''Figure 9.'''

Representation of the Flower Induction and Flower Formation Networks.Proteins are indicated by ovals (red for the flower induction, blue for the flower formation network, green for the hubs), and interactions are represented by lines. The proteins SOC1 and AGL24 form a homodimer,which is indicated with a small dot next to the oval of the protein.

==Stress responsive MADS-box genes in rice==
MADS-box genes have been shown to be affected by low temperature stress in tomato <ref name="ref17" /> and by application of hormones like cytokinins, gibberellins <ref name="ref18" />, ethylene <ref name="ref19" />and auxins <ref name="ref20" /> in other plants. Seven MADS-box genes exhibited differential expression in response to cold, salt and/or desiccation stress in rice. So far, none of these genes has been implicated in stress response. Amongst stress-induced genes, OsMADS18 is a member of AP1/SQUA group that has been shown to express widely during development with its transcripts accumulating at high levels specifically in meristematic tissues <ref name="ref17" />. It has been shown to interact with OsMADS6, 8/24, 7/45, and 47 <ref name="ref21" /><ref name="ref22" />and in our analysis its expression pattern was found to overlap with those of OsMADS6, 8 and 7 in reproductive tissues and with OsMADS47 during vegetative development, suggesting that it might be interacting with different partners during reproductive development and stress. Recently, Tardif and coworkers showed that a large number of genes involved in flower development are associated with abiotic stress responses in wheat <ref name="ref23" />. Our preliminary analysis involving transcript profiling during reproductive development and abiotic stress conditions has also revealed approximately 400 genes that are up regulated during panicle/seed development and three stress conditions, viz. cold, salt, and dehydration (unpublished data). It would be, therefore, interesting to undertake specific investigations, which could establish the interactions of biochemical pathways that are activated during reproductive development and stress response.

==References==
<references>
* <ref name="ref1">
Arora R, Agarwal P, Ray S, et al. MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress[J]. BMC genomics, 2007, 8(1): 242.
</ref>
* <ref name="ref2">
Par̆enicová L, de Folter S, Kieffer M, et al. Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis new openings to the MADS world[J]. The Plant Cell Online, 2003, 15(7): 1538-1551.
</ref>
* <ref name="ref3">
Leseberg C H, Li A, Kang H, et al. Genome-wide analysis of the MADS-box gene family in Populus trichocarpa[J]. Gene, 2006, 378: 84-94.
</ref>
* <ref name="ref4">
Yang Y, Fanning L, Jack T: The K domain mediates heterodimerization of the Arabidopsis floral organ identity proteins,APETALA3 and PISTILLATA[J]. Plant J 2003, 33(1):47-59.
</ref>
* <ref name="ref5">
Egea Cortines M, Saedler H, Sommer H: Ternary complex formation between the MADS-box proteins SQUAMOSA, DEFICIENS and GLOBOSA is involved in the control of floral architecture in Antirrhinum majus[J]. EMBO J 1999, 18(19):5370-5379.
</ref>
* <ref name="ref6">
Cho S, Jang S, Chae S, Chung KM, Moon YH, An G, Jang SK: Analysis of the C-terminal region of Arabidopsis thaliana APETALA1 as a transcription activation domain. Plant Mol Biol 1999,40(3):419-429.
</ref>
* <ref name="ref7">
Rita Arora, Pinky Agarwal, Swatismita Ray.MADS-box gene family in rice: genome-wide identification,organization and expression profiling during reproductive development and stress.BMC Genomics,2007, 8:242.
</ref>
* <ref name="ref8">
Stefan de Folter,Richard G.H. Immink,Martin Kieffer,Lucie Parˇenicova´ ,et al.Comprehensive Interaction Map of the Arabidopsis MADS Box Transcription Factors.The Plant Cell, 2005, 17:1424–1433.
</ref>
* <ref name="ref9">
Alvarez-Buylla, E.R., Pelaz, S., Liljegren, S.J., Gold, S.E., et al. An ancestral MADS-box gene duplication occurred before the divergence of plants and animals. Proc. Natl. Acad. Sci.USA 2000,97:5328–5333.
</ref>
* <ref name="ref10">
Riechmann, J.L., and Meyerowitz, E.M. . MADS domain proteins in plant development. Biol. Chem,1997,378:1079–1101.
</ref>
* <ref name="ref11">
Honma, T., and Goto, K. . Complexes of MADS-box proteins are sufficient to convert leaves into floral organs. Nature ,2001,409:525–529.
</ref>
* <ref name="ref12">
Immink, R.G.H., and Angenent, G.C. . Transcription factors do it together: The hows and whys of studying protein-protein interactions.
Trends Plant Sci,2002, 7:531–534.
</ref>
* <ref name="ref13">
Blazquez,M.A.. Flower development pathways. J. Cell Sci.,2000,113:3547–3548.
</ref>
* <ref name="ref14">
Simpson, G.G., and Dean, C. . Arabidopsis, the Rosetta stone of flowering time? Science ,2002,296:285–289.
</ref>
* <ref name="ref15">
Mandel, M.A., Gustafson-Brown, C., Savidge, B., and Yanofsky,M.F. . Molecular characterization of the Arabidopsis floral homeotic gene APETALA1. Nature ,1992,360:273–277.
</ref>
* <ref name="ref16">
Ferrandiz, C., Gu, Q., Martienssen, R., and Yanofsky, M.F. .Redundant regulation of meristem identity and plant architecture by FRUITFULL, APETALA1 and CAULIFLOWER. Development ,2000,127:725–734.
</ref>
* <ref name="ref17">
Lozano R, Angosto T, Gomez P, Payan C, Capel J, Huijser P, Salinas J,Martinez-Zapater JM: Tomato flower abnormalities induced by low temperatures are associated with changes of expression of MADS-Box genes. Plant Physiol 1998, 117(1):91-100.
</ref>
* <ref name="ref18">
Bonhomme F, Kurz B, Melzer S, Bernier G, Jacqmard A: Cytokinin and gibberellin activate SaMADS A, a gene apparently involved in regulation of the floral transition in Sinapis alba.Plant J 2000, 24(1):103-111.
</ref>
* <ref name="ref19">
Ando S, Sato Y, Kamachi S, Sakai S: Isolation of a MADS-box gene
(ERAF17) and correlation of its expression with the induction of formation of female flowers by ethylene in cucumber plants (Cucumis sativus L.). Planta 2001, 213(6):943-952.
</ref>
* <ref name="ref20">
Zhu C, Perry SE: Control of expression and autoregulation of AGL15, a member of the MADS-box family. Plant J 2005,41(4):583-594.
</ref>
* <ref name="ref21">
Fornara F, Parenicova L, Falasca G, Pelucchi N, Masiero S, Ciannamea S, Lopez-Dee Z, Altamura MM, Colombo L, Kater MM: Functional characterization of OsMADS18, a member of the AP1/SQUA subfamily of MADS box genes. Plant Physiol 2004,135(4):2207-2219.
</ref>
* <ref name="ref22">
Moon YH, Jung JY, Kang HG, An G: Identification of a rice APETALA3 homologue by yeast two-hybrid screening. Plant Mol Biol 1999, 40(1):167-177.
</ref>
* <ref name="ref23">
Tardif G, Kane NA, Adam H, Labrie L, Major G, Gulick P, Sarhan F,
Laliberte JF: Interaction network of proteins associated with abiotic stress response and development in wheat. Plant Mol Biol 2007, 63(5):703-718.
</ref>

</references>

MADS

2014-06-07T11:10:52Z

Kathy: /* The Flower Induction and Flower Organ Formation Subnetworks */

==Brief Introduction==
===Background===
MADS-box family member are known to be involved in many important processes during plant growth and development<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The word MADS finds its origin from the first letters of its founding members, Mini Chromosome Maintenance 1 (MCM1) of yeast (Saccharomyces cerevisiae), Agamous (AG) of Arabidopsis (Arabidopsis thaliana), Deficiens (DEF) of snapdragon (Antirrhinum majus) and Serum Response Factor (SRF) of humans (Homo sapiens)<ref name="ref1" />.

They are characterized by the presence of a conserved domain of approximately 60 amino acids located in the N-terminal region; this domain is named the MADS-box domain and is involved in DNA binding and dimerization<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The MADS-box family has been divided into two main groups. The type I consists of ARG80/SRF-like genes of animals and fungi, also designated as M-type genes in plants, and type II contains MEF2-like genes of animals and yeast as well as MIKC-type genes of plants<ref name="ref1" /><ref name="ref3" />.The plant-specific MIKC-type MADS-box proteins include three additional domains followed by the MADS domain, viz. a less-conserved Intervening region of ~30 amino acids, a moderately conserved Keratin-like domain of ~70 amino acids mainly involved in heterodimerization, and a highly variable C-terminal region of variable length implicated in transcriptional activation and higher-order complex formation<ref name="ref4" /><ref name="ref5" /<ref name="ref6" />.
[[File:mads_box1.jpg|center|thumb|1000px|'''Figure 1.''' ''Protein Structure of '''BGIOSGA004940''' '']]
[[File:Gene_tree_1.jpg]]'''Figure 2.Gene tree'''

===Evolutionary relationships between rice and Arabidopsis MADS-box family genes===
A separate phylogenetic tree was also generated from complete protein sequences of all the MADS-box genes in rice and Arabidopsis (Figure 3). Of the 75 rice MADS-box genes, 38 grouped with MIKCc, six with MIKC*, nine with Mβ, 13 with Mα and 10 grouped with Mγ-type Arabidopsis genes<ref name="ref7" />.

[[File:Gene_tree_2.jpg]]'''Figure 3.Phylogenetic analysis of rice and Arabidopsis MADS-box proteins'''

===MADS-box transcription factors ===
The best studied plant MADS-box transcription factors are those involved in floral organ identity determination. Combinations of A-, B-, and C-function genes determine the development of the four whorls of an Arabidopsis flower: A-function genes determine sepal development; A- and B-function genes determine petal development; B- and C function genes determine the stamen development, and C-function genes are necessary for carpel development<ref name="ref2" /><ref name="ref3" />.

== Organization and structure of MADS-box genes==
===Location of genes===
The individual genes were localized on chromosomes based on the 5' and 3' coordinates for respective gene models in TIGR database.Out of five types of MADS-box genes, the Mγ genes were confined to chromosome 1, 3 and 4, while Mβ genes were present only on chromosome 1. No chromosomal bias was observed in the distribution of MIKCc,MIKC* and Mα genes.<ref name="ref7" />
[[File:Gene_location.jpg]]
'''Figure 4.''' Chromosomal location of rice MADS-box '''

===Distribution of conserved motifs===
The MEME motif search tool was employed to identify the conserved motifs present in MADS-box proteins (Figure 5). Motifs 1, 6 or 2 specifying the MADS domain were found in all the members of the MADS-box family. All proteins belonging to MIKCc and MIKC* groups had motif 1-type MADS domain..Most Mα proteins also had the motif 1-type MADS domain except OsMADS72 and 77 which contained motif 6. Motif 6 was found to be the most common type of MADS domain in Mβ-type proteins.Distinctively, in case of Mγ proteins a larger MADS domain of 83 amino acids was detected, followed by a coiled coil region and a region of unknown complexity as indicated by Simple Modular Architecture Research Tool (SMART) version 3.4<ref name="ref7" />.
[[File:Conserved_motifs.jpg]]'''Figure 5.Distribution of Conserved motifs in rice MADS-box proteins'''

===Expression profiling of MADS-box genes===
Expression profiles have been generated using avadis™ software version 4.2. X-axis represents the developmental stages. Y-axis represents average log2 expression values.Genes exhibiting these expression patterns have been represented by numbers. Dotted lines have been drawn to demarcate vegetative organs, panicle and seed developmental stages（Figure 6）.
[[File:Expression_patterns.jpg]]'''Figure 6.Expression patterns of MADS-box genes in rice in vegetative as well as panicle and seed development.'''
[[File:Differential_expressions.jpg]]'''Figure 7.'''

Differential expressions shown by seven MADS-box genes in response to various abiotic stress conditions.Left panel shows four genes up regulated and right panel shows down regulated genes more than 2 folds with p value less than 0.05 in response to three abiotic stress conditions. X-axis represents seedling followed by stress samples (CS, cold stress; DS, dehydration stress; SS, salt stress). Y-axis represents average expression values obtained using microarrays. Error bars represent standard error for data obtained in three biological replicates(Figure 7).

==''Japonica'' Group==
{| style="background:#A1A3A6; width:85%;" border="0"
|-style="background:white; color:black" align="center"
!
'''[[Os01g0201700]]'''
||
'''[[Os02g0682200]]'''
||
'''[[Os04g0580700]]'''
||
'''[[Os09g0507200]]'''
||
'''[[Os08g0531700]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os07g0605200]]'''
||
'''[[Os07g0108900]]'''
||
'''[[Os05g0203800]]'''
||
'''[[Os12g0207000]]'''
||
'''[[Os03g0752800]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os03g0122600]]'''
||
'''[[Os10g0536100]]'''
||
'''[[Os06g0162800]]'''
||
'''[[Os01g0883100]]'''
||
'''[[Os01g0886200]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os04g0461300]]'''
||
'''[[Os06g0712700]]'''
||
'''[[Os02g0731200]]'''
||
'''[[Os03g0215400]]'''
||
'''[[Os02g0579600]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os12g0206800]]'''
||
'''[[Os08g0531900]]'''
||
'''[[Os03g0753100]]'''
||
'''[[Os05g0203600]]'''
||
'''[[Os02g0170300]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os02g0761000]]'''
||
'''[[Os04g0614100]]'''
||
'''[[Os05g0423400]]'''
||
'''[[Os08g0431900]]'''
||
'''[[Os04g0304400]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os06g0223300]]'''
||
'''[[Os06g0667200]]'''
||
'''[[Os06g0217300]]'''
||
'''[[Os03g0186600]]'''
||
'''[[Os01g0922800]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os12g0501700]]'''
||
'''[[Os08g0112700]]'''
||
'''[[Os01g0726400]]'''
||
'''[[Os12g0407400]]'''
||
'''[[Os11g0658700]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os04g0387400]]'''
||
'''[[Os03g0253400]]'''
||

||

||

|}
==''Indica'' Group==
{| style="background:#A1A3A6; width:85%;" border="0"
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA002178]]'''
||
'''[[BGIOSGA008820]]'''
||
'''[[BGIOSGA016980]]'''
||
'''[[BGIOSGA031056]]'''
||
'''[[BGIOSGA029052]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA026097]]'''
||
'''[[BGIOSGA018621]]'''
||
'''[[BGIOSGA024961]]'''
||
'''[[BGIOSGA009798]]'''
||
'''[[BGIOSGA033356]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA021849]]'''
||
'''[[BGIOSGA000377]]'''
||
'''[[BGIOSGA004940]]'''
||
'''[[BGIOSGA020546]]'''
||
'''[[BGIOSGA007336]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA011213]]'''
||
'''[[BGIOSGA026745]]'''
||
'''[[BGIOSGA008494]]'''
||
'''[[BGIOSGA022872]]'''
||
'''[[BGIOSGA036463]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA009797]]'''
||
'''[[BGIOSGA026939]]'''
||
'''[[BGIOSGA008983]]'''
||
'''[[BGIOSGA007056]]'''
||
'''[[BGIOSGA018624]]''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA007333]]'''
||
'''[[BGIOSGA009093]]'''
||
'''[[BGIOSGA022154]]'''
||
'''[[BGIOSGA019900]]'''
||
'''[[BGIOSGA016106]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA029053]]'''
||
'''[[BGIOSGA017110]]'''
||
'''[[BGIOSGA003731]]'''
||
'''[[BGIOSGA016105]]'''
||
'''[[BGIOSGA005076]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA015021]]'''
||
'''[[BGIOSGA023435]]'''
||
'''[[BGIOSGA021662]]'''
||
'''[[BGIOSGA011317]]'''
||
'''[[BGIOSGA036149]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA027872]]'''
||
'''[[BGIOSGA007600]]'''
||
'''[[BGIOSGA000892]]'''
||
'''[[BGIOSGA018453]]'''
||
'''[[BGIOSGA006672]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA030217]]'''
||
'''[[BGIOSGA005284]]'''
||
'''[[BGIOSGA035654]]'''
||
'''[[BGIOSGA021177]]'''
||
'''[[BGIOSGA003304]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA036334]]'''
||
'''[[BGIOSGA022830]]'''
||
'''[[BGIOSGA028419]]'''
||
'''[[BGIOSGA018341]]'''
||
'''[[BGIOSGA015023]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA000269]]'''
||
'''[[BGIOSGA003303]]'''
||
'''[[BGIOSGA011095]]'''
||
'''[[BGIOSGA016270]]'''
||
'''[[BGIOSGA003441]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA002989]]'''
||
'''[[BGIOSGA034252]]'''
||
'''[[BGIOSGA030219]]'''
||
'''[[BGIOSGA000297]]'''
||
'''[[BGIOSGA003442]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA003440]]'''
||
'''[[BGIOSGA003443]]'''
||

||

||

|}

==MADS Box Protein Interactions==
===Comprehensive Analysis of MADS Box Transcription Factor Dimerization===
Remarkably, the MIKC proteins that contain the K-box, a domain specific for type II plant MADS box proteins that is presumed to fold into an amphipathic a-helical structure<ref name="ref8" /><ref name="ref9" /><ref name="ref10" />,interact preferably with other type II proteins and hardly form dimers with the type I MADS box proteins. However, there are some exceptions. In particular, there is a preference for interactions with type I proteins from the Ma subclade. Among the type I proteins, most heterodimers are found between members of different subclades. Interactions among Ma proteins are rare, but they dimerize preferentially with many proteins of the Mb and Mg clades. Similarly, only a few interactions among members of the Mb and Mg clades were observed, and Mb-Mg heterodimers are rare. This suggests that the participation of a Ma protein is a prerequisite for a stable dimer consisting of only type I proteins. Although many interactions were observed, a relatively large number of MADS domain proteins appeared to have no interactions at all. Possibly these proteins interact only with non-MADS box proteins, or alternatively,particular interactions are not formed in a yeast two-hybrid assay. For example, the interaction between the B-type proteins APETALA3 (AP3) and PISTILLATA (PI) was not found in this screen. Previously, these proteins appeared to interact exclusively in a higher-order complex, with either SEPALLATA3 (SEP3) or AP1<ref name="ref11" /> ,suggesting that the additional factors stabilize the AP3-PI dimer. This requirement for stabilizing factors to maintain specific dimers could be more general.Homodimerization is another form of MADS domain transcription factor interaction that is difficult to detect by yeast two-hybrid analysis <ref name="ref12" />,and hence, many homodimers have probably been missed in this screening.

Subsequently, the proteins were clustered based on the obtained interaction patterns, which allows the identification of proteins with similar interactions and groups of proteins that are highly connected (Figure 8). This analysis gives clues about the involvement of proteins in certain developmental programs. It reveals groups of proteins with common known functions, but more informatively, also shows clusters containing uncharacterized proteins, for which a function can now be predicted, based on their presence in a particular interaction cluster.
[[File:ABC_8.jpg]]'''Figure 8.'''

Interactome Map of the Arabidopsis MADS Box Transcription Factor Family.Proteins are organized based on hierarchical clustering of their protein–protein interaction patterns. Proteins that do not interact in the screen are omitted from this figure. Protein–protein interactions are indicated with red blocks and no interactions with green blocks. Presence of clustered proteins with a putative similar function is indicated with a colored bar on the left and bottom side of the figure: red for embryo, green for root, blue for flowering,and yellow for floral organs.
===The Flower Induction and Flower Organ Formation Subnetworks===
The regulation of flowering time is a complex process in which many environmental and internal signals are integrated, finally giving rise to a switch from vegetative to generative development at the appropriate time. MADS box transcription factors have shown to play pivotal roles in the flowering program and occupy many important positions in the hierarchical network <ref name="ref13" /><ref name="ref14" />.Based on the interaction data obtained in this study, we tried to unravel two subnetworks composed of interactions between known MADS box proteins involved in flower induction and flower organ formation (Figure 9). The proteins AP1 and FRUITFULL (FUL) are present in both subnetworks, which would refer to their early and late function in flowering <ref name="ref15" /><ref name="ref16" />.However, the most striking observation is that many of the floral organ identity proteins, such as AGAMOUS (AG), SEP1/2/3, and SHP1/2 proteins, interact not only with positive regulators of flowering, such as SUPPRESSOR OF CONSTANS 1 (SOC1) and AGAMOUS-LIKE 24(AGL24), but also with a negative regulator, SVP, implying that there is both positive and negative crosstalk between the two pathways via protein interactions, as pointed out above.
[[File:ABC_9..jpg]]'''Figure 9.'''

Representation of the Flower Induction and Flower Formation Networks.Proteins are indicated by ovals (red for the flower induction, blue for the flower formation network, green for the hubs), and interactions are represented by lines. The proteins SOC1 and AGL24 form a homodimer,which is indicated with a small dot next to the oval of the protein.

==Stress responsive MADS-box genes in rice==
MADS-box genes have been shown to be affected by low temperature stress in tomato <ref name="ref17" /> and by application of hormones like cytokinins, gibberellins <ref name="ref18" />, ethylene <ref name="ref19" />and auxins <ref name="ref20" /> in other plants. Seven MADS-box genes exhibited differential expression in response to cold, salt and/or desiccation stress in rice. So far, none of these genes has been implicated in stress response. Amongst stress-induced genes, OsMADS18 is a member of AP1/SQUA group that has been shown to express widely during development with its transcripts accumulating at high levels specifically in meristematic tissues <ref name="ref17" />. It has been shown to interact with OsMADS6, 8/24, 7/45, and 47 <ref name="ref21" /><ref name="ref22" />and in our analysis its expression pattern was found to overlap with those of OsMADS6, 8 and 7 in reproductive tissues and with OsMADS47 during vegetative development, suggesting that it might be interacting with different partners during reproductive development and stress. Recently, Tardif and coworkers showed that a large number of genes involved in flower development are associated with abiotic stress responses in wheat <ref name="ref23" />. Our preliminary analysis involving transcript profiling during reproductive development and abiotic stress conditions has also revealed approximately 400 genes that are up regulated during panicle/seed development and three stress conditions, viz. cold, salt, and dehydration (unpublished data). It would be, therefore, interesting to undertake specific investigations, which could establish the interactions of biochemical pathways that are activated during reproductive development and stress response.

==References==
<references>
* <ref name="ref1">
Arora R, Agarwal P, Ray S, et al. MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress[J]. BMC genomics, 2007, 8(1): 242.
</ref>
* <ref name="ref2">
Par̆enicová L, de Folter S, Kieffer M, et al. Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis new openings to the MADS world[J]. The Plant Cell Online, 2003, 15(7): 1538-1551.
</ref>
* <ref name="ref3">
Leseberg C H, Li A, Kang H, et al. Genome-wide analysis of the MADS-box gene family in Populus trichocarpa[J]. Gene, 2006, 378: 84-94.
</ref>
* <ref name="ref4">
Yang Y, Fanning L, Jack T: The K domain mediates heterodimerization of the Arabidopsis floral organ identity proteins,APETALA3 and PISTILLATA[J]. Plant J 2003, 33(1):47-59.
</ref>
* <ref name="ref5">
Egea Cortines M, Saedler H, Sommer H: Ternary complex formation between the MADS-box proteins SQUAMOSA, DEFICIENS and GLOBOSA is involved in the control of floral architecture in Antirrhinum majus[J]. EMBO J 1999, 18(19):5370-5379.
</ref>
* <ref name="ref6">
Cho S, Jang S, Chae S, Chung KM, Moon YH, An G, Jang SK: Analysis of the C-terminal region of Arabidopsis thaliana APETALA1 as a transcription activation domain. Plant Mol Biol 1999,40(3):419-429.
</ref>
* <ref name="ref7">
Rita Arora, Pinky Agarwal, Swatismita Ray.MADS-box gene family in rice: genome-wide identification,organization and expression profiling during reproductive development and stress.BMC Genomics,2007, 8:242.
</ref>
* <ref name="ref8">
Stefan de Folter,Richard G.H. Immink,Martin Kieffer,Lucie Parˇenicova´ ,et al.Comprehensive Interaction Map of the Arabidopsis MADS Box Transcription Factors.The Plant Cell, 2005, 17:1424–1433.
</ref>
* <ref name="ref9">
Alvarez-Buylla, E.R., Pelaz, S., Liljegren, S.J., Gold, S.E., et al. An ancestral MADS-box gene duplication occurred before the divergence of plants and animals. Proc. Natl. Acad. Sci.USA 2000,97:5328–5333.
</ref>
* <ref name="ref10">
Riechmann, J.L., and Meyerowitz, E.M. . MADS domain proteins in plant development. Biol. Chem,1997,378:1079–1101.
</ref>
* <ref name="ref11">
Honma, T., and Goto, K. . Complexes of MADS-box proteins are sufficient to convert leaves into floral organs. Nature ,2001,409:525–529.
</ref>
* <ref name="ref12">
Immink, R.G.H., and Angenent, G.C. . Transcription factors do it together: The hows and whys of studying protein-protein interactions.
Trends Plant Sci,2002, 7:531–534.
</ref>
* <ref name="ref13">
Blazquez,M.A.. Flower development pathways. J. Cell Sci.,2000,113:3547–3548.
</ref>
* <ref name="ref14">
Simpson, G.G., and Dean, C. . Arabidopsis, the Rosetta stone of flowering time? Science ,2002,296:285–289.
</ref>
* <ref name="ref15">
Mandel, M.A., Gustafson-Brown, C., Savidge, B., and Yanofsky,M.F. . Molecular characterization of the Arabidopsis floral homeotic gene APETALA1. Nature ,1992,360:273–277.
</ref>
* <ref name="ref16">
Ferrandiz, C., Gu, Q., Martienssen, R., and Yanofsky, M.F. .Redundant regulation of meristem identity and plant architecture by FRUITFULL, APETALA1 and CAULIFLOWER. Development ,2000,127:725–734.
</ref>
* <ref name="ref17">
Lozano R, Angosto T, Gomez P, Payan C, Capel J, Huijser P, Salinas J,Martinez-Zapater JM: Tomato flower abnormalities induced by low temperatures are associated with changes of expression of MADS-Box genes. Plant Physiol 1998, 117(1):91-100.
</ref>
* <ref name="ref18">
Bonhomme F, Kurz B, Melzer S, Bernier G, Jacqmard A: Cytokinin and gibberellin activate SaMADS A, a gene apparently involved in regulation of the floral transition in Sinapis alba.Plant J 2000, 24(1):103-111.
</ref>
* <ref name="ref19">
Ando S, Sato Y, Kamachi S, Sakai S: Isolation of a MADS-box gene
(ERAF17) and correlation of its expression with the induction of formation of female flowers by ethylene in cucumber plants (Cucumis sativus L.). Planta 2001, 213(6):943-952.
</ref>
* <ref name="ref20">
Zhu C, Perry SE: Control of expression and autoregulation of AGL15, a member of the MADS-box family. Plant J 2005,41(4):583-594.
</ref>
* <ref name="ref21">
Fornara F, Parenicova L, Falasca G, Pelucchi N, Masiero S, Ciannamea S, Lopez-Dee Z, Altamura MM, Colombo L, Kater MM: Functional characterization of OsMADS18, a member of the AP1/SQUA subfamily of MADS box genes. Plant Physiol 2004,135(4):2207-2219.
</ref>
* <ref name="ref22">
Moon YH, Jung JY, Kang HG, An G: Identification of a rice APETALA3 homologue by yeast two-hybrid screening. Plant Mol Biol 1999, 40(1):167-177.
</ref>
* <ref name="ref23">
Tardif G, Kane NA, Adam H, Labrie L, Major G, Gulick P, Sarhan F,
Laliberte JF: Interaction network of proteins associated with abiotic stress response and development in wheat. Plant Mol Biol 2007, 63(5):703-718.
</ref>

</references>

MADS

2014-06-07T11:10:25Z

Kathy: /* The Flower Induction and Flower Organ Formation Subnetworks */

==Brief Introduction==
===Background===
MADS-box family member are known to be involved in many important processes during plant growth and development<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The word MADS finds its origin from the first letters of its founding members, Mini Chromosome Maintenance 1 (MCM1) of yeast (Saccharomyces cerevisiae), Agamous (AG) of Arabidopsis (Arabidopsis thaliana), Deficiens (DEF) of snapdragon (Antirrhinum majus) and Serum Response Factor (SRF) of humans (Homo sapiens)<ref name="ref1" />.

They are characterized by the presence of a conserved domain of approximately 60 amino acids located in the N-terminal region; this domain is named the MADS-box domain and is involved in DNA binding and dimerization<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The MADS-box family has been divided into two main groups. The type I consists of ARG80/SRF-like genes of animals and fungi, also designated as M-type genes in plants, and type II contains MEF2-like genes of animals and yeast as well as MIKC-type genes of plants<ref name="ref1" /><ref name="ref3" />.The plant-specific MIKC-type MADS-box proteins include three additional domains followed by the MADS domain, viz. a less-conserved Intervening region of ~30 amino acids, a moderately conserved Keratin-like domain of ~70 amino acids mainly involved in heterodimerization, and a highly variable C-terminal region of variable length implicated in transcriptional activation and higher-order complex formation<ref name="ref4" /><ref name="ref5" /<ref name="ref6" />.
[[File:mads_box1.jpg|center|thumb|1000px|'''Figure 1.''' ''Protein Structure of '''BGIOSGA004940''' '']]
[[File:Gene_tree_1.jpg]]'''Figure 2.Gene tree'''

===Evolutionary relationships between rice and Arabidopsis MADS-box family genes===
A separate phylogenetic tree was also generated from complete protein sequences of all the MADS-box genes in rice and Arabidopsis (Figure 3). Of the 75 rice MADS-box genes, 38 grouped with MIKCc, six with MIKC*, nine with Mβ, 13 with Mα and 10 grouped with Mγ-type Arabidopsis genes<ref name="ref7" />.

[[File:Gene_tree_2.jpg]]'''Figure 3.Phylogenetic analysis of rice and Arabidopsis MADS-box proteins'''

===MADS-box transcription factors ===
The best studied plant MADS-box transcription factors are those involved in floral organ identity determination. Combinations of A-, B-, and C-function genes determine the development of the four whorls of an Arabidopsis flower: A-function genes determine sepal development; A- and B-function genes determine petal development; B- and C function genes determine the stamen development, and C-function genes are necessary for carpel development<ref name="ref2" /><ref name="ref3" />.

== Organization and structure of MADS-box genes==
===Location of genes===
The individual genes were localized on chromosomes based on the 5' and 3' coordinates for respective gene models in TIGR database.Out of five types of MADS-box genes, the Mγ genes were confined to chromosome 1, 3 and 4, while Mβ genes were present only on chromosome 1. No chromosomal bias was observed in the distribution of MIKCc,MIKC* and Mα genes.<ref name="ref7" />
[[File:Gene_location.jpg]]
'''Figure 4.''' Chromosomal location of rice MADS-box '''

===Distribution of conserved motifs===
The MEME motif search tool was employed to identify the conserved motifs present in MADS-box proteins (Figure 5). Motifs 1, 6 or 2 specifying the MADS domain were found in all the members of the MADS-box family. All proteins belonging to MIKCc and MIKC* groups had motif 1-type MADS domain..Most Mα proteins also had the motif 1-type MADS domain except OsMADS72 and 77 which contained motif 6. Motif 6 was found to be the most common type of MADS domain in Mβ-type proteins.Distinctively, in case of Mγ proteins a larger MADS domain of 83 amino acids was detected, followed by a coiled coil region and a region of unknown complexity as indicated by Simple Modular Architecture Research Tool (SMART) version 3.4<ref name="ref7" />.
[[File:Conserved_motifs.jpg]]'''Figure 5.Distribution of Conserved motifs in rice MADS-box proteins'''

===Expression profiling of MADS-box genes===
Expression profiles have been generated using avadis™ software version 4.2. X-axis represents the developmental stages. Y-axis represents average log2 expression values.Genes exhibiting these expression patterns have been represented by numbers. Dotted lines have been drawn to demarcate vegetative organs, panicle and seed developmental stages（Figure 6）.
[[File:Expression_patterns.jpg]]'''Figure 6.Expression patterns of MADS-box genes in rice in vegetative as well as panicle and seed development.'''
[[File:Differential_expressions.jpg]]'''Figure 7.'''

Differential expressions shown by seven MADS-box genes in response to various abiotic stress conditions.Left panel shows four genes up regulated and right panel shows down regulated genes more than 2 folds with p value less than 0.05 in response to three abiotic stress conditions. X-axis represents seedling followed by stress samples (CS, cold stress; DS, dehydration stress; SS, salt stress). Y-axis represents average expression values obtained using microarrays. Error bars represent standard error for data obtained in three biological replicates(Figure 7).

==''Japonica'' Group==
{| style="background:#A1A3A6; width:85%;" border="0"
|-style="background:white; color:black" align="center"
!
'''[[Os01g0201700]]'''
||
'''[[Os02g0682200]]'''
||
'''[[Os04g0580700]]'''
||
'''[[Os09g0507200]]'''
||
'''[[Os08g0531700]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os07g0605200]]'''
||
'''[[Os07g0108900]]'''
||
'''[[Os05g0203800]]'''
||
'''[[Os12g0207000]]'''
||
'''[[Os03g0752800]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os03g0122600]]'''
||
'''[[Os10g0536100]]'''
||
'''[[Os06g0162800]]'''
||
'''[[Os01g0883100]]'''
||
'''[[Os01g0886200]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os04g0461300]]'''
||
'''[[Os06g0712700]]'''
||
'''[[Os02g0731200]]'''
||
'''[[Os03g0215400]]'''
||
'''[[Os02g0579600]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os12g0206800]]'''
||
'''[[Os08g0531900]]'''
||
'''[[Os03g0753100]]'''
||
'''[[Os05g0203600]]'''
||
'''[[Os02g0170300]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os02g0761000]]'''
||
'''[[Os04g0614100]]'''
||
'''[[Os05g0423400]]'''
||
'''[[Os08g0431900]]'''
||
'''[[Os04g0304400]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os06g0223300]]'''
||
'''[[Os06g0667200]]'''
||
'''[[Os06g0217300]]'''
||
'''[[Os03g0186600]]'''
||
'''[[Os01g0922800]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os12g0501700]]'''
||
'''[[Os08g0112700]]'''
||
'''[[Os01g0726400]]'''
||
'''[[Os12g0407400]]'''
||
'''[[Os11g0658700]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os04g0387400]]'''
||
'''[[Os03g0253400]]'''
||

||

||

|}
==''Indica'' Group==
{| style="background:#A1A3A6; width:85%;" border="0"
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA002178]]'''
||
'''[[BGIOSGA008820]]'''
||
'''[[BGIOSGA016980]]'''
||
'''[[BGIOSGA031056]]'''
||
'''[[BGIOSGA029052]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA026097]]'''
||
'''[[BGIOSGA018621]]'''
||
'''[[BGIOSGA024961]]'''
||
'''[[BGIOSGA009798]]'''
||
'''[[BGIOSGA033356]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA021849]]'''
||
'''[[BGIOSGA000377]]'''
||
'''[[BGIOSGA004940]]'''
||
'''[[BGIOSGA020546]]'''
||
'''[[BGIOSGA007336]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA011213]]'''
||
'''[[BGIOSGA026745]]'''
||
'''[[BGIOSGA008494]]'''
||
'''[[BGIOSGA022872]]'''
||
'''[[BGIOSGA036463]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA009797]]'''
||
'''[[BGIOSGA026939]]'''
||
'''[[BGIOSGA008983]]'''
||
'''[[BGIOSGA007056]]'''
||
'''[[BGIOSGA018624]]''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA007333]]'''
||
'''[[BGIOSGA009093]]'''
||
'''[[BGIOSGA022154]]'''
||
'''[[BGIOSGA019900]]'''
||
'''[[BGIOSGA016106]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA029053]]'''
||
'''[[BGIOSGA017110]]'''
||
'''[[BGIOSGA003731]]'''
||
'''[[BGIOSGA016105]]'''
||
'''[[BGIOSGA005076]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA015021]]'''
||
'''[[BGIOSGA023435]]'''
||
'''[[BGIOSGA021662]]'''
||
'''[[BGIOSGA011317]]'''
||
'''[[BGIOSGA036149]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA027872]]'''
||
'''[[BGIOSGA007600]]'''
||
'''[[BGIOSGA000892]]'''
||
'''[[BGIOSGA018453]]'''
||
'''[[BGIOSGA006672]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA030217]]'''
||
'''[[BGIOSGA005284]]'''
||
'''[[BGIOSGA035654]]'''
||
'''[[BGIOSGA021177]]'''
||
'''[[BGIOSGA003304]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA036334]]'''
||
'''[[BGIOSGA022830]]'''
||
'''[[BGIOSGA028419]]'''
||
'''[[BGIOSGA018341]]'''
||
'''[[BGIOSGA015023]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA000269]]'''
||
'''[[BGIOSGA003303]]'''
||
'''[[BGIOSGA011095]]'''
||
'''[[BGIOSGA016270]]'''
||
'''[[BGIOSGA003441]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA002989]]'''
||
'''[[BGIOSGA034252]]'''
||
'''[[BGIOSGA030219]]'''
||
'''[[BGIOSGA000297]]'''
||
'''[[BGIOSGA003442]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA003440]]'''
||
'''[[BGIOSGA003443]]'''
||

||

||

|}

==MADS Box Protein Interactions==
===Comprehensive Analysis of MADS Box Transcription Factor Dimerization===
Remarkably, the MIKC proteins that contain the K-box, a domain specific for type II plant MADS box proteins that is presumed to fold into an amphipathic a-helical structure<ref name="ref8" /><ref name="ref9" /><ref name="ref10" />,interact preferably with other type II proteins and hardly form dimers with the type I MADS box proteins. However, there are some exceptions. In particular, there is a preference for interactions with type I proteins from the Ma subclade. Among the type I proteins, most heterodimers are found between members of different subclades. Interactions among Ma proteins are rare, but they dimerize preferentially with many proteins of the Mb and Mg clades. Similarly, only a few interactions among members of the Mb and Mg clades were observed, and Mb-Mg heterodimers are rare. This suggests that the participation of a Ma protein is a prerequisite for a stable dimer consisting of only type I proteins. Although many interactions were observed, a relatively large number of MADS domain proteins appeared to have no interactions at all. Possibly these proteins interact only with non-MADS box proteins, or alternatively,particular interactions are not formed in a yeast two-hybrid assay. For example, the interaction between the B-type proteins APETALA3 (AP3) and PISTILLATA (PI) was not found in this screen. Previously, these proteins appeared to interact exclusively in a higher-order complex, with either SEPALLATA3 (SEP3) or AP1<ref name="ref11" /> ,suggesting that the additional factors stabilize the AP3-PI dimer. This requirement for stabilizing factors to maintain specific dimers could be more general.Homodimerization is another form of MADS domain transcription factor interaction that is difficult to detect by yeast two-hybrid analysis <ref name="ref12" />,and hence, many homodimers have probably been missed in this screening.

Subsequently, the proteins were clustered based on the obtained interaction patterns, which allows the identification of proteins with similar interactions and groups of proteins that are highly connected (Figure 8). This analysis gives clues about the involvement of proteins in certain developmental programs. It reveals groups of proteins with common known functions, but more informatively, also shows clusters containing uncharacterized proteins, for which a function can now be predicted, based on their presence in a particular interaction cluster.
[[File:ABC_8.jpg]]'''Figure 8.'''

Interactome Map of the Arabidopsis MADS Box Transcription Factor Family.Proteins are organized based on hierarchical clustering of their protein–protein interaction patterns. Proteins that do not interact in the screen are omitted from this figure. Protein–protein interactions are indicated with red blocks and no interactions with green blocks. Presence of clustered proteins with a putative similar function is indicated with a colored bar on the left and bottom side of the figure: red for embryo, green for root, blue for flowering,and yellow for floral organs.
===The Flower Induction and Flower Organ Formation Subnetworks===
The regulation of flowering time is a complex process in which many environmental and internal signals are integrated, finally giving rise to a switch from vegetative to generative development at the appropriate time. MADS box transcription factors have shown to play pivotal roles in the flowering program and occupy many important positions in the hierarchical network <ref name="ref13" /><ref name="ref14" />.Based on the interaction data obtained in this study, we tried to unravel two subnetworks composed of interactions between known MADS box proteins involved in flower induction and flower organ formation (Figure 9). The proteins AP1 and FRUITFULL (FUL) are present in both subnetworks, which would refer to their early and late function in flowering <ref name="ref15" /><ref name="ref16" />.However, the most striking observation is that many of the floral organ identity proteins, such as AGAMOUS (AG), SEP1/2/3, and SHP1/2 proteins, interact not only with positive regulators of flowering, such as SUPPRESSOR OF CONSTANS 1 (SOC1) and AGAMOUS-LIKE 24(AGL24), but also with a negative regulator, SVP, implying that there is both positive and negative crosstalk between the two pathways via protein interactions, as pointed out above.
[[File:ABC_9..jpg]]'''Figure 9.'''
Representation of the Flower Induction and Flower Formation Networks.Proteins are indicated by ovals (red for the flower induction, blue for the flower formation network, green for the hubs), and interactions are represented by lines. The proteins SOC1 and AGL24 form a homodimer,which is indicated with a small dot next to the oval of the protein.

==Stress responsive MADS-box genes in rice==
MADS-box genes have been shown to be affected by low temperature stress in tomato <ref name="ref17" /> and by application of hormones like cytokinins, gibberellins <ref name="ref18" />, ethylene <ref name="ref19" />and auxins <ref name="ref20" /> in other plants. Seven MADS-box genes exhibited differential expression in response to cold, salt and/or desiccation stress in rice. So far, none of these genes has been implicated in stress response. Amongst stress-induced genes, OsMADS18 is a member of AP1/SQUA group that has been shown to express widely during development with its transcripts accumulating at high levels specifically in meristematic tissues <ref name="ref17" />. It has been shown to interact with OsMADS6, 8/24, 7/45, and 47 <ref name="ref21" /><ref name="ref22" />and in our analysis its expression pattern was found to overlap with those of OsMADS6, 8 and 7 in reproductive tissues and with OsMADS47 during vegetative development, suggesting that it might be interacting with different partners during reproductive development and stress. Recently, Tardif and coworkers showed that a large number of genes involved in flower development are associated with abiotic stress responses in wheat <ref name="ref23" />. Our preliminary analysis involving transcript profiling during reproductive development and abiotic stress conditions has also revealed approximately 400 genes that are up regulated during panicle/seed development and three stress conditions, viz. cold, salt, and dehydration (unpublished data). It would be, therefore, interesting to undertake specific investigations, which could establish the interactions of biochemical pathways that are activated during reproductive development and stress response.

==References==
<references>
* <ref name="ref1">
Arora R, Agarwal P, Ray S, et al. MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress[J]. BMC genomics, 2007, 8(1): 242.
</ref>
* <ref name="ref2">
Par̆enicová L, de Folter S, Kieffer M, et al. Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis new openings to the MADS world[J]. The Plant Cell Online, 2003, 15(7): 1538-1551.
</ref>
* <ref name="ref3">
Leseberg C H, Li A, Kang H, et al. Genome-wide analysis of the MADS-box gene family in Populus trichocarpa[J]. Gene, 2006, 378: 84-94.
</ref>
* <ref name="ref4">
Yang Y, Fanning L, Jack T: The K domain mediates heterodimerization of the Arabidopsis floral organ identity proteins,APETALA3 and PISTILLATA[J]. Plant J 2003, 33(1):47-59.
</ref>
* <ref name="ref5">
Egea Cortines M, Saedler H, Sommer H: Ternary complex formation between the MADS-box proteins SQUAMOSA, DEFICIENS and GLOBOSA is involved in the control of floral architecture in Antirrhinum majus[J]. EMBO J 1999, 18(19):5370-5379.
</ref>
* <ref name="ref6">
Cho S, Jang S, Chae S, Chung KM, Moon YH, An G, Jang SK: Analysis of the C-terminal region of Arabidopsis thaliana APETALA1 as a transcription activation domain. Plant Mol Biol 1999,40(3):419-429.
</ref>
* <ref name="ref7">
Rita Arora, Pinky Agarwal, Swatismita Ray.MADS-box gene family in rice: genome-wide identification,organization and expression profiling during reproductive development and stress.BMC Genomics,2007, 8:242.
</ref>
* <ref name="ref8">
Stefan de Folter,Richard G.H. Immink,Martin Kieffer,Lucie Parˇenicova´ ,et al.Comprehensive Interaction Map of the Arabidopsis MADS Box Transcription Factors.The Plant Cell, 2005, 17:1424–1433.
</ref>
* <ref name="ref9">
Alvarez-Buylla, E.R., Pelaz, S., Liljegren, S.J., Gold, S.E., et al. An ancestral MADS-box gene duplication occurred before the divergence of plants and animals. Proc. Natl. Acad. Sci.USA 2000,97:5328–5333.
</ref>
* <ref name="ref10">
Riechmann, J.L., and Meyerowitz, E.M. . MADS domain proteins in plant development. Biol. Chem,1997,378:1079–1101.
</ref>
* <ref name="ref11">
Honma, T., and Goto, K. . Complexes of MADS-box proteins are sufficient to convert leaves into floral organs. Nature ,2001,409:525–529.
</ref>
* <ref name="ref12">
Immink, R.G.H., and Angenent, G.C. . Transcription factors do it together: The hows and whys of studying protein-protein interactions.
Trends Plant Sci,2002, 7:531–534.
</ref>
* <ref name="ref13">
Blazquez,M.A.. Flower development pathways. J. Cell Sci.,2000,113:3547–3548.
</ref>
* <ref name="ref14">
Simpson, G.G., and Dean, C. . Arabidopsis, the Rosetta stone of flowering time? Science ,2002,296:285–289.
</ref>
* <ref name="ref15">
Mandel, M.A., Gustafson-Brown, C., Savidge, B., and Yanofsky,M.F. . Molecular characterization of the Arabidopsis floral homeotic gene APETALA1. Nature ,1992,360:273–277.
</ref>
* <ref name="ref16">
Ferrandiz, C., Gu, Q., Martienssen, R., and Yanofsky, M.F. .Redundant regulation of meristem identity and plant architecture by FRUITFULL, APETALA1 and CAULIFLOWER. Development ,2000,127:725–734.
</ref>
* <ref name="ref17">
Lozano R, Angosto T, Gomez P, Payan C, Capel J, Huijser P, Salinas J,Martinez-Zapater JM: Tomato flower abnormalities induced by low temperatures are associated with changes of expression of MADS-Box genes. Plant Physiol 1998, 117(1):91-100.
</ref>
* <ref name="ref18">
Bonhomme F, Kurz B, Melzer S, Bernier G, Jacqmard A: Cytokinin and gibberellin activate SaMADS A, a gene apparently involved in regulation of the floral transition in Sinapis alba.Plant J 2000, 24(1):103-111.
</ref>
* <ref name="ref19">
Ando S, Sato Y, Kamachi S, Sakai S: Isolation of a MADS-box gene
(ERAF17) and correlation of its expression with the induction of formation of female flowers by ethylene in cucumber plants (Cucumis sativus L.). Planta 2001, 213(6):943-952.
</ref>
* <ref name="ref20">
Zhu C, Perry SE: Control of expression and autoregulation of AGL15, a member of the MADS-box family. Plant J 2005,41(4):583-594.
</ref>
* <ref name="ref21">
Fornara F, Parenicova L, Falasca G, Pelucchi N, Masiero S, Ciannamea S, Lopez-Dee Z, Altamura MM, Colombo L, Kater MM: Functional characterization of OsMADS18, a member of the AP1/SQUA subfamily of MADS box genes. Plant Physiol 2004,135(4):2207-2219.
</ref>
* <ref name="ref22">
Moon YH, Jung JY, Kang HG, An G: Identification of a rice APETALA3 homologue by yeast two-hybrid screening. Plant Mol Biol 1999, 40(1):167-177.
</ref>
* <ref name="ref23">
Tardif G, Kane NA, Adam H, Labrie L, Major G, Gulick P, Sarhan F,
Laliberte JF: Interaction network of proteins associated with abiotic stress response and development in wheat. Plant Mol Biol 2007, 63(5):703-718.
</ref>

</references>

File:ABC 9..jpg

2014-06-07T11:08:44Z

Kathy:

MADS

2014-06-07T11:06:48Z

Kathy:

==Brief Introduction==
===Background===
MADS-box family member are known to be involved in many important processes during plant growth and development<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The word MADS finds its origin from the first letters of its founding members, Mini Chromosome Maintenance 1 (MCM1) of yeast (Saccharomyces cerevisiae), Agamous (AG) of Arabidopsis (Arabidopsis thaliana), Deficiens (DEF) of snapdragon (Antirrhinum majus) and Serum Response Factor (SRF) of humans (Homo sapiens)<ref name="ref1" />.

They are characterized by the presence of a conserved domain of approximately 60 amino acids located in the N-terminal region; this domain is named the MADS-box domain and is involved in DNA binding and dimerization<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The MADS-box family has been divided into two main groups. The type I consists of ARG80/SRF-like genes of animals and fungi, also designated as M-type genes in plants, and type II contains MEF2-like genes of animals and yeast as well as MIKC-type genes of plants<ref name="ref1" /><ref name="ref3" />.The plant-specific MIKC-type MADS-box proteins include three additional domains followed by the MADS domain, viz. a less-conserved Intervening region of ~30 amino acids, a moderately conserved Keratin-like domain of ~70 amino acids mainly involved in heterodimerization, and a highly variable C-terminal region of variable length implicated in transcriptional activation and higher-order complex formation<ref name="ref4" /><ref name="ref5" /<ref name="ref6" />.
[[File:mads_box1.jpg|center|thumb|1000px|'''Figure 1.''' ''Protein Structure of '''BGIOSGA004940''' '']]
[[File:Gene_tree_1.jpg]]'''Figure 2.Gene tree'''

===Evolutionary relationships between rice and Arabidopsis MADS-box family genes===
A separate phylogenetic tree was also generated from complete protein sequences of all the MADS-box genes in rice and Arabidopsis (Figure 3). Of the 75 rice MADS-box genes, 38 grouped with MIKCc, six with MIKC*, nine with Mβ, 13 with Mα and 10 grouped with Mγ-type Arabidopsis genes<ref name="ref7" />.

[[File:Gene_tree_2.jpg]]'''Figure 3.Phylogenetic analysis of rice and Arabidopsis MADS-box proteins'''

===MADS-box transcription factors ===
The best studied plant MADS-box transcription factors are those involved in floral organ identity determination. Combinations of A-, B-, and C-function genes determine the development of the four whorls of an Arabidopsis flower: A-function genes determine sepal development; A- and B-function genes determine petal development; B- and C function genes determine the stamen development, and C-function genes are necessary for carpel development<ref name="ref2" /><ref name="ref3" />.

== Organization and structure of MADS-box genes==
===Location of genes===
The individual genes were localized on chromosomes based on the 5' and 3' coordinates for respective gene models in TIGR database.Out of five types of MADS-box genes, the Mγ genes were confined to chromosome 1, 3 and 4, while Mβ genes were present only on chromosome 1. No chromosomal bias was observed in the distribution of MIKCc,MIKC* and Mα genes.<ref name="ref7" />
[[File:Gene_location.jpg]]
'''Figure 4.''' Chromosomal location of rice MADS-box '''

===Distribution of conserved motifs===
The MEME motif search tool was employed to identify the conserved motifs present in MADS-box proteins (Figure 5). Motifs 1, 6 or 2 specifying the MADS domain were found in all the members of the MADS-box family. All proteins belonging to MIKCc and MIKC* groups had motif 1-type MADS domain..Most Mα proteins also had the motif 1-type MADS domain except OsMADS72 and 77 which contained motif 6. Motif 6 was found to be the most common type of MADS domain in Mβ-type proteins.Distinctively, in case of Mγ proteins a larger MADS domain of 83 amino acids was detected, followed by a coiled coil region and a region of unknown complexity as indicated by Simple Modular Architecture Research Tool (SMART) version 3.4<ref name="ref7" />.
[[File:Conserved_motifs.jpg]]'''Figure 5.Distribution of Conserved motifs in rice MADS-box proteins'''

===Expression profiling of MADS-box genes===
Expression profiles have been generated using avadis™ software version 4.2. X-axis represents the developmental stages. Y-axis represents average log2 expression values.Genes exhibiting these expression patterns have been represented by numbers. Dotted lines have been drawn to demarcate vegetative organs, panicle and seed developmental stages（Figure 6）.
[[File:Expression_patterns.jpg]]'''Figure 6.Expression patterns of MADS-box genes in rice in vegetative as well as panicle and seed development.'''
[[File:Differential_expressions.jpg]]'''Figure 7.'''

Differential expressions shown by seven MADS-box genes in response to various abiotic stress conditions.Left panel shows four genes up regulated and right panel shows down regulated genes more than 2 folds with p value less than 0.05 in response to three abiotic stress conditions. X-axis represents seedling followed by stress samples (CS, cold stress; DS, dehydration stress; SS, salt stress). Y-axis represents average expression values obtained using microarrays. Error bars represent standard error for data obtained in three biological replicates(Figure 7).

==''Japonica'' Group==
{| style="background:#A1A3A6; width:85%;" border="0"
|-style="background:white; color:black" align="center"
!
'''[[Os01g0201700]]'''
||
'''[[Os02g0682200]]'''
||
'''[[Os04g0580700]]'''
||
'''[[Os09g0507200]]'''
||
'''[[Os08g0531700]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os07g0605200]]'''
||
'''[[Os07g0108900]]'''
||
'''[[Os05g0203800]]'''
||
'''[[Os12g0207000]]'''
||
'''[[Os03g0752800]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os03g0122600]]'''
||
'''[[Os10g0536100]]'''
||
'''[[Os06g0162800]]'''
||
'''[[Os01g0883100]]'''
||
'''[[Os01g0886200]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os04g0461300]]'''
||
'''[[Os06g0712700]]'''
||
'''[[Os02g0731200]]'''
||
'''[[Os03g0215400]]'''
||
'''[[Os02g0579600]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os12g0206800]]'''
||
'''[[Os08g0531900]]'''
||
'''[[Os03g0753100]]'''
||
'''[[Os05g0203600]]'''
||
'''[[Os02g0170300]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os02g0761000]]'''
||
'''[[Os04g0614100]]'''
||
'''[[Os05g0423400]]'''
||
'''[[Os08g0431900]]'''
||
'''[[Os04g0304400]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os06g0223300]]'''
||
'''[[Os06g0667200]]'''
||
'''[[Os06g0217300]]'''
||
'''[[Os03g0186600]]'''
||
'''[[Os01g0922800]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os12g0501700]]'''
||
'''[[Os08g0112700]]'''
||
'''[[Os01g0726400]]'''
||
'''[[Os12g0407400]]'''
||
'''[[Os11g0658700]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os04g0387400]]'''
||
'''[[Os03g0253400]]'''
||

||

||

|}
==''Indica'' Group==
{| style="background:#A1A3A6; width:85%;" border="0"
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA002178]]'''
||
'''[[BGIOSGA008820]]'''
||
'''[[BGIOSGA016980]]'''
||
'''[[BGIOSGA031056]]'''
||
'''[[BGIOSGA029052]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA026097]]'''
||
'''[[BGIOSGA018621]]'''
||
'''[[BGIOSGA024961]]'''
||
'''[[BGIOSGA009798]]'''
||
'''[[BGIOSGA033356]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA021849]]'''
||
'''[[BGIOSGA000377]]'''
||
'''[[BGIOSGA004940]]'''
||
'''[[BGIOSGA020546]]'''
||
'''[[BGIOSGA007336]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA011213]]'''
||
'''[[BGIOSGA026745]]'''
||
'''[[BGIOSGA008494]]'''
||
'''[[BGIOSGA022872]]'''
||
'''[[BGIOSGA036463]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA009797]]'''
||
'''[[BGIOSGA026939]]'''
||
'''[[BGIOSGA008983]]'''
||
'''[[BGIOSGA007056]]'''
||
'''[[BGIOSGA018624]]''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA007333]]'''
||
'''[[BGIOSGA009093]]'''
||
'''[[BGIOSGA022154]]'''
||
'''[[BGIOSGA019900]]'''
||
'''[[BGIOSGA016106]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA029053]]'''
||
'''[[BGIOSGA017110]]'''
||
'''[[BGIOSGA003731]]'''
||
'''[[BGIOSGA016105]]'''
||
'''[[BGIOSGA005076]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA015021]]'''
||
'''[[BGIOSGA023435]]'''
||
'''[[BGIOSGA021662]]'''
||
'''[[BGIOSGA011317]]'''
||
'''[[BGIOSGA036149]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA027872]]'''
||
'''[[BGIOSGA007600]]'''
||
'''[[BGIOSGA000892]]'''
||
'''[[BGIOSGA018453]]'''
||
'''[[BGIOSGA006672]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA030217]]'''
||
'''[[BGIOSGA005284]]'''
||
'''[[BGIOSGA035654]]'''
||
'''[[BGIOSGA021177]]'''
||
'''[[BGIOSGA003304]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA036334]]'''
||
'''[[BGIOSGA022830]]'''
||
'''[[BGIOSGA028419]]'''
||
'''[[BGIOSGA018341]]'''
||
'''[[BGIOSGA015023]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA000269]]'''
||
'''[[BGIOSGA003303]]'''
||
'''[[BGIOSGA011095]]'''
||
'''[[BGIOSGA016270]]'''
||
'''[[BGIOSGA003441]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA002989]]'''
||
'''[[BGIOSGA034252]]'''
||
'''[[BGIOSGA030219]]'''
||
'''[[BGIOSGA000297]]'''
||
'''[[BGIOSGA003442]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA003440]]'''
||
'''[[BGIOSGA003443]]'''
||

||

||

|}

==MADS Box Protein Interactions==
===Comprehensive Analysis of MADS Box Transcription Factor Dimerization===
Remarkably, the MIKC proteins that contain the K-box, a domain specific for type II plant MADS box proteins that is presumed to fold into an amphipathic a-helical structure<ref name="ref8" /><ref name="ref9" /><ref name="ref10" />,interact preferably with other type II proteins and hardly form dimers with the type I MADS box proteins. However, there are some exceptions. In particular, there is a preference for interactions with type I proteins from the Ma subclade. Among the type I proteins, most heterodimers are found between members of different subclades. Interactions among Ma proteins are rare, but they dimerize preferentially with many proteins of the Mb and Mg clades. Similarly, only a few interactions among members of the Mb and Mg clades were observed, and Mb-Mg heterodimers are rare. This suggests that the participation of a Ma protein is a prerequisite for a stable dimer consisting of only type I proteins. Although many interactions were observed, a relatively large number of MADS domain proteins appeared to have no interactions at all. Possibly these proteins interact only with non-MADS box proteins, or alternatively,particular interactions are not formed in a yeast two-hybrid assay. For example, the interaction between the B-type proteins APETALA3 (AP3) and PISTILLATA (PI) was not found in this screen. Previously, these proteins appeared to interact exclusively in a higher-order complex, with either SEPALLATA3 (SEP3) or AP1<ref name="ref11" /> ,suggesting that the additional factors stabilize the AP3-PI dimer. This requirement for stabilizing factors to maintain specific dimers could be more general.Homodimerization is another form of MADS domain transcription factor interaction that is difficult to detect by yeast two-hybrid analysis <ref name="ref12" />,and hence, many homodimers have probably been missed in this screening.

Subsequently, the proteins were clustered based on the obtained interaction patterns, which allows the identification of proteins with similar interactions and groups of proteins that are highly connected (Figure 8). This analysis gives clues about the involvement of proteins in certain developmental programs. It reveals groups of proteins with common known functions, but more informatively, also shows clusters containing uncharacterized proteins, for which a function can now be predicted, based on their presence in a particular interaction cluster.
[[File:ABC_8.jpg]]'''Figure 8.'''

Interactome Map of the Arabidopsis MADS Box Transcription Factor Family.Proteins are organized based on hierarchical clustering of their protein–protein interaction patterns. Proteins that do not interact in the screen are omitted from this figure. Protein–protein interactions are indicated with red blocks and no interactions with green blocks. Presence of clustered proteins with a putative similar function is indicated with a colored bar on the left and bottom side of the figure: red for embryo, green for root, blue for flowering,and yellow for floral organs.
===The Flower Induction and Flower Organ Formation Subnetworks===
The regulation of flowering time is a complex process in which many environmental and internal signals are integrated, finally giving rise to a switch from vegetative to generative development at the appropriate time. MADS box transcription factors have shown to play pivotal roles in the flowering program and occupy many important positions in the hierarchical network <ref name="ref13" /><ref name="ref14" />.Based on the interaction data obtained in this study, we tried to unravel two subnetworks composed of interactions between known MADS box proteins involved in flower induction and flower organ formation (Figure 9). The proteins AP1 and FRUITFULL (FUL) are present in both subnetworks, which would refer to their early and late function in flowering <ref name="ref15" /><ref name="ref16" />.However, the most striking observation is that many of the floral organ identity proteins, such as AGAMOUS (AG), SEP1/2/3, and SHP1/2 proteins, interact not only with positive regulators of flowering, such as SUPPRESSOR OF CONSTANS 1 (SOC1) and AGAMOUS-LIKE 24(AGL24), but also with a negative regulator, SVP, implying that there is both positive and negative crosstalk between the two pathways via protein interactions, as pointed out above.

==Stress responsive MADS-box genes in rice==
MADS-box genes have been shown to be affected by low temperature stress in tomato <ref name="ref17" /> and by application of hormones like cytokinins, gibberellins <ref name="ref18" />, ethylene <ref name="ref19" />and auxins <ref name="ref20" /> in other plants. Seven MADS-box genes exhibited differential expression in response to cold, salt and/or desiccation stress in rice. So far, none of these genes has been implicated in stress response. Amongst stress-induced genes, OsMADS18 is a member of AP1/SQUA group that has been shown to express widely during development with its transcripts accumulating at high levels specifically in meristematic tissues <ref name="ref17" />. It has been shown to interact with OsMADS6, 8/24, 7/45, and 47 <ref name="ref21" /><ref name="ref22" />and in our analysis its expression pattern was found to overlap with those of OsMADS6, 8 and 7 in reproductive tissues and with OsMADS47 during vegetative development, suggesting that it might be interacting with different partners during reproductive development and stress. Recently, Tardif and coworkers showed that a large number of genes involved in flower development are associated with abiotic stress responses in wheat <ref name="ref23" />. Our preliminary analysis involving transcript profiling during reproductive development and abiotic stress conditions has also revealed approximately 400 genes that are up regulated during panicle/seed development and three stress conditions, viz. cold, salt, and dehydration (unpublished data). It would be, therefore, interesting to undertake specific investigations, which could establish the interactions of biochemical pathways that are activated during reproductive development and stress response.

==References==
<references>
* <ref name="ref1">
Arora R, Agarwal P, Ray S, et al. MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress[J]. BMC genomics, 2007, 8(1): 242.
</ref>
* <ref name="ref2">
Par̆enicová L, de Folter S, Kieffer M, et al. Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis new openings to the MADS world[J]. The Plant Cell Online, 2003, 15(7): 1538-1551.
</ref>
* <ref name="ref3">
Leseberg C H, Li A, Kang H, et al. Genome-wide analysis of the MADS-box gene family in Populus trichocarpa[J]. Gene, 2006, 378: 84-94.
</ref>
* <ref name="ref4">
Yang Y, Fanning L, Jack T: The K domain mediates heterodimerization of the Arabidopsis floral organ identity proteins,APETALA3 and PISTILLATA[J]. Plant J 2003, 33(1):47-59.
</ref>
* <ref name="ref5">
Egea Cortines M, Saedler H, Sommer H: Ternary complex formation between the MADS-box proteins SQUAMOSA, DEFICIENS and GLOBOSA is involved in the control of floral architecture in Antirrhinum majus[J]. EMBO J 1999, 18(19):5370-5379.
</ref>
* <ref name="ref6">
Cho S, Jang S, Chae S, Chung KM, Moon YH, An G, Jang SK: Analysis of the C-terminal region of Arabidopsis thaliana APETALA1 as a transcription activation domain. Plant Mol Biol 1999,40(3):419-429.
</ref>
* <ref name="ref7">
Rita Arora, Pinky Agarwal, Swatismita Ray.MADS-box gene family in rice: genome-wide identification,organization and expression profiling during reproductive development and stress.BMC Genomics,2007, 8:242.
</ref>
* <ref name="ref8">
Stefan de Folter,Richard G.H. Immink,Martin Kieffer,Lucie Parˇenicova´ ,et al.Comprehensive Interaction Map of the Arabidopsis MADS Box Transcription Factors.The Plant Cell, 2005, 17:1424–1433.
</ref>
* <ref name="ref9">
Alvarez-Buylla, E.R., Pelaz, S., Liljegren, S.J., Gold, S.E., et al. An ancestral MADS-box gene duplication occurred before the divergence of plants and animals. Proc. Natl. Acad. Sci.USA 2000,97:5328–5333.
</ref>
* <ref name="ref10">
Riechmann, J.L., and Meyerowitz, E.M. . MADS domain proteins in plant development. Biol. Chem,1997,378:1079–1101.
</ref>
* <ref name="ref11">
Honma, T., and Goto, K. . Complexes of MADS-box proteins are sufficient to convert leaves into floral organs. Nature ,2001,409:525–529.
</ref>
* <ref name="ref12">
Immink, R.G.H., and Angenent, G.C. . Transcription factors do it together: The hows and whys of studying protein-protein interactions.
Trends Plant Sci,2002, 7:531–534.
</ref>
* <ref name="ref13">
Blazquez,M.A.. Flower development pathways. J. Cell Sci.,2000,113:3547–3548.
</ref>
* <ref name="ref14">
Simpson, G.G., and Dean, C. . Arabidopsis, the Rosetta stone of flowering time? Science ,2002,296:285–289.
</ref>
* <ref name="ref15">
Mandel, M.A., Gustafson-Brown, C., Savidge, B., and Yanofsky,M.F. . Molecular characterization of the Arabidopsis floral homeotic gene APETALA1. Nature ,1992,360:273–277.
</ref>
* <ref name="ref16">
Ferrandiz, C., Gu, Q., Martienssen, R., and Yanofsky, M.F. .Redundant regulation of meristem identity and plant architecture by FRUITFULL, APETALA1 and CAULIFLOWER. Development ,2000,127:725–734.
</ref>
* <ref name="ref17">
Lozano R, Angosto T, Gomez P, Payan C, Capel J, Huijser P, Salinas J,Martinez-Zapater JM: Tomato flower abnormalities induced by low temperatures are associated with changes of expression of MADS-Box genes. Plant Physiol 1998, 117(1):91-100.
</ref>
* <ref name="ref18">
Bonhomme F, Kurz B, Melzer S, Bernier G, Jacqmard A: Cytokinin and gibberellin activate SaMADS A, a gene apparently involved in regulation of the floral transition in Sinapis alba.Plant J 2000, 24(1):103-111.
</ref>
* <ref name="ref19">
Ando S, Sato Y, Kamachi S, Sakai S: Isolation of a MADS-box gene
(ERAF17) and correlation of its expression with the induction of formation of female flowers by ethylene in cucumber plants (Cucumis sativus L.). Planta 2001, 213(6):943-952.
</ref>
* <ref name="ref20">
Zhu C, Perry SE: Control of expression and autoregulation of AGL15, a member of the MADS-box family. Plant J 2005,41(4):583-594.
</ref>
* <ref name="ref21">
Fornara F, Parenicova L, Falasca G, Pelucchi N, Masiero S, Ciannamea S, Lopez-Dee Z, Altamura MM, Colombo L, Kater MM: Functional characterization of OsMADS18, a member of the AP1/SQUA subfamily of MADS box genes. Plant Physiol 2004,135(4):2207-2219.
</ref>
* <ref name="ref22">
Moon YH, Jung JY, Kang HG, An G: Identification of a rice APETALA3 homologue by yeast two-hybrid screening. Plant Mol Biol 1999, 40(1):167-177.
</ref>
* <ref name="ref23">
Tardif G, Kane NA, Adam H, Labrie L, Major G, Gulick P, Sarhan F,
Laliberte JF: Interaction network of proteins associated with abiotic stress response and development in wheat. Plant Mol Biol 2007, 63(5):703-718.
</ref>

</references>

MADS

2014-06-07T09:55:37Z

Kathy: /* Comprehensive Analysis of MADS Box Transcription Factor Dimerization */

==Brief Introduction==
===Background===
MADS-box family member are known to be involved in many important processes during plant growth and development<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The word MADS finds its origin from the first letters of its founding members, Mini Chromosome Maintenance 1 (MCM1) of yeast (Saccharomyces cerevisiae), Agamous (AG) of Arabidopsis (Arabidopsis thaliana), Deficiens (DEF) of snapdragon (Antirrhinum majus) and Serum Response Factor (SRF) of humans (Homo sapiens)<ref name="ref1" />.

They are characterized by the presence of a conserved domain of approximately 60 amino acids located in the N-terminal region; this domain is named the MADS-box domain and is involved in DNA binding and dimerization<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The MADS-box family has been divided into two main groups. The type I consists of ARG80/SRF-like genes of animals and fungi, also designated as M-type genes in plants, and type II contains MEF2-like genes of animals and yeast as well as MIKC-type genes of plants<ref name="ref1" /><ref name="ref3" />.The plant-specific MIKC-type MADS-box proteins include three additional domains followed by the MADS domain, viz. a less-conserved Intervening region of ~30 amino acids, a moderately conserved Keratin-like domain of ~70 amino acids mainly involved in heterodimerization, and a highly variable C-terminal region of variable length implicated in transcriptional activation and higher-order complex formation<ref name="ref4" /><ref name="ref5" /<ref name="ref6" />.
[[File:mads_box1.jpg|center|thumb|1000px|'''Figure 1.''' ''Protein Structure of '''BGIOSGA004940''' '']]
[[File:Gene_tree_1.jpg]]'''Figure 2.Gene tree'''

===Evolutionary relationships between rice and Arabidopsis MADS-box family genes===
A separate phylogenetic tree was also generated from complete protein sequences of all the MADS-box genes in rice and Arabidopsis (Figure 3). Of the 75 rice MADS-box genes, 38 grouped with MIKCc, six with MIKC*, nine with Mβ, 13 with Mα and 10 grouped with Mγ-type Arabidopsis genes<ref name="ref7" />.

[[File:Gene_tree_2.jpg]]'''Figure 3.Phylogenetic analysis of rice and Arabidopsis MADS-box proteins'''

===MADS-box transcription factors ===
The best studied plant MADS-box transcription factors are those involved in floral organ identity determination. Combinations of A-, B-, and C-function genes determine the development of the four whorls of an Arabidopsis flower: A-function genes determine sepal development; A- and B-function genes determine petal development; B- and C function genes determine the stamen development, and C-function genes are necessary for carpel development<ref name="ref2" /><ref name="ref3" />.

== Organization and structure of MADS-box genes==
===Location of genes===
The individual genes were localized on chromosomes based on the 5' and 3' coordinates for respective gene models in TIGR database.Out of five types of MADS-box genes, the Mγ genes were confined to chromosome 1, 3 and 4, while Mβ genes were present only on chromosome 1. No chromosomal bias was observed in the distribution of MIKCc,MIKC* and Mα genes.<ref name="ref7" />
[[File:Gene_location.jpg]]
'''Figure 4.''' Chromosomal location of rice MADS-box '''

===Distribution of conserved motifs===
The MEME motif search tool was employed to identify the conserved motifs present in MADS-box proteins (Figure 5). Motifs 1, 6 or 2 specifying the MADS domain were found in all the members of the MADS-box family. All proteins belonging to MIKCc and MIKC* groups had motif 1-type MADS domain..Most Mα proteins also had the motif 1-type MADS domain except OsMADS72 and 77 which contained motif 6. Motif 6 was found to be the most common type of MADS domain in Mβ-type proteins.Distinctively, in case of Mγ proteins a larger MADS domain of 83 amino acids was detected, followed by a coiled coil region and a region of unknown complexity as indicated by Simple Modular Architecture Research Tool (SMART) version 3.4<ref name="ref7" />.
[[File:Conserved_motifs.jpg]]'''Figure 5.Distribution of Conserved motifs in rice MADS-box proteins'''

===Expression profiling of MADS-box genes===
Expression profiles have been generated using avadis™ software version 4.2. X-axis represents the developmental stages. Y-axis represents average log2 expression values.Genes exhibiting these expression patterns have been represented by numbers. Dotted lines have been drawn to demarcate vegetative organs, panicle and seed developmental stages（Figure 6）.
[[File:Expression_patterns.jpg]]'''Figure 6.Expression patterns of MADS-box genes in rice in vegetative as well as panicle and seed development.'''
[[File:Differential_expressions.jpg]]'''Figure 7.'''

Differential expressions shown by seven MADS-box genes in response to various abiotic stress conditions.Left panel shows four genes up regulated and right panel shows down regulated genes more than 2 folds with p value less than 0.05 in response to three abiotic stress conditions. X-axis represents seedling followed by stress samples (CS, cold stress; DS, dehydration stress; SS, salt stress). Y-axis represents average expression values obtained using microarrays. Error bars represent standard error for data obtained in three biological replicates(Figure 7).

==''Japonica'' Group==
{| style="background:#A1A3A6; width:85%;" border="0"
|-style="background:white; color:black" align="center"
!
'''[[Os01g0201700]]'''
||
'''[[Os02g0682200]]'''
||
'''[[Os04g0580700]]'''
||
'''[[Os09g0507200]]'''
||
'''[[Os08g0531700]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os07g0605200]]'''
||
'''[[Os07g0108900]]'''
||
'''[[Os05g0203800]]'''
||
'''[[Os12g0207000]]'''
||
'''[[Os03g0752800]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os03g0122600]]'''
||
'''[[Os10g0536100]]'''
||
'''[[Os06g0162800]]'''
||
'''[[Os01g0883100]]'''
||
'''[[Os01g0886200]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os04g0461300]]'''
||
'''[[Os06g0712700]]'''
||
'''[[Os02g0731200]]'''
||
'''[[Os03g0215400]]'''
||
'''[[Os02g0579600]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os12g0206800]]'''
||
'''[[Os08g0531900]]'''
||
'''[[Os03g0753100]]'''
||
'''[[Os05g0203600]]'''
||
'''[[Os02g0170300]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os02g0761000]]'''
||
'''[[Os04g0614100]]'''
||
'''[[Os05g0423400]]'''
||
'''[[Os08g0431900]]'''
||
'''[[Os04g0304400]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os06g0223300]]'''
||
'''[[Os06g0667200]]'''
||
'''[[Os06g0217300]]'''
||
'''[[Os03g0186600]]'''
||
'''[[Os01g0922800]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os12g0501700]]'''
||
'''[[Os08g0112700]]'''
||
'''[[Os01g0726400]]'''
||
'''[[Os12g0407400]]'''
||
'''[[Os11g0658700]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os04g0387400]]'''
||
'''[[Os03g0253400]]'''
||

||

||

|}
==''Indica'' Group==
{| style="background:#A1A3A6; width:85%;" border="0"
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA002178]]'''
||
'''[[BGIOSGA008820]]'''
||
'''[[BGIOSGA016980]]'''
||
'''[[BGIOSGA031056]]'''
||
'''[[BGIOSGA029052]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA026097]]'''
||
'''[[BGIOSGA018621]]'''
||
'''[[BGIOSGA024961]]'''
||
'''[[BGIOSGA009798]]'''
||
'''[[BGIOSGA033356]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA021849]]'''
||
'''[[BGIOSGA000377]]'''
||
'''[[BGIOSGA004940]]'''
||
'''[[BGIOSGA020546]]'''
||
'''[[BGIOSGA007336]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA011213]]'''
||
'''[[BGIOSGA026745]]'''
||
'''[[BGIOSGA008494]]'''
||
'''[[BGIOSGA022872]]'''
||
'''[[BGIOSGA036463]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA009797]]'''
||
'''[[BGIOSGA026939]]'''
||
'''[[BGIOSGA008983]]'''
||
'''[[BGIOSGA007056]]'''
||
'''[[BGIOSGA018624]]''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA007333]]'''
||
'''[[BGIOSGA009093]]'''
||
'''[[BGIOSGA022154]]'''
||
'''[[BGIOSGA019900]]'''
||
'''[[BGIOSGA016106]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA029053]]'''
||
'''[[BGIOSGA017110]]'''
||
'''[[BGIOSGA003731]]'''
||
'''[[BGIOSGA016105]]'''
||
'''[[BGIOSGA005076]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA015021]]'''
||
'''[[BGIOSGA023435]]'''
||
'''[[BGIOSGA021662]]'''
||
'''[[BGIOSGA011317]]'''
||
'''[[BGIOSGA036149]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA027872]]'''
||
'''[[BGIOSGA007600]]'''
||
'''[[BGIOSGA000892]]'''
||
'''[[BGIOSGA018453]]'''
||
'''[[BGIOSGA006672]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA030217]]'''
||
'''[[BGIOSGA005284]]'''
||
'''[[BGIOSGA035654]]'''
||
'''[[BGIOSGA021177]]'''
||
'''[[BGIOSGA003304]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA036334]]'''
||
'''[[BGIOSGA022830]]'''
||
'''[[BGIOSGA028419]]'''
||
'''[[BGIOSGA018341]]'''
||
'''[[BGIOSGA015023]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA000269]]'''
||
'''[[BGIOSGA003303]]'''
||
'''[[BGIOSGA011095]]'''
||
'''[[BGIOSGA016270]]'''
||
'''[[BGIOSGA003441]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA002989]]'''
||
'''[[BGIOSGA034252]]'''
||
'''[[BGIOSGA030219]]'''
||
'''[[BGIOSGA000297]]'''
||
'''[[BGIOSGA003442]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA003440]]'''
||
'''[[BGIOSGA003443]]'''
||

||

||

|}

==MADS Box Protein Interactions==
===Comprehensive Analysis of MADS Box Transcription Factor Dimerization===
Remarkably, the MIKC proteins that contain the K-box, a domain specific for type II plant MADS box proteins that is presumed to fold into an amphipathic a-helical structure<ref name="ref8" /><ref name="ref9" /><ref name="ref10" />,interact preferably with other type II proteins and hardly form dimers with the type I MADS box proteins. However, there are some exceptions. In particular, there is a preference for interactions with type I proteins from the Ma subclade. Among the type I proteins, most heterodimers are found between members of different subclades. Interactions among Ma proteins are rare, but they dimerize preferentially with many proteins of the Mb and Mg clades. Similarly, only a few interactions among members of the Mb and Mg clades were observed, and Mb-Mg heterodimers are rare. This suggests that the participation of a Ma protein is a prerequisite for a stable dimer consisting of only type I proteins. Although many interactions were observed, a relatively large number of MADS domain proteins appeared to have no interactions at all. Possibly these proteins interact only with non-MADS box proteins, or alternatively,particular interactions are not formed in a yeast two-hybrid assay. For example, the interaction between the B-type proteins APETALA3 (AP3) and PISTILLATA (PI) was not found in this screen. Previously, these proteins appeared to interact exclusively in a higher-order complex, with either SEPALLATA3 (SEP3) or AP1<ref name="ref11" /> ,suggesting that the additional factors stabilize the AP3-PI dimer. This requirement for stabilizing factors to maintain specific dimers could be more general.Homodimerization is another form of MADS domain transcription factor interaction that is difficult to detect by yeast two-hybrid analysis <ref name="ref12" />,and hence, many homodimers have probably been missed in this screening.

Subsequently, the proteins were clustered based on the obtained interaction patterns, which allows the identification of proteins with similar interactions and groups of proteins that are highly connected (Figure 8). This analysis gives clues about the involvement of proteins in certain developmental programs. It reveals groups of proteins with common known functions, but more informatively, also shows clusters containing uncharacterized proteins, for which a function can now be predicted, based on their presence in a particular interaction cluster.
[[File:ABC_8.jpg]]'''Figure 8.'''

Interactome Map of the Arabidopsis MADS Box Transcription Factor Family.Proteins are organized based on hierarchical clustering of their protein–protein interaction patterns. Proteins that do not interact in the screen are omitted from this figure. Protein–protein interactions are indicated with red blocks and no interactions with green blocks. Presence of clustered proteins with a putative similar function is indicated with a colored bar on the left and bottom side of the figure: red for embryo, green for root, blue for flowering,and yellow for floral organs.

==Stress responsive MADS-box genes in rice==
MADS-box genes have been shown to be affected by low temperature stress in tomato <ref name="ref13" /> and by application of hormones like cytokinins, gibberellins <ref name="ref14" />, ethylene <ref name="ref15" />and auxins <ref name="ref16" /> in other plants. Seven MADS-box genes exhibited differential expression in response to cold, salt and/or desiccation stress in rice. So far, none of these genes has been implicated in stress response. Amongst stress-induced genes, OsMADS18 is a member of AP1/SQUA group that has been shown to express widely during development with its transcripts accumulating at high levels specifically in meristematic tissues <ref name="ref17" />. It has been shown to interact with OsMADS6, 8/24, 7/45, and 47 <ref name="ref17" /><ref name="ref18" />and in our analysis its expression pattern was found to overlap with those of OsMADS6, 8 and 7 in reproductive tissues and with OsMADS47 during vegetative development, suggesting that it might be interacting with different partners during reproductive development and stress. Recently, Tardif and coworkers showed that a large number of genes involved in flower development are associated with abiotic stress responses in wheat <ref name="ref19" />. Our preliminary analysis involving transcript profiling during reproductive development and abiotic stress conditions has also revealed approximately 400 genes that are up regulated during panicle/seed development and three stress conditions, viz. cold, salt, and dehydration (unpublished data). It would be, therefore, interesting to undertake specific investigations, which could establish the interactions of biochemical pathways that are activated during reproductive development and stress response.

==References==
<references>
* <ref name="ref1">
Arora R, Agarwal P, Ray S, et al. MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress[J]. BMC genomics, 2007, 8(1): 242.
</ref>
* <ref name="ref2">
Par̆enicová L, de Folter S, Kieffer M, et al. Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis new openings to the MADS world[J]. The Plant Cell Online, 2003, 15(7): 1538-1551.
</ref>
* <ref name="ref3">
Leseberg C H, Li A, Kang H, et al. Genome-wide analysis of the MADS-box gene family in Populus trichocarpa[J]. Gene, 2006, 378: 84-94.
</ref>
* <ref name="ref4">
Yang Y, Fanning L, Jack T: The K domain mediates heterodimerization of the Arabidopsis floral organ identity proteins,APETALA3 and PISTILLATA[J]. Plant J 2003, 33(1):47-59.
</ref>
* <ref name="ref5">
Egea Cortines M, Saedler H, Sommer H: Ternary complex formation between the MADS-box proteins SQUAMOSA, DEFICIENS and GLOBOSA is involved in the control of floral architecture in Antirrhinum majus[J]. EMBO J 1999, 18(19):5370-5379.
</ref>
* <ref name="ref6">
Cho S, Jang S, Chae S, Chung KM, Moon YH, An G, Jang SK: Analysis of the C-terminal region of Arabidopsis thaliana APETALA1 as a transcription activation domain. Plant Mol Biol 1999,40(3):419-429.
</ref>
* <ref name="ref7">
Rita Arora, Pinky Agarwal, Swatismita Ray.MADS-box gene family in rice: genome-wide identification,organization and expression profiling during reproductive development and stress.BMC Genomics,2007, 8:242.
</ref>
* <ref name="ref8">
Stefan de Folter,Richard G.H. Immink,Martin Kieffer,Lucie Parˇenicova´ ,et al.Comprehensive Interaction Map of the Arabidopsis MADS Box Transcription Factors.The Plant Cell, 2005, 17:1424–1433.
</ref>
* <ref name="ref9">
Alvarez-Buylla, E.R., Pelaz, S., Liljegren, S.J., Gold, S.E., et al. An ancestral MADS-box gene duplication occurred before the divergence of plants and animals. Proc. Natl. Acad. Sci.USA 2000,97:5328–5333.
</ref>
* <ref name="ref10">
Riechmann, J.L., and Meyerowitz, E.M. . MADS domain proteins in plant development. Biol. Chem,1997,378:1079–1101.
</ref>
* <ref name="ref11">
Honma, T., and Goto, K. . Complexes of MADS-box proteins are sufficient to convert leaves into floral organs. Nature ,2001,409:525–529.
</ref>
* <ref name="ref12">
Immink, R.G.H., and Angenent, G.C. . Transcription factors do it together: The hows and whys of studying protein-protein interactions.
Trends Plant Sci,2002, 7:531–534.
</ref>
* <ref name="ref13">
Lozano R, Angosto T, Gomez P, Payan C, Capel J, Huijser P, Salinas J,Martinez-Zapater JM: Tomato flower abnormalities induced by low temperatures are associated with changes of expression of MADS-Box genes. Plant Physiol 1998, 117(1):91-100.
</ref>
* <ref name="ref14">
Bonhomme F, Kurz B, Melzer S, Bernier G, Jacqmard A: Cytokinin and gibberellin activate SaMADS A, a gene apparently involved in regulation of the floral transition in Sinapis alba.Plant J 2000, 24(1):103-111.
</ref>
* <ref name="ref15">
Ando S, Sato Y, Kamachi S, Sakai S: Isolation of a MADS-box gene
(ERAF17) and correlation of its expression with the induction of formation of female flowers by ethylene in cucumber plants (Cucumis sativus L.). Planta 2001, 213(6):943-952.
</ref>
* <ref name="ref16">
Zhu C, Perry SE: Control of expression and autoregulation of AGL15, a member of the MADS-box family. Plant J 2005,41(4):583-594.
</ref>
* <ref name="ref17">
Fornara F, Parenicova L, Falasca G, Pelucchi N, Masiero S, Ciannamea S, Lopez-Dee Z, Altamura MM, Colombo L, Kater MM: Functional characterization of OsMADS18, a member of the AP1/SQUA subfamily of MADS box genes. Plant Physiol 2004,135(4):2207-2219.
</ref>
* <ref name="ref18">
Moon YH, Jung JY, Kang HG, An G: Identification of a rice APETALA3 homologue by yeast two-hybrid screening. Plant Mol Biol 1999, 40(1):167-177.
</ref>
* <ref name="ref19">
Tardif G, Kane NA, Adam H, Labrie L, Major G, Gulick P, Sarhan F,
Laliberte JF: Interaction network of proteins associated with abiotic stress response and development in wheat. Plant Mol Biol 2007, 63(5):703-718.
</ref>

</references>

MADS

2014-06-07T09:55:05Z

Kathy: /* Comprehensive Analysis of MADS Box Transcription Factor Dimerization */

==Brief Introduction==
===Background===
MADS-box family member are known to be involved in many important processes during plant growth and development<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The word MADS finds its origin from the first letters of its founding members, Mini Chromosome Maintenance 1 (MCM1) of yeast (Saccharomyces cerevisiae), Agamous (AG) of Arabidopsis (Arabidopsis thaliana), Deficiens (DEF) of snapdragon (Antirrhinum majus) and Serum Response Factor (SRF) of humans (Homo sapiens)<ref name="ref1" />.

They are characterized by the presence of a conserved domain of approximately 60 amino acids located in the N-terminal region; this domain is named the MADS-box domain and is involved in DNA binding and dimerization<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The MADS-box family has been divided into two main groups. The type I consists of ARG80/SRF-like genes of animals and fungi, also designated as M-type genes in plants, and type II contains MEF2-like genes of animals and yeast as well as MIKC-type genes of plants<ref name="ref1" /><ref name="ref3" />.The plant-specific MIKC-type MADS-box proteins include three additional domains followed by the MADS domain, viz. a less-conserved Intervening region of ~30 amino acids, a moderately conserved Keratin-like domain of ~70 amino acids mainly involved in heterodimerization, and a highly variable C-terminal region of variable length implicated in transcriptional activation and higher-order complex formation<ref name="ref4" /><ref name="ref5" /<ref name="ref6" />.
[[File:mads_box1.jpg|center|thumb|1000px|'''Figure 1.''' ''Protein Structure of '''BGIOSGA004940''' '']]
[[File:Gene_tree_1.jpg]]'''Figure 2.Gene tree'''

===Evolutionary relationships between rice and Arabidopsis MADS-box family genes===
A separate phylogenetic tree was also generated from complete protein sequences of all the MADS-box genes in rice and Arabidopsis (Figure 3). Of the 75 rice MADS-box genes, 38 grouped with MIKCc, six with MIKC*, nine with Mβ, 13 with Mα and 10 grouped with Mγ-type Arabidopsis genes<ref name="ref7" />.

[[File:Gene_tree_2.jpg]]'''Figure 3.Phylogenetic analysis of rice and Arabidopsis MADS-box proteins'''

===MADS-box transcription factors ===
The best studied plant MADS-box transcription factors are those involved in floral organ identity determination. Combinations of A-, B-, and C-function genes determine the development of the four whorls of an Arabidopsis flower: A-function genes determine sepal development; A- and B-function genes determine petal development; B- and C function genes determine the stamen development, and C-function genes are necessary for carpel development<ref name="ref2" /><ref name="ref3" />.

== Organization and structure of MADS-box genes==
===Location of genes===
The individual genes were localized on chromosomes based on the 5' and 3' coordinates for respective gene models in TIGR database.Out of five types of MADS-box genes, the Mγ genes were confined to chromosome 1, 3 and 4, while Mβ genes were present only on chromosome 1. No chromosomal bias was observed in the distribution of MIKCc,MIKC* and Mα genes.<ref name="ref7" />
[[File:Gene_location.jpg]]
'''Figure 4.''' Chromosomal location of rice MADS-box '''

===Distribution of conserved motifs===
The MEME motif search tool was employed to identify the conserved motifs present in MADS-box proteins (Figure 5). Motifs 1, 6 or 2 specifying the MADS domain were found in all the members of the MADS-box family. All proteins belonging to MIKCc and MIKC* groups had motif 1-type MADS domain..Most Mα proteins also had the motif 1-type MADS domain except OsMADS72 and 77 which contained motif 6. Motif 6 was found to be the most common type of MADS domain in Mβ-type proteins.Distinctively, in case of Mγ proteins a larger MADS domain of 83 amino acids was detected, followed by a coiled coil region and a region of unknown complexity as indicated by Simple Modular Architecture Research Tool (SMART) version 3.4<ref name="ref7" />.
[[File:Conserved_motifs.jpg]]'''Figure 5.Distribution of Conserved motifs in rice MADS-box proteins'''

===Expression profiling of MADS-box genes===
Expression profiles have been generated using avadis™ software version 4.2. X-axis represents the developmental stages. Y-axis represents average log2 expression values.Genes exhibiting these expression patterns have been represented by numbers. Dotted lines have been drawn to demarcate vegetative organs, panicle and seed developmental stages（Figure 6）.
[[File:Expression_patterns.jpg]]'''Figure 6.Expression patterns of MADS-box genes in rice in vegetative as well as panicle and seed development.'''
[[File:Differential_expressions.jpg]]'''Figure 7.'''

Differential expressions shown by seven MADS-box genes in response to various abiotic stress conditions.Left panel shows four genes up regulated and right panel shows down regulated genes more than 2 folds with p value less than 0.05 in response to three abiotic stress conditions. X-axis represents seedling followed by stress samples (CS, cold stress; DS, dehydration stress; SS, salt stress). Y-axis represents average expression values obtained using microarrays. Error bars represent standard error for data obtained in three biological replicates(Figure 7).

==''Japonica'' Group==
{| style="background:#A1A3A6; width:85%;" border="0"
|-style="background:white; color:black" align="center"
!
'''[[Os01g0201700]]'''
||
'''[[Os02g0682200]]'''
||
'''[[Os04g0580700]]'''
||
'''[[Os09g0507200]]'''
||
'''[[Os08g0531700]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os07g0605200]]'''
||
'''[[Os07g0108900]]'''
||
'''[[Os05g0203800]]'''
||
'''[[Os12g0207000]]'''
||
'''[[Os03g0752800]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os03g0122600]]'''
||
'''[[Os10g0536100]]'''
||
'''[[Os06g0162800]]'''
||
'''[[Os01g0883100]]'''
||
'''[[Os01g0886200]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os04g0461300]]'''
||
'''[[Os06g0712700]]'''
||
'''[[Os02g0731200]]'''
||
'''[[Os03g0215400]]'''
||
'''[[Os02g0579600]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os12g0206800]]'''
||
'''[[Os08g0531900]]'''
||
'''[[Os03g0753100]]'''
||
'''[[Os05g0203600]]'''
||
'''[[Os02g0170300]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os02g0761000]]'''
||
'''[[Os04g0614100]]'''
||
'''[[Os05g0423400]]'''
||
'''[[Os08g0431900]]'''
||
'''[[Os04g0304400]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os06g0223300]]'''
||
'''[[Os06g0667200]]'''
||
'''[[Os06g0217300]]'''
||
'''[[Os03g0186600]]'''
||
'''[[Os01g0922800]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os12g0501700]]'''
||
'''[[Os08g0112700]]'''
||
'''[[Os01g0726400]]'''
||
'''[[Os12g0407400]]'''
||
'''[[Os11g0658700]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os04g0387400]]'''
||
'''[[Os03g0253400]]'''
||

||

||

|}
==''Indica'' Group==
{| style="background:#A1A3A6; width:85%;" border="0"
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA002178]]'''
||
'''[[BGIOSGA008820]]'''
||
'''[[BGIOSGA016980]]'''
||
'''[[BGIOSGA031056]]'''
||
'''[[BGIOSGA029052]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA026097]]'''
||
'''[[BGIOSGA018621]]'''
||
'''[[BGIOSGA024961]]'''
||
'''[[BGIOSGA009798]]'''
||
'''[[BGIOSGA033356]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA021849]]'''
||
'''[[BGIOSGA000377]]'''
||
'''[[BGIOSGA004940]]'''
||
'''[[BGIOSGA020546]]'''
||
'''[[BGIOSGA007336]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA011213]]'''
||
'''[[BGIOSGA026745]]'''
||
'''[[BGIOSGA008494]]'''
||
'''[[BGIOSGA022872]]'''
||
'''[[BGIOSGA036463]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA009797]]'''
||
'''[[BGIOSGA026939]]'''
||
'''[[BGIOSGA008983]]'''
||
'''[[BGIOSGA007056]]'''
||
'''[[BGIOSGA018624]]''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA007333]]'''
||
'''[[BGIOSGA009093]]'''
||
'''[[BGIOSGA022154]]'''
||
'''[[BGIOSGA019900]]'''
||
'''[[BGIOSGA016106]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA029053]]'''
||
'''[[BGIOSGA017110]]'''
||
'''[[BGIOSGA003731]]'''
||
'''[[BGIOSGA016105]]'''
||
'''[[BGIOSGA005076]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA015021]]'''
||
'''[[BGIOSGA023435]]'''
||
'''[[BGIOSGA021662]]'''
||
'''[[BGIOSGA011317]]'''
||
'''[[BGIOSGA036149]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA027872]]'''
||
'''[[BGIOSGA007600]]'''
||
'''[[BGIOSGA000892]]'''
||
'''[[BGIOSGA018453]]'''
||
'''[[BGIOSGA006672]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA030217]]'''
||
'''[[BGIOSGA005284]]'''
||
'''[[BGIOSGA035654]]'''
||
'''[[BGIOSGA021177]]'''
||
'''[[BGIOSGA003304]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA036334]]'''
||
'''[[BGIOSGA022830]]'''
||
'''[[BGIOSGA028419]]'''
||
'''[[BGIOSGA018341]]'''
||
'''[[BGIOSGA015023]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA000269]]'''
||
'''[[BGIOSGA003303]]'''
||
'''[[BGIOSGA011095]]'''
||
'''[[BGIOSGA016270]]'''
||
'''[[BGIOSGA003441]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA002989]]'''
||
'''[[BGIOSGA034252]]'''
||
'''[[BGIOSGA030219]]'''
||
'''[[BGIOSGA000297]]'''
||
'''[[BGIOSGA003442]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA003440]]'''
||
'''[[BGIOSGA003443]]'''
||

||

||

|}

==MADS Box Protein Interactions==
===Comprehensive Analysis of MADS Box Transcription Factor Dimerization===
Remarkably, the MIKC proteins that contain the K-box, a domain specific for type II plant MADS box proteins that is presumed to fold into an amphipathic a-helical structure<ref name="ref8" /><ref name="ref9" /><ref name="ref10" />,interact preferably with other type II proteins and hardly form dimers with the type I MADS box proteins. However, there are some exceptions. In particular, there is a preference for interactions with type I proteins from the Ma subclade. Among the type I proteins, most heterodimers are found between members of different subclades. Interactions among Ma proteins are rare, but they dimerize preferentially with many proteins of the Mb and Mg clades. Similarly, only a few interactions among members of the Mb and Mg clades were observed, and Mb-Mg heterodimers are rare. This suggests that the participation of a Ma protein is a prerequisite for a stable dimer consisting of only type I proteins. Although many interactions were observed, a relatively large number of MADS domain proteins appeared to have no interactions at all. Possibly these proteins interact only with non-MADS box proteins, or alternatively,particular interactions are not formed in a yeast two-hybrid assay. For example, the interaction between the B-type proteins APETALA3 (AP3) and PISTILLATA (PI) was not found in this screen. Previously, these proteins appeared to interact exclusively in a higher-order complex, with either SEPALLATA3 (SEP3) or AP1<ref name="ref11" /> ,suggesting that the additional factors stabilize the AP3-PI dimer. This requirement for stabilizing factors to maintain specific dimers could be more general.Homodimerization is another form of MADS domain transcription factor interaction that is difficult to detect by yeast two-hybrid analysis <ref name="ref12" />,and hence, many homodimers have probably been missed in this screening.

Subsequently, the proteins were clustered based on the obtained interaction patterns, which allows the identification of proteins with similar interactions and groups of proteins that are highly connected (Figure 8). This analysis gives clues about the involvement of proteins in certain developmental programs. It reveals groups of proteins with common known functions, but more informatively, also shows clusters containing uncharacterized proteins, for which a function can now be predicted, based on their presence in a particular interaction cluster.
[[File:ABC_8.jpg]]'''Figure 8.'''
Interactome Map of the Arabidopsis MADS Box Transcription Factor Family.Proteins are organized based on hierarchical clustering of their protein–protein interaction patterns. Proteins that do not interact in the screen are omitted from this figure. Protein–protein interactions are indicated with red blocks and no interactions with green blocks. Presence of clustered proteins with a putative similar function is indicated with a colored bar on the left and bottom side of the figure: red for embryo, green for root, blue for flowering,and yellow for floral organs.

==Stress responsive MADS-box genes in rice==
MADS-box genes have been shown to be affected by low temperature stress in tomato <ref name="ref13" /> and by application of hormones like cytokinins, gibberellins <ref name="ref14" />, ethylene <ref name="ref15" />and auxins <ref name="ref16" /> in other plants. Seven MADS-box genes exhibited differential expression in response to cold, salt and/or desiccation stress in rice. So far, none of these genes has been implicated in stress response. Amongst stress-induced genes, OsMADS18 is a member of AP1/SQUA group that has been shown to express widely during development with its transcripts accumulating at high levels specifically in meristematic tissues <ref name="ref17" />. It has been shown to interact with OsMADS6, 8/24, 7/45, and 47 <ref name="ref17" /><ref name="ref18" />and in our analysis its expression pattern was found to overlap with those of OsMADS6, 8 and 7 in reproductive tissues and with OsMADS47 during vegetative development, suggesting that it might be interacting with different partners during reproductive development and stress. Recently, Tardif and coworkers showed that a large number of genes involved in flower development are associated with abiotic stress responses in wheat <ref name="ref19" />. Our preliminary analysis involving transcript profiling during reproductive development and abiotic stress conditions has also revealed approximately 400 genes that are up regulated during panicle/seed development and three stress conditions, viz. cold, salt, and dehydration (unpublished data). It would be, therefore, interesting to undertake specific investigations, which could establish the interactions of biochemical pathways that are activated during reproductive development and stress response.

==References==
<references>
* <ref name="ref1">
Arora R, Agarwal P, Ray S, et al. MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress[J]. BMC genomics, 2007, 8(1): 242.
</ref>
* <ref name="ref2">
Par̆enicová L, de Folter S, Kieffer M, et al. Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis new openings to the MADS world[J]. The Plant Cell Online, 2003, 15(7): 1538-1551.
</ref>
* <ref name="ref3">
Leseberg C H, Li A, Kang H, et al. Genome-wide analysis of the MADS-box gene family in Populus trichocarpa[J]. Gene, 2006, 378: 84-94.
</ref>
* <ref name="ref4">
Yang Y, Fanning L, Jack T: The K domain mediates heterodimerization of the Arabidopsis floral organ identity proteins,APETALA3 and PISTILLATA[J]. Plant J 2003, 33(1):47-59.
</ref>
* <ref name="ref5">
Egea Cortines M, Saedler H, Sommer H: Ternary complex formation between the MADS-box proteins SQUAMOSA, DEFICIENS and GLOBOSA is involved in the control of floral architecture in Antirrhinum majus[J]. EMBO J 1999, 18(19):5370-5379.
</ref>
* <ref name="ref6">
Cho S, Jang S, Chae S, Chung KM, Moon YH, An G, Jang SK: Analysis of the C-terminal region of Arabidopsis thaliana APETALA1 as a transcription activation domain. Plant Mol Biol 1999,40(3):419-429.
</ref>
* <ref name="ref7">
Rita Arora, Pinky Agarwal, Swatismita Ray.MADS-box gene family in rice: genome-wide identification,organization and expression profiling during reproductive development and stress.BMC Genomics,2007, 8:242.
</ref>
* <ref name="ref8">
Stefan de Folter,Richard G.H. Immink,Martin Kieffer,Lucie Parˇenicova´ ,et al.Comprehensive Interaction Map of the Arabidopsis MADS Box Transcription Factors.The Plant Cell, 2005, 17:1424–1433.
</ref>
* <ref name="ref9">
Alvarez-Buylla, E.R., Pelaz, S., Liljegren, S.J., Gold, S.E., et al. An ancestral MADS-box gene duplication occurred before the divergence of plants and animals. Proc. Natl. Acad. Sci.USA 2000,97:5328–5333.
</ref>
* <ref name="ref10">
Riechmann, J.L., and Meyerowitz, E.M. . MADS domain proteins in plant development. Biol. Chem,1997,378:1079–1101.
</ref>
* <ref name="ref11">
Honma, T., and Goto, K. . Complexes of MADS-box proteins are sufficient to convert leaves into floral organs. Nature ,2001,409:525–529.
</ref>
* <ref name="ref12">
Immink, R.G.H., and Angenent, G.C. . Transcription factors do it together: The hows and whys of studying protein-protein interactions.
Trends Plant Sci,2002, 7:531–534.
</ref>
* <ref name="ref13">
Lozano R, Angosto T, Gomez P, Payan C, Capel J, Huijser P, Salinas J,Martinez-Zapater JM: Tomato flower abnormalities induced by low temperatures are associated with changes of expression of MADS-Box genes. Plant Physiol 1998, 117(1):91-100.
</ref>
* <ref name="ref14">
Bonhomme F, Kurz B, Melzer S, Bernier G, Jacqmard A: Cytokinin and gibberellin activate SaMADS A, a gene apparently involved in regulation of the floral transition in Sinapis alba.Plant J 2000, 24(1):103-111.
</ref>
* <ref name="ref15">
Ando S, Sato Y, Kamachi S, Sakai S: Isolation of a MADS-box gene
(ERAF17) and correlation of its expression with the induction of formation of female flowers by ethylene in cucumber plants (Cucumis sativus L.). Planta 2001, 213(6):943-952.
</ref>
* <ref name="ref16">
Zhu C, Perry SE: Control of expression and autoregulation of AGL15, a member of the MADS-box family. Plant J 2005,41(4):583-594.
</ref>
* <ref name="ref17">
Fornara F, Parenicova L, Falasca G, Pelucchi N, Masiero S, Ciannamea S, Lopez-Dee Z, Altamura MM, Colombo L, Kater MM: Functional characterization of OsMADS18, a member of the AP1/SQUA subfamily of MADS box genes. Plant Physiol 2004,135(4):2207-2219.
</ref>
* <ref name="ref18">
Moon YH, Jung JY, Kang HG, An G: Identification of a rice APETALA3 homologue by yeast two-hybrid screening. Plant Mol Biol 1999, 40(1):167-177.
</ref>
* <ref name="ref19">
Tardif G, Kane NA, Adam H, Labrie L, Major G, Gulick P, Sarhan F,
Laliberte JF: Interaction network of proteins associated with abiotic stress response and development in wheat. Plant Mol Biol 2007, 63(5):703-718.
</ref>

</references>

2014-06-07T09:39:58Z

Kathy:

2014-06-07T02:16:20Z

Kathy: /* Stress responsive MADS-box genes in rice */

MADS

2014-06-07T02:15:22Z

Kathy:

==Brief Introduction==
*1.1 Background
MADS-box family member are known to be involved in many important processes during plant growth and development<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The word MADS finds its origin from the first letters of its founding members, Mini Chromosome Maintenance 1 (MCM1) of yeast (Saccharomyces cerevisiae), Agamous (AG) of Arabidopsis (Arabidopsis thaliana), Deficiens (DEF) of snapdragon (Antirrhinum majus) and Serum Response Factor (SRF) of humans (Homo sapiens)<ref name="ref1" />.

They are characterized by the presence of a conserved domain of approximately 60 amino acids located in the N-terminal region; this domain is named the MADS-box domain and is involved in DNA binding and dimerization<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The MADS-box family has been divided into two main groups. The type I consists of ARG80/SRF-like genes of animals and fungi, also designated as M-type genes in plants, and type II contains MEF2-like genes of animals and yeast as well as MIKC-type genes of plants<ref name="ref1" /><ref name="ref3" />.The plant-specific MIKC-type MADS-box proteins include three additional domains followed by the MADS domain, viz. a less-conserved Intervening region of ~30 amino acids, a moderately conserved Keratin-like domain of ~70 amino acids mainly involved in heterodimerization, and a highly variable C-terminal region of variable length implicated in transcriptional activation and higher-order complex formation<ref name="ref4" /><ref name="ref5" /<ref name="ref6" />.
[[File:mads_box1.jpg|center|thumb|1000px|'''Figure 1.''' ''Protein Structure of '''BGIOSGA004940''' '']]
[[File:Gene_tree_1.jpg]]'''Figure 2.Gene tree'''

*1.2 Evolutionary relationships between rice and Arabidopsis MADS-box family genes.
A separate phylogenetic tree was also generated from complete protein sequences of all the MADS-box genes in rice and Arabidopsis (Figure 3). Of the 75 rice MADS-box genes, 38 grouped with MIKCc, six with MIKC*, nine with Mβ, 13 with Mα and 10 grouped with Mγ-type Arabidopsis genes<ref name="ref7" />.

[[File:Gene_tree_2.jpg]]'''Figure 3.Phylogenetic analysis of rice and Arabidopsis MADS-box proteins'''

*1.3 MADS-box transcription factors
The best studied plant MADS-box transcription factors are those involved in floral organ identity determination. Combinations of A-, B-, and C-function genes determine the development of the four whorls of an Arabidopsis flower: A-function genes determine sepal development; A- and B-function genes determine petal development; B- and C function genes determine the stamen development, and C-function genes are necessary for carpel development<ref name="ref2" /><ref name="ref3" />.

== Organization and structure of MADS-box genes==
*2.1 Location of genes
The individual genes were localized on chromosomes based on the 5' and 3' coordinates for respective gene models in TIGR database.Out of five types of MADS-box genes, the Mγ genes were confined to chromosome 1, 3 and 4, while Mβ genes were present only on chromosome 1. No chromosomal bias was observed in the distribution of MIKCc,MIKC* and Mα genes.<ref name="ref7" />
[[File:Gene_location.jpg]]
'''Figure 4.''' Chromosomal location of rice MADS-box '''

*2.2 Distribution of conserved motifs
The MEME motif search tool was employed to identify the conserved motifs present in MADS-box proteins (Figure 5). Motifs 1, 6 or 2 specifying the MADS domain were found in all the members of the MADS-box family. All proteins belonging to MIKCc and MIKC* groups had motif 1-type MADS domain..Most Mα proteins also had the motif 1-type MADS domain except OsMADS72 and 77 which contained motif 6. Motif 6 was found to be the most common type of MADS domain in Mβ-type proteins.Distinctively, in case of Mγ proteins a larger MADS domain of 83 amino acids was detected, followed by a coiled coil region and a region of unknown complexity as indicated by Simple Modular Architecture Research Tool (SMART) version 3.4<ref name="ref7" />.
[[File:Conserved_motifs.jpg]]'''Figure 5.Distribution of Conserved motifs in rice MADS-box proteins'''

*2.3 Expression profiling of MADS-box genes
Expression profiles have been generated using avadis™ software version 4.2. X-axis represents the developmental stages. Y-axis represents average log2 expression values.Genes exhibiting these expression patterns have been represented by numbers. Dotted lines have been drawn to demarcate vegetative organs, panicle and seed developmental stages（Figure 6）.
[[File:Expression_patterns.jpg]]'''Figure 6.Expression patterns of MADS-box genes in rice in vegetative as well as panicle and seed development.'''
[[File:Differential_expressions.jpg]]'''Figure 7.'''

Differential expressions shown by seven MADS-box genes in response to various abiotic stress conditions.Left panel shows four genes up regulated and right panel shows down regulated genes more than 2 folds with p value less than 0.05 in response to three abiotic stress conditions. X-axis represents seedling followed by stress samples (CS, cold stress; DS, dehydration stress; SS, salt stress). Y-axis represents average expression values obtained using microarrays. Error bars represent standard error for data obtained in three biological replicates(Figure 7).

==''Japonica'' Group==
{| style="background:#A1A3A6; width:85%;" border="0"
|-style="background:white; color:black" align="center"
!
'''[[Os01g0201700]]'''
||
'''[[Os02g0682200]]'''
||
'''[[Os04g0580700]]'''
||
'''[[Os09g0507200]]'''
||
'''[[Os08g0531700]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os07g0605200]]'''
||
'''[[Os07g0108900]]'''
||
'''[[Os05g0203800]]'''
||
'''[[Os12g0207000]]'''
||
'''[[Os03g0752800]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os03g0122600]]'''
||
'''[[Os10g0536100]]'''
||
'''[[Os06g0162800]]'''
||
'''[[Os01g0883100]]'''
||
'''[[Os01g0886200]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os04g0461300]]'''
||
'''[[Os06g0712700]]'''
||
'''[[Os02g0731200]]'''
||
'''[[Os03g0215400]]'''
||
'''[[Os02g0579600]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os12g0206800]]'''
||
'''[[Os08g0531900]]'''
||
'''[[Os03g0753100]]'''
||
'''[[Os05g0203600]]'''
||
'''[[Os02g0170300]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os02g0761000]]'''
||
'''[[Os04g0614100]]'''
||
'''[[Os05g0423400]]'''
||
'''[[Os08g0431900]]'''
||
'''[[Os04g0304400]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os06g0223300]]'''
||
'''[[Os06g0667200]]'''
||
'''[[Os06g0217300]]'''
||
'''[[Os03g0186600]]'''
||
'''[[Os01g0922800]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os12g0501700]]'''
||
'''[[Os08g0112700]]'''
||
'''[[Os01g0726400]]'''
||
'''[[Os12g0407400]]'''
||
'''[[Os11g0658700]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os04g0387400]]'''
||
'''[[Os03g0253400]]'''
||

||

||

|}
==''Indica'' Group==
{| style="background:#A1A3A6; width:85%;" border="0"
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA002178]]'''
||
'''[[BGIOSGA008820]]'''
||
'''[[BGIOSGA016980]]'''
||
'''[[BGIOSGA031056]]'''
||
'''[[BGIOSGA029052]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA026097]]'''
||
'''[[BGIOSGA018621]]'''
||
'''[[BGIOSGA024961]]'''
||
'''[[BGIOSGA009798]]'''
||
'''[[BGIOSGA033356]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA021849]]'''
||
'''[[BGIOSGA000377]]'''
||
'''[[BGIOSGA004940]]'''
||
'''[[BGIOSGA020546]]'''
||
'''[[BGIOSGA007336]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA011213]]'''
||
'''[[BGIOSGA026745]]'''
||
'''[[BGIOSGA008494]]'''
||
'''[[BGIOSGA022872]]'''
||
'''[[BGIOSGA036463]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA009797]]'''
||
'''[[BGIOSGA026939]]'''
||
'''[[BGIOSGA008983]]'''
||
'''[[BGIOSGA007056]]'''
||
'''[[BGIOSGA018624]]''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA007333]]'''
||
'''[[BGIOSGA009093]]'''
||
'''[[BGIOSGA022154]]'''
||
'''[[BGIOSGA019900]]'''
||
'''[[BGIOSGA016106]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA029053]]'''
||
'''[[BGIOSGA017110]]'''
||
'''[[BGIOSGA003731]]'''
||
'''[[BGIOSGA016105]]'''
||
'''[[BGIOSGA005076]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA015021]]'''
||
'''[[BGIOSGA023435]]'''
||
'''[[BGIOSGA021662]]'''
||
'''[[BGIOSGA011317]]'''
||
'''[[BGIOSGA036149]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA027872]]'''
||
'''[[BGIOSGA007600]]'''
||
'''[[BGIOSGA000892]]'''
||
'''[[BGIOSGA018453]]'''
||
'''[[BGIOSGA006672]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA030217]]'''
||
'''[[BGIOSGA005284]]'''
||
'''[[BGIOSGA035654]]'''
||
'''[[BGIOSGA021177]]'''
||
'''[[BGIOSGA003304]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA036334]]'''
||
'''[[BGIOSGA022830]]'''
||
'''[[BGIOSGA028419]]'''
||
'''[[BGIOSGA018341]]'''
||
'''[[BGIOSGA015023]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA000269]]'''
||
'''[[BGIOSGA003303]]'''
||
'''[[BGIOSGA011095]]'''
||
'''[[BGIOSGA016270]]'''
||
'''[[BGIOSGA003441]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA002989]]'''
||
'''[[BGIOSGA034252]]'''
||
'''[[BGIOSGA030219]]'''
||
'''[[BGIOSGA000297]]'''
||
'''[[BGIOSGA003442]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA003440]]'''
||
'''[[BGIOSGA003443]]'''
||

||

||

|}

==Stress responsive MADS-box genes in rice==
MADS-box genes have been shown to be affected by low temperature stress in tomato <ref name="ref8" /> and by application of hormones like cytokinins, gibberellins <ref name="ref9" />, ethylene <ref name="ref10" />and auxins <ref name="ref11" /> in other plants. Seven MADS-box genes exhibited differential expression in response to cold, salt and/or desiccation stress in rice. So far, none of these genes has been implicated in stress response. Amongst stress-induced genes, OsMADS18 is a member of AP1/SQUA group that has been shown to express widely during development with its transcripts accumulating at high levels specifically in meristematic tissues <ref name="ref12" />. It has been shown to interact with OsMADS6, 8/24, 7/45, and 47 <ref name="ref13" /> <ref name="ref12" />and in our analysis its expression pattern was found to overlap with those of OsMADS6, 8 and 7 in reproductive tissues and with OsMADS47 during vegetative development, suggesting that it might be interacting with different partners during reproductive development and stress. Recently, Tardif and coworkers showed that a large number of genes involved in flower development are associated with abiotic stress responses in wheat <ref name="ref14" />. Our preliminary analysis involving transcript profiling during reproductive development and abiotic stress conditions has also revealed approximately 400 genes that are up regulated during panicle/seed development and three stress conditions, viz. cold, salt, and dehydration (unpublished data). It would be, therefore, interesting to undertake specific investigations, which could establish the interactions of biochemical pathways that are activated during reproductive development and stress response.

==References==
<references>
* <ref name="ref1">
Arora R, Agarwal P, Ray S, et al. MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress[J]. BMC genomics, 2007, 8(1): 242.
</ref>
* <ref name="ref2">
Par̆enicová L, de Folter S, Kieffer M, et al. Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis new openings to the MADS world[J]. The Plant Cell Online, 2003, 15(7): 1538-1551.
</ref>
* <ref name="ref3">
Leseberg C H, Li A, Kang H, et al. Genome-wide analysis of the MADS-box gene family in Populus trichocarpa[J]. Gene, 2006, 378: 84-94.
</ref>
* <ref name="ref4">
Yang Y, Fanning L, Jack T: The K domain mediates heterodimerization of the Arabidopsis floral organ identity proteins,APETALA3 and PISTILLATA[J]. Plant J 2003, 33(1):47-59.
</ref>
* <ref name="ref5">
Egea Cortines M, Saedler H, Sommer H: Ternary complex formation between the MADS-box proteins SQUAMOSA, DEFICIENS and GLOBOSA is involved in the control of floral architecture in Antirrhinum majus[J]. EMBO J 1999, 18(19):5370-5379.
</ref>
* <ref name="ref6">
Cho S, Jang S, Chae S, Chung KM, Moon YH, An G, Jang SK: Analysis of the C-terminal region of Arabidopsis thaliana APETALA1 as a transcription activation domain. Plant Mol Biol 1999,40(3):419-429.
</ref>
* <ref name="ref7">
Rita Arora, Pinky Agarwal, Swatismita Ray.MADS-box gene family in rice: genome-wide identification,organization and expression profiling during reproductive development and stress.BMC Genomics,2007, 8:242.
</ref>

</references>

MADS

2014-06-07T01:59:04Z

2014-06-06T13:38:30Z

Kathy: uploaded a new version of "File:Gene location.jpg"

MADS

2014-06-06T13:37:13Z

Kathy:

==Brief Introduction==
* MADS-box family member are known to be involved in many important processes during plant growth and development<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The word MADS finds its origin from the first letters of its founding members, Mini Chromosome Maintenance 1 (MCM1) of yeast (Saccharomyces cerevisiae), Agamous (AG) of Arabidopsis (Arabidopsis thaliana), Deficiens (DEF) of snapdragon (Antirrhinum majus) and Serum Response Factor (SRF) of humans (Homo sapiens)<ref name="ref1" />.
* They are characterized by the presence of a conserved domain of approximately 60 amino acids located in the N-terminal region; this domain is named the MADS-box domain and is involved in DNA binding and dimerization<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The MADS-box family has been divided into two main groups. The type I consists of ARG80/SRF-like genes of animals and fungi, also designated as M-type genes in plants, and type II contains MEF2-like genes of animals and yeast as well as MIKC-type genes of plants<ref name="ref1" /><ref name="ref3" />.The plant-specific MIKC-type MADS-box proteins include three additional domains followed by the MADS domain, viz. a less-conserved Intervening region of ~30 amino acids, a moderately conserved Keratin-like domain of ~70 amino acids mainly involved in heterodimerization, and a highly variable C-terminal region of variable length implicated in transcriptional activation and higher-order complex formation<ref name="ref4" /><ref name="ref6" />.
[[File:mads_box1.jpg|center|thumb|1000px|'''Figure 1.''' ''Protein Structure of '''BGIOSGA004940''' '']]
* The best studied plant MADS-box transcription factors are those involved in floral organ identity determination. Combinations of A-, B-, and C-function genes determine the development of the four whorls of an Arabidopsis flower: A-function genes determine sepal development; A- and B-function genes determine petal development; B- and C function genes determine the stamen development, and C-function genes are necessary for carpel development<ref name="ref2" /><ref name="ref3" />.

== Organization and structure of MADS-box genes==
* The individual genes were localized on chromosomes based on the 5' and 3' coordinates for respective gene models in TIGR database
(Figure 2).[[File:Gene-location.jpg]]

==''Japonica'' Group==
{| style="background:#A1A3A6; width:85%;" border="0"
|-style="background:white; color:black" align="center"
!
'''[[Os01g0201700]]'''
||
'''[[Os02g0682200]]'''
||
'''[[Os04g0580700]]'''
||
'''[[Os09g0507200]]'''
||
'''[[Os08g0531700]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os07g0605200]]'''
||
'''[[Os07g0108900]]'''
||
'''[[Os05g0203800]]'''
||
'''[[Os12g0207000]]'''
||
'''[[Os03g0752800]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os03g0122600]]'''
||
'''[[Os10g0536100]]'''
||
'''[[Os06g0162800]]'''
||
'''[[Os01g0883100]]'''
||
'''[[Os01g0886200]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os04g0461300]]'''
||
'''[[Os06g0712700]]'''
||
'''[[Os02g0731200]]'''
||
'''[[Os03g0215400]]'''
||
'''[[Os02g0579600]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os12g0206800]]'''
||
'''[[Os08g0531900]]'''
||
'''[[Os03g0753100]]'''
||
'''[[Os05g0203600]]'''
||
'''[[Os02g0170300]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os02g0761000]]'''
||
'''[[Os04g0614100]]'''
||
'''[[Os05g0423400]]'''
||
'''[[Os08g0431900]]'''
||
'''[[Os04g0304400]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os06g0223300]]'''
||
'''[[Os06g0667200]]'''
||
'''[[Os06g0217300]]'''
||
'''[[Os03g0186600]]'''
||
'''[[Os01g0922800]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os12g0501700]]'''
||
'''[[Os08g0112700]]'''
||
'''[[Os01g0726400]]'''
||
'''[[Os12g0407400]]'''
||
'''[[Os11g0658700]]'''
|-style="background:white; color:black" align="center"
!
'''[[Os04g0387400]]'''
||
'''[[Os03g0253400]]'''
||

||

||

|}
==''Indica'' Group==
{| style="background:#A1A3A6; width:85%;" border="0"
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA002178]]'''
||
'''[[BGIOSGA008820]]'''
||
'''[[BGIOSGA016980]]'''
||
'''[[BGIOSGA031056]]'''
||
'''[[BGIOSGA029052]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA026097]]'''
||
'''[[BGIOSGA018621]]'''
||
'''[[BGIOSGA024961]]'''
||
'''[[BGIOSGA009798]]'''
||
'''[[BGIOSGA033356]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA021849]]'''
||
'''[[BGIOSGA000377]]'''
||
'''[[BGIOSGA004940]]'''
||
'''[[BGIOSGA020546]]'''
||
'''[[BGIOSGA007336]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA011213]]'''
||
'''[[BGIOSGA026745]]'''
||
'''[[BGIOSGA008494]]'''
||
'''[[BGIOSGA022872]]'''
||
'''[[BGIOSGA036463]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA009797]]'''
||
'''[[BGIOSGA026939]]'''
||
'''[[BGIOSGA008983]]'''
||
'''[[BGIOSGA007056]]'''
||
'''[[BGIOSGA018624]]''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA007333]]'''
||
'''[[BGIOSGA009093]]'''
||
'''[[BGIOSGA022154]]'''
||
'''[[BGIOSGA019900]]'''
||
'''[[BGIOSGA016106]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA029053]]'''
||
'''[[BGIOSGA017110]]'''
||
'''[[BGIOSGA003731]]'''
||
'''[[BGIOSGA016105]]'''
||
'''[[BGIOSGA005076]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA015021]]'''
||
'''[[BGIOSGA023435]]'''
||
'''[[BGIOSGA021662]]'''
||
'''[[BGIOSGA011317]]'''
||
'''[[BGIOSGA036149]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA027872]]'''
||
'''[[BGIOSGA007600]]'''
||
'''[[BGIOSGA000892]]'''
||
'''[[BGIOSGA018453]]'''
||
'''[[BGIOSGA006672]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA030217]]'''
||
'''[[BGIOSGA005284]]'''
||
'''[[BGIOSGA035654]]'''
||
'''[[BGIOSGA021177]]'''
||
'''[[BGIOSGA003304]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA036334]]'''
||
'''[[BGIOSGA022830]]'''
||
'''[[BGIOSGA028419]]'''
||
'''[[BGIOSGA018341]]'''
||
'''[[BGIOSGA015023]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA000269]]'''
||
'''[[BGIOSGA003303]]'''
||
'''[[BGIOSGA011095]]'''
||
'''[[BGIOSGA016270]]'''
||
'''[[BGIOSGA003441]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA002989]]'''
||
'''[[BGIOSGA034252]]'''
||
'''[[BGIOSGA030219]]'''
||
'''[[BGIOSGA000297]]'''
||
'''[[BGIOSGA003442]]'''
|-style="background:white; color:black" align="center"
!
'''[[BGIOSGA003440]]'''
||
'''[[BGIOSGA003443]]'''
||

||

||

|}
==References==
<references>
* <ref name="ref1">
Arora R, Agarwal P, Ray S, et al. MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress[J]. BMC genomics, 2007, 8(1): 242.
</ref>
* <ref name="ref2">
Par̆enicová L, de Folter S, Kieffer M, et al. Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis new openings to the MADS world[J]. The Plant Cell Online, 2003, 15(7): 1538-1551.
</ref>
* <ref name="ref3">
Leseberg C H, Li A, Kang H, et al. Genome-wide analysis of the MADS-box gene family in Populus trichocarpa[J]. Gene, 2006, 378: 84-94.
</ref>
* <ref name="ref4">
Yang Y, Fanning L, Jack T: The K domain mediates heterodimerization of the Arabidopsis floral organ identity proteins,APETALA3 and PISTILLATA[J]. Plant J 2003, 33(1):47-59.
</ref>
* <ref name="ref5">
Egea Cortines M, Saedler H, Sommer H: Ternary complex formation between the MADS-box proteins SQUAMOSA, DEFICIENS and GLOBOSA is involved in the control of floral architecture in Antirrhinum majus[J]. EMBO J 1999,18(19):5370-5379.</ref>
* <ref name="ref6">
Cho S, Jang S, Chae S, Chung KM, Moon YH, An G, Jang SK: Analysis of the C-terminal region of Arabidopsis thaliana APETALA1 as a transcription activation domain. Plant Mol Biol 1999,40(3):419-429.
</ref>
</references>