Difference between revisions of "MADS"
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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. | 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:Figure_8.jpg]] | ||
| + | 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== | ==Stress responsive MADS-box genes in rice== | ||
Revision as of 09:53, 7 June 2014
Contents
Brief Introduction
Background
MADS-box family member are known to be involved in many important processes during plant growth and development[1][2][3]. 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)[1].
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[1][2][3]. 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[1][3].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[4][5].
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[6].
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[2][3].
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.[6]
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[6].
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）.
Figure 6.Expression patterns of MADS-box genes in rice in vegetative as well as panicle and seed development.
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
Indica Group
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[7][8][9],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[10] ,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 [11],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.
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 [12] and by application of hormones like cytokinins, gibberellins [13], ethylene [14]and auxins [15] 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 [16]. It has been shown to interact with OsMADS6, 8/24, 7/45, and 47 [16][17]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 [18]. 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
- ↑ 1.0 1.1 1.2 1.3 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.
- ↑ 2.0 2.1 2.2 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.
- ↑ 3.0 3.1 3.2 3.3 Leseberg C H, Li A, Kang H, et al. Genome-wide analysis of the MADS-box gene family in< i> Populus trichocarpa</i>[J]. Gene, 2006, 378: 84-94.
- ↑ 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.
- ↑ 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.
- ↑ 6.0 6.1 6.2 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.
- ↑ 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.
- ↑ 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.
- ↑ Riechmann, J.L., and Meyerowitz, E.M. . MADS domain proteins in plant development. Biol. Chem,1997,378:1079–1101.
- ↑ Honma, T., and Goto, K. . Complexes of MADS-box proteins are sufficient to convert leaves into floral organs. Nature ,2001,409:525–529.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 16.0 16.1 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.
- ↑ 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.
- ↑ 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.
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