MADS - Revision history

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

2014-06-07T11:11:13Z

‎The Flower Induction and Flower Organ Formation Subnetworks

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

2014-06-07T11:10:52Z

‎The Flower Induction and Flower Organ Formation Subnetworks

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

2014-06-07T11:10:25Z

‎The Flower Induction and Flower Organ Formation Subnetworks

Kathy at 11:06, 7 June 2014

2014-06-07T11:06:48Z

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

2014-06-07T09:55:37Z

‎Comprehensive Analysis of MADS Box Transcription Factor Dimerization

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

2014-06-07T09:55:05Z

‎Comprehensive Analysis of MADS Box Transcription Factor Dimerization

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

2014-06-07T09:53:15Z

‎Comprehensive Analysis of MADS Box Transcription Factor Dimerization

Kathy: /* References */

2014-06-07T09:50:52Z

‎References

Kathy at 09:47, 7 June 2014

2014-06-07T09:47:42Z

Kathy at 09:39, 7 June 2014

2014-06-07T09:39:58Z

@@ Line 302: / Line 302: @@
 ===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.'''

@@ Line 303: / Line 303: @@
 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.

@@ Line 302: / Line 302: @@
 ===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.'''
 ==Stress responsive MADS-box genes in rice==

@@ Line 300: / Line 300: @@
 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.
+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==
@@ Line 344: / Line 347: @@
 </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">
+* <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="ref15">
+* <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="ref16">
+* <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="ref17">
+* <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="ref18">
+* <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="ref19">
+* <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.

@@ Line 298: / Line 298: @@
 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.

← Older revision		Revision as of 09:53, 7 June 2014
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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==

@@ Line 323: / Line 323: @@
 * <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="ref13">

@@ Line 16: / Line 16: @@
 == Organization and structure of MADS-box genes==
-*2.1 Location of 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 '''
-*2.2 Distribution of conserved motifs
+===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 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.'''