Difference between revisions of "MADS"
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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" />. | 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''' | [[File:Conserved_motifs.jpg]]'''Figure 5.Distribution of Conserved motifs in rice MADS-box proteins''' | ||
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| + | *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）. | ||
==''Japonica'' Group== | ==''Japonica'' Group== | ||
Revision as of 01:51, 7 June 2014
Contents
Brief Introduction
- 1.1 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
- 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[6].
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[2][3].
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.[6]
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[6].
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）.
Japonica Group
Indica Group
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.
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