Evolution of the B3 DNA binding superfamily: new insights into REM family gene diversification

The B3 DNA binding domain includes five families: auxin response factor (ARF), abscisic acid-insensitive3 (ABI3), high level expression of sugar inducible (HSI), related to ABI3/VP1 (RAV) and reproductive meristem (REM). The release of the complete genomes of the angiosperm eudicots Arabidopsis thal...

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Bibliographic Details
Published in:PloS one 2009-06, Vol.4 (6), p.e5791-e5791
Main Authors: Romanel, Elisson A C, Schrago, Carlos G, Couñago, Rafael M, Russo, Claudia A M, Alves-Ferreira, Márcio
Format: Article
Language:English
Subjects:
Abscisic acid
Algae
Arabidopsis
Arabidopsis - chemistry
Arabidopsis - genetics
Arabidopsis Proteins - chemistry
Arabidopsis Proteins - genetics
Arabidopsis thaliana
Binding
Bioinformatics
Biological Evolution
Chlamydomonas reinhardtii
Cladistic analysis
Comparative analysis
Conservation
Conserved sequence
Cyanidioschyzon
Deoxyribonucleic acid
Divergence
DNA
DNA binding
Eukaryota - genetics
Evolution
Evolution, Molecular
Evolutionary Biology/Plant Genetics and Gene Expression
Evolutionary Biology/Plant Genomes and Evolution
Gene Duplication
Genes
Genes, Plant
Genetic research
Genomes
Genomics
Identification
Molecular Sequence Data
Multigene Family
Phylogeny
Physcomitrella
Plant Biology
Plant Biology/Plant Genomes and Evolution
Plant evolution
Plant Physiological Phenomena
Plant Proteins
Populus trichocarpa
Protein Conformation
Protein Structure, Tertiary
Proteins
Reproduction (copying)
Sugar
Volvox carteri
Zea mays - chemistry
Zea mays - genetics
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Summary:The B3 DNA binding domain includes five families: auxin response factor (ARF), abscisic acid-insensitive3 (ABI3), high level expression of sugar inducible (HSI), related to ABI3/VP1 (RAV) and reproductive meristem (REM). The release of the complete genomes of the angiosperm eudicots Arabidopsis thaliana and Populus trichocarpa, the monocot Orysa sativa, the bryophyte Physcomitrella patens,the green algae Chlamydomonas reinhardtii and Volvox carteri and the red algae Cyanidioschyzon melorae provided an exceptional opportunity to study the evolution of this superfamily. In order to better understand the origin and the diversification of B3 domains in plants, we combined comparative phylogenetic analysis with exon/intron structure and duplication events. In addition, we investigated the conservation and divergence of the B3 domain during the origin and evolution of each family. Our data indicate that showed that the B3 containing genes have undergone extensive duplication events, and that the REM family B3 domain has a highly diverged DNA binding. Our results also indicate that the founding member of the B3 gene family is likely to be similar to the ABI3/HSI genes found in C. reinhardtii and V. carteri. Among the B3 families, ABI3, HSI, RAV and ARF are most structurally conserved, whereas the REM family has experienced a rapid divergence. These results are discussed in light of their functional and evolutionary roles in plant development.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0005791