Journal Article

Evolution of the B3 DNA Binding Superfamily: New Insights into REM Family Gene Diversification

Couñago, Rafael M., Romanel, Elisson A. C., Russo, Claudia A. M., Alves-Ferreira, Márcio, Schrago, Carlos G.

2009

Overview

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.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: 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