Evolutionary relationship and structural characterization of the EPF/EPFL gene family

PLoS One. 2013 Jun 3;8(6):e65183. doi: 10.1371/journal.pone.0065183. Print 2013.

Abstract

EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Arabidopsis / classification
  • Arabidopsis / genetics*
  • Arabidopsis Proteins / chemistry*
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • Biological Evolution
  • Bryopsida / classification
  • Bryopsida / genetics
  • Carica / classification
  • Carica / genetics
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Gene Expression Regulation, Plant*
  • Medicago truncatula / classification
  • Medicago truncatula / genetics
  • Molecular Dynamics Simulation
  • Oryza / classification
  • Oryza / genetics
  • Phylogeny*
  • Picea / classification
  • Picea / genetics
  • Plant Stomata / anatomy & histology
  • Plant Stomata / genetics*
  • Protein Conformation
  • Selaginellaceae / classification
  • Selaginellaceae / genetics
  • Sequence Homology, Amino Acid
  • Signal Transduction
  • Sorghum / classification
  • Sorghum / genetics
  • Transcription Factors / chemistry*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism

Substances

  • Arabidopsis Proteins
  • DNA-Binding Proteins
  • EPF1 protein, Arabidopsis
  • EPF2 protein, Arabidopsis
  • EPFL9 protein, Arabidopsis
  • Transcription Factors

Grant support

This work was principally supported by the JST Advanced Low Carbon Technology Research and Development Program (ALCA) from the Japan Science and Technology Agency (JST) (to NT, TT and MK). This work was supported in part by JST-SENTAN (to SO and MM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.