Analysis of EF-hand-containing proteins in Arabidopsis

Genome Biol. 2002 Sep 23;3(10):RESEARCH0056. doi: 10.1186/gb-2002-3-10-research0056. Epub 2002 Sep 23.

Abstract

Background: In plants, calcium (Ca2+) has emerged as an important messenger mediating the action of many hormonal and environmental signals, including biotic and abiotic stresses. Many different signals raise cytosolic calcium concentration ([Ca2+]cyt), which in turn is thought to regulate cellular and developmental processes via Ca2+-binding proteins. Three out of the four classes of Ca2+-binding proteins in plants contain Ca2+-binding EF-hand motif(s). This motif is a conserved helix-loop-helix structure that can bind a single Ca2+ ion. To identify all EF-hand-containing proteins in Arabidopsis, we analyzed its completed genome sequence for genes encoding EF-hand-containing proteins.

Results: A maximum of 250 proteins possibly having EF-hands were identified. Diverse proteins, including enzymes, proteins involved in transcription and translation, protein- and nucleic-acid-binding proteins and a large number of unknown proteins, have one or more putative EF-hands. Phylogenetic analysis identified six major groups that contain some families of proteins.

Conclusions: The presence of EF-hand motif(s) in a diversity of proteins is consistent with the involvement of Ca2+ in regulating many cellular and developmental processes. Thus far, only 47 of the possible 250 EF-hand proteins have been reported in the literature. Various domains that we identified in many of the uncharacterized EF-hand-containing proteins should help in elucidating their cellular role(s). Our analyses suggest that the Ca2+ messenger system is widely used in plants and that EF-hand-containing proteins are likely to be the key transducers mediating Ca2+ action.

MeSH terms

  • Arabidopsis / chemistry*
  • Arabidopsis / genetics
  • Arabidopsis Proteins / chemistry*
  • Arabidopsis Proteins / genetics
  • Calcium-Binding Proteins / chemistry
  • Calcium-Binding Proteins / genetics
  • Databases, Protein
  • EF Hand Motifs* / genetics
  • Phylogeny
  • Protein Sorting Signals / genetics
  • Protein Structure, Tertiary / genetics
  • Sequence Analysis, Protein / methods*

Substances

  • Arabidopsis Proteins
  • Calcium-Binding Proteins
  • Protein Sorting Signals