Research

Analysis of EF-hand-containing proteins in Arabidopsis

Irene S Day, Vaka S Reddy, Gul Shad Ali and ASN Reddy

Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA

author email corresponding author email

Genome Biology 2002, 3:research0056.1-0056.24doi:10.1186/gb-2002-3-10-research0056

Published:	23 September 2002

Subject areas: Biochemistry and structural biology, Bioinformatics, Plant biology, Genome studies, Physiology

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.