Genome-wide identification and analyses of the rice calmodulin and related potential calcium sensor proteins

By functional analyses and BLAST searches of the TIGR rice database, a maximum number of 243 proteins that possibly have EF-hand motifs were identified in the rice genome. Using a neighbor-joining tree based on amino acid sequence similarity, five loci were defined as Cam genes and thirty two additional CML genes were identified. Extensive analyses of the gene structures, the chromosome locations, the EF-hand motif organization, expression characteristics including analysis by RT-PCR and a comparative analysis of Cam and CML genes in rice and Arabidopsis are presented.Although many proteins have unknown functions, the complexity of this gene family indicates the importance of Ca2+-signals in regulating cellular responses to stimuli and this family of proteins likely plays a critical role as their transducers.Ca2+ is an essential second messenger in all eukaryotic cells in triggering physiological changes in response to external stimuli. Due to the activities of Ca2+-ATPases and Ca2+-channels on the cellular membrane, rapid and transient changes of its cytosolic concentrations are possible. In plant cells, a wide range of stimuli trigger cytosolic [Ca2+] increases of different magnitude and specialized character [1,2], which are typically transmitted by protein sensors that preferably bind Ca2+. Ca2+ binding results in conformation changes that modulate their activity or their ability to interact with other proteins. For the majority of Ca2+-binding proteins, the Ca2+-binding sites are composed of a characteristic helix-loop-helix motif called an EF hand. Each loop, including the end of the second flanking helix, provides seven ligands for binding Ca2+ with a pentagonal bipyramid geometry. Ca2+-binding ligands are within the region designated as +X*+Y*+Z*-Y*-X**-Z, in which * represents an intervening residue. Three ligands for Ca2+ coordination are provided by carboxylate oxygens from residues 1 (+X), 3 (+Y) and 5 (+Z), one from a carbonyl oxygen from residue 7 (-Y)