Abstract
BackgroundCyclophilins (CYPs) belong to the immunophilin superfamily, and have peptidyl-prolyl cis-trans isomerase (PPIase) activity. PPIase catalyzes cis- and trans-rotamer interconversion of the peptidyl-prolyl amide bond of peptides, a rate-limiting step in protein folding. Studies have demonstrated the importance of many PPIases in plant biology, but no genome-wide analysis of the CYP gene family has been conducted for a legume species.ResultsHere we performed a comprehensive database survey and identified a total of 62 CYP genes, located on 18 different chromosomes in the soybean genome (GmCYP1 to GmCYP62), of which 10 are multi- and 52 are single-domain proteins. Most of the predicted GmCYPs clustered together in pairs, reflecting the ancient genome duplication event. Analysis of gene structure revealed the presence of introns in protein-coding regions as well as in 5′ and 3′ untranslated regions, and that their size, abundance and distribution varied within the gene family. Expression analysis of GmCYP genes in soybean tissues displayed their differential tissue specific expression patterns.ConclusionsOverall, we have identified 62 CYP genes in the soybean genome, the largest CYP gene family known to date. This is the first genome-wide study of the CYP gene family of a legume species. The expansion of GmCYP genes in soybean, and their distribution pattern on the chromosomes strongly suggest genome-wide segmental and tandem duplications.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0282-7) contains supplementary material, which is available to authorized users.
Highlights
Cyclophilins (CYPs) belong to the immunophilin superfamily, and have peptidyl-prolyl cis-trans isomerase (PPIase) activity
Of the 62 GmCYPs, 52 encoded a protein with a single cyclophilin-like domain (CLD) which is responsible for the cis/trans isomerization of the peptidyl prolyl peptide bond
The tetratricopeptide repeats (TPRs) motif is degenerate in nature and consists of a 34 amino acid repeat unit typically arranged in tandem arrays [28]
Summary
Cyclophilins (CYPs) belong to the immunophilin superfamily, and have peptidyl-prolyl cis-trans isomerase (PPIase) activity. Cyclophilins (CYPs) are ubiquitous proteins found in organisms ranging from archaea and bacteria to plants and animals [1,2]. As they were originally identified as receptors for the immunosuppressive drug cyclosporine A (CsA), CYPs are classified in the immunophilin family of proteins possessing peptidyl prolyl cis/trans isomerase activity. In the yeast Saccharomyces cerevisiae there are at least 8 different CYPs, Cpr to Cpr8 [4] These proteins are not essential for growth, but are crucial for survival after heat stress [5].
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