Abstract
Cyclophilins (CYPs) are a member of the immunophilin superfamily (in addition to FKBPs and parvulins) and play a significant role in peptidyl-prolyl cis-trans isomerase (PPIase) activity. Previous studies have shown that CYPs have important functions in plants, but no genome-wide analysis of the cotton CYP gene family has been reported, and the specific biological function of this gene is still elusive. Based on the release of the cotton genome sequence, we identified 75, 78, 40 and 38 CYP gene sequences from G. barbadense, G. hirsutum, G. arboreum, and G. raimondii, respectively; 221 CYP genes were unequally located on chromosomes. Phylogenetic analysis showed that 231 CYP genes clustered into three major groups and eight subgroups. Collinearity analysis showed that segmental duplications played a significant role in the expansion of CYP members in cotton. There were light-responsiveness, abiotic-stress and hormone-response elements upstream of most of the CYPs. In addition, the motif composition analysis revealed that 49 cyclophilin proteins had extra domains, including TPR (tetratricopeptide repeat), coiled coil, U-box, RRM (RNA recognition motif), WD40 (RNA recognition motif) and zinc finger domains, along with the cyclophilin-like domain (CLD). The expression patterns based on qRT-PCR showed that six CYP expression levels showed greater differences between Xinhai21 (long fibres, G. barbadense) and Ashmon (short fibres, G. barbadense) at 10 and 20 days postanthesis (DPA). These results signified that CYP genes are involved in the elongation stage of cotton fibre development. This study provides a valuable resource for further investigations of CYP gene functions and molecular mechanisms in cotton.
Highlights
Cyclophilins (CYPs) are a member of the immunophilin superfamily and are identified by their highly conserved cyclophilin-like domain (CLD) [1]
Using the Hidden Markov Model (HMM) profile of the peptidyl-prolyl cis-trans isomerase (PPIase) domain (PF00160) and CYP sequences from Arabidopsis (29), rice (27) and B. napus (77) as queries, a total of 80, 83, 42 and 38 predicted CYP gene sequences were identified from G. barbadense, G. hirsutum, G. arboreum and G. raimondii, respectively
75, 78, 40 and 38 CYP genes were identified from G. barbadense, G. hirsutum, G. arboreum, and G. raimondii, respectively
Summary
Cyclophilins (CYPs) are a member of the immunophilin superfamily (in addition to FKBPs and Parvulins) and are identified by their highly conserved cyclophilin-like domain (CLD) [1]. In 1984, Handschumacher et al first identified cyclophilin A (CyPA) from bovine thymocytes, which is the receptor of the immunosuppressive drug cyclosporine A (CsA) [2]. An 18-kDa protein with PPIase (peptidyl-prolyl cis-trans isomerase) activity, which can catalyse the cis/trans isomerisation process of Xaa-proline peptide bonds, was found by Fischer and Takahashi et al This process is a rate-limiting step in protein folding. Fischer and Takahashi et al discovered that PPIase is the cyclosporin A-binding protein cyclophilin [3,4]. CYPs are ubiquitous proteins present in bacteria, plants and animals [5,6]. Plants have a higher number of CYPs, with 29 in Arabidopsis thaliana, 27 in rice, 62 in soybean, 77 in B. napus and 39 in maize [9,10,11,12,13]
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