On the role, ecology, phylogeny, and structure of dual-family immunophilins

Abstract

The novel class of dual-family immunophilins (henceforth abbreviated as DFI) represents naturally occurring chimera of classical FK506-binding protein (FKBP) and cyclophilin (CYN), connected by a flexible linker that may include a three-unit tetratricopeptide (TPR) repeat. Here, I report a comprehensive analysis of all current DFI sequences and their host organisms. DFIs are of two kinds: CFBP (cyclosporin-and FK506-binding protein) and FCBP (FK506-and cyclosporin-binding protein), found in eukaryotes. The CFBP type occurs in select bacteria that are mostly extremophiles, such as psychrophilic, thermophilic, halophilic, and sulfur-reducing. Essentially all DFI organisms are unicellular. I suggest that DFIs are specialized bifunctional chaperones that use their flexible interdomain linker to associate with large polypeptides or multisubunit megacomplexes to promote simultaneous folding or renaturation of two clients in proximity, essential in stressful and denaturing environments. Analysis of sequence homology and predicted 3D structures of the FKBP and CYN domains as well as the TPR linkers upheld the modular nature of the DFIs and revealed the uniqueness of their TPR domain. The CFBP and FCBP genes appear to have evolved in parallel pathways with no obvious single common ancestor. The occurrence of both types of DFI in multiple unrelated phylogenetic clades supported their selection in metabolic and environmental niche roles rather than a traditional taxonomic relationship.Nonetheless, organisms with these rare immunophilins may define an operational taxonomic unit (OTU) bound by the commonality of chaperone function.

Dual-Family Peptidylprolyl Isomerases (Immunophilins) of Select Monocellular Organisms

“…Nonetheless, advanced 3D simulation with I-TASSER, using the known crystal structures of similar CYN and FKBP sequences, yielded the expected structures, i.e. the CYN and FKBP domains, linked with TPR or the short linker with ID [14]. Interestingly, the simulations actually yielded an ensemble of multiple structural conformers in which the two domains were oriented at various degrees relative to each other, clearly using the flexible linker as a hinge ( Figure 2).…”

“…Multiple tandem repeats of TPR can be found in a wide variety of proteins, in which they participate in proteinprotein interactions. All FCBPs contain three nonidentical repeats of TPR, referred as 3TPR [14]. In sharp contrast, the CFBPs do not contain TPR, but instead uses short peptide sequences, averaging ~50 amino acids in length, to serve as a linker between the CYN and FKBP domains [16].…”

“…Bioinformatic analysis showed that all CFBP linkers, in spite of their sequence dissimilarity, possess intrinsic disorder (ID), a hallmark of flexible protein linkers [16], as shown later with Flavobacterium johnsoniae CFBP (Figure 3). Thus, both classes of DFPPIs contain flexible linkers, serving as connector between the two classical PPI/immunophilin domains, which offered the first indication that the two domains may function as independent functional modules, able to freely bend against each other [14,16].…”

“…The full-length DFIs as well as the individually expressed CYN and FKBP domains were able to promote refolding of a model substrate protein in vitro, suggesting the DFPPIs are in fact dual-family chaperones [13]. In the years that followed, sequence homology search unraveled several dozen more FCBP and CFBP in the newly sequenced genomes [14], although their biochemical properties were not studied. In this review, I…”

“…collectively refer to these CFBP and FCBP sequences as DFPPIs, and summarize our current knowledge on these proteins along with a broader view of their potential function. More specialized reviews of DFPPI subsets and recent bioinformatic analysis of their structure can be found elsewhere [14][15][16].…”