Focused proteomic analysis of functional network for peptidyl prolyl cis/trans isomerases

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Peptidyl prolyl cis/trans isomerases (PPlases) catalyze the rotation about the peptide bond preceding proline, a step that can be rate-limiting for the folding of newly synthesized proteins. PPlases also have the ability to bind many proteins and to act as chaperones; thus they are believed to regulate folding, assembly and trafficking, and controlling activity of proteins in the cell. PPlases are most familiar as the targets of the immunosuppressive drugs, cyclosporin A (CsA) and FK506, which bind, respectively, to cyclophilin (CyP) and FK506-binding protein (FKBP) and inhibit their cognate PPlaseactivities. Both CyP and FKBP are ubiquitous, highly expressed and conserved from bacteria to human. The third family of PPlases, parvulins, is the target of neither CsA nor FK506, but is also conserved from bacteria to human. Although a number of CyP, FKBP and parvulin homologs have been identified in almost all organisms, the cellular functions of most of those homologs remain to be exploded. In this study, we analyzed systematically potential substrate for 23 different human PPlases including 9 CyP, 11 FKBP, and 3 parvulin homologs by using proteomic approaches that include expression of epitope-tagged PPlase, affinity purification in the presence or absence of PPlase inhibitor, mass-spectrometry based protein identification, and database searching. We identified about 200 potential substrates for the three types of PPlases and constructed a functional protein network for the PPlases. The network included proteins that have roles in translation, cell cycle, proliferation, transcription, stress-responses, DNA/protein metabolism, RNA processing, protein trafficking, and ribosome biogenesis. We investigated further the involvement of PPlases in ribosome biogenesis, and found that parvulin 14, FKBP25, and CyPB have probably roles in different stages of human ribosome biogenesis.