Zdravko Lorkovic Lab

Cyclophilins, multifaceted proteins that regulate diverse cellular processes

Cyclophilins are ubiquitous proteins found in archea, bacteria, and eucaria, with the largest family described so far in the plant Arabidopsis thaliana. They belong to a family of immunosuppressant receptor proteins called immunophilins, which in addition to cyclophilins include the FK506 binding proteins (FK506BPs) and the parvulins. Members of the immunophilin superfamily possess peptidyl-prolyl cis-trans isomerase (PPIase) activity; e.g. they catalyze cis to trans isomerization of peptide bonds preceding proline. Cis to trans isomerization of prolyl imide bonds takes place spontaneously, but is very slow. As this could be a rate limiting step in protein folding the importance of this enzyme family is best highlighted by the fact that over 90% of prolyl imide bonds are in trans conformation.

In eukaryotic cells cyclophilins have been implicated in virtually all cellular processes. These include protein trafficking and maturation, cell signaling, receptor complex stabilization, apoptosis, transcription, RNA processing and spliceosome assembly. However, the mechanisms of how cyclophilins contribute to these cellular events have been difficult to establish and are still largely unknown. Yet, several studies provided evidence for the mechanism of cyclophilin action. For example, the cyclophilin A-cyclosporine A complex inhibits the phosphatase activity of calcineurin, which in turn results in inhibition of T-cell activation by blocking the expression of several immunosuppressive genes. Another example is the parvulin Ess1/Pin1 which has been shown to interact with numerous phosphoproteins through recognition of a pSer/Thr-Pro motif by its amino-terminal WW domain. By promoting the cis to trans isomerisation of the prolyl peptide bonds through its carboxyl-terminal PPIase domain it regulates the activities of p53, tau, RNA polymerase II, and some mitotic proteins. Based on the data reported for TLP40, Pin1, CypRS64, AtCyp59/Rct1, and PTPA it has been proposed that phosphorylation-specific prolyl isomerisation could be a common mechanism for immunophilin function.

Arabidopsis RNA binding proteins, a family with many unknowns

In all aspects of post-transcriptional regulation of gene expression a crucial role for RNA binding proteins (RBP) has been documented. In fact RNAP II transcripts are accompanied by RNA binding proteins from the start of the transcription until they are degraded in the. RBPs are characterized by the presence of one or more RNA binding domain; the most widely spread being the RNA recognition motif (RRM) and the K-homology domain (KH), whereby different types of RNA binding domains are often combined with each other or with other protein domains involved in protein-protein interaction, protein targeting etc. Interestingly, many genes encoding RBPs are differentially expressed (subject to transcriptional and post-transcriptional regulation) depending on the cell type or developmental stage. This is particularly evident for KH domain RBPs which seem to be highly important for differentiation and development in metazoan by regulating different aspects of RNA metabolism.

From the Arabidopsis genomic survey it became clear that plants express a complex set of RBPs whereby the majority of Arabidopsis RRM and KH domain-containing RNA binding proteins seem to be plant-specific. This indicate that in plants RNA-binding proteins with different domain organizations and RNA-binding specificities have evolved and are most likely performing plant-specific functions. Indeed, plant RBPs are beginning to emerge with increasing frequency as regulatory factors acting in floral transition, floral patterning, abscisic acid signaling, low temperature and salinity adaptation, circadian rhythms, and chromatin modification.