The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
CPR4 (UniProt accession: P25334) encodes peptidyl-prolyl cis-trans isomerase CPR4, also designated CYP4, SCC3, YCR069W, or YCR69W/YCR70W. The gene is located on chromosome III of Saccharomyces cerevisiae (strain ATCC 204508 / S288c). The protein belongs to the cyclophilin family of peptidyl-prolyl cis-trans isomerases (PPIases; EC 5.2.1.8), which catalyze the interconversion of cis and trans conformations of peptide bonds preceding proline residues in polypeptide chains (franco1991thenucleotidesequence pages 4-7, franco1991thenucleotidesequence pages 1-2).
The CPR4 gene was originally cloned and sequenced as SCC3 (for S. cerevisiae cyclophilin 3), described as the third cyclophilin-homologous gene identified in budding yeast. The open reading frame comprises 954 nucleotides encoding a polypeptide of 318 amino acids with a predicted molecular weight of approximately 33–36 kDa and an isoelectric point of 6.9 (franco1991thenucleotidesequence pages 4-7, franco1991thenucleotidesequence pages 1-2). The protein has three notable structural features:
CPR4 (also CYP4, SCC3, YCR069W) in Saccharomyces cerevisiae encodes a cyclophilin-family peptidyl-prolyl cis-trans isomerase precursor of 318 amino acids (~33–36 kDa) that contains an N-terminal ~20 aa signal peptide, a central cyclophilin-like/PPIase domain, and a hydrophobic C-terminal membrane anchor; the original SCC3 cloning study concluded that these features make the protein secretory or, more likely, membrane-anchored. (franco1991thenucleotidesequence pages 4-7, franco1991thenucleotidesequence pages 2-4, franco1991thenucleotidesequence pages 1-2, pemberton2005identificationandcomparative pages 6-8)
Sequence comparison showed that CPR4/Scc3 is unusual among yeast cyclophilins because it shares structural organization with Drosophila NinaA, including both a cleavable signal peptide and a C-terminal transmembrane segment, supporting the idea that CPR4 may act on folding or trafficking of proteins in the secretory pathway rather than functioning as a soluble cytosolic cyclophilin. (franco1991thenucleotidesequence pages 4-7, arevalorodriguez2004prolylisomerasesin pages 7-8, colley1991thecyclophilinhomolog pages 1-2, pemberton2005identificationandcomparative pages 11-13)
Franco et al. also noted that the conserved cyclophilin residue equivalent to W121, important for cyclosporin A binding in other cyclophilins, is replaced by glutamate in Scc3/CPR4 (W121E-equivalent substitution), implying that cyclosporin binding may be reduced while leaving catalytic PPIase-related features more intact; however, CPR4-specific CsA sensitivity was not directly established. (franco1991thenucleotidesequence pages 4-7)
Later yeast cyclophilin surveys placed Cpr4 among the eight S. cerevisiae cyclophilins and reported vacuolar localization, while comparative analyses also discussed ER/secretory-pathway association, heat-shock/tunicamycin inducibility, and a relationship to cyclophilin C-like proteins. Taken together, the best-supported model is that CPR4 is a membrane-associated secretory/vacuolar cyclophilin with conserved cyclophilin fold characteristics but an incompletely resolved precise cellular function. (arevalorodriguez2004prolylisomerasesin pages 7-8, arevalorodriguez2004prolylisomerasesin pages 4-6, wang2005thecyclophilins pages 2-3, wang2005thecyclophilins pages 3-4, pemberton2005identificationandcomparative pages 11-13)
Blockquote: This blockquote condenses the main structural and localization evidence for yeast CPR4/Cpr4, including its precursor architecture, NinaA-like topology, and the key W121E-related inference about cyclosporin binding. It is useful as a quick-reference evidence summary for functional annotation.
N-terminal signal peptide. The first ~20 amino acids constitute a hydrophobic signal peptide with a predicted cleavage site between positions A20 and A21, consistent with entry into the secretory pathway (franco1991thenucleotidesequence pages 4-7, franco1991thenucleotidesequence pages 1-2).
Central cyclophilin-like PPIase domain. The core of the protein contains a cyclophilin-like domain (CLD), harboring the canonical PPIase fold (InterPro: IPR002130, IPR029000; Pfam: PF00160). Sequence alignment with other cyclophilins reveals conservation of key catalytic segments, particularly segment IV, which is implicated in PPIase activity (franco1991thenucleotidesequence pages 4-7, pemberton2005identificationandcomparative pages 6-8).
C-terminal transmembrane domain. Unlike the major cytosolic yeast cyclophilin Cpr1, Cpr4 contains a hydrophobic stretch of approximately 17 amino acids at the C-terminus that fits the characteristics of a transmembrane helix domain (franco1991thenucleotidesequence pages 4-7, arevalorodriguez2004prolylisomerasesin pages 7-8). The protein also contains a potential glycosylation site (S-A-T) (franco1991thenucleotidesequence pages 4-7). This combined topology — cleavable signal peptide plus C-terminal membrane anchor — suggests the protein is a type I integral membrane protein with its catalytic domain oriented on the luminal/exoplasmic face (franco1991thenucleotidesequence pages 4-7, franco1991thenucleotidesequence pages 1-2).
As a cyclophilin-family member, Cpr4 is predicted to catalyze the cis-trans isomerization of peptidyl-prolyl bonds in substrate proteins (EC 5.2.1.8). This reaction accelerates the rate-limiting step of protein folding that involves proline-containing segments (franco1991thenucleotidesequence pages 1-2, arevalorodriguez2004prolylisomerasesin pages 2-4). The cyclophilin fold of Cpr4 is well conserved relative to other family members, including canonical segments associated with PPIase catalysis (franco1991thenucleotidesequence pages 4-7). However, direct biochemical measurement of Cpr4's PPIase catalytic activity, substrate specificity, or kinetic parameters has not been reported. The specific in vivo substrates of Cpr4 remain unknown, and its biological function is listed as "unknown" in comprehensive surveys of yeast prolyl isomerases (arevalorodriguez2004prolylisomerasesin pages 4-6).
A notable sequence feature with functional implications is the substitution of the tryptophan residue at the position equivalent to W121 of human cyclophilin A. In human CypA, W121 is critical for cyclosporin A (CsA) binding: mutation to phenylalanine or alanine reduces CsA susceptibility by 75- to 200-fold while diminishing PPIase activity only 2- to 13-fold, demonstrating that CsA binding and PPIase catalytic function are structurally separable. In Cpr4/Scc3, this tryptophan is replaced by glutamic acid, suggesting that Cpr4 may exhibit reduced sensitivity to CsA, though this was not experimentally verified (franco1991thenucleotidesequence pages 4-7).
The localization of Cpr4 has been addressed in multiple studies, with evidence pointing to the vacuole and the endoplasmic reticulum/secretory pathway:
Vacuolar localization: Multiple comprehensive surveys of yeast prolyl isomerases consistently report Cpr4 as a vacuolar protein (arevalorodriguez2004prolylisomerasesin pages 4-6, wang2005thecyclophilins pages 2-3). Wang and Heitman (2005) described both Cpr4 and Cpr8 as vacuolar cyclophilins that share cyclophilin C (CypC) as their mammalian ortholog (wang2005thecyclophilins pages 2-3). Arévalo-Rodríguez et al. (2004) also noted that "recent reports indicate that Cpr4 localizes to the vacuole" (arevalorodriguez2004prolylisomerasesin pages 7-8).
ER and secretory pathway association: Pemberton and Kay (2005), in their comparative PPIase analysis, listed Cpr4 with a predicted ER localization based on its N-terminal signal sequence, and described it as functioning within the secretory pathway. They further noted that CPR4 expression is induced by heat shock and tunicamycin, the latter being an ER stress agent that induces the unfolded protein response (pemberton2005identificationandcomparative pages 6-8, pemberton2005identificationandcomparative pages 11-13).
These observations are not contradictory: membrane proteins with signal peptides transit through the ER en route to other compartments including the vacuole. The presence of both an N-terminal signal peptide and a C-terminal transmembrane domain indicates that Cpr4 enters the secretory pathway and is subsequently trafficked — likely reaching the vacuolar membrane as its final destination.
The most striking structural parallel to Cpr4 is with Drosophila NinaA (neither inactivation nor afterpotential A), an integral membrane cyclophilin essential for rhodopsin biosynthesis and transport. NinaA shares with Cpr4 the combined topology of an N-terminal cleavable signal peptide and a C-terminal transmembrane domain, along with a central cyclophilin catalytic domain (franco1991thenucleotidesequence pages 4-7, arevalorodriguez2004prolylisomerasesin pages 7-8, colley1991thecyclophilinhomolog pages 1-2). NinaA localizes to the ER and secretory vesicles, where it is required for the proper folding and ER-to-Golgi transport of Rh1 opsin (colley1991thecyclophilinhomolog pages 4-6, colley1991thecyclophilinhomolog pages 2-4, colley1991thecyclophilinhomolog pages 1-2). In NinaA mutants, Rh1 opsin accumulates in the ER in an unprocessed high-molecular-weight form, and dramatic ER membrane elaboration occurs (colley1991thecyclophilinhomolog pages 4-6). NinaA acts as a substrate-specific chaperone/foldase, exhibiting selectivity for Rh1 and Rh2 rhodopsin isoforms but not Rh3 or Rh4, and targets the N-terminal P37 proline residue (ferreira2012fromdrosophilato pages 6-8, colley1991thecyclophilinhomolog pages 2-4).
The structural similarity between Cpr4 and NinaA led Franco et al. (1991) to propose that Cpr4 may serve an analogous function in yeast — acting as a membrane-anchored cyclophilin that assists in the folding or transport of specific membrane or secretory proteins — though with different target substrates, as yeast lacks rhodopsins (franco1991thenucleotidesequence pages 4-7, franco1991thenucleotidesequence pages 1-2). This remains the most compelling functional hypothesis for Cpr4, though it has not been experimentally validated.
S. cerevisiae encodes eight cyclophilins (Cpr1–Cpr8) distributed across multiple subcellular compartments. The following table summarizes their properties:
| Gene | Approx. mass | Subcellular localization | Known function / distinguishing features | Mammalian ortholog |
|---|---|---|---|---|
| CPR1 | 17 kDa | Cytoplasm, nucleus | Cyclosporin A receptor; interacts with Sin3-Rpd3 histone deacetylase complex (arevalorodriguez2004prolylisomerasesin pages 4-6, wang2005thecyclophilins pages 3-4) | CypA (wang2005thecyclophilins pages 2-3) |
| CPR2 | 20 kDa | Secreted / secretory pathway | Required for cell survival after heat shock (arevalorodriguez2004prolylisomerasesin pages 4-6, arevalorodriguez2004prolylisomerasesin pages 7-8) | CypB (wang2005thecyclophilins pages 2-3) |
| CPR3 | 20 kDa | Mitochondria | Supports mitochondrial function at high temperature; assists mitochondrial protein folding under stress (arevalorodriguez2004prolylisomerasesin pages 4-6, arevalorodriguez2004prolylisomerasesin pages 7-8) | CypD (wang2005thecyclophilins pages 2-3) |
| CPR4 | 33 kDa | Vacuole; also reported/predicted in ER/secretory pathway | Function remains unknown; cyclophilin-family PPIase domain; N-terminal signal peptide; C-terminal transmembrane domain(s); structurally similar to Drosophila NinaA; reported as induced by heat shock and tunicamycin (arevalorodriguez2004prolylisomerasesin pages 4-6, arevalorodriguez2004prolylisomerasesin pages 7-8, franco1991thenucleotidesequence pages 4-7, pemberton2005identificationandcomparative pages 11-13) | CypC (wang2005thecyclophilins pages 2-3) |
| CPR5 | 23 kDa | Endoplasmic reticulum | Unknown function; secretory-pathway cyclophilin with HDEL retention signal (arevalorodriguez2004prolylisomerasesin pages 4-6, arevalorodriguez2004prolylisomerasesin pages 7-8) | CypB (wang2005thecyclophilins pages 2-3) |
| CPR6 | 45 kDa | Cytoplasm | Interacts with Hsp82/Hsp90; contains TPR domain; chaperone-associated cyclophilin (arevalorodriguez2004prolylisomerasesin pages 4-6, arevalorodriguez2004prolylisomerasesin pages 7-8) | Cyp40 (wang2005thecyclophilins pages 2-3) |
| CPR7 | 45 kDa | Cytoplasm | Interacts with Hsp90; contains TPR domain; required for normal growth (arevalorodriguez2004prolylisomerasesin pages 4-6, arevalorodriguez2004prolylisomerasesin pages 7-8) | Cyp40 (wang2005thecyclophilins pages 2-3) |
| CPR8 | 35 kDa | Vacuole / membrane | Unknown function; membrane-associated vacuolar cyclophilin (arevalorodriguez2004prolylisomerasesin pages 4-6, wang2005thecyclophilins pages 2-3, pemberton2005identificationandcomparative pages 11-13) | CypC (wang2005thecyclophilins pages 2-3) |
Table: This table summarizes the eight Saccharomyces cerevisiae cyclophilins (CPR1-CPR8), including size, localization, functions, and ortholog assignments. CPR4 is highlighted because it is the target gene and has mixed localization/function evidence that is important for interpretation.
A critical finding from genetic studies is that none of the eight yeast cyclophilins is essential for viability. An octuple mutant strain (Δcpr1 Δcpr2 Δcpr3 Δcpr4 Δcpr5 Δcpr6 Δcpr7 Δcpr8) lacking all eight cyclophilins is viable, with little evidence of functional redundancy among the family members (wang2005thecyclophilins pages 3-4, arevalorodriguez2004prolylisomerasesin pages 2-4). This indicates that whatever function Cpr4 performs, it is dispensable under standard laboratory growth conditions. The only essential yeast prolyl isomerase is the parvulin-family member Ess1 (arevalorodriguez2004prolylisomerasesin pages 2-4).
Phylogenetic analyses place Cpr4 and Cpr8 on the same branch, both related to the cyclophilin C family (CypC orthologs), and distinct from the cyclophilin A (CypA/Cpr1) and cyclophilin B (CypB/Cpr2, Cpr5) lineages. The cyclophilin C orthologs appear to have evolved independently from one another and from the cyclophilin B orthologs, rather than sharing a distinct common ancestor (wang2005thecyclophilins pages 3-4, pemberton2005identificationandcomparative pages 10-11, pemberton2005identificationandcomparative pages 11-13).
Northern blot analysis demonstrated that CPR4/SCC3 is constitutively expressed during exponential growth, producing an abundant ~1.2 kb transcript (franco1991thenucleotidesequence pages 4-7). The 5′ regulatory region contains a TATA box at position −135 and other promoter elements but lacks identifiable upstream activating sequences, consistent with constitutive expression (franco1991thenucleotidesequence pages 4-7). Independently, Pemberton and Kay (2005) reported that CPR4 is induced by heat shock and tunicamycin, suggesting regulation under ER-stress or protein-folding-stress conditions (pemberton2005identificationandcomparative pages 11-13).
Cpr4 is a membrane-anchored cyclophilin of the secretory/vacuolar pathway in S. cerevisiae. Based on its domain architecture, it is predicted to catalyze peptidyl-prolyl cis-trans isomerization (EC 5.2.1.8) of substrate proteins within the lumen of the ER, transport vesicles, or the vacuole. Its unique topology — with an N-terminal signal peptide and C-terminal transmembrane anchor — is shared with Drosophila NinaA, suggesting it may function as a chaperone-like PPIase that assists in the folding or intracellular transport of specific membrane or secretory proteins. However, the precise in vivo substrates and biological role of Cpr4 remain experimentally undefined. The protein is non-essential, as demonstrated by the viability of strains lacking all eight yeast cyclophilins. CPR4 is constitutively expressed and may be further upregulated under conditions of ER stress. The replacement of the canonical CsA-binding tryptophan with glutamic acid suggests that Cpr4 may have reduced cyclosporin A affinity compared to other cyclophilins, although this has not been directly tested.
References
(franco1991thenucleotidesequence pages 4-7): L. Franco, A. Jiménez, J. Demolder, F. Molemans, W. Fiers, and R. Contreras. The nucleotide sequence of a third cyclophilin‐homologous gene from saccharomyces cerevisiae. Yeast, 7:971-979, Dec 1991. URL: https://doi.org/10.1002/yea.320070909, doi:10.1002/yea.320070909. This article has 44 citations and is from a peer-reviewed journal.
(franco1991thenucleotidesequence pages 1-2): L. Franco, A. Jiménez, J. Demolder, F. Molemans, W. Fiers, and R. Contreras. The nucleotide sequence of a third cyclophilin‐homologous gene from saccharomyces cerevisiae. Yeast, 7:971-979, Dec 1991. URL: https://doi.org/10.1002/yea.320070909, doi:10.1002/yea.320070909. This article has 44 citations and is from a peer-reviewed journal.
(franco1991thenucleotidesequence pages 2-4): L. Franco, A. Jiménez, J. Demolder, F. Molemans, W. Fiers, and R. Contreras. The nucleotide sequence of a third cyclophilin‐homologous gene from saccharomyces cerevisiae. Yeast, 7:971-979, Dec 1991. URL: https://doi.org/10.1002/yea.320070909, doi:10.1002/yea.320070909. This article has 44 citations and is from a peer-reviewed journal.
(pemberton2005identificationandcomparative pages 6-8): Trevor J. Pemberton and John E. Kay. Identification and comparative analysis of the peptidyl-prolyl cis/trans isomerase repertoires of h. sapiens, d. melanogaster, c. elegans, s. cerevisiae and sz. pombe. Comparative and Functional Genomics, 6:277-300, Jul 2005. URL: https://doi.org/10.1002/cfg.482, doi:10.1002/cfg.482. This article has 74 citations.
(arevalorodriguez2004prolylisomerasesin pages 7-8): M. Arévalo-Rodríguez, Xiaoyun Wu, S. Hanes, and J. Heitman. Prolyl isomerases in yeast. Frontiers in bioscience : a journal and virtual library, 9:2420-46, Sep 2004. URL: https://doi.org/10.2741/1405, doi:10.2741/1405. This article has 151 citations.
(colley1991thecyclophilinhomolog pages 1-2): Nansi Jo Colley, Elizabeth K. Baker, Mark A. Stamnes, and Charles S. Zuker. The cyclophilin homolog ninaa is required in the secretory pathway. Cell, 67:255-263, Oct 1991. URL: https://doi.org/10.1016/0092-8674(91)90177-z, doi:10.1016/0092-8674(91)90177-z. This article has 405 citations and is from a highest quality peer-reviewed journal.
(pemberton2005identificationandcomparative pages 11-13): Trevor J. Pemberton and John E. Kay. Identification and comparative analysis of the peptidyl-prolyl cis/trans isomerase repertoires of h. sapiens, d. melanogaster, c. elegans, s. cerevisiae and sz. pombe. Comparative and Functional Genomics, 6:277-300, Jul 2005. URL: https://doi.org/10.1002/cfg.482, doi:10.1002/cfg.482. This article has 74 citations.
(arevalorodriguez2004prolylisomerasesin pages 4-6): M. Arévalo-Rodríguez, Xiaoyun Wu, S. Hanes, and J. Heitman. Prolyl isomerases in yeast. Frontiers in bioscience : a journal and virtual library, 9:2420-46, Sep 2004. URL: https://doi.org/10.2741/1405, doi:10.2741/1405. This article has 151 citations.
(wang2005thecyclophilins pages 2-3): Ping Wang and Joseph Heitman. The cyclophilins. Genome Biology, 6:226-226, Jun 2005. URL: https://doi.org/10.1186/gb-2005-6-7-226, doi:10.1186/gb-2005-6-7-226. This article has 892 citations and is from a highest quality peer-reviewed journal.
(wang2005thecyclophilins pages 3-4): Ping Wang and Joseph Heitman. The cyclophilins. Genome Biology, 6:226-226, Jun 2005. URL: https://doi.org/10.1186/gb-2005-6-7-226, doi:10.1186/gb-2005-6-7-226. This article has 892 citations and is from a highest quality peer-reviewed journal.
(arevalorodriguez2004prolylisomerasesin pages 2-4): M. Arévalo-Rodríguez, Xiaoyun Wu, S. Hanes, and J. Heitman. Prolyl isomerases in yeast. Frontiers in bioscience : a journal and virtual library, 9:2420-46, Sep 2004. URL: https://doi.org/10.2741/1405, doi:10.2741/1405. This article has 151 citations.
(colley1991thecyclophilinhomolog pages 4-6): Nansi Jo Colley, Elizabeth K. Baker, Mark A. Stamnes, and Charles S. Zuker. The cyclophilin homolog ninaa is required in the secretory pathway. Cell, 67:255-263, Oct 1991. URL: https://doi.org/10.1016/0092-8674(91)90177-z, doi:10.1016/0092-8674(91)90177-z. This article has 405 citations and is from a highest quality peer-reviewed journal.
(colley1991thecyclophilinhomolog pages 2-4): Nansi Jo Colley, Elizabeth K. Baker, Mark A. Stamnes, and Charles S. Zuker. The cyclophilin homolog ninaa is required in the secretory pathway. Cell, 67:255-263, Oct 1991. URL: https://doi.org/10.1016/0092-8674(91)90177-z, doi:10.1016/0092-8674(91)90177-z. This article has 405 citations and is from a highest quality peer-reviewed journal.
(ferreira2012fromdrosophilato pages 6-8): Paulo A. Ferreira and Andrew Orry. From drosophila to humans: reflections on the roles of the prolyl isomerases and chaperones, cyclophilins, in cell function and disease. Journal of Neurogenetics, 26:132-143, Jun 2012. URL: https://doi.org/10.3109/01677063.2011.647143, doi:10.3109/01677063.2011.647143. This article has 23 citations and is from a peer-reviewed journal.
(pemberton2005identificationandcomparative pages 10-11): Trevor J. Pemberton and John E. Kay. Identification and comparative analysis of the peptidyl-prolyl cis/trans isomerase repertoires of h. sapiens, d. melanogaster, c. elegans, s. cerevisiae and sz. pombe. Comparative and Functional Genomics, 6:277-300, Jul 2005. URL: https://doi.org/10.1002/cfg.482, doi:10.1002/cfg.482. This article has 74 citations.