51
|
Barik S. On the role, ecology, phylogeny, and structure of dual-family immunophilins. Cell Stress Chaperones 2017; 22:833-845. [PMID: 28567569 PMCID: PMC5655371 DOI: 10.1007/s12192-017-0813-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 01/26/2023] Open
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.
Collapse
Affiliation(s)
- Sailen Barik
- , EonBio, 3780 Pelham Drive, Mobile, AL, 36619, USA.
| |
Collapse
|
52
|
Zheng Z, Yang X, Fu Y, Zhu L, Wei H, Lin X. Overexpression of PvPin1, a Bamboo Homolog of PIN1-Type Parvulin 1, Delays Flowering Time in Transgenic Arabidopsis and Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1526. [PMID: 28951734 PMCID: PMC5599775 DOI: 10.3389/fpls.2017.01526] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/21/2017] [Indexed: 05/03/2023]
Abstract
Because of the long and unpredictable flowering period in bamboo, the molecular mechanism of bamboo flowering is unclear. Recent study showed that Arabidopsis PIN1-type parvulin 1 (Pin1At) is an important floral activator and regulates floral transition by facilitating the cis/trans isomerization of the phosphorylated Ser/Thr residues preceding proline motifs in suppressor of overexpression of CO 1 (SOC1) and agamous-like 24 (AGL24). Whether bamboo has a Pin1 homolog and whether it works in bamboo flowering are still unknown. In this study, we cloned PvPin1, a homolog of Pin1At, from Phyllostachys violascens (Bambusoideae). Bioinformatics analysis showed that PvPin1 is closely related to Pin1-like proteins in monocots. PvPin1 was widely expressed in all tested bamboo tissues, with the highest expression in young leaf and lowest in floral bud. Moreover, PvPin1 expression was high in leaves before bamboo flowering then declined during flower development. Overexpression of PvPin1 significantly delayed flowering time by downregulating SOC1 and AGL24 expression in Arabidopsis under greenhouse conditions and conferred a significantly late flowering phenotype by upregulating OsMADS56 in rice under field conditions. PvPin1 showed subcellular localization in both the nucleus and cytolemma. The 1500-bp sequence of the PvPin1 promoter was cloned, and cis-acting element prediction showed that ABRE and TGACG-motif elements, which responded to abscisic acid (ABA) and methyl jasmonate (MeJA), respectively, were characteristic of P. violascens in comparison with Arabidopsis. On promoter activity analysis, exogenous ABA and MeJA could significantly inhibit PvPin1 expression. These findings suggested that PvPin1 may be a repressor in flowering, and its delay of flowering time could be regulated by ABA and MeJA in bamboo.
Collapse
Affiliation(s)
- Zhigang Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry UniversityHangzhou, China
| | - Xiaoming Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry UniversityHangzhou, China
| | - Yaping Fu
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Longfei Zhu
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry UniversityHangzhou, China
| | - Hantian Wei
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry UniversityHangzhou, China
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry UniversityHangzhou, China
- *Correspondence: Xinchun Lin,
| |
Collapse
|
53
|
Eb-Levadoux Y, Frelon S, Simon O, Arnaudguilhem C, Lobinski R, Mounicou S. In vivo identification of potential uranium protein targets in zebrafish ovaries after chronic waterborne exposure. Metallomics 2017; 9:525-534. [DOI: 10.1039/c6mt00291a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
54
|
Schumann M, Ihling CH, Prell E, Schierhorn A, Sinz A, Fischer G, Schiene-Fischer C, Malešević M. Identification of low abundance cyclophilins in human plasma. Proteomics 2016; 16:2815-2826. [PMID: 27586231 DOI: 10.1002/pmic.201600221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/19/2016] [Accepted: 08/22/2016] [Indexed: 11/08/2022]
Abstract
Cylophilins (Cyps) belong to the ubiquitously distributed enzyme class of peptidyl prolyl cis/trans isomerases (EC5.2.1.8), which are foldases capable of accelerating slow steps in the refolding of denatured proteins. At least 20 different Cyp isoenzymes are broadly distributed among all organs and cellular compartments in humans. Extracellularly localized Cyps came into the scientific focus recently because of their involvement in the control of inflammatory diseases, as well as viral and bacterial infections. However, detailed insights into Cyp functions are often hampered by the lack of sensitive detection methods. We present an improved method for affinity purification and detection of Cyp in biotic samples in this manuscript. The procedure takes advantage of two novel cyclosporine A derivatives. Derivative 1 was used to capture Cyps from the sample while derivative 2 was applied for selective release from the affinity matrix. Using this approach, eight different Cyp (CypA, CypB, CypC, Cyp40 (PPID), CypE, CypD (PPIF), CypH, and CypL1) were unambiguously detected in healthy human blood plasma. Moreover, extracellular CypA was found to be partially modified by Nε acetylation on residues Lys44, Lys133, Lys155, as well as Nα acetylation at the N-terminal Val residue. Nα acetylation of Ser2 residue was also found for Cyp40.
Collapse
Affiliation(s)
- Michael Schumann
- Department of Enzymology, Institute of Biochemistry und Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Erik Prell
- Branch Office Halle, Max-Planck Institute for Biophysical Chemistry, Göttingen, Halle, Germany
| | - Angelika Schierhorn
- Department of Enzymology, Institute of Biochemistry und Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Gunter Fischer
- Branch Office Halle, Max-Planck Institute for Biophysical Chemistry, Göttingen, Halle, Germany
| | - Cordelia Schiene-Fischer
- Department of Enzymology, Institute of Biochemistry und Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Miroslav Malešević
- Department of Enzymology, Institute of Biochemistry und Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany.
| |
Collapse
|
55
|
Quistgaard EM, Weininger U, Ural-Blimke Y, Modig K, Nordlund P, Akke M, Löw C. Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD. BMC Biol 2016; 14:82. [PMID: 27664121 PMCID: PMC5034536 DOI: 10.1186/s12915-016-0300-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/18/2016] [Indexed: 11/25/2022] Open
Abstract
Background Peptidyl-prolyl isomerases (PPIases) catalyze cis/trans isomerization of peptidyl-prolyl bonds, which is often rate-limiting for protein folding. SlyD is a two-domain enzyme containing both a PPIase FK506-binding protein (FKBP) domain and an insert-in-flap (IF) chaperone domain. To date, the interactions of these domains with unfolded proteins have remained rather obscure, with structural information on binding to the FKBP domain being limited to complexes involving various inhibitor compounds or a chemically modified tetrapeptide. Results We have characterized the binding of 15-residue-long unmodified peptides to SlyD from Thermus thermophilus (TtSlyD) in terms of binding thermodynamics and enzyme kinetics through the use of isothermal titration calorimetry, nuclear magnetic resonance spectroscopy, and site-directed mutagenesis. We show that the affinities and enzymatic activity of TtSlyD towards these peptides are much higher than for the chemically modified tetrapeptides that are typically used for activity measurements on FKBPs. In addition, we present a series of crystal structures of TtSlyD with the inhibitor FK506 bound to the FKBP domain, and with 15-residue-long peptides bound to either one or both domains, which reveals that substrates bind in a highly adaptable fashion to the IF domain through β-strand augmentation, and can bind to the FKBP domain as both types VIa1 and VIb-like cis-proline β-turns. Our results furthermore provide important clues to the catalytic mechanism and support the notion of inter-domain cross talk. Conclusions We found that 15-residue-long unmodified peptides can serve as better substrate mimics for the IF and FKBP domains than chemically modified tetrapeptides. We furthermore show how such peptides are recognized by each of these domains in TtSlyD, and propose a novel general model for the catalytic mechanism of FKBPs that involves C-terminal rotation around the peptidyl-prolyl bond mediated by stabilization of the twisted transition state in the hydrophobic binding site. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0300-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Esben M Quistgaard
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-17177, Stockholm, Sweden.,Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22603, Hamburg, Germany
| | - Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Yonca Ural-Blimke
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22603, Hamburg, Germany
| | - Kristofer Modig
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Pär Nordlund
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-17177, Stockholm, Sweden.,School of Biological Sciences, Nanyang Technological University, 639798, Singapore, Singapore
| | - Mikael Akke
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Christian Löw
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-17177, Stockholm, Sweden. .,Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22603, Hamburg, Germany.
| |
Collapse
|
56
|
Liao Y, Castello A, Fischer B, Leicht S, Föehr S, Frese CK, Ragan C, Kurscheid S, Pagler E, Yang H, Krijgsveld J, Hentze MW, Preiss T. The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease. Cell Rep 2016; 16:1456-1469. [PMID: 27452465 PMCID: PMC4977271 DOI: 10.1016/j.celrep.2016.06.084] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 04/06/2016] [Accepted: 06/07/2016] [Indexed: 11/30/2022] Open
Abstract
RNA functions through the dynamic formation of complexes with RNA-binding proteins (RBPs) in all clades of life. We determined the RBP repertoire of beating cardiomyocytic HL-1 cells by jointly employing two in vivo proteomic methods, mRNA interactome capture and RBDmap. Together, these yielded 1,148 RBPs, 391 of which are shared with all other available mammalian RBP repertoires, while 393 are thus far unique to cardiomyocytes. RBDmap further identified 568 regions of RNA contact within 368 RBPs. The cardiomyocyte mRNA interactome composition reflects their unique biology. Proteins with roles in cardiovascular physiology or disease, mitochondrial function, and intermediary metabolism are all highly represented. Notably, we identified 73 metabolic enzymes as RBPs. RNA-enzyme contacts frequently involve Rossmann fold domains with examples in evidence of both, mutual exclusivity of, or compatibility between RNA binding and enzymatic function. Our findings raise the prospect of previously hidden RNA-mediated regulatory interactions among cardiomyocyte gene expression, physiology, and metabolism. mRNA interactome capture and RBDmap reveal the cardiomyocyte RNA-binding proteome 1,148 RBPs are identified, 393 of which are thus far unique to cardiomyocytes Many cardiac RBPs have links to heart disease and mitochondrial metabolism Contacts of metabolic enzymes with RNA frequently involve Rossmann fold domains
Collapse
Affiliation(s)
- Yalin Liao
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton (Canberra) ACT 2601, Australia
| | - Alfredo Castello
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Bernd Fischer
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stefan Leicht
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Sophia Föehr
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Christian K Frese
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Chikako Ragan
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton (Canberra) ACT 2601, Australia
| | - Sebastian Kurscheid
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton (Canberra) ACT 2601, Australia
| | - Eloisa Pagler
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton (Canberra) ACT 2601, Australia
| | - Hao Yang
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton (Canberra) ACT 2601, Australia
| | - Jeroen Krijgsveld
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton (Canberra) ACT 2601, Australia; Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), NSW 2010, Australia.
| |
Collapse
|
57
|
Dreßen M, Lahm H, Lahm A, Wolf K, Doppler S, Deutsch MA, Cleuziou J, Pabst von Ohain J, Schön P, Ewert P, Malcic I, Lange R, Krane M. A novel de novo TBX5 mutation in a patient with Holt-Oram syndrome leading to a dramatically reduced biological function. Mol Genet Genomic Med 2016; 4:557-67. [PMID: 27652283 PMCID: PMC5023941 DOI: 10.1002/mgg3.234] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 04/29/2016] [Accepted: 05/03/2016] [Indexed: 01/26/2023] Open
Abstract
Background The Holt–Oram syndrome (HOS) is an autosomal dominant disorder affecting 1/100.000 live births. It is defined by upper limb anomalies and congenital heart defects with variable severity. We describe a dramatic phenotype of a male, 15‐month‐old patient being investigated for strict diagnostic criteria of HOS. Methods and results Genetic analysis revealed a so far unpublished TBX5 mutation, which occurs de novo in the patient with healthy parents. TBX5 belongs to the large family of T‐box transcription factors playing major roles in morphogenesis and cell‐type specification. The mutation located in the DNA‐binding domain at position 920 (C→A) leads to an amino acid change at position 85 (proline → threonine). Three‐dimensional analysis of the protein structure predicted a cis to trans change in the respective peptide bond, thereby probably provoking major conformational and functional alterations of the protein. The p.Pro85Thr mutation showed a dramatically reduced activation (97%) of the NPPA promoter in luciferase assays and failed to induce NPPA expression in HEK 293 cells compared to wild‐type TBX5 protein. The mutation did not interfere with the nuclear localization of the protein. Conclusion These results suggest that the dramatic functional alteration of the p.Pro85Thr mutation leads to the distinctive phenotype of the patient.
Collapse
Affiliation(s)
- Martina Dreßen
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Harald Lahm
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Armin Lahm
- Bioinformatics Project Support Rome Italy
| | - Klaudia Wolf
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Stefanie Doppler
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Marcus-André Deutsch
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Julie Cleuziou
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Jelena Pabst von Ohain
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Patric Schön
- Department of Paediatric Cardiology and Congenital Heart Defects German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Peter Ewert
- Department of Paediatric Cardiology and Congenital Heart Defects German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Ivan Malcic
- Department of Pediatrics Division of Cardiology and Intensive Care Unit University Hospital Zagreb Zagreb Croatia
| | - Rüdiger Lange
- Department of Cardiovascular SurgeryDivision of Experimental SurgeryGerman Heart Center Munich at the Technical University of MunichMunichGermany; DZHK (German Center for Cardiovascular Research) - partner site Munich Heart AllianceMunichGermany
| | - Markus Krane
- Department of Cardiovascular SurgeryDivision of Experimental SurgeryGerman Heart Center Munich at the Technical University of MunichMunichGermany; DZHK (German Center for Cardiovascular Research) - partner site Munich Heart AllianceMunichGermany
| |
Collapse
|
58
|
Meduri G, Guillemeau K, Dounane O, Sazdovitch V, Duyckaerts C, Chambraud B, Baulieu EE, Giustiniani J. Caspase-cleaved Tau-D(421) is colocalized with the immunophilin FKBP52 in the autophagy-endolysosomal system of Alzheimer's disease neurons. Neurobiol Aging 2016; 46:124-37. [PMID: 27479154 DOI: 10.1016/j.neurobiolaging.2016.06.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 04/27/2016] [Accepted: 06/24/2016] [Indexed: 01/06/2023]
Abstract
Pathologic modifications of the Tau protein leading to neurofibrillary tangle (NFT) formation are a common feature of a wide range of neurodegenerative diseases known as tauopathies, which include Alzheimer's disease (AD). We previously showed that the immunophilin FKBP52 physically and functionally interacts with Tau, and we recently reported that FKBP52 levels are abnormally low in AD patients' brains. To decipher the mechanism of FKBP52 decrease in AD brains, we performed multiple labeling immunohistofluorescence and lysosomal purification using postmortem brain samples of healthy controls (n = 8) and AD (n = 20) patients. Confocal analysis revealed that FKBP52 localizes to the endolysosomal system. We also report FKBP52 colocalization with the truncated Tau-D(421) in the autophagy-endolysosomal system in some AD neurons and that the decrease of FKBP52 correlates with NFT formation. Additional experiments of autophagy inhibition in Tau-inducible SH-SY5Y cells allowed demonstrating FKBP52 release in the extracellular milieu. Our findings point out the possibility that FKBP52 could be abnormally released from NFTs negative neurons in AD brains in correlation with the early pathologic Tau-D(421) neuronal accumulation.
Collapse
Affiliation(s)
- Geri Meduri
- INSERM, Unité mixte de recherche 1195, Université Paris-Saclay, Le Kremlin Bicêtre, France
| | - Kevin Guillemeau
- INSERM, Unité mixte de recherche 1195, Université Paris-Saclay, Le Kremlin Bicêtre, France
| | - Omar Dounane
- INSERM, Unité mixte de recherche 1195, Université Paris-Saclay, Le Kremlin Bicêtre, France
| | - Véronique Sazdovitch
- Laboratoire de Neuropathologie Escourolle, Hôpital de La Salpêtrière, AP-HP, Paris, France
| | - Charles Duyckaerts
- Laboratoire de Neuropathologie Escourolle, Hôpital de La Salpêtrière, AP-HP, Paris, France
| | - Béatrice Chambraud
- INSERM, Unité mixte de recherche 1195, Université Paris-Saclay, Le Kremlin Bicêtre, France
| | - Etienne Emile Baulieu
- INSERM, Unité mixte de recherche 1195, Université Paris-Saclay, Le Kremlin Bicêtre, France.
| | - Julien Giustiniani
- INSERM, Unité mixte de recherche 1195, Université Paris-Saclay, Le Kremlin Bicêtre, France.
| |
Collapse
|
59
|
Structural and Functional Characterization of a Novel Family of Cyclophilins, the AquaCyps. PLoS One 2016; 11:e0157070. [PMID: 27276069 PMCID: PMC4898713 DOI: 10.1371/journal.pone.0157070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/24/2016] [Indexed: 01/19/2023] Open
Abstract
Cyclophilins are ubiquitous cis-trans-prolyl isomerases (PPIases) found in all kingdoms of life. Here, we identify a novel family of cyclophilins, termed AquaCyps, which specifically occurs in marine Alphaproteobacteria, but not in related terrestric species. In addition to a canonical PPIase domain, AquaCyps contain large extensions and insertions. The crystal structures of two representatives from Hirschia baltica, AquaCyp293 and AquaCyp300, reveal the formation of a compact domain, the NIC domain, by the N- and C-terminal extensions together with a central insertion. The NIC domain adopts a novel mixed alpha-helical, beta-sheet fold that is linked to the cyclophilin domain via a conserved disulfide bond. In its overall fold, AquaCyp293 resembles AquaCyp300, but the two proteins utilize distinct sets of active site residues, consistent with differences in their PPIase catalytic properties. While AquaCyp293 is a highly active general PPIase, AquaCyp300 is specific for hydrophobic substrate peptides and exhibits lower overall activity.
Collapse
|
60
|
Humbert MV, Almonacid Mendoza HL, Jackson AC, Hung MC, Bielecka MK, Heckels JE, Christodoulides M. Vaccine potential of bacterial macrophage infectivity potentiator (MIP)-like peptidyl prolyl cis/trans isomerase (PPIase) proteins. Expert Rev Vaccines 2015; 14:1633-49. [PMID: 26468663 DOI: 10.1586/14760584.2015.1095638] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Peptidyl prolyl cis/trans isomerases (PPIases) are a superfamily of proteins ubiquitously distributed among living organisms, which function primarily to assist the folding and structuring of unfolded and partially folded polypeptide chains and proteins. In this review, we focus specifically on the Macrophage Infectivity Potentiator (MIP)-like PPIases, which are members of the immunophilin family of FK506-binding proteins (FKBP). MIP-like PPIases have accessory roles in virulence and are candidates for inclusion in vaccines protective against both animal and human bacterial pathogens. A structural vaccinology approach obviates any issues over molecular mimicry and potential cross-reactivity with human FKBP proteins and studies with a representative antigen, the Neisseria meningitidis-MIP, support this strategy. Moreover, a dual approach of vaccination and drug targeting could be considered for controlling bacterial infectious diseases of humans and animals.
Collapse
Affiliation(s)
- María Victoria Humbert
- a Neisseria Research, Molecular Microbiology, Academic Unit of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories , University of Southampton Faculty of Medicine , Southampton , UK
| | - Hannia L Almonacid Mendoza
- a Neisseria Research, Molecular Microbiology, Academic Unit of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories , University of Southampton Faculty of Medicine , Southampton , UK
| | - Alexandra C Jackson
- a Neisseria Research, Molecular Microbiology, Academic Unit of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories , University of Southampton Faculty of Medicine , Southampton , UK
| | - Miao-Chiu Hung
- a Neisseria Research, Molecular Microbiology, Academic Unit of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories , University of Southampton Faculty of Medicine , Southampton , UK
| | - Magdalena K Bielecka
- a Neisseria Research, Molecular Microbiology, Academic Unit of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories , University of Southampton Faculty of Medicine , Southampton , UK
| | - John E Heckels
- a Neisseria Research, Molecular Microbiology, Academic Unit of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories , University of Southampton Faculty of Medicine , Southampton , UK
| | - Myron Christodoulides
- a Neisseria Research, Molecular Microbiology, Academic Unit of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories , University of Southampton Faculty of Medicine , Southampton , UK
| |
Collapse
|
61
|
Ben-Gedalya T, Moll L, Bejerano-Sagie M, Frere S, Cabral WA, Friedmann-Morvinski D, Slutsky I, Burstyn-Cohen T, Marini JC, Cohen E. Alzheimer's disease-causing proline substitutions lead to presenilin 1 aggregation and malfunction. EMBO J 2015; 34:2820-39. [PMID: 26438723 DOI: 10.15252/embj.201592042] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/25/2015] [Indexed: 12/15/2022] Open
Abstract
Do different neurodegenerative maladies emanate from the failure of a mutual protein folding mechanism? We have addressed this question by comparing mutational patterns that are linked to the manifestation of distinct neurodegenerative disorders and identified similar neurodegeneration-linked proline substitutions in the prion protein and in presenilin 1 that underlie the development of a prion disorder and of familial Alzheimer's disease (fAD), respectively. These substitutions were found to prevent the endoplasmic reticulum (ER)-resident chaperone, cyclophilin B, from assisting presenilin 1 to fold properly, leading to its aggregation, deposition in the ER, reduction of γ-secretase activity, and impaired mitochondrial distribution and function. Similarly, reduced quantities of the processed, active presenilin 1 were observed in brains of cyclophilin B knockout mice. These discoveries imply that reduced cyclophilin activity contributes to the development of distinct neurodegenerative disorders, propose a novel mechanism for the development of certain fAD cases, and support the emerging theme that this disorder can stem from aberrant presenilin 1 function. This study also points at ER chaperones as targets for the development of counter-neurodegeneration therapies.
Collapse
Affiliation(s)
- Tziona Ben-Gedalya
- Biochemistry and Molecular Biology, The Institute for Medical Research Israel - Canada (IMRIC), The Hebrew University Medical School, Jerusalem, Israel
| | - Lorna Moll
- Biochemistry and Molecular Biology, The Institute for Medical Research Israel - Canada (IMRIC), The Hebrew University Medical School, Jerusalem, Israel
| | - Michal Bejerano-Sagie
- Biochemistry and Molecular Biology, The Institute for Medical Research Israel - Canada (IMRIC), The Hebrew University Medical School, Jerusalem, Israel
| | - Samuel Frere
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Wayne A Cabral
- Bone and Extracellular Matrix Branch, NICHD, NIH, Bethesda, MD, USA
| | | | - Inna Slutsky
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tal Burstyn-Cohen
- Institute for Dental Sciences, Faculty of Dental Medicine Hebrew University - Hadassah, Jerusalem, Israel
| | - Joan C Marini
- Bone and Extracellular Matrix Branch, NICHD, NIH, Bethesda, MD, USA
| | - Ehud Cohen
- Biochemistry and Molecular Biology, The Institute for Medical Research Israel - Canada (IMRIC), The Hebrew University Medical School, Jerusalem, Israel
| |
Collapse
|
62
|
von Brunn A, Ciesek S, von Brunn B, Carbajo-Lozoya J. Genetic deficiency and polymorphisms of cyclophilin A reveal its essential role for Human Coronavirus 229E replication. Curr Opin Virol 2015; 14:56-61. [PMID: 26318518 PMCID: PMC7102849 DOI: 10.1016/j.coviro.2015.08.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/06/2015] [Accepted: 08/10/2015] [Indexed: 12/15/2022]
Abstract
Replication of coronaviruses is inhibited in vitro by cyclosporin A, a well-known immunosuppressive drug which binds to cellular cyclophilins thus inactivating their enzymatic cis-trans peptidyl-prolyl isomerase function. Latter is required for proper folding of cellular proteins and of proteins of several viruses. Here, we summarize present knowledge on the role of cyclophilin A during coronavirus replication. We present data on the effect of cyclophilin A single nucleotide polymorphism mutants on the replication of human CoV-229E demonstrating the requirement of proper cyclophilin A function for virus propagation. Results define cellular cyclophilin A as a host target for inhibition of coronaviruses ranging from relatively mild common cold to highly pathogenic SARS-CoV and MERS-CoV viruses with the perspective of disclosing non-immunosuppressive cyclosporin A analogs to broadly inactivate the coronavirus family.
Collapse
Affiliation(s)
- Albrecht von Brunn
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-Universität, München, Germany; German Center for Infection Research (DZIF), Germany.
| | - Sandra Ciesek
- German Center for Infection Research (DZIF), Germany; Department of Gastroenterology, Hepatology und Endocrinology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Brigitte von Brunn
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-Universität, München, Germany; German Center for Infection Research (DZIF), Germany
| | - Javier Carbajo-Lozoya
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-Universität, München, Germany; German Center for Infection Research (DZIF), Germany
| |
Collapse
|
63
|
Follis AV, Llambi F, Merritt P, Chipuk JE, Green DR, Kriwacki RW. Pin1-Induced Proline Isomerization in Cytosolic p53 Mediates BAX Activation and Apoptosis. Mol Cell 2015; 59:677-84. [PMID: 26236013 PMCID: PMC4546541 DOI: 10.1016/j.molcel.2015.06.029] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/15/2015] [Accepted: 06/22/2015] [Indexed: 12/31/2022]
Abstract
The cytosolic fraction of the tumor suppressor p53 activates the apoptotic effector protein BAX to trigger apoptosis. Here we report that p53 activates BAX through a mechanism different from that associated with activation by BH3 only proteins (BIM and BID). We observed that cis-trans isomerization of proline 47 (Pro47) within p53, an inherently rare molecular event, was required for BAX activation. The prolyl isomerase Pin1 enhanced p53-dependent BAX activation by catalyzing cis-trans interconversion of p53 Pro47. Our results reveal a signaling mechanism whereby proline cis-trans isomerization in one protein triggers conformational and functional changes in a downstream signaling partner. Activation of BAX through the concerted action of cytosolic p53 and Pin1 may integrate cell stress signals to induce a direct apoptotic response.
Collapse
Affiliation(s)
- Ariele Viacava Follis
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Fabien Llambi
- Department of Immunology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Parker Merritt
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jerry E Chipuk
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA; Department of Dermatology, The Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, 920 Court Avenue, Memphis, TN 38163, USA.
| |
Collapse
|
64
|
Schmid F. Preface. Special Issue on Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets. Biochim Biophys Acta Gen Subj 2015; 1850:1963-4. [PMID: 25999160 DOI: 10.1016/j.bbagen.2015.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Franz Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95440 Bayreuth, Germany
| |
Collapse
|
65
|
Roles of Prolyl Isomerases in RNA-Mediated Gene Expression. Biomolecules 2015; 5:974-99. [PMID: 25992900 PMCID: PMC4496705 DOI: 10.3390/biom5020974] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/01/2015] [Accepted: 05/07/2015] [Indexed: 12/16/2022] Open
Abstract
The peptidyl-prolyl cis-trans isomerases (PPIases) that include immunophilins (cyclophilins and FKBPs) and parvulins (Pin1, Par14, Par17) participate in cell signaling, transcription, pre-mRNA processing and mRNA decay. The human genome encodes 19 cyclophilins, 18 FKBPs and three parvulins. Immunophilins are receptors for the immunosuppressive drugs cyclosporin A, FK506, and rapamycin that are used in organ transplantation. Pin1 has also been targeted in the treatment of Alzheimer’s disease, asthma, and a number of cancers. While these PPIases are characterized as molecular chaperones, they also act in a nonchaperone manner to promote protein-protein interactions using surfaces outside their active sites. The immunosuppressive drugs act by a gain-of-function mechanism by promoting protein-protein interactions in vivo. Several immunophilins have been identified as components of the spliceosome and are essential for alternative splicing. Pin1 plays roles in transcription and RNA processing by catalyzing conformational changes in the RNA Pol II C-terminal domain. Pin1 also binds several RNA binding proteins such as AUF1, KSRP, HuR, and SLBP that regulate mRNA decay by remodeling mRNP complexes. The functions of ribonucleoprotein associated PPIases are largely unknown. This review highlights PPIases that play roles in RNA-mediated gene expression, providing insight into their structures, functions and mechanisms of action in mRNP remodeling in vivo.
Collapse
|
66
|
Schmidpeter PAM, Schmid FX. Prolyl isomerization and its catalysis in protein folding and protein function. J Mol Biol 2015; 427:1609-31. [PMID: 25676311 DOI: 10.1016/j.jmb.2015.01.023] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/30/2015] [Indexed: 12/20/2022]
Abstract
Prolyl isomerizations are intrinsically slow processes. They determine the rates of many protein folding reactions and control regulatory events in folded proteins. Prolyl isomerases are able to catalyze these isomerizations, and thus, they have the potential to assist protein folding and to modulate protein function. Here, we provide examples for how prolyl isomerizations limit protein folding and are accelerated by prolyl isomerases and how native-state prolyl isomerizations regulate protein functions. The roles of prolines in protein folding and protein function are closely interrelated because both of them depend on the coupling between cis/trans isomerization and conformational changes that can involve extended regions of a protein.
Collapse
Affiliation(s)
- Philipp A M Schmidpeter
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Franz X Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biologie, Universität Bayreuth, 95440 Bayreuth, Germany.
| |
Collapse
|