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Da Silva WM, Bei J, Amigo N, Valacco MP, Amadio A, Zhang Q, Wu X, Yu T, Larzabal M, Chen Z, Cataldi A. Quantification of enterohemorrhagic Escherichia coli O157:H7 protein abundance by high-throughput proteome. PLoS One 2018; 13:e0208520. [PMID: 30596662 PMCID: PMC6312284 DOI: 10.1371/journal.pone.0208520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/19/2018] [Indexed: 12/22/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a human pathogen responsible for diarrhea, hemorrhagic colitis and hemolytic uremic syndrome (HUS). To promote a comprehensive insight into the molecular basis of EHEC O157:H7 physiology and pathogenesis, the combined proteome of EHEC O157:H7 strains, Clade 8 and Clade 6 isolated from cattle in Argentina, and the standard EDL933 (clade 3) strain has been analyzed. From shotgun proteomic analysis a total of 2,644 non-redundant proteins of EHEC O157:H7 were identified, which correspond approximately 47% of the predicted proteome of this pathogen. Normalized spectrum abundance factor analysis was performed to estimate the protein abundance. According this analysis, 50 proteins were detected as the most abundant of EHEC O157:H7 proteome. COG analysis showed that the majority of the most abundant proteins are associated with translation processes. A KEGG enrichment analysis revealed that Glycolysis / Gluconeogenesis was the most significant pathway. On the other hand, the less abundant detected proteins are those related to DNA processes, cell respiration and prophage. Among the proteins that composed the Type III Secretion System, the most abundant protein was EspA. Altogether, the results show a subset of important proteins that contribute to physiology and pathogenicity of EHEC O157:H7.
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Affiliation(s)
- Wanderson Marques Da Silva
- Institute of Biotechnology, CICVyA, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina
| | - Jinlong Bei
- AGRO-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Natalia Amigo
- Institute of Biotechnology, CICVyA, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina
| | - María Pía Valacco
- CEQUIBIEM (Mass Spectrometry Facility), Faculty of Exact and Natural Sciences, University of Buenos Aires and CONICET (National Research Council), Buenos Aires, Argentina
| | - Ariel Amadio
- Rafaela Experimental Station, National Institute of Agricultural Technology, Rafaela, Santa Fe, Argentina
| | - Qi Zhang
- AGRO-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Xiuju Wu
- AGRO-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Ting Yu
- AGRO-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Mariano Larzabal
- Institute of Biotechnology, CICVyA, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina
| | - Zhuang Chen
- AGRO-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Angel Cataldi
- Institute of Biotechnology, CICVyA, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina
- * E-mail:
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Peptidylarginine Deiminases Post-Translationally Deiminate Prohibitin and Modulate Extracellular Vesicle Release and MicroRNAs in Glioblastoma Multiforme. Int J Mol Sci 2018; 20:ijms20010103. [PMID: 30597867 PMCID: PMC6337164 DOI: 10.3390/ijms20010103] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 12/22/2018] [Accepted: 12/25/2018] [Indexed: 12/19/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most aggressive form of adult primary malignant brain tumour with poor prognosis. Extracellular vesicles (EVs) are a key-mediator through which GBM cells promote a pro-oncogenic microenvironment. Peptidylarginine deiminases (PADs), which catalyze the post-translational protein deimination of target proteins, are implicated in cancer, including via EV modulation. Pan-PAD inhibitor Cl-amidine affected EV release from GBM cells, and EV related microRNA cargo, with reduced pro-oncogenic microRNA21 and increased anti-oncogenic microRNA126, also in combinatory treatment with the chemotherapeutic agent temozolomide (TMZ). The GBM cell lines under study, LN18 and LN229, differed in PAD2, PAD3 and PAD4 isozyme expression. Various cytoskeletal, nuclear and mitochondrial proteins were identified to be deiminated in GBM, including prohibitin (PHB), a key protein in mitochondrial integrity and also involved in chemo-resistance. Post-translational deimination of PHB, and PHB protein levels, were reduced after 1 h treatment with pan-PAD inhibitor Cl-amidine in GBM cells. Histone H3 deimination was also reduced following Cl-amidine treatment. Multifaceted roles for PADs on EV-mediated pathways, as well as deimination of mitochondrial, nuclear and invadopodia related proteins, highlight PADs as novel targets for modulating GBM tumour communication.
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Magnadóttir B, Hayes P, Gísladóttir B, Bragason BÞ, Hristova M, Nicholas AP, Guðmundsdóttir S, Lange S. Pentraxins CRP-I and CRP-II are post-translationally deiminated and differ in tissue specificity in cod (Gadus morhua L.) ontogeny. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 87:1-11. [PMID: 29777721 DOI: 10.1016/j.dci.2018.05.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 06/08/2023]
Abstract
Pentraxins are fluid phase pattern recognition molecules that form an important part of the innate immune defence and are conserved between fish and human. In Atlantic cod (Gadus morhua L.), two pentraxin-like proteins have been described, CRP-I and CRP-II. Here we show for the first time that these two CRP forms are post-translationally deiminated (an irreversible conversion of arginine to citrulline) and differ with respect to tissue specific localisation in cod ontogeny from 3 to 84 days post hatching. While both forms are expressed in liver, albeit at temporally differing levels, CRP-I shows a strong association with nervous tissue while CRP-II is strongly associated to mucosal tissues of gut and skin. This indicates differing roles for the two pentraxin types in immune responses and tissue remodelling, also elucidating novel roles for CRP-I in the nervous system. The presence of deimination positive bands for cod CRPs varied somewhat between mucus and serum, possibly facilitating CRP protein moonlighting, allowing the same protein to exhibit a range of biological functions and thus meeting different functional requirements in different tissues. The presented findings may further current understanding of the diverse roles of pentraxins in teleost immune defences and tissue remodelling, as well as in various human pathologies, including autoimmune diseases, amyloidosis and cancer.
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Affiliation(s)
- Bergljót Magnadóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Polly Hayes
- Department of Biomedical Sciences, University of Westminster, London W1W 6UW, UK.
| | - Berglind Gísladóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Birkir Þór Bragason
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Mariya Hristova
- Perinatal Brain Protection and Repair Group, EGA Institute for Women's Health, University College London, WC1E 6HX London, UK.
| | - Anthony P Nicholas
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Sigríður Guðmundsdóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, Department of Biomedical Sciences, University of Westminster, London W1W 6UW, UK.
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Magnadóttir B, Hayes P, Hristova M, Bragason BT, Nicholas AP, Dodds AW, Guðmundsdóttir S, Lange S. Post-translational protein deimination in cod (Gadus morhua L.) ontogeny novel roles in tissue remodelling and mucosal immune defences? DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 87:157-170. [PMID: 29908202 DOI: 10.1016/j.dci.2018.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 06/08/2023]
Abstract
Peptidylarginine deiminases (PADs) are calcium dependent enzymes with physiological and pathophysiological roles conserved throughout phylogeny. PADs promote post-translational deimination of protein arginine to citrulline, altering the structure and function of target proteins. Deiminated proteins were detected in the early developmental stages of cod from 11 days post fertilisation to 70 days post hatching. Deiminated proteins were present in mucosal surfaces and in liver, pancreas, spleen, gut, muscle, brain and eye during early cod larval development. Deiminated protein targets identified in skin mucosa included nuclear histones; cytoskeletal proteins such as tubulin and beta-actin; metabolic and immune related proteins such as galectin, mannan-binding lectin, toll-like receptor, kininogen, Beta2-microglobulin, aldehyde dehydrogenase, bloodthirsty and preproapolipoprotein A-I. Deiminated histone H3, a marker for anti-pathogenic neutrophil extracellular traps, was particularly elevated in mucosal tissues in immunostimulated cod larvae. PAD-mediated protein deimination may facilitate protein moonlighting, allowing the same protein to exhibit a range of biological functions, in tissue remodelling and mucosal immune defences in teleost ontogeny.
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Affiliation(s)
- Bergljót Magnadóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Polly Hayes
- Department of Biomedical Sciences, University of Westminster, London, W1W 6UW, UK.
| | - Mariya Hristova
- Perinatal Brain Protection and Repair Group, EGA Institute for Women's Health, University College London, WC1E 6HX, London, UK.
| | - Birkir Thor Bragason
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Anthony P Nicholas
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Alister W Dodds
- MRC Immunochemistry Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Sigríður Guðmundsdóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, Department of Biomedical Sciences, University of Westminster, London, W1W 6UW, UK.
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56
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Zhao Q, Yang W, Qin T, Huang Z. Moonlighting Phosphatase Activity of Klenow DNA Polymerase in the Presence of RNA. Biochemistry 2018; 57:5127-5135. [PMID: 30059615 DOI: 10.1021/acs.biochem.8b00688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
RNA is a key player in the cellular central dogma, including RNA transcription and protein synthesis. However, it is unknown whether RNA can directly interfere with DNA synthesis. Recently, we have found in vitro that while binding to DNA polymerase nonspecifically, RNA can transform DNA polymerase to display a moonlighting activity, dNTP phosphatase, in turn interfering with DNA synthesis. This phosphatase activity removes the γ-phosphate from dNTPs (generating dNDPs) and subsequently removes the β-phosphate from the formed dNDPs (generating dNMPs), confirmed by the noncleavable α,β-CH2-dGTP and β,γ-CH2-dGTP analogues. We also found that dGTP is the best substrate for the phosphatase, and the dNTP phosphatase activity is sensitive to the reaction medium. In addition, we have revealed that RNA can tune the activity of closely related proteins and give rise to new catalytic functions with subtle differences. Moreover, we have demonstrated in vitro that at the lower dNTP level, this phosphatase can directly inhibit DNA synthesis by dNTP depletion, though the phosphatase activity is 690-fold slower than the polymerase activity. Our observation in vitro suggests a plausible strategy for RNA to directly interfere with DNA polymerase and DNA synthesis in vivo.
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Affiliation(s)
- Qianwei Zhao
- College of Life Sciences , Sichuan University , Chengdu , China
| | - Wen Yang
- College of Life Sciences , Sichuan University , Chengdu , China
| | - Tong Qin
- College of Life Sciences , Sichuan University , Chengdu , China
| | - Zhen Huang
- College of Life Sciences , Sichuan University , Chengdu , China.,Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
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57
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Veyel D, Sokolowska EM, Moreno JC, Kierszniowska S, Cichon J, Wojciechowska I, Luzarowski M, Kosmacz M, Szlachetko J, Gorka M, Méret M, Graf A, Meyer EH, Willmitzer L, Skirycz A. PROMIS, global analysis of PROtein-metabolite interactions using size separation in Arabidopsis thaliana. J Biol Chem 2018; 293:12440-12453. [PMID: 29853640 PMCID: PMC6093232 DOI: 10.1074/jbc.ra118.003351] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/25/2018] [Indexed: 12/19/2022] Open
Abstract
Small molecules not only represent cellular building blocks and metabolic intermediates, but also regulatory ligands and signaling molecules that interact with proteins. Although these interactions affect cellular metabolism, growth, and development, they have been largely understudied. Herein, we describe a method, which we named PROtein–Metabolite Interactions using Size separation (PROMIS), that allows simultaneous, global analysis of endogenous protein–small molecule and of protein–protein complexes. To this end, a cell-free native lysate from Arabidopsis thaliana cell cultures was fractionated by size-exclusion chromatography, followed by quantitative metabolomic and proteomic analyses. Proteins and small molecules showing similar elution behavior, across protein-containing fractions, constituted putative interactors. Applying PROMIS to an A. thaliana extract, we ascertained known protein–protein (PPIs) and protein–metabolite (PMIs) interactions and reproduced binding between small-molecule protease inhibitors and their respective proteases. More importantly, we present examples of two experimental strategies that exploit the PROMIS dataset to identify novel PMIs. By looking for similar elution behavior of metabolites and enzymes belonging to the same biochemical pathways, we identified putative feedback and feed-forward regulations in pantothenate biosynthesis and the methionine salvage cycle, respectively. By combining PROMIS with an orthogonal affinity purification approach, we identified an interaction between the dipeptide Tyr–Asp and the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase. In summary, we present proof of concept for a powerful experimental tool that enables system-wide analysis of PMIs and PPIs across all biological systems. The dataset obtained here comprises nearly 140 metabolites and 5000 proteins, which can be mined for putative interactors.
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Affiliation(s)
- Daniel Veyel
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Ewelina M Sokolowska
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Juan C Moreno
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | | | - Justyna Cichon
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Izabela Wojciechowska
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Marcin Luzarowski
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Monika Kosmacz
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Jagoda Szlachetko
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Michal Gorka
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | | | - Alexander Graf
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Etienne H Meyer
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Lothar Willmitzer
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Aleksandra Skirycz
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
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Celebioglu HU, Svensson B. Exo- and surface proteomes of the probiotic bacterium Lactobacillus acidophilus NCFM. Proteomics 2018; 17. [PMID: 28393464 DOI: 10.1002/pmic.201700019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/30/2017] [Accepted: 04/06/2017] [Indexed: 11/09/2022]
Abstract
Lactobacillus acidophilus NCFM is a well-known probiotic bacterium extensively studied for its beneficial health effects. Exoproteome (proteins exported into culture medium) and surface proteome (proteins attached to S-layer) of this probiotic were identified by using 2DE followed by MALDI TOF MS to find proteins potentially involved in bacteria-host interactions. The exo- and surface proteomes included 43 and 39 different proteins from 72 and 49 successfully identified spots, respectively. Twenty-two proteins were shared between the two proteomes; both contained the major surface layer protein that participates in host interaction as well as several well-known and putative moonlighting proteins. The exoproteome contained nine classically-secreted (containing a signal sequence) and ten nonclassically-secreted proteins, while the surface proteome contained four classically-secreted and eight nonclassically secreted proteins. Identification of exo- and surface proteomes contributes describing potential protein-mediated probiotic-host interactions.
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Affiliation(s)
- Hasan Ufuk Celebioglu
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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Artier J, da Silva Zandonadi F, de Souza Carvalho FM, Pauletti BA, Leme AFP, Carnielli CM, Selistre‐de‐Araujo HS, Bertolini MC, Ferro JA, Belasque Júnior J, de Oliveira JCF, Novo‐Mansur MTM. Comparative proteomic analysis of Xanthomonas citri ssp. citri periplasmic proteins reveals changes in cellular envelope metabolism during in vitro pathogenicity induction. MOLECULAR PLANT PATHOLOGY 2018; 19:143-157. [PMID: 27798950 PMCID: PMC6638008 DOI: 10.1111/mpp.12507] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Citrus canker is a plant disease caused by Gram-negative bacteria from the genus Xanthomonas. The most virulent species is Xanthomonas citri ssp. citri (XAC), which attacks a wide range of citrus hosts. Differential proteomic analysis of the periplasm-enriched fraction was performed for XAC cells grown in pathogenicity-inducing (XAM-M) and pathogenicity-non-inducing (nutrient broth) media using two-dimensional electrophoresis combined with liquid chromatography-tandem mass spectrometry. Amongst the 40 proteins identified, transglycosylase was detected in a highly abundant spot in XAC cells grown under inducing condition. Additional up-regulated proteins related to cellular envelope metabolism included glucose-1-phosphate thymidylyltransferase, dTDP-4-dehydrorhamnose-3,5-epimerase and peptidyl-prolyl cis-trans-isomerase. Phosphoglucomutase and superoxide dismutase proteins, known to be involved in pathogenicity in other Xanthomonas species or organisms, were also detected. Western blot and quantitative real-time polymerase chain reaction analyses for transglycosylase and superoxide dismutase confirmed that these proteins were up-regulated under inducing condition, consistent with the proteomic results. Multiple spots for the 60-kDa chaperonin and glyceraldehyde-3-phosphate dehydrogenase were identified, suggesting the presence of post-translational modifications. We propose that substantial alterations in cellular envelope metabolism occur during the XAC infectious process, which are related to several aspects, from defence against reactive oxygen species to exopolysaccharide synthesis. Our results provide new candidates for virulence-related proteins, whose abundance correlates with the induction of pathogenicity and virulence genes, such as hrpD6, hrpG, hrpB7, hpa1 and hrpX. The results present new potential targets against XAC to be investigated in further functional studies.
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Affiliation(s)
- Juliana Artier
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e EvoluçãoUniversidade Federal de São Carlos, UFSCarSão CarlosSP13565‐905Brazil
| | - Flávia da Silva Zandonadi
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e EvoluçãoUniversidade Federal de São Carlos, UFSCarSão CarlosSP13565‐905Brazil
| | - Flávia Maria de Souza Carvalho
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESPUniversidade Estadual PaulistaJaboticabalSP14884‐900Brazil
| | - Bianca Alves Pauletti
- LNBio, CNPEMLaboratório de Espectrometria de Massas, Laboratório Nacional de BiociênciasCampinasSP13083‐970Brazil
| | - Adriana Franco Paes Leme
- LNBio, CNPEMLaboratório de Espectrometria de Massas, Laboratório Nacional de BiociênciasCampinasSP13083‐970Brazil
| | - Carolina Moretto Carnielli
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e EvoluçãoUniversidade Federal de São Carlos, UFSCarSão CarlosSP13565‐905Brazil
| | | | - Maria Célia Bertolini
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESPUniversidade Estadual PaulistaAraraquaraSP14800‐060Brazil
| | - Jesus Aparecido Ferro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESPUniversidade Estadual PaulistaJaboticabalSP14884‐900Brazil
| | - José Belasque Júnior
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura ‘Luiz de Queiroz’Universidade de São PauloPiracicabaSP13418‐900Brazil
| | - Julio Cezar Franco de Oliveira
- Laboratório de Interações Microbianas, Departamento de Ciências BiológicasUniversidade Federal de São Paulo, UNIFESPDiademaSP09913‐030Brazil
| | - Maria Teresa Marques Novo‐Mansur
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e EvoluçãoUniversidade Federal de São Carlos, UFSCarSão CarlosSP13565‐905Brazil
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60
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Pinto G, Radulovic M, Godovac-Zimmermann J. Spatial perspectives in the redox code-Mass spectrometric proteomics studies of moonlighting proteins. MASS SPECTROMETRY REVIEWS 2018; 37:81-100. [PMID: 27186965 DOI: 10.1002/mas.21508] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/03/2016] [Indexed: 06/05/2023]
Abstract
The Redox Code involves specific, reversible oxidative changes in proteins that modulate protein tertiary structure, interactions, trafficking, and activity, and hence couple the proteome to the metabolic/oxidative state of cells. It is currently a major focus of study in cell biology. Recent studies of dynamic cellular spatial reorganization with MS-based subcellular-spatial-razor proteomics reveal that protein constituents of many subcellular structures, including mitochondria, the endoplasmic reticulum, the plasma membrane, and the extracellular matrix, undergo changes in their subcellular abundance/distribution in response to oxidative stress. These proteins are components of a diverse variety of functional processes spatially distributed across cells. Many of the same proteins are involved in response to suppression of DNA replication indicate that oxidative stress is strongly intertwined with DNA replication/proliferation. Both are replete with networks of moonlighting proteins that show coordinated changes in subcellular location and that include primary protein actuators of the redox code involved in the processing of NAD+ /NADH, NADP+ /NADPH, Cys/CySS, and GSH/GSSG redox couples. Small groups of key proteins such as {KPNA2, KPNB1, PCNA, PTMA, SET} constitute "spatial switches" that modulate many nuclear processes. Much of the functional response involves subcellular protein trafficking, including nuclear import/export processes, vesicle-mediated trafficking, the endoplasmic reticulum/Golgi pathway, chaperone-assisted processes, and other transport systems. This is not visible to measurements of total protein abundance by transcriptomics or proteomics. Comprehensive pictures of cellular function will require collection of data on the subcellular transport and local functions of many moonlighting proteins, especially of those with critical roles in spatial coordination across cells. The proteome-wide analysis of coordinated changes in abundance and trafficking of proteins offered by MS-based proteomics has a unique, crucial role to play in deciphering the complex adaptive systems that underlie cellular function. © 2016 Wiley Periodicals, Inc. Mass Spec Rev.
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Affiliation(s)
- Gabriella Pinto
- Division of Medicine, Center for Nephrology, Royal Free Campus, University College London, Rowland Hill Street, London, NW3 2PF, United Kingdom
| | - Marko Radulovic
- Insitute of Oncology and Radiology, Pasterova 14, Belgrade, 11000, Serbia
| | - Jasminka Godovac-Zimmermann
- Division of Medicine, Center for Nephrology, Royal Free Campus, University College London, Rowland Hill Street, London, NW3 2PF, United Kingdom
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Wong SL, To J, Santos J, Allam VSRR, Dalton JP, Djordjevic SP, Donnelly S, Padula MP, Sukkar MB. Proteomic Analysis of Extracellular HMGB1 Identifies Binding Partners and Exposes Its Potential Role in Airway Epithelial Cell Homeostasis. J Proteome Res 2017; 17:33-45. [PMID: 28976774 DOI: 10.1021/acs.jproteome.7b00212] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The release of damage-associated molecular patterns (DAMPs) by airway epithelial cells is believed to play a crucial role in the initiation and development of chronic airway conditions such as asthma and chronic obstructive pulmonary disease (COPD). Intriguingly, the classic DAMP high-mobility group box-1 (HMGB1) is detected in the culture supernatant of airway epithelial cells under basal conditions, indicating a role for HMGB1 in the regulation of epithelial cellular and immune homeostasis. To gain contextual insight into the potential role of HMGB1 in airway epithelial cell homeostasis, we used the orthogonal and complementary methods of high-resolution clear native electrophoresis, immunoprecipitation, and pull-downs coupled to liquid chromatography-tandem mass spectrometry (LC-MS/MS) to profile HMGB1 and its binding partners in the culture supernatant of unstimulated airway epithelial cells. We found that HMGB1 presents exclusively as a protein complex under basal conditions. Moreover, protein network analysis performed on 185 binding proteins revealed 14 that directly associate with HMGB1: amyloid precursor protein, F-actin-capping protein subunit alpha-1 (CAPZA1), glyceraldehyde-3 phosphate dehydrogenase (GAPDH), ubiquitin, several members of the heat shock protein family (HSPA8, HSP90B1, HSP90AA1), XRCC5 and XRCC6, high mobility group A1 (HMGA1), histone 3 (H3F3B), the FACT (facilitates chromatin transcription) complex constituents SUPT1H and SSRP1, and heterogeneous ribonucleoprotein K (HNRNPK). These studies provide a new understanding of the extracellular functions of HMGB1 in cellular and immune homeostasis at the airway mucosal surface and could have implications for therapeutic targeting.
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Affiliation(s)
- Sharon L Wong
- Discipline of Pharmacy, Graduate School of Health, The University of Technology Sydney , Ultimo, New South Wales 2007, Australia
| | - Joyce To
- School of Life Sciences, Faculty of Science, The University of Technology Sydney , Ultimo, New South Wales 2007, Australia
| | - Jerran Santos
- School of Life Sciences, Faculty of Science, The University of Technology Sydney , Ultimo, New South Wales 2007, Australia
| | - Venkata Sita Rama Raju Allam
- Discipline of Pharmacy, Graduate School of Health, The University of Technology Sydney , Ultimo, New South Wales 2007, Australia
| | - John P Dalton
- School of Life Sciences, Faculty of Science, The University of Technology Sydney , Ultimo, New South Wales 2007, Australia.,School of Biological Sciences, Queen's University , Belfast BT9 7BL, Northern Ireland
| | - Steven P Djordjevic
- The ithree institute, The University of Technology Sydney , Ultimo, New South Wales 2007, Australia
| | - Sheila Donnelly
- School of Life Sciences, Faculty of Science, The University of Technology Sydney , Ultimo, New South Wales 2007, Australia
| | - Matthew P Padula
- School of Life Sciences, Faculty of Science, The University of Technology Sydney , Ultimo, New South Wales 2007, Australia.,The ithree institute, The University of Technology Sydney , Ultimo, New South Wales 2007, Australia
| | - Maria B Sukkar
- Discipline of Pharmacy, Graduate School of Health, The University of Technology Sydney , Ultimo, New South Wales 2007, Australia
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Deacon OM, Karsisiotis AI, Moreno-Chicano T, Hough MA, Macdonald C, Blumenschein TMA, Wilson MT, Moore GR, Worrall JAR. Heightened Dynamics of the Oxidized Y48H Variant of Human Cytochrome c Increases Its Peroxidatic Activity. Biochemistry 2017; 56:6111-6124. [PMID: 29083920 DOI: 10.1021/acs.biochem.7b00890] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Proteins performing multiple biochemical functions are called "moonlighting proteins" or extreme multifunctional (EMF) proteins. Mitochondrial cytochrome c is an EMF protein that binds multiple partner proteins to act as a signaling molecule, transfers electrons in the respiratory chain, and acts as a peroxidase in apoptosis. Mutations in the cytochrome c gene lead to the disease thrombocytopenia, which is accompanied by enhanced apoptotic activity. The Y48H variant arises from one such mutation and is found in the 40-57 Ω-loop, the lowest-unfolding free energy substructure of the cytochrome c fold. A 1.36 Å resolution X-ray structure of the Y48H variant reveals minimal structural changes compared to the wild-type structure, with the axial Met80 ligand coordinated to the heme iron. Despite this, the intrinsic peroxidase activity is enhanced, implying that a pentacoordinate heme state is more prevalent in the Y48H variant, corroborated through determination of a Met80 "off rate" of >125 s-1 compared to a rate of ∼6 s-1 for the wild-type protein. Heteronuclear nuclear magnetic resonance measurements with the oxidized Y48H variant reveal heightened dynamics in the 40-57 Ω-loop and the Met80-containing 71-85 Ω-loop relative to the wild-type protein, illustrating communication between these substructures. Placed into context with the G41S cytochrome c variant, also implicated in thrombocytopenia, a dynamic picture associated with this disease relative to cytochrome c is emerging whereby increasing dynamics in substructures of the cytochrome c fold serve to facilitate an increased population of the peroxidatic pentacoordinate heme state in the following order: wild type < G41S < Y48H.
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Affiliation(s)
- Oliver M Deacon
- School of Biological Sciences, University of Essex , Wivenhoe Park, Colchester CO4 3SQ, U.K
| | | | - Tadeo Moreno-Chicano
- School of Biological Sciences, University of Essex , Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Michael A Hough
- School of Biological Sciences, University of Essex , Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Colin Macdonald
- School of Chemistry, University of East Anglia , Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Tharin M A Blumenschein
- School of Chemistry, University of East Anglia , Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Michael T Wilson
- School of Biological Sciences, University of Essex , Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Geoffrey R Moore
- School of Chemistry, University of East Anglia , Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Jonathan A R Worrall
- School of Biological Sciences, University of Essex , Wivenhoe Park, Colchester CO4 3SQ, U.K
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63
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Thomas G, Aslan JE, Thomas L, Shinde P, Shinde U, Simmen T. Caught in the act - protein adaptation and the expanding roles of the PACS proteins in tissue homeostasis and disease. J Cell Sci 2017; 130:1865-1876. [PMID: 28476937 PMCID: PMC5482974 DOI: 10.1242/jcs.199463] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Vertebrate proteins that fulfill multiple and seemingly disparate functions are increasingly recognized as vital solutions to maintaining homeostasis in the face of the complex cell and tissue physiology of higher metazoans. However, the molecular adaptations that underpin this increased functionality remain elusive. In this Commentary, we review the PACS proteins - which first appeared in lower metazoans as protein traffic modulators and evolved in vertebrates to integrate cytoplasmic protein traffic and interorganellar communication with nuclear gene expression - as examples of protein adaptation 'caught in the act'. Vertebrate PACS-1 and PACS-2 increased their functional density and roles as metabolic switches by acquiring phosphorylation sites and nuclear trafficking signals within disordered regions of the proteins. These findings illustrate one mechanism by which vertebrates accommodate their complex cell physiology with a limited set of proteins. We will also highlight how pathogenic viruses exploit the PACS sorting pathways as well as recent studies on PACS genes with mutations or altered expression that result in diverse diseases. These discoveries suggest that investigation of the evolving PACS protein family provides a rich opportunity for insight into vertebrate cell and organ homeostasis.
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Affiliation(s)
- Gary Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15239, USA
- University of Pittsburgh Cancer Institute, Pittsburgh, PA 15239, USA
| | - Joseph E Aslan
- Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Laurel Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15239, USA
| | - Pushkar Shinde
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ujwal Shinde
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Thomas Simmen
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada T6G2H7
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64
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Gutiérrez T, Simmen T. Endoplasmic reticulum chaperones tweak the mitochondrial calcium rheostat to control metabolism and cell death. Cell Calcium 2017; 70:64-75. [PMID: 28619231 DOI: 10.1016/j.ceca.2017.05.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/24/2017] [Accepted: 05/24/2017] [Indexed: 12/16/2022]
Abstract
The folding of secretory proteins is a well-understood mechanism, based on decades of research on endoplasmic reticulum (ER) chaperones. These chaperones interact with newly imported polypeptides close to the ER translocon. Classic examples for these proteins include the immunoglobulin binding protein (BiP/GRP78), and the lectins calnexin and calreticulin. Although not considered chaperones per se, the ER oxidoreductases of the protein disulfide isomerase (PDI) family complete the folding job by catalyzing the formation of disulfide bonds through cysteine oxidation. Research from the past decade has demonstrated that ER chaperones are multifunctional proteins. The regulation of ER-mitochondria Ca2+ crosstalk is one of their additional functions, as shown for calnexin, BiP/GRP78 or the oxidoreductases Ero1α and TMX1. This function depends on interactions of this group of proteins with the ER Ca2+ handling machinery. This novel function makes perfect sense for two reasons: i. It allows ER chaperones to control mitochondrial apoptosis instantly without a lengthy bypass involving the upregulation of pro-apoptotic transcription factors via the unfolded protein response (UPR); and ii. It allows the ER protein folding machinery to fine-tune ATP import via controlling the speed of mitochondrial oxidative phosphorylation. Therefore, the role of ER chaperones in regulating ER-mitochondria Ca2+ flux identifies the progression of secretory protein folding as a central regulator of cell survival and death, at least in cell types that secrete large amount of proteins. In other cell types, ER protein folding might serve as a sentinel mechanism that monitors cellular well-being to control cell metabolism and apoptosis. The selenoprotein SEPN1 is a classic example for such a role. Through the control of ER-mitochondria Ca2+-flux, ER chaperones and folding assistants guide cellular apoptosis and mitochondrial metabolism.
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Affiliation(s)
- Tomas Gutiérrez
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, T6G2H7, Canada
| | - Thomas Simmen
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, T6G2H7, Canada,.
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65
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Raj M, Langley M, McArthur SJ, Jean F. Moonlighting glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is required for efficient hepatitis C virus and dengue virus infections in human Huh-7.5.1 cells. J Gen Virol 2017; 98:977-991. [PMID: 28548037 DOI: 10.1099/jgv.0.000754] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Hijacking of cellular biosynthetic pathways by human enveloped viruses is a shared molecular event essential for the viral lifecycle. In this study, the accumulating evidence of the importance of human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in the host secretory pathway led us to hypothesize that this moonlighting enzyme could play a key role in the lifecycle steps of two important Flaviviridae members, hepatitis C virus (HCV) and dengue virus (DENV). We used short interfering RNA (siRNA)-mediated knockdown of human GAPDH in Huh-7.5.1 cells- both pre- and post-HCV infection- to demonstrate that GAPDH is a host factor for HCV infection. siRNA-induced GAPDH knockdown performed pre-HCV infection inhibits HCV core production in infected cells and leads to a decrease in infectivity of the HCV-infected cell supernatants. siRNA-induced GAPDH knockdown performed post-HCV infection does not have an effect on HCV core abundance in infected cells, but does lead to a decrease in infectivity of the HCV-infected cell supernatants. Exogenous expression of V5-tagged human GAPDH, pre- and post-infection, increases the infectivity of HCV-infected cell supernatants, suggesting a role for GAPDH during HCV post-replication steps. Interestingly, siRNA-induced GAPDH knockdown in HCV replicon-harbouring cells had no effect on viral RNA replication. Importantly, we confirmed the important role of GAPDH in the HCV lifecycle using Huh-7-derived stable GAPDH-knockdown clones. Finally, siRNA-induced GAPDH knockdown inhibits intracellular DENV-2 E glycoprotein production in infected cells. Collectively, our findings suggest that the moonlighting enzyme, GAPDH, is an important host factor for HCV infection, and they support its potential role in the DENV lifecycle.
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Affiliation(s)
- Meera Raj
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.,Present address: Canadian Blood Services and the Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Mary Langley
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.,Present address: School of Medicine, Flinders University, Adelaide, South Australia
| | - Steven J McArthur
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - François Jean
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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66
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Jobin PG, Butler GS, Overall CM. New intracellular activities of matrix metalloproteinases shine in the moonlight. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:2043-2055. [PMID: 28526562 DOI: 10.1016/j.bbamcr.2017.05.013] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 02/04/2023]
Abstract
Adaption of a single protein to perform multiple independent functions facilitates functional plasticity of the proteome allowing a limited number of protein-coding genes to perform a multitude of cellular processes. Multifunctionality is achievable by post-translational modifications and by modulating subcellular localization. Matrix metalloproteinases (MMPs), classically viewed as degraders of the extracellular matrix (ECM) responsible for matrix protein turnover, are more recently recognized as regulators of a range of extracellular bioactive molecules including chemokines, cytokines, and their binders. However, growing evidence has convincingly identified select MMPs in intracellular compartments with unexpected physiological and pathological roles. Intracellular MMPs have both proteolytic and non-proteolytic functions, including signal transduction and transcription factor activity thereby challenging their traditional designation as extracellular proteases. This review highlights current knowledge of subcellular location and activity of these "moonlighting" MMPs. Intracellular roles herald a new era of MMP research, rejuvenating interest in targeting these proteases in therapeutic strategies. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman.
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Affiliation(s)
- Parker G Jobin
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Georgina S Butler
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada; Department of Oral Biological & Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher M Overall
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada; Department of Oral Biological & Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, Canada.
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67
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Peng G, McEwen AG, Olieric V, Schmitt C, Albrecht S, Cavarelli J, Tarnus C. Insight into the remarkable affinity and selectivity of the aminobenzosuberone scaffold for the M1 aminopeptidases family based on structure analysis. Proteins 2017; 85:1413-1421. [DOI: 10.1002/prot.25301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/17/2017] [Accepted: 04/03/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Guanya Peng
- Paul Scherrer Institut (SLS) WSLB; 5232 Villigen Suisse Switzerland
| | - Alastair G. McEwen
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; Illkirch France
- Centre National de la Recherche Scientifique; UMR7104; Illkirch France
- Institut National de la Santé et de la Recherche Médicale; U964; Illkirch France
- Université de Strasbourg; Illkirch France
| | - Vincent Olieric
- Paul Scherrer Institut (SLS) WSLB; 5232 Villigen Suisse Switzerland
| | - Celine Schmitt
- Laboratoire de Chimie Organique et Bioorganique; EA4566; Université de Haute Alsace, Institut Jean Baptiste Donnet; Mulhouse France
| | - Sebastien Albrecht
- Laboratoire de Chimie Organique et Bioorganique; EA4566; Université de Haute Alsace, Institut Jean Baptiste Donnet; Mulhouse France
| | - Jean Cavarelli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; Illkirch France
- Centre National de la Recherche Scientifique; UMR7104; Illkirch France
- Institut National de la Santé et de la Recherche Médicale; U964; Illkirch France
- Université de Strasbourg; Illkirch France
| | - Celine Tarnus
- Laboratoire de Chimie Organique et Bioorganique; EA4566; Université de Haute Alsace, Institut Jean Baptiste Donnet; Mulhouse France
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68
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Biaggini K, Borrel V, Szunerits S, Boukherroub R, N'Diaye A, Zébré A, Bonnin-Jusserand M, Duflos G, Feuilloley M, Drider D, Déchelotte P, Connil N. Substance P enhances lactic acid and tyramine production in Enterococcus faecalis V583 and promotes its cytotoxic effect on intestinal Caco-2/TC7 cells. Gut Pathog 2017; 9:20. [PMID: 28439299 PMCID: PMC5399405 DOI: 10.1186/s13099-017-0171-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 04/13/2017] [Indexed: 12/22/2022] Open
Abstract
Background Enterococcus faecalis, generally considered as a saprophytic bowel commensal, has recently emerged as an important nosocomial pathogen causing severe urinary tract infections, surgical wound infections, bacteremia, and bacterial endocarditis. This bacterium is capable of forming biofilms on various surfaces and its high level of antibiotic resistance contributes to its pathogenicity. The aim of this study was to evaluate the effect on E. faecalis, of Substance P (SP), an antimicrobial peptide that is produced in the gut and skin. Results We found that SP did not have antibacterial activity against E. faecalis V583 (MIC >1000 µg/ml). Conversely, SP stimulated aggregation, hydrophobicity, lactic acid and tyramine production in this bacterium. The cytotoxicity and bacterial translocation were also accelerated when E. faecalis V583 were pretreated with SP before infection of intestinal Caco-2/TC7 cells. Conclusion SP can modulate the physiology of E. faecalis. Extensive studies are now needed to screen within the human microbiota which bacteria are responsive to host molecules, and to identify their sensors.
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Affiliation(s)
- Kelly Biaggini
- Laboratoire de Microbiologie, Signaux et Microenvironnement (EA4312), Université de Rouen/IUT d'Evreux, 55, rue saint Germain, 27000 Evreux, France
| | - Valérie Borrel
- Laboratoire de Microbiologie, Signaux et Microenvironnement (EA4312), Université de Rouen/IUT d'Evreux, 55, rue saint Germain, 27000 Evreux, France
| | - Sabine Szunerits
- Institute of Electronics, Microelectronics and Nanotechnology, UMR-CNRS 8520, Université Lille 1, Villeneuve d'Ascq, France
| | - Rabah Boukherroub
- Institute of Electronics, Microelectronics and Nanotechnology, UMR-CNRS 8520, Université Lille 1, Villeneuve d'Ascq, France
| | - Awa N'Diaye
- Laboratoire de Microbiologie, Signaux et Microenvironnement (EA4312), Université de Rouen/IUT d'Evreux, 55, rue saint Germain, 27000 Evreux, France
| | - Arthur Zébré
- Laboratoire de Microbiologie, Signaux et Microenvironnement (EA4312), Université de Rouen/IUT d'Evreux, 55, rue saint Germain, 27000 Evreux, France
| | - Maryse Bonnin-Jusserand
- Institut Charles Viollette, EA7394, Université du Littoral Côte d'Opale, Boulogne Sur Mer, France
| | - Guillaume Duflos
- Laboratoire de Sécurité des Aliments, Département des Produits de la Pêche et de l'Aquaculture, ANSES, Boulogne Sur Mer, France
| | - Marc Feuilloley
- Laboratoire de Microbiologie, Signaux et Microenvironnement (EA4312), Université de Rouen/IUT d'Evreux, 55, rue saint Germain, 27000 Evreux, France
| | - Djamel Drider
- Institut Charles Viollette, EA7394, Université Lille 1 - Sciences et Technologies, Villeneuve d'Ascq, France
| | - Pierre Déchelotte
- INSERM Unité 1073 «Nutrition, Inflammation et dysfonction de l'axe intestin-cerveau», Université de Rouen, Rouen, France
| | - Nathalie Connil
- Laboratoire de Microbiologie, Signaux et Microenvironnement (EA4312), Université de Rouen/IUT d'Evreux, 55, rue saint Germain, 27000 Evreux, France
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69
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Gao Z, Niu X, Zhang Q, Chen H, Gao A, Qi S, Xiang R, Belting M, Zhang S. Mitochondria chaperone GRP75 moonlighting as a cell cycle controller to derail endocytosis provides an opportunity for nanomicrosphere intracellular delivery. Oncotarget 2017; 8:58536-58552. [PMID: 28938577 PMCID: PMC5601673 DOI: 10.18632/oncotarget.17234] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/27/2017] [Indexed: 12/15/2022] Open
Abstract
Understanding how cancer cells regulate endocytosis during the cell cycle could lead us to capitalize this event pharmacologically. Although certain endocytosis pathways are attenuated during mitosis, the endocytosis shift and regulation during the cell cycle have not been well clarified. The conventional concept of glucose-regulated proteins (GRPs) as protein folding chaperones was updated by discoveries that translocated GRPs assume moonlighting functions that modify the immune response, regulate viral release, and control intracellular trafficking. In this study, GRP75, a mitochondria matrix chaperone, was discovered to be highly expressed in mitotic cancer cells. Using synchronized cell models and the GRP75 gene knockdown and ectopic overexpression strategy, we showed that: (1) clathrin-mediated endocytosis (CME) was inhibited whereas clathrin-independent endocytosis (CIE) was unchanged or even up-regulated in the cell cycle M-phase; (2) GRP75 inhibited CME but promoted CIE in the M-phase, which is largely due to its high expression in cancer cell mitochondria; (3) GRP75 targeting by its small molecular inhibitor MKT-077 enhanced cell cycle G1 phase-privileged CME, which provides an opportunity for intracellular delivery of nanomicrospheres sized from 40 nm to 100 nm. Together, our results revealed that GRP75 moonlights as a cell cycle controller and endocytosis regulator in cancer cells, and thus has potential as a novel interference target for nanoparticle drugs delivery into dormant cancer cells.
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Affiliation(s)
- Zhihui Gao
- Department of Biochemistry & Cell Biology, School of Medicine, Nankai University, Tianjin, China
| | - Xiuran Niu
- Department of Biochemistry & Cell Biology, School of Medicine, Nankai University, Tianjin, China
| | - Qing Zhang
- Department of Clinical Laboratory, Cancer Hospital of Tianjin Medical University, Tianjin, China
| | - Hang Chen
- Department of Biochemistry & Cell Biology, School of Medicine, Nankai University, Tianjin, China
| | - Aiai Gao
- Department of Biochemistry & Cell Biology, School of Medicine, Nankai University, Tianjin, China
| | - Shanshan Qi
- Department of Biochemistry & Cell Biology, School of Medicine, Nankai University, Tianjin, China
| | - Rong Xiang
- Department of Biochemistry & Cell Biology, School of Medicine, Nankai University, Tianjin, China
| | - Mattias Belting
- Department of Clinical Sciences, Section of Oncology, Lund University, Lund, Sweden
| | - Sihe Zhang
- Department of Biochemistry & Cell Biology, School of Medicine, Nankai University, Tianjin, China
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70
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Querol-García J, Fernández FJ, Marin AV, Gómez S, Fullà D, Melchor-Tafur C, Franco-Hidalgo V, Albertí S, Juanhuix J, Rodríguez de Córdoba S, Regueiro JR, Vega MC. Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from the Gram-Positive Bacterial Pathogen A. vaginae, an Immunoevasive Factor that Interacts with the Human C5a Anaphylatoxin. Front Microbiol 2017; 8:541. [PMID: 28443070 PMCID: PMC5385343 DOI: 10.3389/fmicb.2017.00541] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 03/14/2017] [Indexed: 01/05/2023] Open
Abstract
The Gram-positive anaerobic human pathogenic bacterium Atopobium vaginae causes most diagnosed cases of bacterial vaginosis as well as opportunistic infections in immunocompromised patients. In addition to its well-established role in carbohydrate metabolism, D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Streptococcus pyogenes and S. pneumoniae have been reported to act as extracellular virulence factors during streptococcal infections. Here, we report the crystal structure of GAPDH from A. vaginae (AvGAPDH) at 2.19 Å resolution. The refined model has a crystallographic Rfree of 22.6%. AvGAPDH is a homotetramer wherein each subunit is bound to a nicotinamide adenine dinucleotide (NAD+) molecule. The AvGAPDH enzyme fulfills essential glycolytic as well as moonlight (non-glycolytic) functions, both of which might be targets of chemotherapeutic intervention. We report that AvGAPDH interacts in vitro with the human C5a anaphylatoxin and inhibits C5a-specific granulocyte chemotaxis, thereby suggesting the participation of AvGAPDH in complement-targeted immunoevasion in a context of infection. The availability of high-quality structures of AvGAPDH and other homologous virulence factors from Gram-positive pathogens is critical for drug discovery programs. In this study, sequence and structural differences between AvGAPDH and related bacterial and eukaryotic GAPDH enzymes are reported in an effort to understand how to subvert the immunoevasive properties of GAPDH and evaluate the potential of AvGAPDH as a druggable target.
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Affiliation(s)
- Javier Querol-García
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | - Francisco J Fernández
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain.,Department of Immunology, Complutense University School of MedicineMadrid, Spain.,Hospital 12 de Octubre Health Research InstituteMadrid, Spain.,Abvance Biotech srlMadrid, Spain
| | - Ana V Marin
- Department of Immunology, Complutense University School of MedicineMadrid, Spain.,Hospital 12 de Octubre Health Research InstituteMadrid, Spain
| | - Sara Gómez
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | - Daniel Fullà
- ALBA Synchrotron, Cerdanyola del VallèsCatalonia, Spain
| | - Cecilia Melchor-Tafur
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | - Virginia Franco-Hidalgo
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | | | | | - Santiago Rodríguez de Córdoba
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | - José R Regueiro
- Department of Immunology, Complutense University School of MedicineMadrid, Spain.,Hospital 12 de Octubre Health Research InstituteMadrid, Spain
| | - M Cristina Vega
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
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71
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Andre GO, Converso TR, Politano WR, Ferraz LFC, Ribeiro ML, Leite LCC, Darrieux M. Role of Streptococcus pneumoniae Proteins in Evasion of Complement-Mediated Immunity. Front Microbiol 2017; 8:224. [PMID: 28265264 PMCID: PMC5316553 DOI: 10.3389/fmicb.2017.00224] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 01/31/2017] [Indexed: 12/14/2022] Open
Abstract
The complement system plays a central role in immune defense against Streptococcus pneumoniae. In order to evade complement attack, pneumococci have evolved a number of mechanisms that limit complement mediated opsonization and subsequent phagocytosis. This review focuses on the strategies employed by pneumococci to circumvent complement mediated immunity, both in vitro and in vivo. At last, since many of the proteins involved in interactions with complement components are vaccine candidates in different stages of validation, we explore the use of these antigens alone or in combination, as potential vaccine approaches that aim at elimination or drastic reduction in the ability of this bacterium to evade complement.
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Affiliation(s)
- Greiciely O Andre
- Laboratório de Biologia Celular e Molecular de Microrganismos, Universidade São Francisco Bragança Paulista, Brazil
| | - Thiago R Converso
- Centro de Biotecnologia, Instituto ButantanSão Paulo, Brazil; Programa de Pós-graduação Interunidades em Biotecnologia, Universidade de São PauloSão Paulo, Brazil
| | - Walter R Politano
- Laboratório de Biologia Celular e Molecular de Microrganismos, Universidade São Francisco Bragança Paulista, Brazil
| | - Lucio F C Ferraz
- Laboratório de Biologia Celular e Molecular de Microrganismos, Universidade São Francisco Bragança Paulista, Brazil
| | - Marcelo L Ribeiro
- Laboratório de Farmacologia, Universidade São Francisco Bragança Paulista, Brazil
| | | | - Michelle Darrieux
- Laboratório de Biologia Celular e Molecular de Microrganismos, Universidade São Francisco Bragança Paulista, Brazil
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72
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Liu Z, Tavares R, Forsythe ES, André F, Lugan R, Jonasson G, Boutet-Mercey S, Tohge T, Beilstein MA, Werck-Reichhart D, Renault H. Evolutionary interplay between sister cytochrome P450 genes shapes plasticity in plant metabolism. Nat Commun 2016; 7:13026. [PMID: 27713409 PMCID: PMC5059761 DOI: 10.1038/ncomms13026] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 08/26/2016] [Indexed: 12/19/2022] Open
Abstract
Expansion of the cytochrome P450 gene family is often proposed to have a critical role in the evolution of metabolic complexity, in particular in microorganisms, insects and plants. However, the molecular mechanisms underlying the evolution of this complexity are poorly understood. Here we describe the evolutionary history of a plant P450 retrogene, which emerged and underwent fixation in the common ancestor of Brassicales, before undergoing tandem duplication in the ancestor of Brassicaceae. Duplication leads first to gain of dual functions in one of the copies. Both sister genes are retained through subsequent speciation but eventually return to a single copy in two of three diverging lineages. In the lineage in which both copies are maintained, the ancestral functions are split between paralogs and a novel function arises in the copy under relaxed selection. Our work illustrates how retrotransposition and gene duplication can favour the emergence of novel metabolic functions.
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Affiliation(s)
- Zhenhua Liu
- Institute of Plant Molecular Biology, CNRS, University of Strasbourg, 12 rue du Général Zimmer, Strasbourg 67084 France
| | - Raquel Tavares
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, 16 rue Raphael Dubois, 69622 Villeurbanne Cedex, France
| | - Evan S Forsythe
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - François André
- iBiTec-S/SB2SM, UMR 9198 CNRS, University Paris Sud, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Raphaël Lugan
- Institute of Plant Molecular Biology, CNRS, University of Strasbourg, 12 rue du Général Zimmer, Strasbourg 67084 France
| | - Gabriella Jonasson
- iBiTec-S/SB2SM, UMR 9198 CNRS, University Paris Sud, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Stéphanie Boutet-Mercey
- Institut Jean-Pierre Bourgin, UMR 1318 INRA-AgroParisTech, Saclay Plant Sciences RD10, 78026 Versailles, France
| | - Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology, 14476 Potsdam-Golm, Germany
| | - Mark A Beilstein
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Danièle Werck-Reichhart
- Institute of Plant Molecular Biology, CNRS, University of Strasbourg, 12 rue du Général Zimmer, Strasbourg 67084 France.,University of Strasbourg Institute for Advanced Study, 67000 Strasbourg, France.,Freiburg Institute for Advanced Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Hugues Renault
- Institute of Plant Molecular Biology, CNRS, University of Strasbourg, 12 rue du Général Zimmer, Strasbourg 67084 France.,University of Strasbourg Institute for Advanced Study, 67000 Strasbourg, France.,Freiburg Institute for Advanced Studies, University of Freiburg, 79104 Freiburg, Germany
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73
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Quereda JJ, García-Del Portillo F, Pucciarelli MG. Listeria monocytogenes remodels the cell surface in the blood-stage. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:641-648. [PMID: 27085096 DOI: 10.1111/1758-2229.12416] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
After crossing the intestinal barrier, the bacterial pathogen Listeria monocytogenes disseminates via the blood to the liver, spleen, brain and placenta. Transcriptomic studies have shown that L. monocytogenes changes expression of many genes during this blood-stage. However, no comparable data at the protein level are known. As main interactors with the environment, we focused in surface proteins produced by L. monocytogenes in an ex vivo bovine blood model. Bacteria exposed to blood alter selectively the amount of several surface proteins compared with bacteria grown in laboratory media. Increased levels were detected for Lmo0514 and Internalin A, two surface proteins covalently bound to peptidoglycan, and the moonlighting protein alcohol-acetaldehyde dehydrogenase, also known as Lap for 'Listeria adhesion protein'. Lmo0514, induced by L. monocytogenes inside epithelial cells, is required for survival in plasma and for virulence in mice at early infection stages. Lmo0514 is also important to cope with low pH stress. By contrast, L. monocytogenes down-regulates other surface proteins following exposure to blood and plasma such as Internalin I. These data provide evidence for remodelling of the L. monocytogenes cell surface during the blood-stage, which it could facilitate pathogen dissemination to deep organs.
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Affiliation(s)
- Juan J Quereda
- Laboratory of Intracellular Bacterial Pathogens, Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Francisco García-Del Portillo
- Laboratory of Intracellular Bacterial Pathogens, Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - M Graciela Pucciarelli
- Laboratory of Intracellular Bacterial Pathogens, Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
- Centro de Biología Molecular 'Severo Ochoa' (CBMSO-CSIC), Departamento de Biología Molecular, Universidad Autónoma de Madrid, Spain
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74
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Górska S, Dylus E, Rudawska A, Brzozowska E, Srutkova D, Schwarzer M, Razim A, Kozakova H, Gamian A. Immunoreactive Proteins of Bifidobacterium longum ssp. longum CCM 7952 and Bifidobacterium longum ssp. longum CCDM 372 Identified by Gnotobiotic Mono-Colonized Mice Sera, Immune Rabbit Sera and Non-immune Human Sera. Front Microbiol 2016; 7:1537. [PMID: 27746766 PMCID: PMC5040718 DOI: 10.3389/fmicb.2016.01537] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 09/14/2016] [Indexed: 12/23/2022] Open
Abstract
The Bifidobacteria show great diversity in the cell surface architecture which may influence the physicochemical properties of the bacterial cell and strain specific properties. The immunomodulatory role of bifidobacteria has been extensively studied, however studies on the immunoreactivity of their protein molecules are very limited. Here, we compared six different methods of protein isolation and purification and we report identification of immunogenic and immunoreactive protein of two human Bifidobacterium longum ssp. longum strains. We evaluated potential immunoreactive properties of proteins employing polyclonal sera obtained from germ free mouse, rabbit and human. The protein yield was isolation method-dependent and the reactivity of proteins detected by SDS-PAGE and Western blotting was heterogeneous and varied between different serum samples. The proteins with the highest immunoreactivity were isolated, purified and have them sequenced. Among the immunoreactive proteins we identified enolase, aspartokinase, pyruvate kinase, DnaK (B. longum ssp. longum CCM 7952) and sugar ABC transporter ATP-binding protein, phosphoglycerate kinase, peptidoglycan synthethase penicillin-binding protein 3, transaldolase, ribosomal proteins and glyceraldehyde 3-phosphate dehydrogenase (B. longum ssp. longum CCDM 372).
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Affiliation(s)
- Sabina Górska
- Department of Medical Microbiology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences Wroclaw, Poland
| | - Ewa Dylus
- Department of Medical Microbiology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences Wroclaw, Poland
| | - Angelika Rudawska
- Department of Medical Microbiology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences Wroclaw, Poland
| | - Ewa Brzozowska
- Department of Medical Microbiology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences Wroclaw, Poland
| | - Dagmar Srutkova
- Laboratory of Gnotobiology, Institute of Microbiology, Academy of Sciences of the Czech Republic v. v. i., Novy Hradek, Czech Republic
| | - Martin Schwarzer
- Laboratory of Gnotobiology, Institute of Microbiology, Academy of Sciences of the Czech Republic v. v. i., Novy Hradek, Czech Republic
| | - Agnieszka Razim
- Department of Medical Microbiology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences Wroclaw, Poland
| | - Hana Kozakova
- Laboratory of Gnotobiology, Institute of Microbiology, Academy of Sciences of the Czech Republic v. v. i., Novy Hradek, Czech Republic
| | - Andrzej Gamian
- Department of Medical Microbiology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences Wroclaw, Poland
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75
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Kylväjä R, Ojalehto T, Kainulainen V, Virkola R, Westerlund-Wikström B. Penicillin binding protein 3 of Staphylococcus aureus NCTC 8325-4 binds and activates human plasminogen. BMC Res Notes 2016; 9:389. [PMID: 27488131 PMCID: PMC4972960 DOI: 10.1186/s13104-016-2190-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/28/2016] [Indexed: 11/25/2022] Open
Abstract
Background Staphylococcus aureus is a versatile pathogen expressing a number of virulence-associated adhesive molecules. In a previous study, we generated in a secretion-competent Escherichia coli strain a library of random FLAG-tag positive (FTP) polypeptides of S. aureus. To identify adhesive proteins and gain additional knowledge on putative virulence factors of S. aureus, we here screened the FTP library against human serum proteins. Findings Staphylococcus aureus NCTC 8325-4, origin of the FTP library, adhered to immobilized plasminogen in vitro. In an enzyme-linked immunoassay a C-terminal part of penicillin binding protein 3 (PBP3), included in the FTP library, bound to immobilized plasminogen. We expressed and purified full-length PBP3 and its C-terminal fragments as recombinant proteins. In a time-resolved fluorometry—based assay the PBP3 polypeptides bound to immobilized plasminogen. The polypeptides enhanced formation of plasmin from plasminogen as analyzed by cleavage of a chromogenic plasmin substrate. Conclusions The present findings, although preliminary, demonstrate reliably that S. aureus NCTC 8325-4 adheres to immobilized plasminogen in vitro and that the adhesion may be mediated by a C-terminal fragment of the PBP3 protein. The full length PBP3 and the penicillin binding C-terminal domain of PBP3 expressed as recombinant proteins bound plasminogen and activated plasminogen to plasmin. These phenomena were inhibited by the lysine analogue ε-aminocaproic acid suggesting that the binding is mediated by lysine residues. A detailed molecular description of surface molecules enhancing the virulence of S. aureus will aid in understanding of its pathogenicity and help in design of antibacterial drugs in the future. Electronic supplementary material The online version of this article (doi:10.1186/s13104-016-2190-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Riikka Kylväjä
- General Microbiology, Department of Biosciences, University of Helsinki, P.O.Box 56, FI-00014, University of Helsinki, Helsinki, Finland.,Thermo Fisher Scientific, Ratastie 2, 01620, Vantaa, Finland
| | - Tuomas Ojalehto
- General Microbiology, Department of Biosciences, University of Helsinki, P.O.Box 56, FI-00014, University of Helsinki, Helsinki, Finland.,Orion Diagnostica, Koivu-Mankkaan tie 6, 02200, Espoo, Finland
| | - Veera Kainulainen
- General Microbiology, Department of Biosciences, University of Helsinki, P.O.Box 56, FI-00014, University of Helsinki, Helsinki, Finland.,Pharmacology, Faculty of Medicine, University of Helsinki, P.O.Box 63, FI-00014, University of Helsinki, Helsinki, Finland
| | - Ritva Virkola
- General Microbiology, Department of Biosciences, University of Helsinki, P.O.Box 56, FI-00014, University of Helsinki, Helsinki, Finland
| | - Benita Westerlund-Wikström
- General Microbiology, Department of Biosciences, University of Helsinki, P.O.Box 56, FI-00014, University of Helsinki, Helsinki, Finland.
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76
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Tytgat HLP, Schoofs G, Vanderleyden J, Van Damme EJM, Wattiez R, Lebeer S, Leroy B. Systematic Exploration of the Glycoproteome of the Beneficial Gut Isolate Lactobacillus rhamnosus GG. J Mol Microbiol Biotechnol 2016; 26:345-58. [PMID: 27463506 DOI: 10.1159/000447091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/25/2016] [Indexed: 11/19/2022] Open
Abstract
Glycoproteins form an interesting class of macromolecules involved in bacterial-host interactions, but they are not yet widely explored in Gram-positive and beneficial species. Here, an integrated and widely applicable approach was followed to identify putative bacterial glycoproteins, combining proteome fractionation with 2D protein and glycostained gels and lectin blots. This approach was validated for the microbiota isolate Lactobacillus rhamnosus GG. The approach resulted in a list of putative glycosylated proteins receiving a 'glycosylation score'. Ultimately, we could identify 41 unique glycosylated proteins in L. rhamnosus GG (6 top-confidence, 10 high-confidence and 25 putative hits; classification based on glycosylation score). Most glycoproteins are associated with the cell wall and membrane. Identified glycoproteins include proteins involved in transport, translation, and sugar metabolism processes. A robust screening resulted in a comprehensive mapping of glycoproteins in L. rhamnosus GG. Our results reflect the glycosylation of sugar metabolism enzymes, transporters, and other proteins crucial for cell physiology. We hypothesize that protein glycosylation can confer an extra level of regulation, for example by affecting enzyme functions. This is the first systematic study of the glycoproteome of a probiotic and beneficial gut isolate.
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Affiliation(s)
- Hanne L P Tytgat
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
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77
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Keighren MA, Flockhart JH, West JD. Survival of glucose phosphate isomerase null somatic cells and germ cells in adult mouse chimaeras. Biol Open 2016; 5:596-610. [PMID: 27103217 PMCID: PMC4874354 DOI: 10.1242/bio.017111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/22/2016] [Indexed: 01/22/2023] Open
Abstract
The mouse Gpi1 gene encodes the glycolytic enzyme glucose phosphate isomerase. Homozygous Gpi1(-/-) null mouse embryos die but a previous study showed that some homozygous Gpi1(-/-) null cells survived when combined with wild-type cells in fetal chimaeras. One adult female Gpi1(-/-)↔Gpi1(c/c) chimaera with functional Gpi1(-/-) null oocytes was also identified in a preliminary study. The aims were to characterise the survival of Gpi1(-/-) null cells in adult Gpi1(-/-)↔Gpi1(c/c) chimaeras and determine if Gpi1(-/-) null germ cells are functional. Analysis of adult Gpi1(-/-)↔Gpi1(c/c) chimaeras with pigment and a reiterated transgenic lineage marker showed that low numbers of homozygous Gpi1(-/-) null cells could survive in many tissues of adult chimaeras, including oocytes. Breeding experiments confirmed that Gpi1(-/-) null oocytes in one female Gpi1(-/-)↔Gpi1(c/c) chimaera were functional and provided preliminary evidence that one male putative Gpi1(-/-)↔Gpi1(c/c) chimaera produced functional spermatozoa from homozygous Gpi1(-/-) null germ cells. Although the male chimaera was almost certainly Gpi1(-/-)↔Gpi1(c/c), this part of the study is considered preliminary because only blood was typed for GPI. Gpi1(-/-) null germ cells should survive in a chimaeric testis if they are supported by wild-type Sertoli cells. It is also feasible that spermatozoa could bypass a block at GPI, but not blocks at some later steps in glycolysis, by using fructose, rather than glucose, as the substrate for glycolysis. Although chimaera analysis proved inefficient for studying the fate of Gpi1(-/-) null germ cells, it successfully identified functional Gpi1(-/-) null oocytes and revealed that some Gpi1(-/-) null cells could survive in many adult tissues.
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Affiliation(s)
- Margaret A Keighren
- Genes and Development Group, Centre for Integrative Physiology, Clinical Sciences, University of Edinburgh Medical School, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - Jean H Flockhart
- Genes and Development Group, Centre for Integrative Physiology, Clinical Sciences, University of Edinburgh Medical School, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - John D West
- Genes and Development Group, Centre for Integrative Physiology, Clinical Sciences, University of Edinburgh Medical School, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
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78
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Itri F, Monti DM, Della Ventura B, Vinciguerra R, Chino M, Gesuele F, Lombardi A, Velotta R, Altucci C, Birolo L, Piccoli R, Arciello A. Femtosecond UV-laser pulses to unveil protein-protein interactions in living cells. Cell Mol Life Sci 2016; 73:637-48. [PMID: 26265182 PMCID: PMC11108384 DOI: 10.1007/s00018-015-2015-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/30/2015] [Accepted: 08/06/2015] [Indexed: 12/30/2022]
Abstract
A hallmark to decipher bioprocesses is to characterize protein-protein interactions in living cells. To do this, the development of innovative methodologies, which do not alter proteins and their natural environment, is particularly needed. Here, we report a method (LUCK, Laser UV Cross-linKing) to in vivo cross-link proteins by UV-laser irradiation of living cells. Upon irradiation of HeLa cells under controlled conditions, cross-linked products of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were detected, whose yield was found to be a linear function of the total irradiation energy. We demonstrated that stable dimers of GAPDH were formed through intersubunit cross-linking, as also observed when the pure protein was irradiated by UV-laser in vitro. We proposed a defined patch of aromatic residues located at the enzyme subunit interface as the cross-linking sites involved in dimer formation. Hence, by this technique, UV-laser is able to photofix protein surfaces that come in direct contact. Due to the ultra-short time scale of UV-laser-induced cross-linking, this technique could be extended to weld even transient protein interactions in their native context.
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Affiliation(s)
- Francesco Itri
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Daria M Monti
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome, Italy
| | | | - Roberto Vinciguerra
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Felice Gesuele
- Department of Physics, University of Naples Federico II, 80126, Naples, Italy
| | - Angelina Lombardi
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Raffaele Velotta
- Department of Physics, University of Naples Federico II, 80126, Naples, Italy
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR, Naples, Italy
| | - Carlo Altucci
- Department of Physics, University of Naples Federico II, 80126, Naples, Italy.
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR, Naples, Italy.
| | - Leila Birolo
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy.
| | - Renata Piccoli
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome, Italy
| | - Angela Arciello
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy.
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome, Italy.
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79
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Kumar S, Parameswaran S, Sharma RK. Novel myristoylation of the sperm-specific hexokinase 1 isoform regulates its atypical localization. Biol Open 2015; 4:1679-87. [PMID: 26581589 PMCID: PMC4736023 DOI: 10.1242/bio.012831] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hexokinase 1 variant in mammalian spermatozoa (HK1S) has a unique N-terminus and this isoform atypically localizes to the plasma membrane. However, the mechanism of this process currently remains ambiguous. In this report, we show that fatty acylation underlies the specific sorting of HK1S. Employing chimeric reporter constructs, we first established that compartmentalization of HK1S does not function exclusively in sperm cells and that this feature is swappable to somatic HEK293 cells. Although the N-terminus lacks the classical consensus signature for myristoylation and the sequence-based predictions fail to predict myristoylation of HK1S, complementary experimental approaches confirmed that HK1S is myristoylated. Using live-cell confocal microscopy, we show that the mutation of a single amino acid, the myristoyl recipient Gly(2), impedes the prominent feature of plasma membrane association and relocates the enzyme to the cytosol but not the nucleus. Additionally, substitutions of the putatively palmitoylated Cys(5) is also reflected in a similar loss of compartmentalization of the protein. Taken together, our findings conclusively demonstrate that the N-terminal 'MGQICQ' motif in the unique GCS domain of HK1S acquires hydrophobicity by dual lipidic modifications, N-myristoylation and palmitoylation, to serve the requirements for membranous associations and thus its compartmentalization.
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Affiliation(s)
- Sujeet Kumar
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Sreejit Parameswaran
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Rajendra K Sharma
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
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80
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Savreux-Lenglet G, Depauw S, David-Cordonnier MH. Protein Recognition in Drug-Induced DNA Alkylation: When the Moonlight Protein GAPDH Meets S23906-1/DNA Minor Groove Adducts. Int J Mol Sci 2015; 16:26555-81. [PMID: 26556350 PMCID: PMC4661830 DOI: 10.3390/ijms161125971] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/25/2015] [Accepted: 10/27/2015] [Indexed: 12/11/2022] Open
Abstract
DNA alkylating drugs have been used in clinics for more than seventy years. The diversity of their mechanism of action (major/minor groove; mono-/bis-alkylation; intra-/inter-strand crosslinks; DNA stabilization/destabilization, etc.) has undoubtedly major consequences on the cellular response to treatment. The aim of this review is to highlight the variety of established protein recognition of DNA adducts to then particularly focus on glyceraldehyde-3-phosphate dehydrogenase (GAPDH) function in DNA adduct interaction with illustration using original experiments performed with S23906-1/DNA adduct. The introduction of this review is a state of the art of protein/DNA adducts recognition, depending on the major or minor groove orientation of the DNA bonding as well as on the molecular consequences in terms of double-stranded DNA maintenance. It reviews the implication of proteins from both DNA repair, transcription, replication and chromatin maintenance in selective DNA adduct recognition. The main section of the manuscript is focusing on the implication of the moonlighting protein GAPDH in DNA adduct recognition with the model of the peculiar DNA minor groove alkylating and destabilizing drug S23906-1. The mechanism of action of S23906-1 alkylating drug and the large variety of GAPDH cellular functions are presented prior to focus on GAPDH direct binding to S23906-1 adducts.
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Affiliation(s)
- Gaëlle Savreux-Lenglet
- UMR-S1172-Jean-Pierre Aubert Research Centre (JPARC), INSERM, University of Lille, Lille Hospital, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun F-59045 Lille cedex, France.
| | - Sabine Depauw
- UMR-S1172-Jean-Pierre Aubert Research Centre (JPARC), INSERM, University of Lille, Lille Hospital, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun F-59045 Lille cedex, France.
| | - Marie-Hélène David-Cordonnier
- UMR-S1172-Jean-Pierre Aubert Research Centre (JPARC), INSERM, University of Lille, Lille Hospital, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun F-59045 Lille cedex, France.
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81
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Terrasse R, Amoroso A, Vernet T, Di Guilmi AM. Streptococcus pneumoniae GAPDH Is Released by Cell Lysis and Interacts with Peptidoglycan. PLoS One 2015; 10:e0125377. [PMID: 25927608 PMCID: PMC4415926 DOI: 10.1371/journal.pone.0125377] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/23/2015] [Indexed: 11/26/2022] Open
Abstract
Release of conserved cytoplasmic proteins is widely spread among Gram-positive and Gram-negative bacteria. Because these proteins display additional functions when located at the bacterial surface, they have been qualified as moonlighting proteins. The GAPDH is a glycolytic enzyme which plays an important role in the virulence processes of pathogenic microorganisms like bacterial invasion and host immune system modulation. However, GAPDH, like other moonlighting proteins, cannot be secreted through active secretion systems since they do not contain an N-terminal predicted signal peptide. In this work, we investigated the mechanism of GAPDH export and surface retention in Streptococcus pneumoniae, a major human pathogen. We addressed the role of the major autolysin LytA in the delivery process of GAPDH to the cell surface. Pneumococcal lysis is abolished in the ΔlytA mutant strain or when 1% choline chloride is added in the culture media. We showed that these conditions induce a marked reduction in the amount of surface-associated GAPDH. These data suggest that the presence of GAPDH at the surface of pneumococcal cells depends on the LytA-mediated lysis of a fraction of the cell population. Moreover, we demonstrated that pneumococcal GAPDH binds to the bacterial cell wall independently of the presence of the teichoic acids component, supporting peptidoglycan as a ligand to surface GAPDH. Finally, we showed that peptidoglycan-associated GAPDH recruits C1q from human serum but does not activate the complement pathway.
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Affiliation(s)
- Rémi Terrasse
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044 Grenoble, France
- CNRS UMR5075, IBS, F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
| | - Ana Amoroso
- Centre for Protein Engineering, Department of Life Sciences, University of Liege, Liege, Belgium
| | - Thierry Vernet
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044 Grenoble, France
- CNRS UMR5075, IBS, F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
| | - Anne Marie Di Guilmi
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044 Grenoble, France
- CNRS UMR5075, IBS, F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- * E-mail:
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Rasch J, Theuerkorn M, Ünal C, Heinsohn N, Tran S, Fischer G, Weiwad M, Steinert M. Novel Cycloheximide Derivatives Targeting the Moonlighting Protein Mip Exhibit Specific Antimicrobial Activity Against Legionella pneumophila. Front Bioeng Biotechnol 2015; 3:41. [PMID: 25870856 PMCID: PMC4376002 DOI: 10.3389/fbioe.2015.00041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/15/2015] [Indexed: 12/28/2022] Open
Abstract
Macrophage infectivity potentiator (Mip) and Mip-like proteins are virulence factors in a wide range of pathogens including Legionella pneumophila. These proteins belong to the FK506 binding protein (FKBP) family of peptidyl-prolyl-cis/trans-isomerases (PPIases). In L. pneumophila, the PPIase activity of Mip is required for invasion of macrophages, transmigration through an in vitro lung–epithelial barrier, and full virulence in the guinea pig infection model. Additionally, Mip is a moonlighting protein that binds to collagen IV in the extracellular matrix. Here, we describe the development and synthesis of cycloheximide derivatives with adamantyl moieties as novel FKBP ligands, and analyze their effect on the viability of L. pneumophila and other bacteria. All compounds efficiently inhibited PPIase activity of the prototypic human FKBP12 as well as Mip with IC50-values as low as 180 nM and 1.7 μM, respectively. Five of these derivatives inhibited the growth of L. pneumophila at concentrations of 30–40 μM, but exhibited no effect on other tested bacterial species indicating a specific spectrum of antibacterial activity. The derivatives carrying a 3,5-dimethyladamantan-1-[yl]acetamide substitution (MT_30.32), and a 3-ethyladamantan-1-[yl]acetamide substitution (MT_30.51) had the strongest effects in PPIase- and liquid growth assays. MT_30.32 and MT_30.51 were also inhibitory in macrophage infection studies without being cytotoxic. Accordingly, by applying a combinatorial approach, we were able to generate novel, hybrid inhibitors consisting of cycloheximide and adamantane, two known FKBP inhibitors that interact with different parts of the PPIase domain, respectively. Interestingly, despite the proven Mip-inhibitory activity, the viability of a Mip-deficient strain was affected to the same degree as its wild type. Hence, we also propose that cycloheximide derivatives with adamantyl moieties are potent PPIase inhibitors with multiple targets in L. pneumophila.
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Affiliation(s)
- Janine Rasch
- Institut für Mikrobiologie, Technische Universität Braunschweig , Braunschweig , Germany
| | - Martin Theuerkorn
- Max Planck Institute of Biophysical Chemistry Göttingen BO Halle , Halle , Germany
| | - Can Ünal
- Institut für Mikrobiologie, Technische Universität Braunschweig , Braunschweig , Germany ; Türk-Alman Üniversitesi, Fen Fakültesi , Istanbul , Turkey
| | - Natascha Heinsohn
- Institut für Mikrobiologie, Technische Universität Braunschweig , Braunschweig , Germany
| | - Stefan Tran
- Institut für Mikrobiologie, Technische Universität Braunschweig , Braunschweig , Germany
| | - Gunter Fischer
- Max Planck Institute of Biophysical Chemistry Göttingen BO Halle , Halle , Germany ; Institut für Biochemie und Biotechnologie, Universität Halle-Wittenberg , Halle-Wittenberg , Germany
| | - Matthias Weiwad
- Max Planck Institute of Biophysical Chemistry Göttingen BO Halle , Halle , Germany ; Institut für Biochemie und Biotechnologie, Universität Halle-Wittenberg , Halle-Wittenberg , Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig , Braunschweig , Germany ; Helmholtz Centre for Infection Research , Braunschweig , Germany
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