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Pham MT, Tran TD, Zayabaatar E. Leuconostoc mesenteroides utilizes glucose fermentation to produce electricity and ameliorates high-fat diet-induced abdominal fat mass. Arch Microbiol 2022; 204:670. [PMID: 36241916 DOI: 10.1007/s00203-022-03281-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/21/2022] [Accepted: 10/06/2022] [Indexed: 11/02/2022]
Abstract
Bacteria capable of producing electricity in intestinal microbiota have been discovered. However, no studies have explored butyric acid which generated by electrogenic bacteria on the host organism have significant physiological impacts on certain organs. We found that the capacity for electrical current generation by the commensal gut Leuconostoc mesenteroides EH-1 (L. mesenteroides EH-1) during glucose fermentation. The electricity production was essential for the gut colonization of L. mesenteroides EH-1 since the inhibition of electricity production by cyclophilin A inhibitor (TMN355) significantly diminished the number of bacteria attached to the human gut epithelial cell surface. The adipocyte differentiation contributes to the increased 4-hydroxy-2-nonenal (4-HNE), considered as a biomarker of reactive oxygen species (ROS). The effect of intestinal electrogenic microbiota in the high-fat diet (HFD)-induced 4-HNE and abdominal fat accumulation in mice was investigated in this study. The oral administration of glucose with a butyric acid-producing L. mesenteroides EH-1 bacterium attenuated the expression of 4-HNE and abdominal fat. The level of 4-HNE and abdominal fat depot were markedly increased in mice administered with cyclophilin A inhibitor-pretreated bacteria or GLPG-0974, an antagonist of free fatty acid receptor 2 (Ffar2). Our studies suggest a novel means by which the probiotic bacteria can modulate fat mass deposition and oxidative stress via the cyclophilin A-mediated electron production and the butyric acid-activated Ffar2 pathway.
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Affiliation(s)
- Minh Tan Pham
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
| | - Thi Dung Tran
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Enkhbat Zayabaatar
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
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2
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Xu J, Li Q, Zhang J, Li X, Sun T. In Silico Structural and Functional Analysis of Cold Shock Proteins in Pseudomonas fluorescens PF08 from Marine Fish. J Food Prot 2021; 84:1446-1454. [PMID: 33852731 DOI: 10.4315/jfp-21-044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/08/2021] [Indexed: 12/18/2022]
Abstract
ABSTRACT Pseudomonas fluorescens is a specific spoilage microorganism of refrigerated marine fish, and is highly adapted to low temperature. Cold shock proteins (CSPs) play an important role in cold adaptation of bacteria. In this study, CSP genes were identified from the genome of P. fluorescens PF08 by search of the conserved domain of CSPs with HMMER software, and the CSP physicochemical properties, structures, and functions were analyzed through bioinformatics. Five typical CSPs were identified in the P. fluorescens PF08 genome (PfCSPs). All five PfCSPs are small hydrophilic acidic proteins with a molecular mass of ca. 7.4 kDa. They are located in the cytoplasm and are nonsecretory and nontransmembrane proteins. Multiple sequence alignment analysis indicated that the CSPs are highly conserved between species, especially in DNA-binding sites and RNA-binding motifs that can bind to single-stranded DNA and RNA. The five PfCSPs clustered with CspD from Escherichia coli and Salmonella Typhimurium, which suggests a close homology and high functional similarity among the five PfCSPs and CspD. The secondary and tertiary structures of the PfCSPs are in accordance with the characteristics of the CSP family, and ligand binding sites with higher likelihood were found in PfCSPs. The five PfCSPs were predicted to interact with some of the same proteins that are involved in virulence, stress responses (including to low temperature), cell growth, ribosome assembly, and RNA degradation. The results provide further elucidation of the function of CSPs in adaptation to low temperatures by P. fluorescens. HIGHLIGHTS
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Affiliation(s)
- Jinxiu Xu
- College of Food Science and Engineering, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, People's Republic of China
| | - Qiuying Li
- College of Food Science and Engineering, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, People's Republic of China
| | - Jingyang Zhang
- College of Food Science and Engineering, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, People's Republic of China
| | - Xuepeng Li
- College of Food Science and Engineering, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, People's Republic of China
| | - Tong Sun
- College of Food Science and Engineering, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, People's Republic of China
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3
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Pham MT, Yang JJ, Balasubramaniam A, Rahim AR, Adi P, Do TTM, Herr DR, Huang CM. Leuconostoc mesenteroides mediates an electrogenic pathway to attenuate the accumulation of abdominal fat mass induced by high fat diet. Sci Rep 2020; 10:21916. [PMID: 33318546 PMCID: PMC7736347 DOI: 10.1038/s41598-020-78835-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/27/2020] [Indexed: 11/26/2022] Open
Abstract
Although several electrogenic bacteria have been identified, the physiological effect of electricity generated by bacteria on host health remains elusive. We found that probiotic Leuconostoc mesenteroides (L. mesenteroides) can metabolize linoleic acid to yield electricity via an intracellular cyclophilin A-dependent pathway. Inhibition of cyclophilin A significantly abolished bacterial electricity and lowered the adhesion of L. mesenteroides to the human gut epithelial cell line. Butyrate from L. mesenteroides in the presence of linoleic acid were detectable and mediated free fatty acid receptor 2 (Ffar2) to reduce the lipid contents in differentiating 3T3-L1 adipocytes. Oral administration of L. mesenteroides plus linoleic acid remarkably reduced high-fat-diet (HFD)-induced formation of 4-hydroxy-2-nonenal (4-HNE), a reactive oxygen species (ROS) biomarker, and decreased abdominal fat mass in mice. The reduction of 4-HNE and abdominal fat mass was reversed when cyclophilin A inhibitor-pretreated bacteria were administered to mice. Our studies present a novel mechanism of reducing abdominal fat mass by electrogenic L. mesenteroides which may yield electrons to enhance colonization and sustain high amounts of butyrate to limit ROS during adipocyte differentiation.
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Affiliation(s)
- Minh Tan Pham
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, 32001, Taiwan
| | - John Jackson Yang
- Department of Life Sciences, National Central University, Taoyuan, Taiwan
| | - Arun Balasubramaniam
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, 32001, Taiwan
| | - Adelia Riezka Rahim
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, 32001, Taiwan
| | - Prakoso Adi
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, 32001, Taiwan
| | - Thi Tra My Do
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, 32001, Taiwan
| | - Deron Raymond Herr
- Department of Pharmacology, National University of Singapore, Singapore, Singapore
| | - Chun-Ming Huang
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, 32001, Taiwan.
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4
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Mamipour M, Yousefi M, Hasanzadeh M. An overview on molecular chaperones enhancing solubility of expressed recombinant proteins with correct folding. Int J Biol Macromol 2017; 102:367-375. [PMID: 28412337 PMCID: PMC7185796 DOI: 10.1016/j.ijbiomac.2017.04.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/14/2017] [Accepted: 04/06/2017] [Indexed: 02/07/2023]
Abstract
The majority of research topics declared that most of the recombinant proteins have been expressed by Escherichia coli in basic investigations. But the majority of high expressed proteins formed as inactive recombinant proteins that are called inclusion body. To overcome this problem, several methods have been used including suitable promoter, environmental factors, ladder tag to secretion of proteins into the periplasm, gene protein optimization, chemical chaperones and molecular chaperones sets. Co-expression of the interest protein with molecular chaperones is one of the common methods The chaperones are a group of proteins, which are involved in making correct folding of recombinant proteins. Chaperones are divided two groups including; cytoplasmic and periplasmic chaperones. Moreover, periplasmic chaperones and proteases can be manipulated to increase the yields of secreted proteins. In this article, we attempted to review cytoplasmic chaperones such as Hsp families and periplasmic chaperones including; generic chaperones, specialized chaperones, PPIases, and proteins involved in disulfide bond formation.
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Affiliation(s)
- Mina Mamipour
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammadreza Yousefi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Biotechnology, Higher Education Institute of Rab-Rashid, Tabriz, Iran
| | - Mohammad Hasanzadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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5
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Microbial cyclophilins: specialized functions in virulence and beyond. World J Microbiol Biotechnol 2017; 33:164. [PMID: 28791545 DOI: 10.1007/s11274-017-2330-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/05/2017] [Indexed: 01/18/2023]
Abstract
Cyclophilins belong to the superfamily of peptidyl-prolyl cis/trans isomerases (PPIases, EC: 5.2.1.8), the enzymes that catalyze the cis/trans isomerization of peptidyl-prolyl peptide bonds in unfolded and partially folded polypeptide chains and native state proteins. Cyclophilins have been extensively studied, since they are involved in multiple cellular processes related to human pathologies, such as neurodegenerative disorders, infectious diseases, and cancer. However, the presence of cyclophilins in all domains of life indicates a broader biological importance. In this mini-review, we summarize current advances in the study of microbial cyclophilins. Apart from their anticipated role in protein folding and chaperoning, cyclophilins are involved in several other biological processes, such as cellular signal transduction, adaptation to stress, control of pathogens virulence, and modulation of host immune response. Since many existing family members do not have well-defined functions and novel ones are being characterized, the requirement for further studies on their biological role and molecular mechanism of action is apparent.
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Ikolo F, Zhang M, Harrington DJ, Robinson C, Waller AS, Sutcliffe IC, Black GW. Characterisation of SEQ0694 (PrsA/PrtM) of Streptococcus equi as a functional peptidyl-prolyl isomerase affecting multiple secreted protein substrates. MOLECULAR BIOSYSTEMS 2016; 11:3279-86. [PMID: 26466087 DOI: 10.1039/c5mb00543d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptidyl-prolyl isomerase (PPIase) lipoproteins have been shown to influence the virulence of a number of Gram-positive bacterial human and animal pathogens, most likely through facilitating the folding of cell envelope and secreted virulence factors. Here, we used a proteomic approach to demonstrate that the Streptococcus equi PPIase SEQ0694 alters the production of multiple secreted proteins, including at least two putative virulence factors (FNE and IdeE2). We demonstrate also that, despite some unusual sequence features, recombinant SEQ0694 and its central parvulin domain are functional PPIases. These data add to our knowledge of the mechanisms by which lipoprotein PPIases contribute to the virulence of streptococcal pathogens.
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Affiliation(s)
- Felicia Ikolo
- Department of Applied Sciences, Faculty of Health & Life Sciences, University of Northumbria at Newcastle, Newcastle upon Tyne, NE1 8ST, UK. and Department of Biochemistry, School of Medicine, St. George's University, True Blue, St. George's, Grenada
| | - Meng Zhang
- Department of Applied Sciences, Faculty of Health & Life Sciences, University of Northumbria at Newcastle, Newcastle upon Tyne, NE1 8ST, UK.
| | - Dean J Harrington
- Division of Biomedical Science, School of Life Sciences, University of Bradford, West Yorkshire, BD7 1DP, UK
| | - Carl Robinson
- Centre for Preventive Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK
| | - Andrew S Waller
- Centre for Preventive Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK
| | - Iain C Sutcliffe
- Department of Applied Sciences, Faculty of Health & Life Sciences, University of Northumbria at Newcastle, Newcastle upon Tyne, NE1 8ST, UK.
| | - Gary W Black
- Department of Applied Sciences, Faculty of Health & Life Sciences, University of Northumbria at Newcastle, Newcastle upon Tyne, NE1 8ST, UK.
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7
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Skagia A, Zografou C, Vezyri E, Venieraki A, Katinakis P, Dimou M. Cyclophilin PpiB is involved in motility and biofilm formation via its functional association with certain proteins. Genes Cells 2016; 21:833-51. [PMID: 27306110 DOI: 10.1111/gtc.12383] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/09/2016] [Indexed: 12/24/2022]
Abstract
PpiB belongs to the superfamily of peptidyl-prolyl cis/trans isomerases (PPIases, EC: 5.2.1.8), which catalyze the rate-limiting protein folding step at peptidyl-prolyl bonds and control several biological processes. In this study, we show that PpiB acts as a negative effector of motility and biofilm formation ability of Escherichia coli. We identify multicopy suppressors of each ΔppiB phenotype among putative PpiB prey proteins which upon deletion are often characterized by analogous phenotypes. Many putative preys show similar gene expression in wild-type and ΔppiB genetic backgrounds implying possible post-translational modifications by PpiB. We further conducted in vivo and in vitro interaction screens to determine which of them represent true preys. For DnaK, acetyl-CoA carboxylase, biotin carboxylase subunit (AccC) and phosphate acetyltransferase (Pta) we also showed a direct role of PpiB in the functional control of these proteins because it increased the measured enzyme activity of each protein and further interfered with DnaK localization and the correct folding of AccC. Taken together, these results indicate that PpiB is involved in diverse regulatory mechanisms to negatively modulate motility and biofilm formation via its functional association with certain protein substrates.
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Affiliation(s)
- Aggeliki Skagia
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Chrysoula Zografou
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Eleni Vezyri
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Anastasia Venieraki
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Panagiotis Katinakis
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Maria Dimou
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
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8
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Douillard FP, Rasinkangas P, Bhattacharjee A, Palva A, de Vos WM. The N-Terminal GYPSY Motif Is Required for Pilin-Specific Sortase SrtC1 Functionality in Lactobacillus rhamnosus Strain GG. PLoS One 2016; 11:e0153373. [PMID: 27070897 PMCID: PMC4829219 DOI: 10.1371/journal.pone.0153373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/29/2016] [Indexed: 12/31/2022] Open
Abstract
Predominantly identified in pathogenic Gram-positive bacteria, sortase-dependent pili are also found in commensal species, such as the probiotic-marketed strain Lactobacillus rhamnosus strain GG. Pili are typically associated with host colonization, immune signalling and biofilm formation. Comparative analysis of the N-terminal domains of pilin-specific sortases from various piliated Gram-positive bacteria identified a conserved motif, called GYPSY, within the signal sequence. We investigated the function and role of the GYPSY residues by directed mutagenesis in homologous (rod-shaped) and heterologous (coccoid-shaped) expression systems for pilus formation. Substitutions of some of the GYPSY residues, and more specifically the proline residue, were found to have a direct impact on the degree of piliation of Lb. rhamnosus GG. The present findings uncover a new signalling element involved in the functionality of pilin-specific sortases controlling the pilus biogenesis of Lb. rhamnosus GG and related piliated Gram-positive species.
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Affiliation(s)
- François P. Douillard
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- * E-mail: (FPD); (WMdV)
| | - Pia Rasinkangas
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Arnab Bhattacharjee
- Research Programs Unit Immunobiology, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Airi Palva
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Willem M. de Vos
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Research Programs Unit Immunobiology, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- * E-mail: (FPD); (WMdV)
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9
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Humbert MV, Almonacid Mendoza HL, Jackson AC, Hung MC, Bielecka MK, Heckels JE, Christodoulides M. Vaccine potential of bacterial macrophage infectivity potentiator (MIP)-like peptidyl prolyl cis/trans isomerase (PPIase) proteins. Expert Rev Vaccines 2015; 14:1633-49. [PMID: 26468663 DOI: 10.1586/14760584.2015.1095638] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Peptidyl prolyl cis/trans isomerases (PPIases) are a superfamily of proteins ubiquitously distributed among living organisms, which function primarily to assist the folding and structuring of unfolded and partially folded polypeptide chains and proteins. In this review, we focus specifically on the Macrophage Infectivity Potentiator (MIP)-like PPIases, which are members of the immunophilin family of FK506-binding proteins (FKBP). MIP-like PPIases have accessory roles in virulence and are candidates for inclusion in vaccines protective against both animal and human bacterial pathogens. A structural vaccinology approach obviates any issues over molecular mimicry and potential cross-reactivity with human FKBP proteins and studies with a representative antigen, the Neisseria meningitidis-MIP, support this strategy. Moreover, a dual approach of vaccination and drug targeting could be considered for controlling bacterial infectious diseases of humans and animals.
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Affiliation(s)
- María Victoria Humbert
- a Neisseria Research, Molecular Microbiology, Academic Unit of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories , University of Southampton Faculty of Medicine , Southampton , UK
| | - Hannia L Almonacid Mendoza
- a Neisseria Research, Molecular Microbiology, Academic Unit of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories , University of Southampton Faculty of Medicine , Southampton , UK
| | - Alexandra C Jackson
- a Neisseria Research, Molecular Microbiology, Academic Unit of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories , University of Southampton Faculty of Medicine , Southampton , UK
| | - Miao-Chiu Hung
- a Neisseria Research, Molecular Microbiology, Academic Unit of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories , University of Southampton Faculty of Medicine , Southampton , UK
| | - Magdalena K Bielecka
- a Neisseria Research, Molecular Microbiology, Academic Unit of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories , University of Southampton Faculty of Medicine , Southampton , UK
| | - John E Heckels
- a Neisseria Research, Molecular Microbiology, Academic Unit of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories , University of Southampton Faculty of Medicine , Southampton , UK
| | - Myron Christodoulides
- a Neisseria Research, Molecular Microbiology, Academic Unit of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories , University of Southampton Faculty of Medicine , Southampton , UK
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10
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Kumar A, Baycin-Hizal D, Wolozny D, Pedersen LE, Lewis NE, Heffner K, Chaerkady R, Cole RN, Shiloach J, Zhang H, Bowen MA, Betenbaugh MJ. Elucidation of the CHO Super-Ome (CHO-SO) by Proteoinformatics. J Proteome Res 2015; 14:4687-703. [PMID: 26418914 DOI: 10.1021/acs.jproteome.5b00588] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chinese hamster ovary (CHO) cells are the preferred host cell line for manufacturing a variety of complex biotherapeutic drugs including monoclonal antibodies. We performed a proteomics and bioinformatics analysis on the spent medium from adherent CHO cells. Supernatant from CHO-K1 culture was collected and subjected to in-solution digestion followed by LC/LC-MS/MS analysis, which allowed the identification of 3281 different host cell proteins (HCPs). To functionally categorize them, we applied multiple bioinformatics tools to the proteins identified in our study including SignalP, TargetP, SecretomeP, TMHMM, WoLF PSORT, and Phobius. This analysis provided information on the presence of signal peptides, transmembrane domains, and cellular localization and showed that both secreted and intracellular proteins were constituents of the supernatant. Identified proteins were shown to be localized to the secretory pathway including ones playing roles in cell growth, proliferation, and folding as well as those involved in protein degradation and removal. After combining proteins predicted to be secreted or having a signal peptide, we identified 1015 proteins, which we termed as CHO supernatant-ome (CHO-SO), or superome. As a part of this effort, we created a publically accessible web-based tool called GO-CHO to functionally categorize proteins found in CHO-SO and identify enriched molecular functions, biological processes, and cellular components. We also used a tool to evaluate the immunogenicity potential of high-abundance HCPs. Among enriched functions were catalytic activity and structural constituents of the cytoskeleton. Various transport related biological processes, such as vesicle mediated transport, were found to be highly enriched. Extracellular space and vesicular exosome associated proteins were found to be the most enriched cellular components. The superome also contained proteins secreted from both classical and nonclassical secretory pathways. The work and database described in our study will enable the CHO community to rapidly identify high-abundance HCPs in their cultures and therefore help assess process and purification methods used in the production of biologic drugs.
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Affiliation(s)
- Amit Kumar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States.,Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases , National Institute of Health, Building 14A, Bethesda, Maryland 20892, United States
| | - Deniz Baycin-Hizal
- Antibody Discovery and Protein Engineering, MedImmune LLC , 1 MedImmune Way, Gaithersburg, Maryland 20878, United States
| | - Daniel Wolozny
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , DK-2970 Hørsholm, Denmark
| | - Nathan E Lewis
- Department of Biology, Brigham Young University , Provo, Utah 84602, United States.,Department of Pediatrics, University of California , San Diego, California 92093, United States
| | - Kelley Heffner
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Raghothama Chaerkady
- Institute of Basic Biomedical Sciences, Mass Spectrometry and Proteomics Facility, Johns Hopkins University School of Medicine , 733 North Broadway Street, Baltimore, Maryland 21205, United States
| | - Robert N Cole
- Institute of Basic Biomedical Sciences, Mass Spectrometry and Proteomics Facility, Johns Hopkins University School of Medicine , 733 North Broadway Street, Baltimore, Maryland 21205, United States
| | - Joseph Shiloach
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases , National Institute of Health, Building 14A, Bethesda, Maryland 20892, United States
| | - Hui Zhang
- Department of Pathology, Johns Hopkins School of Medicine , 400 North Broadway Street, Baltimore, Maryland 21287, United States
| | - Michael A Bowen
- Antibody Discovery and Protein Engineering, MedImmune LLC , 1 MedImmune Way, Gaithersburg, Maryland 20878, United States
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
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11
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Identification of Conserved and Species-Specific Functions of the Listeria monocytogenes PrsA2 Secretion Chaperone. Infect Immun 2015. [PMID: 26216425 DOI: 10.1128/iai.00504-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Gram-positive bacterium Listeria monocytogenes is a facultative intracellular pathogen that relies on the regulated secretion and activity of a variety of proteins that sustain life within diverse environments. PrsA2 has recently been identified as a secreted peptidyl-prolyl cis/trans isomerase and chaperone that is dispensable for bacterial growth in broth culture but essential for L. monocytogenes virulence. Following host infection, PrsA2 contributes to the proper folding and activity of secreted proteins that are required for bacterial replication within the host cytosol and for bacterial spread to adjacent cells. PrsA2 is one member of a family of Gram-positive secretion chaperones that appear to play important roles in bacterial physiology; however, it is not known how these proteins recognize their substrate proteins or the degree to which their function is conserved across diverse Gram-positive species. We therefore examined PrsA proteins encoded by a variety of Gram-positive bacteria for functional complementation of L. monocytogenes mutants lacking prsA2. PrsA homologues encoded by Bacillus subtilis, Streptococcus pyogenes, Streptococcus pneumoniae, Streptococcus mutans, Staphylococcus aureus, and Lactococcus lactis were examined for functional complementation of a variety of L. monocytogenes PrsA2-associated phenotypes central to L. monocytogenes pathogenesis and bacterial cell physiology. Our results indicate that while selected aspects of PrsA2 function are broadly conserved among diverse Gram-positive bacteria, PrsA2 exhibits unique specificity for L. monocytogenes target proteins required for pathogenesis. The L. monocytogenes PrsA2 chaperone thus appears evolutionarily optimized for virulence factor secretion within the host cell cytosol while still maintaining aspects of activity relevant to more general features of Gram-positive protein translocation.
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12
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Samazan F, Rokbi B, Seguin D, Telles F, Gautier V, Richarme G, Chevret D, Varela PF, Velours C, Poquet I. Production, secretion and purification of a correctly folded staphylococcal antigen in Lactococcus lactis. Microb Cell Fact 2015; 14:104. [PMID: 26178240 PMCID: PMC4502909 DOI: 10.1186/s12934-015-0271-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 05/08/2015] [Indexed: 11/23/2022] Open
Abstract
Background Lactococcus lactis, a lactic acid bacterium traditionally used to ferment milk and manufacture cheeses, is also, in the biotechnology field, an interesting host to produce proteins of medical interest, as it is “Generally Recognized As Safe”. Furthermore, as L. lactis naturally secretes only one major endogenous protein (Usp45), the secretion of heterologous proteins in this species facilitates their purification from a protein-poor culture medium. Here, we developed and optimized protein production and secretion in L. lactis to obtain proteins of high quality, both correctly folded and pure to a high extent. As proteins to be produced, we chose the two transmembrane members of the HtrA protease family in Staphylococcus aureus, an important extra-cellular pathogen, as these putative surface-exposed antigens could constitute good targets for vaccine development. Results A recombinant ORF encoding a C-terminal, soluble, proteolytically inactive and tagged form of each staphylococcal HtrA protein was cloned into a lactococcal expression-secretion vector. After growth and induction of recombinant gene expression, L. lactis was able to produce and secrete each recombinant rHtrA protein as a stable form that accumulated in the culture medium in similar amounts as the naturally secreted endogenous protein, Usp45. L. lactis growth in fermenters, in particular in a rich optimized medium, led to higher yields for each rHtrA protein. Protein purification from the lactococcal culture medium was easily achieved in one step and allowed recovery of highly pure and stable proteins whose identity was confirmed by mass spectrometry. Although rHtrA proteins were monomeric, they displayed the same secondary structure content, thermal stability and chaperone activity as many other HtrA family members, indicating that they were correctly folded. rHtrA protein immunogenicity was established in mice. The raised polyclonal antibodies allowed studying the expression and subcellular localization of wild type proteins in S. aureus: although both proteins were expressed, only HtrA1 was found to be, as predicted, exposed at the staphylococcal cell surface suggesting that it could be a better candidate for vaccine development. Conclusions In this study, an efficient process was developed to produce and secrete putative staphylococcal surface antigens in L. lactis and to purify them to homogeneity in one step from the culture supernatant. This allowed recovering fully folded, stable and pure proteins which constitute promising vaccine candidates to be tested for protection against staphylococcal infection. L. lactis thus proved to be an efficient and competitive cell factory to produce proteins of high quality for medical applications. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0271-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Frédéric Samazan
- INRA, UMR1319 Micalis (Microbiologie de l'Alimentation au service de la Santé), Domaine de Vilvert, 78352, Jouy-en-Josas Cedex, France. .,Institut Curie/CNRS, UMR3244, 25 rue d'Ulm, 75248, Paris Cedex 05, France.
| | - Bachra Rokbi
- Sanofi Pasteur, Campus Mérieux, 1541 avenue Marcel Mérieux, 69280, Marcy L'Etoile, France.
| | - Delphine Seguin
- Sanofi Pasteur, Campus Mérieux, 1541 avenue Marcel Mérieux, 69280, Marcy L'Etoile, France.
| | - Fabienne Telles
- Sanofi Pasteur, Campus Mérieux, 1541 avenue Marcel Mérieux, 69280, Marcy L'Etoile, France.
| | - Valérie Gautier
- Stress molecules, Institut Jacques Monod, Université Paris 7, 15 rue Hélène Brion, 75013, Paris, France.
| | - Gilbert Richarme
- Stress molecules, Institut Jacques Monod, Université Paris 7, 15 rue Hélène Brion, 75013, Paris, France.
| | - Didier Chevret
- INRA, UMR1319 Micalis (Microbiologie de l'Alimentation au service de la Santé), Domaine de Vilvert, 78352, Jouy-en-Josas Cedex, France.
| | | | | | - Isabelle Poquet
- INRA, UMR1319 Micalis (Microbiologie de l'Alimentation au service de la Santé), Domaine de Vilvert, 78352, Jouy-en-Josas Cedex, France. .,LPBA, Institut Pasteur, Bât. Calmette, 75015, Paris, France.
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Microbial peptidyl-prolyl cis/trans isomerases (PPIases): virulence factors and potential alternative drug targets. Microbiol Mol Biol Rev 2015; 78:544-71. [PMID: 25184565 DOI: 10.1128/mmbr.00015-14] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Initially discovered in the context of immunomodulation, peptidyl-prolyl cis/trans isomerases (PPIases) were soon identified as enzymes catalyzing the rate-limiting protein folding step at peptidyl bonds preceding proline residues. Intense searches revealed that PPIases are a superfamily of proteins consisting of three structurally distinguishable families with representatives in every described species of prokaryote and eukaryote and, recently, even in some giant viruses. Despite the clear-cut enzymatic activity and ubiquitous distribution of PPIases, reports on solely PPIase-dependent biological roles remain scarce. Nevertheless, they have been found to be involved in a plethora of biological processes, such as gene expression, signal transduction, protein secretion, development, and tissue regeneration, underscoring their general importance. Hence, it is not surprising that PPIases have also been identified as virulence-associated proteins. The extent of contribution to virulence is highly variable and dependent on the pleiotropic roles of a single PPIase in the respective pathogen. The main objective of this review is to discuss this variety in virulence-related bacterial and protozoan PPIases as well as the involvement of host PPIases in infectious processes. Moreover, a special focus is given to Legionella pneumophila macrophage infectivity potentiator (Mip) and Mip-like PPIases of other pathogens, as the best-characterized virulence-related representatives of this family. Finally, the potential of PPIases as alternative drug targets and first tangible results are highlighted.
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Peptidylprolyl cis–trans isomerases of Legionella pneumophila: virulence, moonlighting and novel therapeutic targets. Biochem Soc Trans 2014; 42:1728-33. [DOI: 10.1042/bst20140202] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Legionella pneumophila, typically a parasite of free-living protozoa, can also replicate in human alveolar macrophages and lung epithelial cells causing Legionnaires’ disease in humans, a severe atypical pneumonia. The pathogen encodes six peptidylprolyl cis–trans isomerases (PPIases), which generally accelerate folding of prolyl peptide bonds, and influence protein folding. PPIases can be divided into three classes, cyclophilins, parvulins and FK506-binding proteins (FKBPs). They contribute to a multitude of cellular functions including bacterial virulence. In the present review, we provide an overview of L. pneumophila PPIases, discussing their known and anticipated functions as well as moonlighting phenomena. By taking the example of the macrophage infectivity potentiator (Mip) of L. pneumophila, we highlight the potential of PPIases as promising drug targets.
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Olaya-Abril A, Jiménez-Munguía I, Gómez-Gascón L, Rodríguez-Ortega MJ. Surfomics: shaving live organisms for a fast proteomic identification of surface proteins. J Proteomics 2013; 97:164-76. [PMID: 23624344 DOI: 10.1016/j.jprot.2013.03.035] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 02/25/2013] [Accepted: 03/24/2013] [Indexed: 12/11/2022]
Abstract
Surface proteins play a critical role in the interaction between cells and their environment, as they take part in processes like signaling, adhesion, transport, etc. In pathogenic microorganisms, they can also participate in virulence or cytotoxicity. As these proteins have the highest chances to be recognized by the immune system, they are often the targets for the discovery of new vaccines. In addition, they can serve for the development of serological-based tools to diagnose infectious diseases. First-generation proteomic strategies for the identification of surface proteins rely on the biochemical fractionation and/or enrichment of this group of molecules or organelles containing them. However, in the last years, a novel second-generation approach has been developed, consisting of the digestion of live, intact cells with proteases, so that surface-exposed moieties (i.e. the "surfome" of a cell) are "shaved" and analyzed by LC/MS/MS. Here we review such a strategy, firstly set up and developed in Gram-positive bacteria, and further applied to Gram-negative bacteria, unicellular fungi, and also pluricellular organisms. We also discuss the advantages and inconvenients of the approach, and the still unresolved question about the intriguing presence of proteins predicted as cytoplasmic in the surfomes. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Campus de Excelencia Internacional CeiA3, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Irene Jiménez-Munguía
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Campus de Excelencia Internacional CeiA3, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Lidia Gómez-Gascón
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Campus de Excelencia Internacional CeiA3, Córdoba, Spain; Departamento de Sanidad Animal, Universidad de Córdoba, Córdoba, Spain
| | - Manuel J Rodríguez-Ortega
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Campus de Excelencia Internacional CeiA3, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.
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