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Sadones O, Kramarska E, Laverde D, Berisio R, Huebner J, Romero-Saavedra F. Investigation of cross-opsonic effect leads to the discovery of PPIase-domain containing protein vaccine candidate to prevent infections by Gram-positive ESKAPE pathogens. BMC Microbiol 2024; 24:280. [PMID: 39068414 PMCID: PMC11282748 DOI: 10.1186/s12866-024-03427-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 07/15/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Enterococcus faecium and Staphylococcus aureus are the Gram-positive pathogens of the ESKAPE group, known to represent a great threat to human health due to their high virulence and multiple resistances to antibiotics. Combined, enterococci and S. aureus account for 26% of healthcare-associated infections and are the most common organisms responsible for blood stream infections. We previously showed that the peptidyl-prolyl cis/trans isomerase (PPIase) PpiC of E. faecium elicits the production of specific, opsonic, and protective antibodies that are effective against several strains of E. faecium and E. faecalis. Due to the ubiquitous characteristics of PPIases and their essential function within Gram-positive cells, we hypothesized a potential cross-reactive effect of anti-PpiC antibodies. RESULTS Opsonophagocytic assays combined with bioinformatics led to the identification of the foldase protein PrsA as a new potential vaccine antigen in S. aureus. We show that PrsA is a stable dimeric protein able to elicit opsonic antibodies against the S. aureus strain MW2, as well as cross-binding and cross-opsonic in several S. aureus, E. faecium and E. faecalis strains. CONCLUSIONS Given the multiple antibiotic resistances S. aureus and enterococci present, finding preventive strategies is essential to fight those two nosocomial pathogens. The study shows the potential of PrsA as an antigen to use in vaccine formulation against the two dangerous Gram-positive ESKAPE bacteria. Our findings support the idea that PPIases should be further investigated as vaccine targets in the frame of pan-vaccinomics strategy.
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Affiliation(s)
- Océane Sadones
- Division of pediatric infectious disease, Hauner children's hospital, LMU, Munich, Germany.
| | - Eliza Kramarska
- Institute of Biostructures and Bioimaging, Italian Research Council (CNR), Naples, Italy
| | - Diana Laverde
- Division of pediatric infectious disease, Hauner children's hospital, LMU, Munich, Germany
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, Italian Research Council (CNR), Naples, Italy
| | - Johannes Huebner
- Division of pediatric infectious disease, Hauner children's hospital, LMU, Munich, Germany.
| | - Felipe Romero-Saavedra
- Division of pediatric infectious disease, Hauner children's hospital, LMU, Munich, Germany
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2
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Agbavor C, Zimnicka A, Kumar A, George JL, Torres M, Prehna G, Alonzo F, Durrant JD, Freitag NE, Cahoon LA. The chaperone PrsA2 regulates the secretion, stability, and folding of listeriolysin O during Listeria monocytogenes infection. mBio 2024; 15:e0074324. [PMID: 38809022 PMCID: PMC11253611 DOI: 10.1128/mbio.00743-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 04/22/2024] [Indexed: 05/30/2024] Open
Abstract
Pathogenic bacteria rely on secreted virulence factors to cause disease in susceptible hosts. However, in Gram-positive bacteria, the mechanisms underlying secreted protein activation and regulation post-membrane translocation remain largely unknown. Using proteomics, we identified several proteins that are dependent on the secreted chaperone PrsA2. We followed with phenotypic, biochemical, and biophysical assays and computational analyses to examine the regulation of a detected key secreted virulence factor, listeriolysin O (LLO), and its interaction with PrsA2 from the bacterial pathogen Listeria monocytogenes (Lm). Critical to Lm virulence is internalization by host cells and the subsequent action of the cholesterol-dependent pore-forming toxin, LLO, which enables bacterial escape from the host cell phagosome. Since Lm is a Gram-positive organism, the space between the cell membrane and wall is solvent exposed. Therefore, we hypothesized that the drop from neutral to acidic pH as the pathogen is internalized into a phagosome is critical to regulating the interaction of PrsA2 with LLO. Here, we demonstrate that PrsA2 directly interacts with LLO in a pH-dependent manner. We show that PrsA2 protects and sequesters LLO under neutral pH conditions where LLO can be observed to aggregate. In addition, we identify molecular features of PrsA2 that are required for interaction and ultimately the folding and activity of LLO. Moreover, protein-complex modeling suggests that PrsA2 interacts with LLO via its cholesterol-binding domain. These findings highlight a mechanism by which a Gram-positive secretion chaperone regulates the secretion, stability, and folding of a pore-forming toxin under conditions relevant to host cell infection. IMPORTANCE Lm is a ubiquitous food-borne pathogen that can cause severe disease to vulnerable populations. During infection, Lm relies on a wide repertoire of secreted virulence factors including the LLO that enables the bacterium to invade the host and spread from cell to cell. After membrane translocation, secreted factors must become active in the challenging bacterial cell membrane-wall interface. However, the mechanisms required for secreted protein folding and function are largely unknown. Lm encodes a chaperone, PrsA2, that is critical for the activity of secreted factors. Here, we show that PrsA2 directly associates and protects the major Lm virulence factor, LLO, under conditions corresponding to the host cytosol, where LLO undergoes irreversible denaturation. Additionally, we identify molecular features of PrsA2 that enable its interaction with LLO. Together, our results suggest that Lm and perhaps other Gram-positive bacteria utilize secreted chaperones to regulate the activity of pore-forming toxins during infection.
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Affiliation(s)
- Charles Agbavor
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adriana Zimnicka
- Department of Pharmaceutical Sciences, University of Illinois Chicago, Chicago, Illinois, USA
| | - Allison Kumar
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jada L. George
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Madeline Torres
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Gerd Prehna
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Francis Alonzo
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Nancy E. Freitag
- Department of Pharmaceutical Sciences, University of Illinois Chicago, Chicago, Illinois, USA
| | - Laty A. Cahoon
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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3
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Rahman MM, Zamakhaeva S, Rush JS, Chaton CT, Kenner CW, Hla YM, Tsui HCT, Uversky VN, Winkler ME, Korotkov KV, Korotkova N. O-glycosylation of intrinsically disordered regions regulates homeostasis of membrane proteins in streptococci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592596. [PMID: 38746434 PMCID: PMC11092751 DOI: 10.1101/2024.05.05.592596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Proteins harboring intrinsically disordered regions (IDRs) lacking stable secondary or tertiary structures are abundant across the three domains of life. These regions have not been systematically studied in prokaryotes. Our genome-wide analysis identifies extracytoplasmic serine/threonine-rich IDRs in several biologically important membrane proteins in streptococci. We demonstrate that these IDRs are O-glycosylated with glucose by glycosyltransferases GtrB and PgtC2 in Streptococcus pyogenes and Streptococcus pneumoniae, and with N-acetylgalactosamine by a Pgf-dependent mechanism in Streptococcus mutans. Absence of glycosylation leads to a defect in biofilm formation under ethanol-stressed conditions in S. mutans. We link this phenotype to the C-terminal IDR of a post-translocation secretion chaperone PrsA. O-glycosylation of the IDR protects this region from proteolytic degradation. The IDR length attenuates the efficiency of glycosylation and, consequently, the expression level of PrsA. Taken together, our data reveal that O-glycosylation of IDRs functions as a dynamic switch of protein homeostasis in streptococci.
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Affiliation(s)
- Mohammad M. Rahman
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA
| | - Svetlana Zamakhaeva
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA
| | - Jeffrey S. Rush
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Catherine T. Chaton
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Cameron W. Kenner
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA
| | - Yin Mon Hla
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA
| | | | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Malcolm E. Winkler
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Konstantin V. Korotkov
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Natalia Korotkova
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
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4
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Lin MH, Liu CC, Lu CW, Shu JC. Staphylococcus aureus foldase PrsA contributes to the folding and secretion of protein A. BMC Microbiol 2024; 24:108. [PMID: 38566014 PMCID: PMC10986000 DOI: 10.1186/s12866-024-03268-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Staphylococcus aureus secretes a variety of proteins including virulence factors that cause diseases. PrsA, encoded by many Gram-positive bacteria, is a membrane-anchored lipoprotein that functions as a foldase to assist in post-translocational folding and helps maintain the stability of secreted proteins. Our earlier proteomic studies found that PrsA is required for the secretion of protein A, an immunoglobulin-binding protein that contributes to host immune evasion. This study aims to investigate how PrsA influences protein A secretion. RESULTS We found that in comparison with the parental strain HG001, the prsA-deletion mutant HG001ΔprsA secreted less protein A. Deleting prsA also decreased the stability of exported protein A. Pulldown assays indicated that PrsA interacts with protein A in vivo. The domains in PrsA that interact with protein A are mapped to both the N- and C-terminal regions (NC domains). Additionally, the NC domains are essential for promoting PrsA dimerization. Furthermore, an immunoglobulin-binding assay revealed that, compared to the parental strain HG001, fewer immunoglobulins bound to the surface of the mutant strain HG001ΔprsA. CONCLUSIONS This study demonstrates that PrsA is critical for the folding and secretion of protein A. The information derived from this study provides a better understanding of virulent protein export pathways that are crucial to the pathogenicity of S. aureus.
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Affiliation(s)
- Mei-Hui Lin
- Graduate Institute of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Tao-Yuan, 333, Taiwan.
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Tao-Yuan, 333, Taiwan.
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao- Yuan, 333, Taiwan.
| | - Chao-Chin Liu
- Graduate Institute of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Tao-Yuan, 333, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao- Yuan, 333, Taiwan
| | - Chiao-Wen Lu
- Graduate Institute of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Tao-Yuan, 333, Taiwan
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Tao-Yuan, 333, Taiwan
| | - Jwu-Ching Shu
- Graduate Institute of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Tao-Yuan, 333, Taiwan.
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Tao-Yuan, 333, Taiwan.
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao- Yuan, 333, Taiwan.
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5
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George JL, Agbavor C, Cabo LF, Cahoon LA. Streptococcus pneumoniae secretion chaperones PrsA, SlrA, and HtrA are required for competence, antibiotic resistance, colonization, and invasive disease. Infect Immun 2024; 92:e0049023. [PMID: 38226817 PMCID: PMC10863415 DOI: 10.1128/iai.00490-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/19/2023] [Indexed: 01/17/2024] Open
Abstract
Streptococcus pneumoniae is a Gram-positive bacterium and a significant health threat with the populations most at risk being children, the elderly, and the immuno-compromised. To colonize and transition into an invasive infectious organism, S. pneumoniae secretes virulence factors that are translocated across the bacterial membrane and destined for surface exposure, attachment to the cell wall, or secretion into the host. The surface exposed protein chaperones PrsA, SlrA, and HtrA facilitate S. pneumoniae protein secretion; however, the distinct roles contributed by each of these secretion chaperones have not been well defined. Tandem Mass-Tagged Mass Spectrometry and virulence, adhesion, competence, and cell wall integrity assays were used to interrogate the individual and collective contributions of PrsA, SlrA, and HtrA to multiple aspects of S. pneumoniae physiology and virulence. PrsA, SlrA, and HtrA were found to play critical roles in S. pneumoniae host cell infection and competence, and the absence of each of these secretion chaperones significantly altered the S. pneumoniae secretome in distinct ways. PrsA and SlrA were additionally found to contribute to cell wall assembly and resistance to cell wall-active antimicrobials and were important for enabling S. pneumoniae host cell adhesion during colonization and invasive infection. These findings serve to further illustrate the pivotal contributions of PrsA, SlrA, and HtrA to S. pneumoniae protein secretion and virulence.
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Affiliation(s)
- Jada L. George
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Charles Agbavor
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Leah F. Cabo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Laty A. Cahoon
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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6
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Jiang K, Li W, Tong M, Xu J, Chen Z, Yang Y, Zang Y, Jiao X, Liu C, Lim B, Jiang X, Wang J, Wu D, Wang M, Liu SJ, Shao F, Gao X. Bacteroides fragilis ubiquitin homologue drives intraspecies bacterial competition in the gut microbiome. Nat Microbiol 2024; 9:70-84. [PMID: 38082149 DOI: 10.1038/s41564-023-01541-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 10/26/2023] [Indexed: 12/21/2023]
Abstract
Interbacterial antagonism and associated defensive strategies are both essential during bacterial competition. The human gut symbiont Bacteroides fragilis secretes a ubiquitin homologue (BfUbb) that is toxic to a subset of B. fragilis strains in vitro. In the present study, we demonstrate that BfUbb lyses certain B. fragilis strains by non-covalently binding and inactivating an essential peptidyl-prolyl isomerase (PPIase). BfUbb-sensitivity profiling of B. fragilis strains revealed a key tyrosine residue (Tyr119) in the PPIase and strains that encode a glutamic acid residue at Tyr119 are resistant to BfUbb. Crystal structural analysis and functional studies of BfUbb and the BfUbb-PPIase complex uncover a unique disulfide bond at the carboxy terminus of BfUbb to mediate the interaction with Tyr119 of the PPIase. In vitro coculture assays and mouse studies show that BfUbb confers a competitive advantage for encoding strains and this is further supported by human gut metagenome analyses. Our findings reveal a previously undescribed mechanism of bacterial intraspecies competition.
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Affiliation(s)
- Kun Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Weixun Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ming Tong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jinghua Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zhe Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yan Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yuanrong Zang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xuyao Jiao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Bentley Lim
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Xianzhi Jiang
- Microbiome Research Center, Moon (Guangzhou) Biotech Co. Ltd., Guangzhou, China
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Dalei Wu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Mingyu Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Feng Shao
- National Institute of Biological Sciences, Beijing, China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
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7
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Foor SD, Brangulis K, Shakya AK, Rana VS, Bista S, Kitsou C, Ronzetti M, Alreja AB, Linden SB, Altieri AS, Baljinnyam B, Akopjana I, Nelson DC, Simeonov A, Herzberg O, Caimano MJ, Pal U. A unique borrelial protein facilitates microbial immune evasion. mBio 2023; 14:e0213523. [PMID: 37830812 PMCID: PMC10653885 DOI: 10.1128/mbio.02135-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Lyme disease is a major tick-borne infection caused by a bacterial pathogen called Borrelia burgdorferi, which is transmitted by ticks and affects hundreds of thousands of people every year. These bacterial pathogens are distinct from other genera of microbes because of their distinct features and ability to transmit a multi-system infection to a range of vertebrates, including humans. Progress in understanding the infection biology of Lyme disease, and thus advancements towards its prevention, are hindered by an incomplete understanding of the microbiology of B. burgdorferi, partly due to the occurrence of many unique borrelial proteins that are structurally unrelated to proteins of known functions yet are indispensable for pathogen survival. We herein report the use of diverse technologies to examine the structure and function of a unique B. burgdorferi protein, annotated as BB0238-an essential virulence determinant. We show that the protein is structurally organized into two distinct domains, is involved in multiplex protein-protein interactions, and facilitates tick-to-mouse pathogen transmission by aiding microbial evasion of early host cellular immunity. We believe that our findings will further enrich our understanding of the microbiology of B. burgdorferi, potentially impacting the future development of novel prevention strategies against a widespread tick-transmitted infection.
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Affiliation(s)
- Shelby D. Foor
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Kalvis Brangulis
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- Department of Human Physiology and Biochemistry, Riga Stradins University, Riga, Latvia
| | - Anil K. Shakya
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Vipin S. Rana
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Sandhya Bista
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Chrysoula Kitsou
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Michael Ronzetti
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Adit B. Alreja
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Sara B. Linden
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Amanda S. Altieri
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Bolormaa Baljinnyam
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Inara Akopjana
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Daniel C. Nelson
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Osnat Herzberg
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Melissa J. Caimano
- Departments of Medicine, Pediatrics, and Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Utpal Pal
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
- Virginia-Maryland College of Veterinary Medicine, College Park, Maryland, USA
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8
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He B, Sachla AJ, Helmann JD. TerC proteins function during protein secretion to metalate exoenzymes. Nat Commun 2023; 14:6186. [PMID: 37794032 PMCID: PMC10550928 DOI: 10.1038/s41467-023-41896-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/14/2023] [Indexed: 10/06/2023] Open
Abstract
Cytosolic metalloenzymes acquire metals from buffered intracellular pools. How exported metalloenzymes are appropriately metalated is less clear. We provide evidence that TerC family proteins function in metalation of enzymes during export through the general secretion (Sec-dependent) pathway. Bacillus subtilis strains lacking MeeF(YceF) and MeeY(YkoY) have a reduced capacity for protein export and a greatly reduced level of manganese (Mn) in the secreted proteome. MeeF and MeeY copurify with proteins of the general secretory pathway, and in their absence the FtsH membrane protease is essential for viability. MeeF and MeeY are also required for efficient function of the Mn2+-dependent lipoteichoic acid synthase (LtaS), a membrane-localized enzyme with an extracytoplasmic active site. Thus, MeeF and MeeY, representative of the widely conserved TerC family of membrane transporters, function in the co-translocational metalation of Mn2+-dependent membrane and extracellular enzymes.
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Affiliation(s)
- Bixi He
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, NY, 14853-8101, USA
| | - Ankita J Sachla
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, NY, 14853-8101, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, NY, 14853-8101, USA.
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9
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Wang L, Li A, Fang J, Wang Y, Chen L, Qiao L, Wang W. Enhanced Cell Wall and Cell Membrane Activity Promotes Heat Adaptation of Enterococcus faecium. Int J Mol Sci 2023; 24:11822. [PMID: 37511581 PMCID: PMC10380804 DOI: 10.3390/ijms241411822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/09/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Enterococcus faecium (E. faecium) is widely used in foods and is known as a probiotic to treat or prevent diarrhea in pets and livestock. However, the poor resistance of E. faecium to high temperature processing procedures limits its use. Strain domestication is a low-cost and effective method to obtain high-temperature-resistant strains. In this study, heat treatment was performed from 45 °C to 70 °C and the temperature was gradually increased by 5 °C every 3 days. After domestication, the survival rates of the high temperature adaptation strain RS047-wl under 65 °C water bath for 40 min was 11.5 times higher than WT RS047. Moreover, the saturated fatty acid (SFA) contents in cell membrane and the cell volume significantly increased in the RS047-wl. The combined transcriptomic, metabolomic, and proteomics analysis results showed a significant enhancement of cell wall and membrane synthesis ability in the RS047-wl. In conclusion, one of the main factors contributing to the improved high temperature resistance of RS047-wl was its enhanced ability to synthesize cell wall and membrane, which helped maintain normal cell morphology. Developing a high-temperature-resistant strain and understanding its mechanism enables it to adapt to high temperatures. This lays the groundwork for its future development and application.
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Affiliation(s)
- Li Wang
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Aike Li
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Yongwei Wang
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
| | - Lixian Chen
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
| | - Lin Qiao
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
| | - Weiwei Wang
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
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10
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Zhu X, Zhang K, Luo H, Wu J. Overexpression of the class A penicillin-binding protein PonA in Bacillus improves recombinant protein production. BIORESOURCE TECHNOLOGY 2023; 383:129219. [PMID: 37217145 DOI: 10.1016/j.biortech.2023.129219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
The bottleneck of recombinant protein production in microbial cell factories is sometimes determined by limited manipulable targets and the lack of gene annotation related to protein expression. PonA is the major class A penicillin-binding protein in Bacillus, which polymerizes and cross-links peptidoglycan. Here, we described its novel functions during recombinant protein expression in Bacillus subtilis and analyzed the mechanism of its chaperone activity. When PonA was overexpressed, the expression of hyperthermophilic amylase significantly increased 3.96- and 1.26-fold in shake flasks and fed-batch processes, respectively. Increased cell diameter and reinforced cell walls were observed in PonA-overexpressing strains. Furthermore, the FN3 structural domain and the natural dimeric structure of PonA may be critical for exerting its chaperone activity. These data suggest that PonA can be an effective target for modification of the expression of recombinant proteins in B. subtilis.
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Affiliation(s)
- Xuyang Zhu
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Kang Zhang
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Hui Luo
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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11
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He B, Sachla AJ, Helmann JD. TerC Proteins Function During Protein Secretion to Metalate Exoenzymes. RESEARCH SQUARE 2023:rs.3.rs-2860473. [PMID: 37292672 PMCID: PMC10246235 DOI: 10.21203/rs.3.rs-2860473/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cytosolic metalloenzymes acquire metals from buffered intracellular pools. How exported metalloenzymes are appropriately metalated is less clear. We provide evidence that TerC family proteins function in metalation of enzymes during export through the general secretion (Sec-dependent) pathway. Bacillus subtilis strains lacking MeeF(YceF) and MeeY(YkoY) have a reduced capacity for protein export and a greatly reduced level of manganese (Mn) in the secreted proteome. MeeF and MeeY copurify with proteins of the general secretory pathway, and in their absence the FtsH membrane protease is essential for viability. MeeF and MeeY are also required for efficient function of the Mn2+-dependent lipoteichoic acid synthase (LtaS), a membrane-localized enzyme with an extracytoplasmic active site. Thus, MeeF and MeeY, representative of the widely conserved TerC family of membrane transporters, function in the co-translocational metalation of Mn2+-dependent membrane and extracellular enzymes.
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Affiliation(s)
- Bixi He
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, New York 14853-8101, USA
| | - Ankita J. Sachla
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, New York 14853-8101, USA
| | - John D. Helmann
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, New York 14853-8101, USA
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12
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He B, Sachla AJ, Helmann JD. TerC Proteins Function During Protein Secretion to Metalate Exoenzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536223. [PMID: 37090602 PMCID: PMC10120614 DOI: 10.1101/2023.04.10.536223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Cytosolic metalloenzymes acquire metals from buffered intracellular pools. How exported metalloenzymes are appropriately metalated is less clear. We provide evidence that TerC family proteins function in metalation of enzymes during export through the general secretion (Sec-dependent) pathway. Bacillus subtilis strains lacking MeeF(YceF) and MeeY(YkoY) have a reduced capacity for protein export and a greatly reduced level of manganese (Mn) in the secreted proteome. MeeF and MeeY copurify with proteins of the general secretory pathway, and in their absence the FtsH membrane protease is essential for viability. MeeF and MeeY are also required for efficient function of the Mn 2+ -dependent lipoteichoic acid synthase (LtaS), a membrane-localized enzyme with an extracytoplasmic active site. Thus, MeeF and MeeY, representative of the widely conserved TerC family of membrane transporters, function in the co-translocational metalation of Mn 2+ -dependent membrane and extracellular enzymes.
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Affiliation(s)
- Bixi He
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, New York 14853-8101, USA
| | - Ankita J. Sachla
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, New York 14853-8101, USA
| | - John D. Helmann
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, New York 14853-8101, USA
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13
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Dipten L, Amenti, Rajkrishna M. Molecular docking analysis of juglone with parvulin-type PPiase PrsA from Staphylococcus aureus. Bioinformation 2023; 19:48-52. [PMID: 37720298 PMCID: PMC10504509 DOI: 10.6026/97320630019048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 09/19/2023] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen that causes variety of infections range from mild skin diseases to life-threatening sepsis. It is also notorious for acquiring resistance to numerous antibiotics. Parvulin-type peptidyl-prolyl cis-trans isomerase (PPiase) domain containing PrsA protein is considered as an essential folding factor for secreted proteins of Gram-positive bacteria. Therefore, it is considered as a potential target for anti-staphylococcal drug discovery. Juglone, plant-derived 1,4-naphthoquinone, shows confirmed antitumor and antibacterial activities. Destruction of bacterial biofilm, inhibition of enzyme expression, degradation of nucleic acids, and other pathways are likely the major possible mechanisms for Staphylococcus aureus inactivation by juglone. Selective inhibition of parvulin type PPiase by juglone has been proven biochemically. However, detail structural information of parvulin-juglone interaction and mechanism of enzymatic inhibition till unexplored. Past hypothesis on inactivation of parvulin type PPiase due to covalent attachment of juglone molecules to its cysteine residues is not acceptable for the S. aureus PrsA parvulin domain as that lacks cysteine. Docking studies showed that juglone binds to the active site residues of S. aureus PrsA parvulin domain involved in enzymatic reaction. Active site conserved histidine residue of parvulin may be involved in juglone interaction as it was found to be the common interactive residue in majority of docking complexes. Data shows Juglone possibly inhibits parvulin type PPiase through competitive inhibition mechanism. Subtle differences of juglone interactions with other orthologous parvulin domains will help to develop semisynthetic drug with higher specificity against S. aureus.
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Affiliation(s)
- Laskar Dipten
- Department of Biotechnology, Nagaland University, Dimapur, Nagaland-797112, India
| | - Amenti
- Department of Biotechnology, Nagaland University, Dimapur, Nagaland-797112, India
| | - Mondal Rajkrishna
- Department of Biotechnology, Nagaland University, Dimapur, Nagaland-797112, India
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14
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Miyazaki R, Ai M, Tanaka N, Suzuki T, Dhomae N, Tsukazaki T, Akiyama Y, Mori H. Inner membrane YfgM–PpiD heterodimer acts as a functional unit that associates with the SecY/E/G translocon and promotes protein translocation. J Biol Chem 2022; 298:102572. [PMID: 36209828 PMCID: PMC9643414 DOI: 10.1016/j.jbc.2022.102572] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/24/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022] Open
Abstract
PpiD and YfgM are inner membrane proteins that are both composed of an N-terminal transmembrane segment and a C-terminal periplasmic domain. Escherichia coli YfgM and PpiD form a stable complex that interacts with the SecY/E/G (Sec) translocon, a channel that allows protein translocation across the cytoplasmic membrane. Although PpiD is known to function in protein translocation, the functional significance of PpiD–YfgM complex formation as well as the molecular mechanisms of PpiD–YfgM and PpiD/YfgM–Sec translocon interactions remain unclear. Here, we conducted genetic and biochemical studies using yfgM and ppiD mutants and demonstrated that a lack of YfgM caused partial PpiD degradation at its C-terminal region and hindered the membrane translocation of Vibrio protein export monitoring polypeptide (VemP), a Vibrio secretory protein, in both E. coli and Vibrio alginolyticus. While ppiD disruption also impaired VemP translocation, we found that the yfgM and ppiD double deletion exhibited no additive or synergistic effects. Together, these results strongly suggest that both PpiD and YfgM are required for efficient VemP translocation. Furthermore, our site-directed in vivo photocrosslinking analysis revealed that the tetratricopeptide repeat domain of YfgM and a conserved structural domain (NC domain) in PpiD interact with each other and that YfgM, like PpiD, directly interacts with the SecG translocon subunit. Crosslinking analysis also suggested that PpiD–YfgM complex formation is required for these proteins to interact with SecG. In summary, we propose that PpiD and YfgM form a functional unit that stimulates protein translocation by facilitating their proper interactions with the Sec translocon.
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Affiliation(s)
- Ryoji Miyazaki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Mengting Ai
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Natsuko Tanaka
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Naoshi Dhomae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Tomoya Tsukazaki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yoshinori Akiyama
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hiroyuki Mori
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
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15
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Naorem RS, Pangabam BD, Bora SS, Goswami G, Barooah M, Hazarika DJ, Fekete C. Identification of Putative Vaccine and Drug Targets against the Methicillin-Resistant Staphylococcus aureus by Reverse Vaccinology and Subtractive Genomics Approaches. Molecules 2022; 27:2083. [PMID: 35408485 PMCID: PMC9000511 DOI: 10.3390/molecules27072083] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 01/23/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an opportunistic pathogen and responsible for causing life-threatening infections. The emergence of hypervirulent and multidrug-resistant (MDR) S. aureus strains led to challenging issues in antibiotic therapy. Consequently, the morbidity and mortality rates caused by S. aureus infections have a substantial impact on health concerns. The current worldwide prevalence of MRSA infections highlights the need for long-lasting preventive measures and strategies. Unfortunately, effective measures are limited. In this study, we focus on the identification of vaccine candidates and drug target proteins against the 16 strains of MRSA using reverse vaccinology and subtractive genomics approaches. Using the reverse vaccinology approach, 4 putative antigenic proteins were identified; among these, PrsA and EssA proteins were found to be more promising vaccine candidates. We applied a molecular docking approach of selected 8 drug target proteins with the drug-like molecules, revealing that the ZINC4235426 as potential drug molecule with favorable interactions with the target active site residues of 5 drug target proteins viz., biotin protein ligase, HPr kinase/phosphorylase, thymidylate kinase, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase, and pantothenate synthetase. Thus, the identified proteins can be used for further rational drug or vaccine design to identify novel therapeutic agents for the treatment of multidrug-resistant staphylococcal infection.
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Affiliation(s)
- Romen Singh Naorem
- Department of General and Environmental Microbiology, Institute of Biology and Sport Biology, University of Pécs, Ifusag utja. 6, 7624 Pecs, Hungary; (R.S.N.); (B.D.P.)
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India; (M.B.); (D.J.H.)
| | - Bandana Devi Pangabam
- Department of General and Environmental Microbiology, Institute of Biology and Sport Biology, University of Pécs, Ifusag utja. 6, 7624 Pecs, Hungary; (R.S.N.); (B.D.P.)
| | - Sudipta Sankar Bora
- DBT—North East Centre for Agricultural Biotechnology (DBT-AAU Center), Assam Agricultural University, Jorhat 785013, India;
| | - Gunajit Goswami
- Multidisciplinary Research Unit, Jorhat Medical College and Hospital, Jorhat 785008, India;
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India; (M.B.); (D.J.H.)
- DBT—North East Centre for Agricultural Biotechnology (DBT-AAU Center), Assam Agricultural University, Jorhat 785013, India;
| | - Dibya Jyoti Hazarika
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India; (M.B.); (D.J.H.)
| | - Csaba Fekete
- Department of General and Environmental Microbiology, Institute of Biology and Sport Biology, University of Pécs, Ifusag utja. 6, 7624 Pecs, Hungary; (R.S.N.); (B.D.P.)
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16
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Structural and Kinetic Views of Molecular Chaperones in Multidomain Protein Folding. Int J Mol Sci 2022; 23:ijms23052485. [PMID: 35269628 PMCID: PMC8910466 DOI: 10.3390/ijms23052485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/10/2022] Open
Abstract
Despite recent developments in protein structure prediction, the process of the structure formation, folding, remains poorly understood. Notably, folding of multidomain proteins, which involves multiple steps of segmental folding, is one of the biggest questions in protein science. Multidomain protein folding often requires the assistance of molecular chaperones. Molecular chaperones promote or delay the folding of the client protein, but the detailed mechanisms are still unclear. This review summarizes the findings of biophysical and structural studies on the mechanism of multidomain protein folding mediated by molecular chaperones and explains how molecular chaperones recognize the client proteins and alter their folding properties. Furthermore, we introduce several recent studies that describe the concept of kinetics-activity relationships to explain the mechanism of functional diversity of molecular chaperones.
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17
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Matos AL, Curto P, Simões I. Moonlighting in Rickettsiales: Expanding Virulence Landscape. Trop Med Infect Dis 2022; 7:32. [PMID: 35202227 PMCID: PMC8877226 DOI: 10.3390/tropicalmed7020032] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/05/2022] [Accepted: 02/17/2022] [Indexed: 12/22/2022] Open
Abstract
The order Rickettsiales includes species that cause a range of human diseases such as human granulocytic anaplasmosis (Anaplasma phagocytophilum), human monocytic ehrlichiosis (Ehrlichia chaffeensis), scrub typhus (Orientia tsutsugamushi), epidemic typhus (Rickettsia prowazekii), murine typhus (R. typhi), Mediterranean spotted fever (R. conorii), or Rocky Mountain spotted fever (R. rickettsii). These diseases are gaining a new momentum given their resurgence patterns and geographical expansion due to the overall rise in temperature and other human-induced pressure, thereby remaining a major public health concern. As obligate intracellular bacteria, Rickettsiales are characterized by their small genome sizes due to reductive evolution. Many pathogens employ moonlighting/multitasking proteins as virulence factors to interfere with multiple cellular processes, in different compartments, at different times during infection, augmenting their virulence. The utilization of this multitasking phenomenon by Rickettsiales as a strategy to maximize the use of their reduced protein repertoire is an emerging theme. Here, we provide an overview of the role of various moonlighting proteins in the pathogenicity of these species. Despite the challenges that lie ahead to determine the multiple potential faces of every single protein in Rickettsiales, the available examples anticipate this multifunctionality as an essential and intrinsic feature of these obligates and should be integrated into available moonlighting repositories.
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Affiliation(s)
- Ana Luísa Matos
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (A.L.M.); (P.C.)
| | - Pedro Curto
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (A.L.M.); (P.C.)
| | - Isaura Simões
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (A.L.M.); (P.C.)
- IIIUC—Institute of Interdisciplinary Research, University of Coimbra, 3004-504 Coimbra, Portugal
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18
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Wu ZY, Campeau A, Liu CH, Gonzalez DJ, Yamaguchi M, Kawabata S, Lu CH, Lai CY, Chiu HC, Chang YC. Unique virulence role of post-translocational chaperone PrsA in shaping Streptococcus pyogenes secretome. Virulence 2021; 12:2633-2647. [PMID: 34592883 PMCID: PMC8489961 DOI: 10.1080/21505594.2021.1982501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/17/2021] [Accepted: 09/14/2021] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pyogenes (group A Streptococcus, GAS) is a strict human pathogen causing a broad spectrum of diseases and a variety of autoimmune sequelae. The pathogenesis of GAS infection mostly relies on the production of an extensive network of cell wall-associated and secreted virulence proteins, such as adhesins, toxins, and exoenzymes. PrsA, the only extracellular parvulin-type peptidyl-prolyl isomerase expressed ubiquitously in Gram-positive bacteria, has been suggested to assist the folding and maturation of newly exported proteins to acquire their native conformation and activity. Two PrsA proteins, PrsA1 and PrsA2, have been identified in GAS, but the respective contribution of each PrsA in GAS pathogenesis remains largely unknown. By combining comparative proteomic and phenotypic analysis approaches, we demonstrate that both PrsA isoforms are required to maintain GAS proteome homeostasis and virulence-associated traits in a unique and overlapping manner. The inactivation of both PrsA in GAS caused remarkable impairment in biofilm formation, host adherence, infection-induced cytotoxicity, and in vivo virulence in a murine soft tissue infection model. The concordance of proteomic and phenotypic data clearly features the essential role of PrsA in GAS full virulence.
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Affiliation(s)
- Zhao-Yi Wu
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Anaamika Campeau
- Department of Pharmacology and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Chao-Hsien Liu
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - David J. Gonzalez
- Department of Pharmacology and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Masaya Yamaguchi
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Shigetada Kawabata
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Chieh-Hsien Lu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chian-Yu Lai
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hao-Chieh Chiu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yung-Chi Chang
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
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19
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Zhang K, Tan R, Yao D, Su L, Xia Y, Wu J. Enhanced Production of Soluble Pyrococcus furiosus α-Amylase in Bacillus subtilis through Chaperone Co-Expression, Heat Treatment and Fermentation Optimization. J Microbiol Biotechnol 2021; 31:570-583. [PMID: 33753701 PMCID: PMC9723276 DOI: 10.4014/jmb.2101.01039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/15/2022]
Abstract
Pyrococcus furiosus α-amylase can hydrolyze α-1,4 linkages in starch and related carbohydrates under hyperthermophilic condition (~ 100°C), showing great potential in a wide range of industrial applications, while its relatively low productivity from heterologous hosts has limited the industrial applications. Bacillus subtilis, a gram-positive bacterium, has been widely used in industrial production for its non-pathogenic and powerful secretory characteristics. This study was conducted to increase production of P. furiosus α-amylase in B. subtilis through three strategies. Initial experiments showed that co-expression of P. furiosus molecular chaperone peptidyl-prolyl cis-trans isomerase through genomic integration mode, using a CRISPR/Cas9 system, increased soluble amylase production. Therefore, considering that native P. furiosus α-amylase is produced within a hyperthermophilic environment and is highly thermostable, heat treatment of intact culture at 90°C for 15 min was performed, thereby greatly increasing soluble amylase production. After optimization of the culture conditions (nitrogen source, carbon source, metal ion, temperature and pH), experiments in a 3-L fermenter yielded a soluble activity of 3,806.7 U/ml, which was 3.3- and 28.2-fold those of a control without heat treatment (1,155.1 U/ml) and an empty expression vector control (135.1 U/ml), respectively. This represents the highest P. furiosus α-amylase production reported to date and should promote innovation in the starch liquefaction process and related industrial productions. Meanwhile, heat treatment, which may promote folding of aggregated P. furiosus α-amylase into a soluble, active form through the transfer of kinetic energy, may be of general benefit when producing proteins from thermophilic archaea.
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Affiliation(s)
- Kang Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P.R. China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, P.R. China
| | - Ruiting Tan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P.R. China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, P.R. China
| | - Dongbang Yao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P.R. China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, P.R. China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P.R. China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, P.R. China
| | - Yongmei Xia
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P.R. China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, P.R. China,Corresponding author Phone: 86-510-85327802 Fax: 86-510-85326653 E-mail:
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20
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Butanol Tolerance of Lactiplantibacillus plantarum: A Transcriptome Study. Genes (Basel) 2021; 12:genes12020181. [PMID: 33514005 PMCID: PMC7911632 DOI: 10.3390/genes12020181] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/17/2021] [Accepted: 01/26/2021] [Indexed: 12/26/2022] Open
Abstract
Biobutanol is a promising alternative fuel with impaired microbial production thanks to its toxicity. Lactiplantibacillus plantarum (L. plantarum) is among the few bacterial species that can naturally tolerate 3% (v/v) butanol. This study aims to identify the genetic factors involved in the butanol stress response of L. plantarum by comparing the differential gene expression in two strains with very different butanol tolerance: the highly resistant Ym1, and the relatively sensitive 8-1. During butanol stress, a total of 319 differentially expressed genes (DEGs) were found in Ym1, and 516 in 8-1. Fifty genes were upregulated and 54 were downregulated in both strains, revealing the common species-specific effects of butanol stress: upregulation of multidrug efflux transporters (SMR, MSF), toxin-antitoxin system, transcriptional regulators (TetR/AcrR, Crp/Fnr, and DeoR/GlpR), Hsp20, and genes involved in polysaccharide biosynthesis. Strong inhibition of the pyrimidine biosynthesis occurred in both strains. However, the strains differed greatly in DEGs responsible for the membrane transport, tryptophan synthesis, glycerol metabolism, tRNAs, and some important transcriptional regulators (Spx, LacI). Uniquely upregulated in the butanol-resistant strain Ym1 were the genes encoding GntR, GroEL, GroES, and foldase PrsA. The phosphoenolpyruvate flux and the phosphotransferase system (PTS) also appear to be major factors in butanol tolerance.
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21
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Scardaci R, Varese F, Manfredi M, Marengo E, Mazzoli R, Pessione E. Enterococcus faecium NCIMB10415 responds to norepinephrine by altering protein profiles and phenotypic characters. J Proteomics 2020; 231:104003. [PMID: 33038511 DOI: 10.1016/j.jprot.2020.104003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/29/2020] [Accepted: 10/04/2020] [Indexed: 12/13/2022]
Abstract
The long-term established symbiosis between gut microbiota and humans is based upon a dynamic equilibrium that, if unbalanced, could lead to the development of diseases. Despite the huge amount of data concerning the microbiota-gut-brain-axis, little information is available on what happens at the molecular level in bacteria, when exposed to human signals. In the present study, the physiological effects exerted by norepinephrine (NE), a human hormone present in significant amounts in the host gut, were analyzed using the commensal/probiotic strain Enterococcus faecium NCIMB10415 as a target. The aim was to compare the protein profiles of treated and untreated bacteria and relating these proteome patterns to some phenotypic modifications important for bacteria-host interaction. Actually, to date, only pathogens have been considered. Combining a gel-free/label-free proteomic analysis with the evaluation of bile salts resistance, biofilm formation and autoaggregation ability (as well as with the bacterial growth kinetics), allowed to detect changes induced by NE treatment on all the tested probiotic properties. Furthermore, exposure to the bioactive molecule increased the abundance of proteins related to stress response and to host-microbe interaction, such as moonlight proteins involved in adhesion and immune stimulation. The results of this investigation demonstrated that, not only pathogens, but also commensal gut bacteria are affected by host-derived hormones, underlining the importance of a correct cross-signalling in the maintenance of gut homeostasis. SIGNIFICANCE: The crucial role played by the human gut microbiota in ensuring host homeostasis and health is definitively ascertained as suggested by the holobiome concept. The present research was intended to shed light on the endocrinological perturbations possibly affecting microbiota. The microbial model used in this study belongs to Enterococcus faecium species, whose controversial role as gut commensal and opportunistic pathogen in the gut ecosystem is well recognized. The results obtained in the present investigation clearly demonstrate that E. faecium NCIMB10415 can sense and respond to norepinephrine, a human hormone abundant at the gut level, by changing protein profiles and physiology, inducing changes that could favor survival and colonization of the host tissues. To our knowledge, this is the first proteomic report concerning the impact of a human hormone on a commensal/probiotic bacterium, since previous research has focused on exploring the effects of neuroendocrine molecules on growth and virulence of pathogenic species.
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Affiliation(s)
- R Scardaci
- Structural and Functional Biochemistry, Laboratory of Microbial Biochemistry and Proteomics, Department of Life Sciences and Systems Biology, Università di Torino, Torino, Italy.
| | - F Varese
- Structural and Functional Biochemistry, Laboratory of Microbial Biochemistry and Proteomics, Department of Life Sciences and Systems Biology, Università di Torino, Torino, Italy
| | - M Manfredi
- Center for Translational Research on Autoimmune and Allergic Diseases, Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
| | - E Marengo
- Center for Translational Research on Autoimmune and Allergic Diseases, Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
| | - R Mazzoli
- Structural and Functional Biochemistry, Laboratory of Microbial Biochemistry and Proteomics, Department of Life Sciences and Systems Biology, Università di Torino, Torino, Italy
| | - E Pessione
- Structural and Functional Biochemistry, Laboratory of Microbial Biochemistry and Proteomics, Department of Life Sciences and Systems Biology, Università di Torino, Torino, Italy.
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22
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Deletion of a Peptidylprolyl Isomerase Gene Results in the Inability of Caldicellulosiruptor bescii To Grow on Crystalline Cellulose without Affecting Protein Glycosylation or Growth on Soluble Substrates. Appl Environ Microbiol 2020; 86:AEM.00909-20. [PMID: 32769195 DOI: 10.1128/aem.00909-20] [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: 04/16/2020] [Accepted: 07/30/2020] [Indexed: 11/20/2022] Open
Abstract
Caldicellulosiruptor bescii secretes a large number of complementary multifunctional enzymes with unique activities for biomass deconstruction. The most abundant enzymes in the C. bescii secretome are found in a unique gene cluster containing a glycosyl transferase (GT39) and a putative peptidyl prolyl cis-trans isomerase. Deletion of the glycosyl transferase in this cluster resulted in loss of detectable protein glycosylation in C. bescii, and its activity has been shown to be responsible for the glycosylation of the proline-threonine rich linkers found in many of the multifunctional cellulases. The presence of a putative peptidyl prolyl cis-trans isomerase within this gene cluster suggested that it might also play a role in cellulase modification. Here, we identify this gene as a putative prsA prolyl cis-trans isomerase. Deletion of prsA2 leads to the inability of C. bescii to grow on insoluble substrates such as Avicel, the model cellulose substrate, while exhibiting no differences in phenotype with the wild-type strain on soluble substrates. Finally, we provide evidence that the prsA2 gene is likely needed to increase solubility of multifunctional cellulases and that this unique gene cluster was likely acquired by members of the Caldicellulosiruptor genus with a group of genes to optimize the production and activity of multifunctional cellulases.IMPORTANCE Caldicellulosiruptor has the ability to digest complex plant biomass without pretreatment and have been engineered to convert biomass, a sustainable, carbon neutral substrate, to fuels. Their strategy for deconstructing plant cell walls relies on an interesting class of cellulases consisting of multiple catalytic modules connected by linker regions and carbohydrate binding modules. The best studied of these enzymes, CelA, has a unique deconstruction mechanism. CelA is located in a cluster of genes that likely allows for optimal expression, secretion, and activity. One of the genes in this cluster is a putative isomerase that modifies the CelA protein. In higher eukaryotes, these isomerases are essential for the proper folding of glycoproteins in the endoplasmic reticulum, but little is known about the role of isomerization in cellulase activity. We show that the stability and activity of CelA is dependent on the activity of this isomerase.
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Roch M, Lelong E, Panasenko OO, Sierra R, Renzoni A, Kelley WL. Thermosensitive PBP2a requires extracellular folding factors PrsA and HtrA1 for Staphylococcus aureus MRSA β-lactam resistance. Commun Biol 2019; 2:417. [PMID: 31754647 PMCID: PMC6858329 DOI: 10.1038/s42003-019-0667-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/25/2019] [Indexed: 12/21/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen and represents a clinical challenge because of widespread antibiotic resistance. Methicillin resistant Staphylococcus aureus (MRSA) is particularly problematic and originates by the horizontal acquisition of mecA encoding PBP2a, an extracellular membrane anchored transpeptidase, which confers resistance to β-lactam antibiotics by allosteric gating of its active site channel. Herein, we show that dual disruption of PrsA, a lipoprotein chaperone displaying anti-aggregation activity, together with HtrA1, a membrane anchored chaperone/serine protease, resulted in severe and synergistic attenuation of PBP2a folding that restores sensitivity to β-lactams such as oxacillin. Purified PBP2a has a pronounced unfolding transition initiating at physiological temperatures that leads to irreversible precipitation and complete loss of activity. The concordance of genetic and biochemical data highlights the necessity for extracellular protein folding factors governing MRSA β-lactam resistance. Targeting the PBP2a folding pathway represents a particularly attractive adjuvant strategy to combat antibiotic resistance.
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Affiliation(s)
- Mélanie Roch
- Department of Microbiology and Molecular Medicine, University Hospital and Medical School of Geneva, 1 rue Michel-Servet, Geneva, CH-1211 Switzerland
| | - Emmanuelle Lelong
- Service of Infectious Diseases and Department of Medical Specialties, University Hospital and Medical School of Geneva, 4 rue Gabrielle-Perret-Gentil, Geneva, CH-1206 Switzerland
| | - Olesya O. Panasenko
- Department of Microbiology and Molecular Medicine, University Hospital and Medical School of Geneva, 1 rue Michel-Servet, Geneva, CH-1211 Switzerland
- Service of Infectious Diseases and Department of Medical Specialties, University Hospital and Medical School of Geneva, 4 rue Gabrielle-Perret-Gentil, Geneva, CH-1206 Switzerland
| | - Roberto Sierra
- Department of Microbiology and Molecular Medicine, University Hospital and Medical School of Geneva, 1 rue Michel-Servet, Geneva, CH-1211 Switzerland
| | - Adriana Renzoni
- Service of Infectious Diseases and Department of Medical Specialties, University Hospital and Medical School of Geneva, 4 rue Gabrielle-Perret-Gentil, Geneva, CH-1206 Switzerland
| | - William L. Kelley
- Department of Microbiology and Molecular Medicine, University Hospital and Medical School of Geneva, 1 rue Michel-Servet, Geneva, CH-1211 Switzerland
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24
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Quesada-Ganuza A, Antelo-Varela M, Mouritzen JC, Bartel J, Becher D, Gjermansen M, Hallin PF, Appel KF, Kilstrup M, Rasmussen MD, Nielsen AK. Identification and optimization of PrsA in Bacillus subtilis for improved yield of amylase. Microb Cell Fact 2019; 18:158. [PMID: 31530286 PMCID: PMC6749698 DOI: 10.1186/s12934-019-1203-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/03/2019] [Indexed: 12/19/2022] Open
Abstract
Background PrsA is an extracytoplasmic folding catalyst essential in Bacillus subtilis. Overexpression of the native PrsA from B. subtilis has repeatedly lead to increased amylase yields. Nevertheless, little is known about how the overexpression of heterologous PrsAs can affect amylase secretion. Results In this study, the final yield of five extracellular alpha-amylases was increased by heterologous PrsA co-expression up to 2.5 fold. The effect of the overexpression of heterologous PrsAs on alpha-amylase secretion is specific to the co-expressed alpha-amylase. Co-expression of a heterologous PrsA can significantly reduce the secretion stress response. Engineering of the B. licheniformis PrsA lead to a further increase in amylase secretion and reduced secretion stress. Conclusions In this work we show how heterologous PrsA overexpression can give a better result on heterologous amylase secretion than the native PrsA, and that PrsA homologs show a variety of specificity towards different alpha-amylases. We also demonstrate that on top of increasing amylase yield, a good PrsA–amylase pairing can lower the secretion stress response of B. subtilis. Finally, we present a new recombinant PrsA variant with increased performance in both supporting amylase secretion and lowering secretion stress.
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Affiliation(s)
- Ane Quesada-Ganuza
- Research and Technology, Novozymes A/S, Krogshoejvej 36, 2880, Basgvaerd, Denmark
| | - Minia Antelo-Varela
- Institute for Microbiology, Department of Microbial Proteomics, Ernst-Moritz-Arndt-University Greifswald, F.- Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Jeppe C Mouritzen
- Research and Technology, Novozymes A/S, Krogshoejvej 36, 2880, Basgvaerd, Denmark
| | - Jürgen Bartel
- Institute for Microbiology, Department of Microbial Proteomics, Ernst-Moritz-Arndt-University Greifswald, F.- Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Dörte Becher
- Institute for Microbiology, Department of Microbial Proteomics, Ernst-Moritz-Arndt-University Greifswald, F.- Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Morten Gjermansen
- Research and Technology, Novozymes A/S, Krogshoejvej 36, 2880, Basgvaerd, Denmark
| | - Peter F Hallin
- Research and Technology, Novozymes A/S, Krogshoejvej 36, 2880, Basgvaerd, Denmark
| | - Karen F Appel
- Research and Technology, Novozymes A/S, Krogshoejvej 36, 2880, Basgvaerd, Denmark
| | - Mogens Kilstrup
- Technical University of Denmark, Søltofts Plads, Building 221, Room 204, 2800, Lyngby, Denmark
| | - Michael D Rasmussen
- Research and Technology, Novozymes A/S, Krogshoejvej 36, 2880, Basgvaerd, Denmark
| | - Allan K Nielsen
- Research and Technology, Novozymes A/S, Krogshoejvej 36, 2880, Basgvaerd, Denmark.
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25
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Abstract
We developed a new approach that couples Southwestern blotting and mass spectrometry to discover proteins that bind extracellular DNA (eDNA) in bacterial biofilms. Using Staphylococcus aureus as a model pathogen, we identified proteins with known DNA-binding activity and uncovered a series of lipoproteins with previously unrecognized DNA-binding activity. We demonstrated that expression of these lipoproteins results in an eDNA-dependent biofilm enhancement. Additionally, we found that while deletion of lipoproteins had a minimal impact on biofilm accumulation, these lipoprotein mutations increased biofilm porosity, suggesting that lipoproteins and their associated interactions contribute to biofilm structure. For one of the lipoproteins, SaeP, we showed that the biofilm phenotype requires the lipoprotein to be anchored to the outside of the cellular membrane, and we further showed that increased SaeP expression correlates with more retention of high-molecular-weight DNA on the bacterial cell surface. SaeP is a known auxiliary protein of the SaeRS system, and we also demonstrated that the levels of SaeP correlate with nuclease production, which can further impact biofilm development. It has been reported that S. aureus biofilms are stabilized by positively charged cytoplasmic proteins that are released into the extracellular environment, where they make favorable electrostatic interactions with the negatively charged cell surface and eDNA. In this work we extend this electrostatic net model to include secreted eDNA-binding proteins and membrane-attached lipoproteins that can function as anchor points between eDNA in the biofilm matrix and the bacterial cell surface.IMPORTANCE Many bacteria are capable of forming biofilms encased in a matrix of self-produced extracellular polymeric substances (EPS) that protects them from chemotherapies and the host defenses. As a result of these inherent resistance mechanisms, bacterial biofilms are extremely difficult to eradicate and are associated with chronic wounds, orthopedic and surgical wound infections, and invasive infections, such as infective endocarditis and osteomyelitis. It is therefore important to understand the nature of the interactions between the bacterial cell surface and EPS that stabilize biofilms. Extracellular DNA (eDNA) has been recognized as an EPS constituent for many bacterial species and has been shown to be important in promoting biofilm formation. Using Staphylococcus aureus biofilms, we show that membrane-attached lipoproteins can interact with the eDNA in the biofilm matrix and promote biofilm formation, which suggests that lipoproteins are potential targets for novel therapies aimed at disrupting bacterial biofilms.
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26
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Savijoki K, Nyman TA, Kainulainen V, Miettinen I, Siljamäki P, Fallarero A, Sandholm J, Satokari R, Varmanen P. Growth Mode and Carbon Source Impact the Surfaceome Dynamics of Lactobacillus rhamnosus GG. Front Microbiol 2019; 10:1272. [PMID: 31231350 PMCID: PMC6560171 DOI: 10.3389/fmicb.2019.01272] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/22/2019] [Indexed: 12/17/2022] Open
Abstract
Bacterial biofilms have clear implications in disease and in food applications involving probiotics. Here, we show that switching the carbohydrate source from glucose to fructose increased the biofilm formation and the total surface-antigenicity of a well-known probiotic, Lactobacillus rhamnosus GG. Surfaceomes (all cell surface-associated proteins) of GG cells grown with glucose and fructose in planktonic and biofilm cultures were identified and compared, which indicated carbohydrate source-dependent variations, especially during biofilm growth. The most distinctive differences under these conditions were detected with several surface adhesins (e.g., MBF, SpaC pilus protein and penicillin-binding proteins), enzymes (glycoside hydrolases, PrsA, PrtP, PrtR, and HtrA) and moonlighting proteins (glycolytic, transcription/translation and stress-associated proteins, r-proteins, tRNA synthetases, Clp family proteins, PepC, PepN, and PepA). The abundance of several known adhesins and candidate moonlighters, including enzymes acting on casein-derived peptides (ClpP, PepC, and PepN), increased in the biofilm cells grown on fructose, from which the surface-associated aminopeptidase activity mediated by PepC and PepN was further confirmed by an enzymatic assay. The mucus binding factor (MBF) was found most abundant in fructose grown biofilm cells whereas SpaC adhesin was identified specifically from planktonic cells growing on fructose. An additional indirect ELISA indicated both growth mode- and carbohydrate-dependent differences in abundance of SpaC, whereas the overall adherence of GG assessed with porcine mucus indicated that the carbon source and the growth mode affected mucus adhesion. The adherence of GG cells to mucus was almost completely inhibited by anti-SpaC antibodies regardless of growth mode and/or carbohydrate source, indicating the key role of the SpaCBA pilus in adherence under the tested conditions. Altogether, our results suggest that carbon source and growth mode coordinate mechanisms shaping the proteinaceous composition of GG cell surface, which potentially contributes to resistance, nutrient acquisition and cell-cell interactions under different conditions. In conclusion, the present study shows that different growth regimes and conditions can have a profound impact on the adherent and antigenic features of GG, thereby providing new information on how to gain additional benefits from this probiotic.
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Affiliation(s)
- Kirsi Savijoki
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
- Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Tuula A. Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Veera Kainulainen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ilkka Miettinen
- Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Pia Siljamäki
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Adyary Fallarero
- Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Jouko Sandholm
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
| | - Reetta Satokari
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Pekka Varmanen
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
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27
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Jiang X, Yang Y, Zhou J, Liu H, Liao X, Luo J, Li X, Fang W. Peptidyl isomerase PrsA is surface-associated onStreptococcus suisand offers cross-protection against serotype 9 strain. FEMS Microbiol Lett 2019; 366:5281431. [DOI: 10.1093/femsle/fnz002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/06/2019] [Indexed: 12/27/2022] Open
Affiliation(s)
- Xiaowu Jiang
- College of Animal Sciences of Zhejiang Unversity and Key Laboratory of Preventive Veterinary Medicine of Zhejiang Province, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, China
- Ningbo International Travel Healthcare Center, 336 Liuting Road, Ningbo 315012, Zhejiang, China
| | - Yunkai Yang
- College of Animal Sciences of Zhejiang Unversity and Key Laboratory of Preventive Veterinary Medicine of Zhejiang Province, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, China
| | - Jingjing Zhou
- College of Animal Sciences of Zhejiang Unversity and Key Laboratory of Preventive Veterinary Medicine of Zhejiang Province, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, China
| | - Hanze Liu
- College of Animal Sciences of Zhejiang Unversity and Key Laboratory of Preventive Veterinary Medicine of Zhejiang Province, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, China
| | - Xiayi Liao
- College of Animal Sciences of Zhejiang Unversity and Key Laboratory of Preventive Veterinary Medicine of Zhejiang Province, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, China
| | - Jie Luo
- Ningbo International Travel Healthcare Center, 336 Liuting Road, Ningbo 315012, Zhejiang, China
| | - Xiaoliang Li
- College of Animal Sciences of Zhejiang Unversity and Key Laboratory of Preventive Veterinary Medicine of Zhejiang Province, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, China
| | - Weihuan Fang
- College of Animal Sciences of Zhejiang Unversity and Key Laboratory of Preventive Veterinary Medicine of Zhejiang Province, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, China
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28
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The conserved mosaic prophage protein paratox inhibits the natural competence regulator ComR in Streptococcus. Sci Rep 2018; 8:16535. [PMID: 30409983 PMCID: PMC6224593 DOI: 10.1038/s41598-018-34816-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 10/25/2018] [Indexed: 01/05/2023] Open
Abstract
Horizontal gene transfer is an important means of bacterial evolution. This includes natural genetic transformation, where bacterial cells become “competent” and DNA is acquired from the extracellular environment. Natural competence in many species of Streptococcus, is regulated by quorum sensing via the ComRS receptor-signal pair. The ComR-XIP (mature ComS peptide) complex induces expression of the alternative sigma factor SigX, which targets RNA polymerase to CIN-box promoters to activate genes involved in DNA uptake and recombination. In addition, the widely distributed Streptococcus prophage gene paratox (prx) also contains a CIN-box, and here we demonstrate it to be transcriptionally activated by XIP. In vitro experiments demonstrate that Prx binds ComR directly and prevents the ComR-XIP complex from interacting with DNA. Mutations of prx in vivo caused increased expression of the late competence gene ssb when induced with XIP as compared to wild-type, and Prx orthologues are able to inhibit ComR activation by XIP in a reporter strain which lacks an endogenous prx. Additionally, an X-ray crystal structure of Prx reveals a unique fold that implies a novel molecular mechanism to inhibit ComR. Overall, our results suggest Prx functions to inhibit the acquisition of new DNA by Streptococcus.
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29
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Yaseen A, Audette GF. Structural flexibility in the Helicobacter pylori peptidyl-prolyl cis,trans-isomerase HP0175 is achieved through an extension of the chaperone helices. J Struct Biol 2018; 204:261-269. [PMID: 30179659 DOI: 10.1016/j.jsb.2018.08.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 08/08/2018] [Accepted: 08/31/2018] [Indexed: 01/19/2023]
Abstract
Helicobacter pylori infects the gastric epithelium of half the global population, where infections can persist into adenocarcinomas and peptic ulcers. H. pylori secretes several proteins that lend to its pathogenesis and survival including VacA, CagA, γ-glutamyltransferase and HP0175. HP0175, also known as HpCBF2, classified as a peptidyl-prolyl cis,trans-isomerase, has been shown to induce apoptosis through a cascade of mechanisms initiated though its interaction with toll like receptor 4 (TLR4). Here, we report the structure of apo-HP0175 at 2.09 Å with a single monomer in the asymmetric unit. Chromatographic, light scattering and mass spectrometric analysis of HP0175 in solution indicate that the protein is mainly monomeric under low salt conditions, while increasing ionic interactions facilitates protein dimerization. A comparison of the apo-HP0175 structure to that of the indole-2-carboxylic acid-bound form shows movement of the N- and C-terminal helices upon interaction of the catalytic residues in the binding pocket. Helix extension of the N/C chaperone domains between apo and I2CA-bound HP0175 supports previous findings in parvulin PPIases for their role in protein stabilization (and accommodation of variable protein lengths) of those undergoing catalysis.
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Affiliation(s)
- Ayat Yaseen
- Department of Chemistry, York University, Toronto M3J 1P3, Canada
| | - Gerald F Audette
- Department of Chemistry, York University, Toronto M3J 1P3, Canada; Centre for Research of Biomolecular Interactions, York University, Toronto M3J 1P3, Canada.
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30
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Hiller S, Burmann BM. Chaperone-client complexes: A dynamic liaison. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 289:142-155. [PMID: 29544626 DOI: 10.1016/j.jmr.2017.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/08/2017] [Accepted: 12/10/2017] [Indexed: 06/08/2023]
Abstract
Living cells contain molecular chaperones that are organized in intricate networks to surveil protein homeostasis by avoiding polypeptide misfolding, aggregation, and the generation of toxic species. In addition, cellular chaperones also fulfill a multitude of alternative functionalities: transport of clients towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver clients towards proteolysis machineries. Until recently, the only available source of atomic resolution information for virtually all chaperones were crystal structures of their client-free, apo-forms. These structures were unable to explain details of the functional mechanisms underlying chaperone-client interactions. The difficulties to crystallize chaperones in complexes with clients arise from their highly dynamic nature, making solution NMR spectroscopy the method of choice for their study. With the advent of advanced solution NMR techniques, in the past few years a substantial number of structural and functional studies on chaperone-client complexes have been resolved, allowing unique insight into the chaperone-client interaction. This review summarizes the recent insights provided by advanced high-resolution NMR-spectroscopy to understand chaperone-client interaction mechanisms at the atomic scale.
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Affiliation(s)
- Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Björn M Burmann
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University for Gothenburg, 405 30 Göteborg, Sweden.
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31
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Arnold JW, Simpson JB, Roach J, Kwintkiewicz J, Azcarate-Peril MA. Intra-species Genomic and Physiological Variability Impact Stress Resistance in Strains of Probiotic Potential. Front Microbiol 2018; 9:242. [PMID: 29515537 PMCID: PMC5826259 DOI: 10.3389/fmicb.2018.00242] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/31/2018] [Indexed: 12/28/2022] Open
Abstract
Large-scale microbiome studies have established that most of the diversity contained in the gastrointestinal tract is represented at the strain level; however, exhaustive genomic and physiological characterization of human isolates is still lacking. With increased use of probiotics as interventions for gastrointestinal disorders, genomic and functional characterization of novel microorganisms becomes essential. In this study, we explored the impact of strain-level genomic variability on bacterial physiology of two novel human Lactobacillus rhamnosus strains (AMC143 and AMC010) of probiotic potential in relation to stress resistance. The strains showed differences with known probiotic strains (L. rhamnosus GG, Lc705, and HN001) at the genomic level, including nucleotide polymorphisms, mutations in non-coding regulatory regions, and rearrangements of genomic architecture. Transcriptomics analysis revealed that gene expression profiles differed between strains when exposed to simulated gastrointestinal stresses, suggesting the presence of unique regulatory systems in each strain. In vitro physiological assays to test resistance to conditions mimicking the gut environment (acid, alkali, and bile stress) showed that growth of L. rhamnosus AMC143 was inhibited upon exposure to alkaline pH, while AMC010 and control strain LGG were unaffected. AMC143 also showed a significant survival advantage compared to the other strains upon bile exposure. Reverse transcription qPCR targeting the bile salt hydrolase gene (bsh) revealed that AMC143 expressed bsh poorly (a consequence of a deletion in the bsh promoter and truncation of bsh gene in AMC143), while AMC010 had significantly higher expression levels than AMC143 or LGG. Insertional inactivation of the bsh gene in AMC010 suggested that bsh could be detrimental to bacterial survival during bile stress. Together, these findings show that coupling of classical microbiology with functional genomics methods for the characterization of bacterial strains is critical for the development of novel probiotics, as variability between strains can dramatically alter bacterial physiology and functionality.
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Affiliation(s)
- Jason W. Arnold
- Division of Gastroenterology and Hepatology, Department of Medicine, Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Joshua B. Simpson
- Department of Chemistry, College of Arts and Sciences, University of North Carolina, Chapel Hill, NC, United States
| | - Jeffrey Roach
- Research Computing, University of North Carolina, Chapel Hill, NC, United States
| | - Jakub Kwintkiewicz
- Division of Gastroenterology and Hepatology, Department of Medicine, Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - M. Andrea Azcarate-Peril
- Division of Gastroenterology and Hepatology, Department of Medicine, Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
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32
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Yan S, Wu G. Bottleneck in secretion of α-amylase in Bacillus subtilis. Microb Cell Fact 2017; 16:124. [PMID: 28724440 PMCID: PMC5518135 DOI: 10.1186/s12934-017-0738-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/10/2017] [Indexed: 11/10/2022] Open
Abstract
Amylase plays an important role in biotechnology industries, and Gram-positive bacterium Bacillus subtilis is a major host to produce heterogeneous α-amylases. However, the secretion stress limits the high yield of α-amylase in B. subtilis although huge efforts have been made to address this secretion bottleneck. In this question-oriented review, every effort is made to answer the following questions, which look simple but are long-standing, through reviewing of literature: (1) Does α-amylase need a specific and dedicated chaperone? (2) What signal sequence does CsaA recognize? (3) Does CsaA require ATP for its operation? (4) Does an unfolded α-amylase is less soluble than a folded one? (5) Does α-amylase aggregate before transporting through Sec secretion system? (6) Is α-amylase sufficient stable to prevent itself from misfolding? (7) Does α-amylase need more disulfide bonds to be stabilized? (8) Which secretion system does PrsA pass through? (9) Is PrsA ATP-dependent? (10) Is PrsA reused after folding of α-amylase? (11) What is the fate of PrsA? (12) Is trigger factor (TF) ATP-dependent? The literature review suggests that not only the most of those questions are still open to answers but also it is necessary to calculate ATP budget in order to better understand how B. subtilis uses its energy for production and secretion.
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Affiliation(s)
- Shaomin Yan
- National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China
| | - Guang Wu
- National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China.
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33
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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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Cahoon LA, Freitag NE, Prehna G. A structural comparison of Listeria monocytogenes protein chaperones PrsA1 and PrsA2 reveals molecular features required for virulence. Mol Microbiol 2016; 101:42-61. [PMID: 27007641 PMCID: PMC4925323 DOI: 10.1111/mmi.13367] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/29/2016] [Indexed: 12/26/2022]
Abstract
Listeria monocytogenes is a Gram-positive environmental bacterium that lives within soil but transitions into a pathogen upon contact with a mammalian host. The transition of L. monocytogenes from soil dweller to cytosolic pathogen is dependent upon secreted virulence factors that mediate cell invasion and intracellular growth. PrsA1 and PrsA2 are secreted bacterial lipoprotein chaperones that contribute to the folding of proteins translocated across the bacterial membrane; PrsA2 is required for L. monocytogenes virulence, whereas the function of PrsA1 remains to be determined. We have solved an X-ray crystal structure of PrsA1 and have used this model to guide comparison structure-based mutagenesis studies with PrsA2. Targeted mutagenesis of PrsA2 demonstrates that oligomerization of PrsA2 as well as molecular features of the foldase domain are required for protein secretion and virulence, whereas a functional role was uncovered for PrsA1 in bacterial resistance to alcohol. Interestingly, PrsA2 membrane localization is not required for all PrsA2-dependent activities, suggesting that the lipoprotein retains function when released from the bacterial cell. PrsA chaperones are thus multifaceted proteins with distinct domains adapted to accommodate the functional needs of a diverse array of secreted substrates.
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Affiliation(s)
- Laty A. Cahoon
- Department of Microbiology and Immunology, University of Illinois at Chicago
| | - Nancy E. Freitag
- Department of Microbiology and Immunology, University of Illinois at Chicago
| | - Gerd Prehna
- Department of Microbiology and Immunology, University of Illinois at Chicago
- Center for Structural Biology Research Resources Center, University of Illinois at Chicago
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Structural and Functional Characterization of a Novel Family of Cyclophilins, the AquaCyps. PLoS One 2016; 11:e0157070. [PMID: 27276069 PMCID: PMC4898713 DOI: 10.1371/journal.pone.0157070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/24/2016] [Indexed: 01/19/2023] Open
Abstract
Cyclophilins are ubiquitous cis-trans-prolyl isomerases (PPIases) found in all kingdoms of life. Here, we identify a novel family of cyclophilins, termed AquaCyps, which specifically occurs in marine Alphaproteobacteria, but not in related terrestric species. In addition to a canonical PPIase domain, AquaCyps contain large extensions and insertions. The crystal structures of two representatives from Hirschia baltica, AquaCyp293 and AquaCyp300, reveal the formation of a compact domain, the NIC domain, by the N- and C-terminal extensions together with a central insertion. The NIC domain adopts a novel mixed alpha-helical, beta-sheet fold that is linked to the cyclophilin domain via a conserved disulfide bond. In its overall fold, AquaCyp293 resembles AquaCyp300, but the two proteins utilize distinct sets of active site residues, consistent with differences in their PPIase catalytic properties. While AquaCyp293 is a highly active general PPIase, AquaCyp300 is specific for hydrophobic substrate peptides and exhibits lower overall activity.
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Naveen V, Chu CH, Chen BW, Tsai YC, Hsiao CD, Sun YJ. Helicobacter pylori cell binding factor 2: Insights into domain motion. J Struct Biol 2016; 194:90-101. [PMID: 26850168 DOI: 10.1016/j.jsb.2016.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 12/22/2015] [Accepted: 02/02/2016] [Indexed: 12/18/2022]
Abstract
Helicobacter pylori cell binding factor 2 (HpCBF2) is an antigenic virulence factor belonging to the SurA-like peptidyl-prolyl cis-trans isomerase family with implications for pathogenicity in the human gastrointestinal tract. HpCBF2 possesses PPIase activity and could act as a periplasmic chaperone to regulate outer membrane protein assembly. Here, we measured the isomerization and chaperone activity of HpCBF2, and determined the crystal structure of HpCBF2 in complex with an inhibitor, indole-2-carboxylic acid (I2CA), at 2.4Å resolution. HpCBF2-I2CA forms a homodimer encasing a large central hydrophobic cavity with a basket-like structure, and each monomer contains a PPIase and a chaperone domain. In the HpCBF2-I2CA dimer, the two PPIase domains separate by a distance of 22.8Å, while the two chaperone domains arrange in a domain-swap manner. The PPIase domains bound with I2CA ligand face towards the chaperone domains and are shielded by surrounding hydrophobic residues. With the aid of SAXS experiments, we also revealed domain motion between the apo- and I2CA-bound states of HpCBF2. The domain motion in HpCBF2 might be necessary for the isomerization activity of PPIase and the accommodation of the unfolded and partially folded peptides to refold by chaperone domain.
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Affiliation(s)
- Vankadari Naveen
- Molecular Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei 115, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Chen-Hsi Chu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Bo-Wei Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Yen-Chun Tsai
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Chwan-Deng Hsiao
- Molecular Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei 115, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan.
| | - Yuh-Ju Sun
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan.
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Burmann BM, Hiller S. Chaperones and chaperone-substrate complexes: Dynamic playgrounds for NMR spectroscopists. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 86-87:41-64. [PMID: 25919198 DOI: 10.1016/j.pnmrs.2015.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/19/2015] [Accepted: 02/19/2015] [Indexed: 05/20/2023]
Abstract
The majority of proteins depend on a well-defined three-dimensional structure to obtain their functionality. In the cellular environment, the process of protein folding is guided by molecular chaperones to avoid misfolding, aggregation, and the generation of toxic species. To this end, living cells contain complex networks of molecular chaperones, which interact with substrate polypeptides by a multitude of different functionalities: transport them towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver them towards a proteolysis machinery. Despite the availability of high-resolution crystal structures of many important chaperones in their substrate-free apo forms, structural information about how substrates are bound by chaperones and how they are protected from misfolding and aggregation is very sparse. This lack of information arises from the highly dynamic nature of chaperone-substrate complexes, which so far has largely hindered their crystallization. This highly dynamic nature makes chaperone-substrate complexes good targets for NMR spectroscopy. Here, we review the results achieved by NMR spectroscopy to understand chaperone function in general and details of chaperone-substrate interactions in particular. We assess the information content and applicability of different NMR techniques for the characterization of chaperones and chaperone-substrate complexes. Finally, we highlight three recent studies, which have provided structural descriptions of chaperone-substrate complexes at atomic resolution.
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Affiliation(s)
- Björn M Burmann
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland.
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Schmidpeter PAM, Schmid FX. Prolyl isomerization and its catalysis in protein folding and protein function. J Mol Biol 2015; 427:1609-31. [PMID: 25676311 DOI: 10.1016/j.jmb.2015.01.023] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/30/2015] [Indexed: 12/20/2022]
Abstract
Prolyl isomerizations are intrinsically slow processes. They determine the rates of many protein folding reactions and control regulatory events in folded proteins. Prolyl isomerases are able to catalyze these isomerizations, and thus, they have the potential to assist protein folding and to modulate protein function. Here, we provide examples for how prolyl isomerizations limit protein folding and are accelerated by prolyl isomerases and how native-state prolyl isomerizations regulate protein functions. The roles of prolines in protein folding and protein function are closely interrelated because both of them depend on the coupling between cis/trans isomerization and conformational changes that can involve extended regions of a protein.
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Affiliation(s)
- Philipp A M Schmidpeter
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Franz X Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biologie, Universität Bayreuth, 95440 Bayreuth, Germany.
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