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Hu Y, Wang Y, Hu X, Chao H, Li S, Ni Q, Zhu Y, Hu Y, Zhao Z, Chen M. T4SEpp: A pipeline integrating protein language models to predict bacterial type IV secreted effectors. Comput Struct Biotechnol J 2024; 23:801-812. [PMID: 38328004 PMCID: PMC10847861 DOI: 10.1016/j.csbj.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/20/2024] [Accepted: 01/20/2024] [Indexed: 02/09/2024] Open
Abstract
Many pathogenic bacteria use type IV secretion systems (T4SSs) to deliver effectors (T4SEs) into the cytoplasm of eukaryotic cells, causing diseases. The identification of effectors is a crucial step in understanding the mechanisms of bacterial pathogenicity, but this remains a major challenge. In this study, we used the full-length embedding features generated by six pre-trained protein language models to train classifiers predicting T4SEs and compared their performance. We integrated three modules into a model called T4SEpp. The first module searched for full-length homologs of known T4SEs, signal sequences, and effector domains; the second module fine-tuned a machine learning model using data for a signal sequence feature; and the third module used the three best-performing pre-trained protein language models. T4SEpp outperformed other state-of-the-art (SOTA) software tools, achieving ∼0.98 accuracy at a high specificity of ∼0.99, based on the assessment of an independent validation dataset. T4SEpp predicted 13 T4SEs from Helicobacter pylori, including the well-known CagA and 12 other potential ones, among which eleven could potentially interact with human proteins. This suggests that these potential T4SEs may be associated with the pathogenicity of H. pylori. Overall, T4SEpp provides a better solution to assist in the identification of bacterial T4SEs and facilitates studies of bacterial pathogenicity. T4SEpp is freely accessible at https://bis.zju.edu.cn/T4SEpp.
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Affiliation(s)
- Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yejun Wang
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen, China
- Department of Cell Biology and Genetics, College of Basic Medicine, Shenzhen University Medical School, Shenzhen, China
| | - Xiaotian Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Sida Li
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qinyang Ni
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yanyan Zhu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yixue Hu
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen, China
| | - Ziyi Zhao
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou 310058, China
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Abdelhamed H, Mannan SB, Riman MM, Tekedar HC, Lawrence ML. Comparative analysis of three plasmids from Plesiomonas shigelloides strain MS-17-188 and their role in antimicrobial resistance. JAC Antimicrob Resist 2024; 6:dlae109. [PMID: 39035015 PMCID: PMC11258559 DOI: 10.1093/jacamr/dlae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024] Open
Abstract
Background Plesiomonas shigelloides strain MS-17-188 was isolated from a deceased catfish from East Mississippi and showed resistance to florfenicol, tetracyclines and a sulphonamide. WGS of strain MS-17-188 revealed three plasmids (pPSMS-171881, pPSMS-171882 and pPSMS-171883). Objectives To accurately determine the impact of three plasmids found in P. shigelloides strain MS-17-188 on the dissemination of antibiotic resistance genes and to provide insights into the molecular structure of these plasmids. Methods The genetic features of these plasmids in terms of genes associated with antimicrobial resistance (AMR), virulence, transfer, maintenance and replication were identified using bioinformatic tools. Additionally, we investigated the in vitro mobilization and stability of plasmid-mediated resistance. The Comprehensive Antibiotic Resistance Database and Virulence Factors Database were used to detect the AMR genes and virulence genes of P. shigelloides plasmids. Moreover, plasmid mobility was evaluated by a filter-mating assay using strain MS-17-188 as a donor and azide-resistant Escherichia coli J53 as a recipient strain. A stability experiment was conducted to explore the persistence of plasmid-mediated antibiotic resistance in strain MS-17-188 in the absence and presence of selection. Results pPSMS-171881 harboured multidrug efflux complex (adeF) and two genes responsible for arsenic resistance (arsB and arsC). pPSMS-171882 had a region of 7085 bp encoding type IV secretion system proteins. pPSMS-171883 carried the tetracycline resistance genes tet(A) and tet(R), and a phenicol resistance gene (floR), which were flanked by two transposable elements and mobilization proteins, suggesting that there is a conjugative mechanism by which this plasmid can be mobilized. Results from the stability experiment indicated that pPSMS-171883 is lost over time in the absence of selective pressure. Moreover, pPSMS-171883 is more stable in P. shigelloides at growth temperatures of 30°C and 37°C compared with 40°C and 43°C. After intraperitoneal injection in catfish, P. shigelloides strain MS-17-188 resulted in no mortalities. Conclusions This is the first study to report plasmid-mediated AMR in Plesiomonas isolated from cultured fish, which needs continued monitoring. This study will provide an understanding of the genetic mechanisms of AMR and virulence of P. shigelloides.
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Affiliation(s)
- Hossam Abdelhamed
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Shahnewaj Bin Mannan
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Munshi Mustafiz Riman
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Hasan C Tekedar
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Mark L Lawrence
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
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Cobe BL, Dey S, Minasov G, Inniss N, Satchell KJF, Cianciotto NP. Bactericidal effectors of the Stenotrophomonas maltophilia type IV secretion system: functional definition of the nuclease TfdA and structural determination of TfcB. mBio 2024; 15:e0119824. [PMID: 38832773 PMCID: PMC11253643 DOI: 10.1128/mbio.01198-24] [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: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 06/05/2024] Open
Abstract
Stenotrophomonas maltophilia expresses a type IV protein secretion system (T4SS) that promotes contact-dependent killing of other bacteria and does so partly by secreting the effector TfcB. Here, we report the structure of TfcB, comprising an N-terminal domain similar to the catalytic domain of glycosyl hydrolase (GH-19) chitinases and a C-terminal domain for recognition and translocation by the T4SS. Utilizing a two-hybrid assay to measure effector interactions with the T4SS coupling protein VirD4, we documented the existence of five more T4SS substrates. One of these was protein 20845, an annotated nuclease. A S. maltophilia mutant lacking the gene for 20845 was impaired for killing Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Moreover, the cloned 20845 gene conferred robust toxicity, with the recombinant E. coli being rescued when 20845 was co-expressed with its cognate immunity protein. The 20845 effector was an 899 amino-acid protein, comprised of a GHH-nuclease domain in its N-terminus, a large central region of indeterminant function, and a C-terminus for secretion. Engineered variants of the 20845 gene that had mutations in the predicted catalytic site did not impede E. coli, indicating that the antibacterial effect of 20845 involves its nuclease activity. Using flow cytometry with DNA staining, we determined that 20845, but not its mutant variants, confers a loss in DNA content of target bacteria. Database searches revealed that uncharacterized homologs of 20845 occur within a range of bacteria. These data indicate that the S. maltophilia T4SS promotes interbacterial competition through the action of multiple toxic effectors, including a potent, novel DNase.IMPORTANCEStenotrophomonas maltophilia is a multi-drug-resistant, Gram-negative bacterium that is an emerging pathogen of humans. Patients with cystic fibrosis are particularly susceptible to S. maltophilia infection. In hospital water systems and various types of infections, S. maltophilia co-exists with other bacteria, including other pathogens such as Pseudomonas aeruginosa. We previously demonstrated that S. maltophilia has a functional VirB/D4 type VI protein secretion system (T4SS) that promotes contact-dependent killing of other bacteria. Since most work on antibacterial systems involves the type VI secretion system, this observation remains noteworthy. Moreover, S. maltophilia currently stands alone as a model for a human pathogen expressing an antibacterial T4SS. Using biochemical, genetic, and cell biological approaches, we now report both the discovery of a novel antibacterial nuclease (TfdA) and the first structural determination of a bactericidal T4SS effector (TfcB).
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Affiliation(s)
- Brandi L. Cobe
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Supratim Dey
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - George Minasov
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Nicole Inniss
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Karla J. F. Satchell
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Nicholas P. Cianciotto
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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Cianciotto NP. The type II secretion system as an underappreciated and understudied mediator of interbacterial antagonism. Infect Immun 2024:e0020724. [PMID: 38980047 DOI: 10.1128/iai.00207-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024] Open
Abstract
Interbacterial antagonism involves all major phyla, occurs across the full range of ecological niches, and has great significance for the environment, clinical arena, and agricultural and industrial sectors. Though the earliest insight into interbacterial antagonism traces back to the discovery of antibiotics, a paradigm shift happened when it was learned that protein secretion systems (e.g., types VI and IV secretion systems) deliver toxic "effectors" against competitors. However, a link between interbacterial antagonism and the Gram-negative type II secretion system (T2SS), which exists in many pathogens and environmental species, is not evident in prior reviews on bacterial competition or T2SS function. A current examination of the literature revealed four examples of a T2SS or one of its known substrates having a bactericidal activity against a Gram-positive target or another Gram-negative. When further studied, the T2SS effectors proved to be peptidases that target the peptidoglycan of the competitor. There are also reports of various bacteriolytic enzymes occurring in the culture supernatants of some other Gram-negative species, and a link between these bactericidal activities and T2SS is suggested. Thus, a T2SS can be a mediator of interbacterial antagonism, and it is possible that many T2SSs have antibacterial outputs. Yet, at present, the T2SS remains relatively understudied for its role in interbacterial competition. Arguably, there is a need to analyze the T2SSs of a broader range of species for their role in interbacterial antagonism. Such investigation offers, among other things, a possible pathway toward developing new antimicrobials for treating disease.
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Affiliation(s)
- Nicholas P Cianciotto
- Department of Microbiology-Immunology, Northwestern University School of Medicine, Chicago, Illinois, USA
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5
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Lee YT, Senturk M, Guan Y, Wang MC. Bacteria-organelle communication in physiology and disease. J Cell Biol 2024; 223:e202310134. [PMID: 38748249 PMCID: PMC11096858 DOI: 10.1083/jcb.202310134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/03/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
Bacteria, omnipresent in our environment and coexisting within our body, exert dual beneficial and pathogenic influences. These microorganisms engage in intricate interactions with the human body, impacting both human health and disease. Simultaneously, certain organelles within our cells share an evolutionary relationship with bacteria, particularly mitochondria, best known for their energy production role and their dynamic interaction with each other and other organelles. In recent years, communication between bacteria and mitochondria has emerged as a new mechanism for regulating the host's physiology and pathology. In this review, we delve into the dynamic communications between bacteria and host mitochondria, shedding light on their collaborative regulation of host immune response, metabolism, aging, and longevity. Additionally, we discuss bacterial interactions with other organelles, including chloroplasts, lysosomes, and the endoplasmic reticulum (ER).
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Affiliation(s)
- Yi-Tang Lee
- Waisman Center, University of Wisconsin, Madison, WI, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Integrative Program of Molecular and Biochemical Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Mumine Senturk
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, USA
| | - Youchen Guan
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Meng C. Wang
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
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Al Mamun AAM, Kissoon K, Li YG, Hancock E, Christie PJ. The F plasmid conjutome: the repertoire of E. coli proteins translocated through an F-encoded type IV secretion system. mSphere 2024:e0035424. [PMID: 38940509 DOI: 10.1128/msphere.00354-24] [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: 04/25/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024] Open
Abstract
Bacterial conjugation systems pose a major threat to human health through their widespread dissemination of mobile genetic elements (MGEs) carrying cargoes of antibiotic resistance genes. Using the Cre Recombinase Assay for Translocation (CRAfT), we recently reported that the IncFV pED208 conjugation system also translocates at least 16 plasmid-encoded proteins to recipient bacteria. Here, we deployed a high-throughput CRAfT screen to identify the repertoire of chromosomally encoded protein substrates of the pED208 system. We identified 32 substrates encoded by the Escherichia coli W3110 genome with functions associated with (i) DNA/nucleotide metabolism, (ii) stress tolerance/physiology, (iii) transcriptional regulation, or (iv) toxin inhibition. The respective gene deletions did not impact pED208 transfer proficiencies, nor did Group 1 (DNA/nucleotide metabolism) mutations detectably alter the SOS response elicited in new transconjugants upon acquisition of pED208. However, MC4100(pED208) donor cells intrinsically exhibit significantly higher SOS activation than plasmid-free MC4100 cells, and this plasmid carriage-induced stress response is further elevated in donor cells deleted of several Group 1 genes. Among 10 characterized substrates, we gained evidence of C-terminal or internal translocation signals that could function independently or synergistically for optimal protein transfer. Remarkably, nearly all tested proteins were also translocated through the IncN pKM101 and IncP RP4 conjugation systems. This repertoire of E. coli protein substrates, here termed the F plasmid "conjutome," is thus characterized by functions of potential benefit to new transconjugants, diverse TSs, and the capacity for promiscuous transfer through heterologous conjugation systems. IMPORTANCE Conjugation systems comprise a major subfamily of the type IV secretion systems (T4SSs) and are the progenitors of a second large T4SS subfamily dedicated to translocation of protein effectors. This study examined the capacity of conjugation machines to function as protein translocators. Using a high-throughput reporter screen, we determined that 32 chromosomally encoded proteins are delivered through an F plasmid conjugation system. The translocated proteins potentially enhance the establishment of the co-transferred F plasmid or mitigate mating-induced stresses. Translocation signals located C-terminally or internally conferred substrate recognition by the F system and, remarkably, many substrates also were translocated through heterologous conjugation systems. Our findings highlight the plasticity of conjugation systems in their capacities to co-translocate DNA and many protein substrates.
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Affiliation(s)
- Abu Amar M Al Mamun
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Kimberley Kissoon
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Yang Grace Li
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Erin Hancock
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, USA
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Roberts JR, Tran SC, Frick-Cheng AE, Bryant KN, Okoye CD, McDonald WH, Cover TL, Ohi MD. Subdomains of the Helicobacter pylori Cag T4SS outer membrane core complex exhibit structural independence. Life Sci Alliance 2024; 7:e202302560. [PMID: 38631913 PMCID: PMC11024343 DOI: 10.26508/lsa.202302560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024] Open
Abstract
The Helicobacter pylori Cag type IV secretion system (Cag T4SS) has an important role in the pathogenesis of gastric cancer. The Cag T4SS outer membrane core complex (OMCC) is organized into three regions: a 14-fold symmetric outer membrane cap (OMC) composed of CagY, CagX, CagT, CagM, and Cag3; a 17-fold symmetric periplasmic ring (PR) composed of CagY and CagX; and a stalk with unknown composition. We investigated how CagT, CagM, and a conserved antenna projection (AP) region of CagY contribute to the structural organization of the OMCC. Single-particle cryo-EM analyses showed that complexes purified from ΔcagT or ΔcagM mutants no longer had organized OMCs, but the PRs remained structured. OMCCs purified from a CagY antenna projection mutant (CagY∆AP) were structurally similar to WT OMCCs, except for the absence of the α-helical antenna projection. These results indicate that CagY and CagX are sufficient for maintaining a stable PR, but the organization of the OMC requires CagY, CagX, CagM, and CagT. Our results highlight an unexpected structural independence of two major subdomains of the Cag T4SS OMCC.
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Affiliation(s)
- Jacquelyn R Roberts
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Sirena C Tran
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Arwen E Frick-Cheng
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Kaeli N Bryant
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Chiamaka D Okoye
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - W Hayes McDonald
- Proteomics Laboratory, Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN USA
| | - Timothy L Cover
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Melanie D Ohi
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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Zhang M, Yang B, Shi J, Wang Z, Liu Y. Host defense peptides mitigate the spread of antibiotic resistance in physiologically relevant condition. Antimicrob Agents Chemother 2024; 68:e0126123. [PMID: 38415983 PMCID: PMC10994823 DOI: 10.1128/aac.01261-23] [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: 09/30/2023] [Accepted: 02/06/2024] [Indexed: 02/29/2024] Open
Abstract
Antibiotic resistance represents a significant challenge to public health and human safety. The primary driver behind the dissemination of antibiotic resistance is the horizontal transfer of plasmids. Current conjugative transfer assay is generally performed in a standardized manner, ignoring the effect of the host environment. Host defense peptides (HDPs) possess a wide range of biological targets and play an essential role in the innate immune system. Herein, we reveal that sub-minimum inhibitory concentrations of HDPs facilitate the conjugative transfer of RP4-7 plasmid in the Luria Broth medium, and this observation is reversed in the RPMI medium, designed to simulate the host environment. Out of these HDPs, indolicidin (Ind), a cationic tridecapeptide from bovine neutrophils, significantly inhibits the conjugation of multidrug resistance plasmids in a dose-dependent manner, including blaNDM- and tet(X4)-bearing plasmids. We demonstrate that the addition of Ind to RPMI medium as the incubation substrate downregulates the expression of conjugation-related genes. In addition, Ind weakens the tricarboxylic acid cycle, impedes the electron transport chain, and disrupts the proton motive force, consequently diminishing the synthesis of adenosine triphosphate and limiting the energy supply. Our findings highlight the importance of the host-like environments for the development of horizontal transfer inhibitors and demonstrate the potential of HDPs in preventing the spread of resistance plasmids.
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Affiliation(s)
- Miao Zhang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Bingqing Yang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Jingru Shi
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zhiqiang Wang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Yuan Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
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Malmsheimer S, Grin I, Bohn E, Franz-Wachtel M, Macek B, Sahr T, Smollich F, Chetrit D, Meir A, Roy C, Buchrieser C, Wagner S. The T4bSS of Legionella features a two-step secretion pathway with an inner membrane intermediate for secretion of transmembrane effectors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.584949. [PMID: 38559167 PMCID: PMC10980071 DOI: 10.1101/2024.03.14.584949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
To promote intracellular survival and infection, Legionella spp. translocate hundreds of effector proteins into eukaryotic host cells using a type IV b protein secretion system (T4bSS). T4bSS are well known to translocate soluble as well as transmembrane domain-containing effector proteins (TMD-effectors) but the mechanisms of secretion are still poorly understood. Herein we investigated the secretion of hydrophobic TMD-effectors, of which about 80 were previously reported to be encoded by L. pneumophila. A proteomic analysis of fractionated membranes revealed that TMD-effectors are targeted to and inserted into the bacterial inner membranes of L. pneumophila independent of the presence of a functional T4bSS. While the T4bSS chaperones IcmS and IcmW were critical for secretion of all tested TMD-effectors, they did not influence inner membrane targeting of these proteins. As for soluble effector proteins, translocation of TMD-effectors into host cells depended on a C-terminal secretion signal and this signal needed to be presented towards the cytoplasmic side of the inner membrane. A different secretion behavior of TMD- and soluble effectors and the need for small periplasmic loops within TMD-effectors provided strong evidence that TMD-effectors are secreted in a two-step secretion process: Initially, an inner membrane intermediate is formed, that is extracted towards the cytoplasmic side, possibly by the help of the type IV coupling protein complex and subsequently secreted into eukaryotic host cells by the T4bSS core complex. Overall, our study highlights the amazing versatility of T4bSS to secrete soluble and TMD-effectors from different subcellular locations of the bacterial cell.
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Affiliation(s)
- Silke Malmsheimer
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Section of Cellular and Molecular Microbiology, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
- Current address: Institut de Recherche en Infectiologie de Montpellier, Equipe Kremer, UMR 9004 - CNRS / UM, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Iwan Grin
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Section of Cellular and Molecular Microbiology, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
| | - Erwin Bohn
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Institute of Medical Microbiology and Hygiene, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
| | - Mirita Franz-Wachtel
- University of Tübingen, Proteome Center Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Boris Macek
- University of Tübingen, Proteome Center Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Tobias Sahr
- Institute Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, 75015 Paris, France
| | - Fabian Smollich
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Section of Cellular and Molecular Microbiology, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
| | - David Chetrit
- Yale University, Department of Microbial Pathogenesis, 295 Congress Avenue, New Haven, CT 06536-0812, USA
| | - Amit Meir
- Yale University, Department of Microbial Pathogenesis, 295 Congress Avenue, New Haven, CT 06536-0812, USA
- Birkbeck Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK
- Current address: University of Glasgow, MRC Centre for Virus Research, School of Infection and Immunity, Glasgow, UK
| | - Craig Roy
- Yale University, Department of Microbial Pathogenesis, 295 Congress Avenue, New Haven, CT 06536-0812, USA
| | - Carmen Buchrieser
- Institute Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, 75015 Paris, France
| | - Samuel Wagner
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Section of Cellular and Molecular Microbiology, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Elfriede-Aulhorn-Str. 6, 72076 Tébingen, Germany
- German Center for Infection Research (DZIF), partner-site Tübingen, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
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10
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Costa TRD, Patkowski JB, Macé K, Christie PJ, Waksman G. Structural and functional diversity of type IV secretion systems. Nat Rev Microbiol 2024; 22:170-185. [PMID: 37814112 DOI: 10.1038/s41579-023-00974-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2023] [Indexed: 10/11/2023]
Abstract
Considerable progress has been made in recent years in the structural and molecular biology of type IV secretion systems in Gram-negative bacteria. The latest advances have substantially improved our understanding of the mechanisms underlying the recruitment and delivery of DNA and protein substrates to the extracellular environment or target cells. In this Review, we aim to summarize these exciting structural and molecular biology findings and to discuss their functional implications for substrate recognition, recruitment and translocation, as well as the biogenesis of extracellular pili. We also describe adaptations necessary for deploying a breadth of processes, such as bacterial survival, host-pathogen interactions and biotic and abiotic adhesion. We highlight the functional and structural diversity that allows this extremely versatile secretion superfamily to function under different environmental conditions and in different bacterial species. Additionally, we emphasize the importance of further understanding the mechanism of type IV secretion, which will support us in combating antimicrobial resistance and treating type IV secretion system-related infections.
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Affiliation(s)
- Tiago R D Costa
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College, London, UK.
| | - Jonasz B Patkowski
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College, London, UK
| | - Kévin Macé
- Institute of Structural and Molecular Biology, Birkbeck and UCL, London, UK
- Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes and CNRS, Rennes, France
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX, USA.
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, Birkbeck and UCL, London, UK.
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11
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Oka GU, Souza DP, Sgro GG, Guzzo CR, Dunger G, Farah CS. Xanthomonas immunity proteins protect against the cis-toxic effects of their cognate T4SS effectors. EMBO Rep 2024; 25:1436-1452. [PMID: 38332152 PMCID: PMC10933484 DOI: 10.1038/s44319-024-00060-6] [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: 09/07/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 02/10/2024] Open
Abstract
Many bacteria kill rival species by translocating toxic effectors into target cells. Effectors are often encoded along with cognate immunity proteins that could (i) protect against "friendly-fire" (trans-intoxication) from neighboring sister cells and/or (ii) protect against internal cis-intoxication (suicide). Here, we distinguish between these two mechanisms in the case of the bactericidal Xanthomonas citri Type IV Secretion System (X-T4SS). We use a set of X. citri mutants lacking multiple effector/immunity protein (X-Tfe/X-Tfi) pairs to show that X-Tfis are not absolutely required to protect against trans-intoxication by wild-type cells. Our investigation then focused on the in vivo function of the lysozyme-like effector X-TfeXAC2609 and its cognate immunity protein X-TfiXAC2610. In the absence of X-TfiXAC2610, we observe X-TfeXAC2609-dependent and X-T4SS-independent accumulation of damage in the X. citri cell envelope, cell death, and inhibition of biofilm formation. While immunity proteins in other systems have been shown to protect against attacks by sister cells (trans-intoxication), this is an example of an antibacterial secretion system in which the immunity proteins are dedicated to protecting cells against cis-intoxication.
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Affiliation(s)
- Gabriel U Oka
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Structure and Function of Bacterial Nanomachines, Institut Européen de Chimie et Biologie-CNRS, UMR 5234 Microbiologie Fondamentale et Pathogénicité University of Bordeaux, Pessac, France
| | - Diorge P Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Germán G Sgro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Cristiane R Guzzo
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - German Dunger
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Instituto de Ciencias Agropecuarias del Litoral (ICiAgro Litoral), Universidad Nacional del Litoral, CONICET, Facultad de Ciencias Agrarias, Esperanza, Argentina
| | - Chuck S Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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12
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Kishida K, Li YG, Ogawa-Kishida N, Khara P, Al Mamun AAM, Bosserman RE, Christie PJ. Chimeric systems composed of swapped Tra subunits between distantly-related F plasmids reveal striking plasticity among type IV secretion machines. PLoS Genet 2024; 20:e1011088. [PMID: 38437248 PMCID: PMC10939261 DOI: 10.1371/journal.pgen.1011088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 03/14/2024] [Accepted: 02/20/2024] [Indexed: 03/06/2024] Open
Abstract
Bacterial type IV secretion systems (T4SSs) are a versatile family of macromolecular translocators, collectively able to recruit diverse DNA and protein substrates and deliver them to a wide range of cell types. Presently, there is little understanding of how T4SSs recognize substrate repertoires and form productive contacts with specific target cells. Although T4SSs are composed of a number of conserved subunits and adopt certain conserved structural features, they also display considerable compositional and structural diversity. Here, we explored the structural bases underlying the functional versatility of T4SSs through systematic deletion and subunit swapping between two conjugation systems encoded by the distantly-related IncF plasmids, pED208 and F. We identified several regions of intrinsic flexibility among the encoded T4SSs, as evidenced by partial or complete functionality of chimeric machines. Swapping of VirD4-like TraD type IV coupling proteins (T4CPs) yielded functional chimeras, indicative of relaxed specificity at the substrate-TraD and TraD-T4SS interfaces. Through mutational analyses, we further delineated domains of the TraD T4CPs contributing to recruitment of cognate vs heterologous DNA substrates. Remarkably, swaps of components comprising the outer membrane core complexes, a few F-specific subunits, or the TraA pilins supported DNA transfer in the absence of detectable pilus production. Among sequenced enterobacterial species in the NCBI database, we identified many strains that harbor two or more F-like plasmids and many F plasmids lacking one or more T4SS components required for self-transfer. We confirmed that host cells carrying co-resident, non-selftransmissible variants of pED208 and F elaborate chimeric T4SSs, as evidenced by transmission of both plasmids. We propose that T4SS plasticity enables the facile assembly of functional chimeras, and this intrinsic flexibility at the structural level can account for functional diversification of this superfamily over evolutionary time and, on a more immediate time-scale, to proliferation of transfer-defective MGEs in nature.
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Affiliation(s)
- Kouhei Kishida
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, United States of America
| | - Yang Grace Li
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, United States of America
| | - Natsumi Ogawa-Kishida
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, United States of America
| | - Pratick Khara
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, United States of America
| | - Abu Amar M. Al Mamun
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, United States of America
| | - Rachel E. Bosserman
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, United States of America
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, United States of America
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13
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Graham CI, MacMartin TL, de Kievit TR, Brassinga AKC. Molecular regulation of virulence in Legionella pneumophila. Mol Microbiol 2024; 121:167-195. [PMID: 37908155 DOI: 10.1111/mmi.15172] [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: 05/31/2023] [Revised: 09/15/2023] [Accepted: 09/17/2023] [Indexed: 11/02/2023]
Abstract
Legionella pneumophila is a gram-negative bacteria found in natural and anthropogenic aquatic environments such as evaporative cooling towers, where it reproduces as an intracellular parasite of cohabiting protozoa. If L. pneumophila is aerosolized and inhaled by a susceptible person, bacteria may colonize their alveolar macrophages causing the opportunistic pneumonia Legionnaires' disease. L. pneumophila utilizes an elaborate regulatory network to control virulence processes such as the Dot/Icm Type IV secretion system and effector repertoire, responding to changing nutritional cues as their host becomes depleted. The bacteria subsequently differentiate to a transmissive state that can survive in the environment until a replacement host is encountered and colonized. In this review, we discuss the lifecycle of L. pneumophila and the molecular regulatory network that senses nutritional depletion via the stringent response, a link to stationary phase-like metabolic changes via alternative sigma factors, and two-component systems that are homologous to stress sensors in other pathogens, to regulate differentiation between the intracellular replicative phase and more transmissible states. Together, we highlight how this prototypic intracellular pathogen offers enormous potential in understanding how molecular mechanisms enable intracellular parasitism and pathogenicity.
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Affiliation(s)
- Christopher I Graham
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Teassa L MacMartin
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Teresa R de Kievit
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ann Karen C Brassinga
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, Manitoba, Canada
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14
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Murata T, Gotoh Y, Hayashi T. A comprehensive list of genes required for the efficient conjugation of plasmid Rts1 was determined by systematic deletion analysis. DNA Res 2024; 31:dsae002. [PMID: 38300630 PMCID: PMC10838148 DOI: 10.1093/dnares/dsae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/08/2024] [Accepted: 01/31/2024] [Indexed: 02/02/2024] Open
Abstract
While conjugation-related genes have been identified in many plasmids by genome sequencing, functional analyses have not yet been performed in most cases, and a full set of conjugation genes has been identified for only a few plasmids. Rts1, a prototype IncT plasmid, is a conjugative plasmid that was originally isolated from Proteus vulgaris. Here, we conducted a systematic deletion analysis of Rts1 to fully understand its conjugation system. Through this analysis along with complementation assays, we identified 32 genes that are required for the efficient conjugation of Rts1 from Escherichia coli to E. coli. In addition, the functions of the 28 genes were determined or predicted; 21 were involved in mating-pair formation, three were involved in DNA transfer and replication, including a relaxase gene belonging to the MOBH12 family, one was involved in coupling, and three were involved in transcriptional regulation. Among the functionally well-analysed conjugation systems, most of the 28 genes showed the highest similarity to those of the SXT element, which is an integrative conjugative element of Vibrio cholerae. The Rts1 conjugation gene set included all 23 genes required for the SXT system. Two groups of plasmids with conjugation systems nearly identical or very similar to that of Rts1 were also identified.
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Affiliation(s)
- Takahiro Murata
- Department of Pediatrics, Teikyo University School of Medicine, Mizonokuchi Hospital, Takatsu-ku, Kawasaki, Kanagawa 213-8507, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
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15
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Tran SC, Bryant KN, Cover TL. The Helicobacter pylori cag pathogenicity island as a determinant of gastric cancer risk. Gut Microbes 2024; 16:2314201. [PMID: 38391242 PMCID: PMC10896142 DOI: 10.1080/19490976.2024.2314201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 01/31/2024] [Indexed: 02/24/2024] Open
Abstract
Helicobacter pylori strains can be broadly classified into two groups based on whether they contain or lack a chromosomal region known as the cag pathogenicity island (cag PAI). Colonization of the human stomach with cag PAI-positive strains is associated with an increased risk of gastric cancer and peptic ulcer disease, compared to colonization with cag PAI-negative strains. The cag PAI encodes a secreted effector protein (CagA) and components of a type IV secretion system (Cag T4SS) that delivers CagA and non-protein substrates into host cells. Animal model experiments indicate that CagA and the Cag T4SS stimulate a gastric mucosal inflammatory response and contribute to the development of gastric cancer. In this review, we discuss recent studies defining structural and functional features of CagA and the Cag T4SS and mechanisms by which H. pylori strains containing the cag PAI promote the development of gastric cancer and peptic ulcer disease.
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Affiliation(s)
- Sirena C Tran
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kaeli N Bryant
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy L Cover
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
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16
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Zehra M, Heo J, Chung JM, Durie CL. Comparative Analysis of T4SS Molecular Architectures. J Microbiol Biotechnol 2023; 33:1543-1551. [PMID: 37528551 PMCID: PMC10772558 DOI: 10.4014/jmb.2307.07006] [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: 07/06/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/03/2023]
Abstract
The recently published high-resolution R388 T4SS structure provides exciting new details about the complete complex of T4SS, including the components making up the stalk and arches, numerous symmetry mismatches between regions of the complex, and an intriguing interpretation of the closed stalk and radial symmetry of the inner membrane complex, which is related to pilus biogenesis assembly. However, there are a few unidentified densities in the electron microscopy map and portions of the identified component sequences for which the structure is not yet known. It is also unclear how well this minimized DNA-transporting T4SS predicts the structure of other T4SSs, such as expanded systems and those that transport proteins rather than DNA. In this review, we evaluate what can be inferred from the recent high-resolution structure of the R388 T4SS with respect to the Cag and Dot/Icm systems. These systems were selected because, given what is currently known about these systems, we expect them to present most structural differences compared to the R388 T4SS structure. Furthermore, we discuss bacterial physiology and diversity, the T4SS structures and their variations between different bacterial species. These insights may prove beneficial for researchers who elucidate the structure and functions of T4SS in different bacterial species.
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Affiliation(s)
- Mishghan Zehra
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Jiwon Heo
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Gyeonggi, Republic of Korea
| | - Jeong Min Chung
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Gyeonggi, Republic of Korea
| | - Clarissa L Durie
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
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17
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Kishida K, Li YG, Ogawa-Kishida N, Khara P, Al Mamun AAM, Bosserman RE, Christie PJ. Chimeric systems composed of swapped Tra subunits between distantly-related F plasmids reveal striking plasticity among type IV secretion machines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570194. [PMID: 38106057 PMCID: PMC10723329 DOI: 10.1101/2023.12.05.570194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Bacterial type IV secretion systems (T4SSs) are a versatile family of macromolecular translocators, collectively able to recruit diverse DNA and protein substrates and deliver them to a wide range of cell types. Presently, there is little understanding of how T4SSs recognize substrate repertoires and form productive contacts with specific target cells. Although T4SSs are composed of a number of conserved subunits and adopt certain conserved structural features, they also display considerable compositional and structural diversity. Here, we explored the structural bases underlying the functional versatility of T4SSs through systematic deletion and subunit swapping between two conjugation systems encoded by the distantly-related IncF plasmids, pED208 and F. We identified several regions of intrinsic flexibility among the encoded T4SSs, as evidenced by partial or complete functionality of chimeric machines. Swapping of VirD4-like TraD type IV coupling proteins (T4CPs) yielded functional chimeras, indicative of relaxed specificity at the substrate - TraD and TraD - T4SS interfaces. Through mutational analyses, we further delineated domains of the TraD T4CPs contributing to recruitment of cognate vs heterologous DNA substrates. Remarkably, swaps of components comprising the outer membrane core complexes, a few F-specific subunits, or the TraA pilins supported DNA transfer in the absence of detectable pilus production. Among sequenced enterobacterial species in the NCBI database, we identified many strains that harbor two or more F-like plasmids and many F plasmids lacking one or more T4SS components required for self-transfer. We confirmed that host cells carrying co-resident, non-selftransmissible variants of pED208 and F elaborate chimeric T4SSs, as evidenced by transmission of both plasmids. We propose that T4SS plasticity enables the facile assembly of functional chimeras, and this intrinsic flexibility at the structural level can account for functional diversification of this superfamily over evolutionary time and, on a more immediate time-scale, to proliferation of transfer-defective MGEs in nature.
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Affiliation(s)
- Kouhei Kishida
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, 6431 Fannin St, Houston, Texas 77030, United States of America
| | - Yang Grace Li
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, 6431 Fannin St, Houston, Texas 77030, United States of America
| | - Natsumi Ogawa-Kishida
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, 6431 Fannin St, Houston, Texas 77030, United States of America
| | - Pratick Khara
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, 6431 Fannin St, Houston, Texas 77030, United States of America
| | - Abu Amar M Al Mamun
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, 6431 Fannin St, Houston, Texas 77030, United States of America
| | - Rachel E. Bosserman
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, 6431 Fannin St, Houston, Texas 77030, United States of America
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, 6431 Fannin St, Houston, Texas 77030, United States of America
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18
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Cabezón E, Valenzuela-Gómez F, Arechaga I. Primary architecture and energy requirements of Type III and Type IV secretion systems. Front Cell Infect Microbiol 2023; 13:1255852. [PMID: 38089815 PMCID: PMC10711112 DOI: 10.3389/fcimb.2023.1255852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
Many pathogens use Type III and Type IV protein secretion systems to secrete virulence factors from the bacterial cytosol into host cells. These systems operate through a one-step mechanism. The secreted substrates (protein or nucleo-protein complexes in the case of Type IV conjugative systems) are guided to the base of the secretion channel, where they are directly delivered into the host cell in an ATP-dependent unfolded state. Despite the numerous disparities between these secretion systems, here we have focused on the structural and functional similarities between both systems. In particular, on the structural similarity shared by one of the main ATPases (EscN and VirD4 in Type III and Type IV secretion systems, respectively). Interestingly, these ATPases also exhibit a structural resemblance to F1-ATPases, which suggests a common mechanism for substrate secretion. The correlation between structure and function of essential components in both systems can provide significant insights into the molecular mechanisms involved. This approach is of great interest in the pursuit of identifying inhibitors that can effectively target these systems.
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Affiliation(s)
- Elena Cabezón
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria- CSIC, Santander, Spain
| | | | - Ignacio Arechaga
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria- CSIC, Santander, Spain
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19
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López-Luis MA, Soriano-Pérez EE, Parada-Fabián JC, Torres J, Maldonado-Rodríguez R, Méndez-Tenorio A. A Proposal for a Consolidated Structural Model of the CagY Protein of Helicobacter pylori. Int J Mol Sci 2023; 24:16781. [PMID: 38069104 PMCID: PMC10706595 DOI: 10.3390/ijms242316781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
CagY is the largest and most complex protein from Helicobacter pylori's (Hp) type IV secretion system (T4SS), playing a critical role in the modulation of gastric inflammation and risk for gastric cancer. CagY spans from the inner to the outer membrane, forming a channel through which Hp molecules are injected into human gastric cells. Yet, a tridimensional structure has been reported for only short segments of the protein. This intricate protein was modeled using different approaches, including homology modeling, ab initio, and deep learning techniques. The challengingly long middle repeat region (MRR) was modeled using deep learning and optimized using equilibrium molecular dynamics. The previously modeled segments were assembled into a 1595 aa chain and a 14-chain CagY multimer structure was assembled by structural alignment. The final structure correlated with published structures and allowed to show how the multimer may form the T4SS channel through which CagA and other molecules are translocated to gastric cells. The model confirmed that MRR, the most polymorphic and complex region of CagY, presents numerous cysteine residues forming disulfide bonds that stabilize the protein and suggest this domain may function as a contractile region playing an essential role in the modulating activity of CagY on tissue inflammation.
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Affiliation(s)
- Mario Angel López-Luis
- Laboratorio de Biotecnología y Bioinformática Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Lázaro Cárdenas, Mexico City 11340, Mexico; (M.A.L.-L.); (E.E.S.-P.); (J.C.P.-F.); (R.M.-R.)
| | - Eva Elda Soriano-Pérez
- Laboratorio de Biotecnología y Bioinformática Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Lázaro Cárdenas, Mexico City 11340, Mexico; (M.A.L.-L.); (E.E.S.-P.); (J.C.P.-F.); (R.M.-R.)
| | - José Carlos Parada-Fabián
- Laboratorio de Biotecnología y Bioinformática Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Lázaro Cárdenas, Mexico City 11340, Mexico; (M.A.L.-L.); (E.E.S.-P.); (J.C.P.-F.); (R.M.-R.)
| | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico;
| | - Rogelio Maldonado-Rodríguez
- Laboratorio de Biotecnología y Bioinformática Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Lázaro Cárdenas, Mexico City 11340, Mexico; (M.A.L.-L.); (E.E.S.-P.); (J.C.P.-F.); (R.M.-R.)
| | - Alfonso Méndez-Tenorio
- Laboratorio de Biotecnología y Bioinformática Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Lázaro Cárdenas, Mexico City 11340, Mexico; (M.A.L.-L.); (E.E.S.-P.); (J.C.P.-F.); (R.M.-R.)
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20
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Tran SC, McClain MS, Cover TL. Role of the CagY antenna projection in Helicobacter pylori Cag type IV secretion system activity. Infect Immun 2023; 91:e0015023. [PMID: 37638724 PMCID: PMC10501215 DOI: 10.1128/iai.00150-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/07/2023] [Indexed: 08/29/2023] Open
Abstract
Helicobacter pylori strains containing the cag pathogenicity island (PAI) are associated with the development of gastric adenocarcinoma and peptic ulcer disease. The cag PAI encodes a secreted effector protein (CagA) and a type IV secretion system (Cag T4SS). Cag T4SS activity is required for the delivery of CagA and non-protein substrates into host cells. The Cag T4SS outer membrane core complex (OMCC) contains a channel-like domain formed by helix-loop-helix elements (antenna projections, AP) from 14 copies of the CagY protein (a VirB10 ortholog). Similar VirB10 antenna regions are present in T4SS OMCCs from multiple bacterial species and are predicted to span the outer membrane. In this study, we investigated the role of the CagY antenna region in Cag T4SS OMCC assembly and Cag T4SS function. An H. pylori mutant strain with deletion of the entire CagY AP (∆AP) retained the capacity to produce CagY and assemble an OMCC, but it lacked T4SS activity (CagA translocation and IL-8 induction in AGS gastric epithelial cells). In contrast, a mutant strain with Gly-Ser substitutions in the unstructured CagY AP loop retained Cag T4SS activity. Mutants containing CagY AP loops with shortened lengths were defective in CagA translocation and exhibited reduced IL-8-inducing activity compared to control strains. These data indicate that the CagY AP region is required for Cag T4SS activity and that Cag T4SS activity can be modulated by altering the length of the CagY AP unstructured loop.
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Affiliation(s)
- Sirena C. Tran
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mark S. McClain
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Timothy L. Cover
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA
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21
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Drehkopf S, Scheibner F, Büttner D. Functional characterization of VirB/VirD4 and Icm/Dot type IV secretion systems from the plant-pathogenic bacterium Xanthomonas euvesicatoria. Front Cell Infect Microbiol 2023; 13:1203159. [PMID: 37593760 PMCID: PMC10432156 DOI: 10.3389/fcimb.2023.1203159] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/17/2023] [Indexed: 08/19/2023] Open
Abstract
Introduction Many Gram-negative plant- and animal-pathogenic bacteria employ type IV secretion (T4S) systems to transport proteins or DNA/protein complexes into eukaryotic or bacterial target cells. T4S systems have been divided into minimized and expanded T4S systems and resemble the VirB/VirD4 T4S system from the plant pathogen Agrobacterium tumefaciens and the Icm/Dot T4S system from the human pathogen Legionella pneumophila, respectively. The only known plant pathogen with both types of T4S systems is Xanthomonas euvesicatoria which is the causal agent of bacterial spot disease on pepper and tomato plants. Results and discussion In the present study, we show that virB/virD4 and icm/dot T4S genes are expressed and encode components of oligomeric complexes corresponding to known assemblies of VirB/VirD4 and Icm/Dot proteins. Both T4S systems are dispensable for the interaction of X. euvesicatoria with its host plants and do not seem to confer contact-dependent lysis of other bacteria, which was previously shown for the chromosomally encoded VirB/VirD4 T4S system from Xanthomonas axonopodis pv. citri. The corresponding chromosomal T4S gene cluster from X. euvesicatoria is incomplete, however, the second plasmid-localized vir gene cluster encodes a functional VirB/VirD4 T4S system which contributes to plasmid transfer. In agreement with this finding, we identified the predicted relaxase TraI as substrate of the T4S systems from X. euvesicatoria. TraI and additional candidate T4S substrates with homology to T4S effectors from X. axonopodis pv. citri interact with the T4S coupling protein VirD4. Interestingly, however, the predicted C-terminal VirD4-binding sites are not sufficient for T4S, suggesting the contribution of additional yet unknown mechanisms to the targeting of T4S substrates from X. euvesicatoria to both VirB/VirD4 and Icm/Dot T4S systems.
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Affiliation(s)
| | | | - Daniela Büttner
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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22
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Wiehlmann L, Klockgether J, Hammerbacher AS, Salunkhe P, Horatzek S, Munder A, Peilert JF, Gulbins E, Eberl L, Tümmler B. A VirB4 ATPase of the mobile accessory genome orchestrates core genome-encoded features of physiology, metabolism, and virulence of Pseudomonas aeruginosa TBCF10839. Front Cell Infect Microbiol 2023; 13:1234420. [PMID: 37577372 PMCID: PMC10413270 DOI: 10.3389/fcimb.2023.1234420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Pseudomonas aeruginosa TBCF10839 is a highly virulent strain that can persist and replicate in human neutrophils. Screening of a signature-tagged mutagenesis (STM) TBCF10839 transposon library in phagocytosis tests identified a mutant that carried the transposon in the VirB4 homolog 5PG21 of an integrative and conjugative element (ICE)-associated type IV secretion system of the pKLC102 subtype. 5P21 TBCF10839 insertion mutants were deficient in metabolic versatility, secretion, quorum sensing, and virulence. The mutants were efficiently killed in phagocytosis tests in vitro and were avirulent in an acute murine airway infection model in vivo. The inactivation of 5PG21 silenced the rhl, las, and pqs operons and the gene expression for the synthesis of hydrogen cyanide, the antimetabolite l-2-amino-4-methoxy-trans-3-butenoic acid, and the H2- and H3-type VI secretion systems and their associated effectors. The mutants were impaired in the utilization of carbon sources and stored compounds that are not funneled into intermediary metabolism. This showcase demonstrates that a single gene of the mobile accessory genome can become an essential element to operate the core genome-encoded features of metabolism and virulence.
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Affiliation(s)
- Lutz Wiehlmann
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Jens Klockgether
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Anna-Silke Hammerbacher
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Prabhakar Salunkhe
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Sonja Horatzek
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Antje Munder
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
| | | | - Erich Gulbins
- Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Institute of Molecular Biology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Burkhard Tümmler
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
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23
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Ryan ME, Damke PP, Bryant C, Sheedlo MJ, Shaffer CL. Architectural asymmetry enables DNA transport through the Helicobacter pylori cag type IV secretion system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550604. [PMID: 37546756 PMCID: PMC10402047 DOI: 10.1101/2023.07.25.550604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Structural asymmetry within secretion system architecture is fundamentally important for apparatus diversification and biological function. However, the mechanism by which symmetry mismatch contributes to nanomachine assembly and interkingdom effector translocation are undefined. Here, we show that architectural asymmetry orchestrates dynamic substrate selection and enables trans-kingdom DNA conjugation through the Helicobacter pylori cag type IV secretion system (cag T4SS). Structural analyses of asymmetric units within the cag T4SS periplasmic ring complex (PRC) revealed intermolecular π-π stacking interactions that coordinate DNA binding and license trans-kingdom conjugation without disrupting the translocation of protein and peptidoglycan effector molecules. Additionally, we identified a novel proximal translocation channel gating mechanism that regulates cargo loading and governs substrate transport across the outer membrane. We thus propose a model whereby the organization and geometry of architectural symmetry mismatch exposes π-π interfaces within the PRC to facilitate DNA transit through the cag T4SS translocation channel.
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Affiliation(s)
- Mackenzie E. Ryan
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, 40506, USA
| | - Prashant P. Damke
- Department of Veterinary Sciences, University of Kentucky College of Agriculture, Lexington, KY, 40546, USA
| | - Caitlynn Bryant
- Department of Veterinary Sciences, University of Kentucky College of Agriculture, Lexington, KY, 40546, USA
| | - Michael J. Sheedlo
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Carrie L. Shaffer
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, 40506, USA
- Department of Veterinary Sciences, University of Kentucky College of Agriculture, Lexington, KY, 40546, USA
- Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, KY, 40536, USA
- Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40506, USA
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24
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Sorokina J, Sokolova I, Majorina M, Ungur A, Troitskiy V, Tukhvatulin A, Melnik B, Belyi Y. Oligomerization and Adjuvant Activity of Peptides Derived from the VirB4-like ATPase of Clostridioides difficile. Biomolecules 2023; 13:1012. [PMID: 37371592 DOI: 10.3390/biom13061012] [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: 05/21/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
In a previous study, we demonstrated that the Clostridioides difficile VirB4-like ATPase forms oligomers in vitro. In the current investigation, to study the observed phenomenon in more detail, we prepared a library of VirB4-derived peptides (delVirB4s) fused to a carrier maltose-binding protein (MBP). Using gel chromatography and polyacrylamide gel electrophoresis, we found a set of overlapping fragments that contribute most significantly to protein aggregation, which were represented as water-soluble oligomers with molecular masses ranging from ~300 kD to several megadaltons. Membrane filtration experiments, sucrose gradient ultracentrifugation, and dynamic light scattering measurements indicated the size of the soluble complex to be 15-100 nm. It was sufficiently stable to withstand treatment with 1 M urea; however, it dissociated in a 6 M urea solution. As shown by the changes in GFP fluorescence and the circular dichroism spectra, the attachment of the delVirB4 peptide significantly altered the structure of the partner MBP. The immunization of mice with the hybrid consisting of the selected VirB4-derived peptide and MBP, GST, or GFP resulted in increased production of specific antibodies compared to the peptide-free carrier proteins, suggesting significant adjuvant activity of the VirB4 fragment. This feature could be useful for the development of new vaccines, especially in the case of "weak" antigens that are unable to elicit a strong immune response by themselves.
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Affiliation(s)
- Julya Sorokina
- Gamaleya Research Centre for Epidemiology and Microbiology, Moscow 123098, Russia
| | - Irina Sokolova
- Gamaleya Research Centre for Epidemiology and Microbiology, Moscow 123098, Russia
| | - Mariya Majorina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Anastasia Ungur
- Gamaleya Research Centre for Epidemiology and Microbiology, Moscow 123098, Russia
| | - Vasiliy Troitskiy
- Department of Infectious Diseases, Institute of Clinical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 2 Bolshaya Pirogovskaya St., Moscow 119435, Russia
| | - Amir Tukhvatulin
- Gamaleya Research Centre for Epidemiology and Microbiology, Moscow 123098, Russia
| | - Bogdan Melnik
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Pushchino Branch, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Yury Belyi
- Gamaleya Research Centre for Epidemiology and Microbiology, Moscow 123098, Russia
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25
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Conners R, León-Quezada RI, McLaren M, Bennett NJ, Daum B, Rakonjac J, Gold VAM. Cryo-electron microscopy of the f1 filamentous phage reveals insights into viral infection and assembly. Nat Commun 2023; 14:2724. [PMID: 37169795 PMCID: PMC10175506 DOI: 10.1038/s41467-023-37915-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/04/2023] [Indexed: 05/13/2023] Open
Abstract
Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular biology and biotechnology. This is particularly true for the Ff (f1, fd or M13) phages, which represent a widely distributed group of filamentous viruses. Over nearly five decades, Ffs have seen an extraordinary range of applications, yet the complete structure of the phage capsid and consequently the mechanisms of infection and assembly remain largely mysterious. In this work, we use cryo-electron microscopy and a highly efficient system for production of short Ff-derived nanorods to determine a structure of a filamentous virus including the tips. We show that structure combined with mutagenesis can identify phage domains that are important in bacterial attack and for release of new progeny, allowing new models to be proposed for the phage lifecycle.
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Affiliation(s)
- Rebecca Conners
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Rayén Ignacia León-Quezada
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Nanophage Technologies, Palmerston North, New Zealand
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Nicholas J Bennett
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Jasna Rakonjac
- School of Natural Sciences, Massey University, Palmerston North, New Zealand.
- Nanophage Technologies, Palmerston North, New Zealand.
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
- Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK.
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26
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Blanc M, Lettl C, Guérin J, Vieille A, Furler S, Briand-Schumacher S, Dreier B, Bergé C, Plückthun A, Vadon-Le Goff S, Fronzes R, Rousselle P, Fischer W, Terradot L. Designed Ankyrin Repeat Proteins provide insights into the structure and function of CagI and are potent inhibitors of CagA translocation by the Helicobacter pylori type IV secretion system. PLoS Pathog 2023; 19:e1011368. [PMID: 37155700 DOI: 10.1371/journal.ppat.1011368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 05/18/2023] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
The bacterial human pathogen Helicobacter pylori produces a type IV secretion system (cagT4SS) to inject the oncoprotein CagA into gastric cells. The cagT4SS external pilus mediates attachment of the apparatus to the target cell and the delivery of CagA. While the composition of the pilus is unclear, CagI is present at the surface of the bacterium and required for pilus formation. Here, we have investigated the properties of CagI by an integrative structural biology approach. Using Alpha Fold 2 and Small Angle X-ray scattering, it was found that CagI forms elongated dimers mediated by rod-shape N-terminal domains (CagIN) prolonged by globular C-terminal domains (CagIC). Three Designed Ankyrin Repeat Proteins (DARPins) K2, K5 and K8 selected against CagI interacted with CagIC with subnanomolar affinities. The crystal structures of the CagI:K2 and CagI:K5 complexes were solved and identified the interfaces between the molecules, thereby providing a structural explanation for the difference in affinity between the two binders. Purified CagI and CagIC were found to interact with adenocarcinoma gastric (AGS) cells, induced cell spreading and the interaction was inhibited by K2. The same DARPin inhibited CagA translocation by up to 65% in AGS cells while inhibition levels were 40% and 30% with K8 and K5, respectively. Our study suggests that CagIC plays a key role in cagT4SS-mediated CagA translocation and that DARPins targeting CagI represent potent inhibitors of the cagT4SS, a crucial risk factor for gastric cancer development.
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Affiliation(s)
- Marine Blanc
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Clara Lettl
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Jérémy Guérin
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Anaïs Vieille
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Sven Furler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Célia Bergé
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Sandrine Vadon-Le Goff
- University of Lyon, CNRS UMR5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), Lyon, France
| | - Rémi Fronzes
- European Institute of Chemistry and Biology, CNRS UMR 5234 Microbiologie Fondamentale et Pathogénicité, Univ. Bordeaux, Pessac, France
| | - Patricia Rousselle
- University of Lyon, CNRS UMR5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), Lyon, France
| | - Wolfgang Fischer
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Laurent Terradot
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
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27
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Han K, Li Y, Zhang Z, Sun L, Wang ET, Li Y. Comparative genome analysis of Sesbania cannabina-nodulating Rhizobium spp. revealing the symbiotic and transferrable characteristics of symbiosis plasmids. Microb Genom 2023; 9. [PMID: 37133904 DOI: 10.1099/mgen.0.001004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
Symbiotic nitrogen fixation between legumes and rhizobia makes a great contribution to the terrestrial ecosystem. The successful symbiosis between the partners mainly depends on the nod and nif genes in rhizobia, while the specific symbiosis is mainly determined by the structure of Nod factors and the corresponding secretion systems (type III secretion system; T3SS), etc. These symbiosis genes are usually located on symbiotic plasmids or a chromosomal symbiotic island, both could be transferred interspecies. In our previous studies, Sesbania cannabina-nodulating rhizobia across the world were classified into 16 species of four genera and all the strains, especially those of Rhizobium spp., harboured extraordinarily highly conserved symbiosis genes, suggesting that horizontal transfer of symbiosis genes might have happened among them. In order to learn the genomic basis of diversification of rhizobia under the selection of host specificity, we performed this study to compare the complete genome sequences of four Rhizobium strains associated with S. cannabina, YTUBH007, YTUZZ027, YTUHZ044 and YTUHZ045. Their complete genomes were sequenced and assembled at the replicon level. Each strain represents a different species according to the average nucleotide identity (ANI) values calculated using the whole-genome sequences; furthermore, except for YTUBH007, which was classified as Rhizobium binae, the remaining three strains were identified as new candidate species. A single symbiotic plasmid sized 345-402 kb containing complete nod, nif, fix, T3SS and conjugal transfer genes was detected in each strain. The high ANI and amino acid identity (AAI) values, as well as the close phylogenetic relationships among the entire symbiotic plasmid sequences, indicate that they have the same origin and the entire plasmid has been transferred among different Rhizobium species. These results indicate that S. cannabina stringently selects a certain symbiosis gene background of the rhizobia for nodulation, which might have forced the symbiosis genes to transfer from some introduced rhizobia to the related native or local-condition-adapted bacteria. The existence of almost complete conjugal transfer related elements, but not the gene virD, indicated that the self-transfer of the symbiotic plasmid in these rhizobial strains may be realized via a virD-independent pathway or through another unidentified gene. This study provides insight for the better understanding of high-frequency symbiotic plasmid transfer, host-specific nodulation and the host shift for rhizobia.
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Affiliation(s)
- Kunming Han
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - Zhenpeng Zhang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, PR China
| | - Liqin Sun
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
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28
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Machtens DA, Willerding JM, Eschenburg S, Reubold TF. Crystal structure of the N-terminal domain of the effector protein SidI of Legionella pneumophila reveals a glucosyl transferase domain. Biochem Biophys Res Commun 2023; 661:50-55. [PMID: 37087798 DOI: 10.1016/j.bbrc.2023.04.029] [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: 03/30/2023] [Accepted: 04/13/2023] [Indexed: 04/25/2023]
Abstract
The Gram-negative bacterium Legionella pneumophila is an accidental human pathogen that can cause a life-threatening respiratory infection called Legionellosis. In the course of infection, L. pneumophila injects more than 300 effector proteins into the host cell. The effector proteins modify the intracellular environment in order to create a stable compartment for proliferation within the host cell. The effector protein SidI has been shown to potently inhibit host translation upon translocation. SidI is able to interact with the translation elongation factor eEF1A, which has been hypothesized to be a target of SidI. A postulated glycosyltransferase domain in the C-terminal half may be responsible for the toxic effect of SidI. Here, we present the crystal structure of an N-terminal fragment of SidI containing residues 37-573. The structure is divided into three subdomains, two of which display a novel fold. The third subdomain shows close structural homology to GT-B fold glycosyltransferases. Based on structural analysis we predict that the two previously identified residues R453 and E482 assume roles in the catalytic activity of SidI. Furthermore, we show that the N-terminal fragment of SidI is able to directly interact with a postulated target, the translation elongation factor eEF1A.
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Affiliation(s)
- Dominik A Machtens
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Jonas M Willerding
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Susanne Eschenburg
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Thomas F Reubold
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany.
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29
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Maphosa S, Moleleki LN, Motaung TE. Bacterial secretion system functions: evidence of interactions and downstream implications. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37083586 DOI: 10.1099/mic.0.001326] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Unprecedented insights into the biology and functions of bacteria have been and continue to be gained through studying bacterial secretion systems in isolation. This method, however, results in our understanding of the systems being primarily based on the idea that they operate independently, ignoring the subtleties of downstream interconnections. Gram-negative bacteria are naturally able to adapt to and navigate their frequently varied and dynamic surroundings, mostly because of the covert connections between secretion systems. Therefore, to comprehend some of the linked downstream repercussions for organisms that follow this discourse, it is vital to have mechanistic insights into how the intersecretion system functions in bacterial rivalry, virulence, and survival, among other things. To that purpose, this paper discusses a few key instances of molecular antagonistic and interdependent relationships between bacterial secretion systems and their produced functional products.
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Affiliation(s)
- Silindile Maphosa
- Division of Microbiology, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Hatfield, Pretoria, South Africa
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Hatfield, Pretoria, South Africa
| | - Lucy N Moleleki
- Division of Microbiology, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Hatfield, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Hatfield, Pretoria, South Africa
| | - Thabiso E Motaung
- Division of Microbiology, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Hatfield, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Hatfield, Pretoria, South Africa
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30
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Dutka P, Liu Y, Maggi S, Ghosal D, Wang J, Carter SD, Zhao W, Vijayrajratnam S, Vogel JP, Jensen GJ. Structure and Function of the Dot/Icm T4SS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.22.533729. [PMID: 36993699 PMCID: PMC10055428 DOI: 10.1101/2023.03.22.533729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The Legionella pneumophila Dot/Icm type IV secretion system (T4SS) delivers effector proteins into host cells during infection. Despite its significance as a potential drug target, our current understanding of its atomic structure is limited to isolated subcomplexes. In this study, we used subtomogram averaging and integrative modeling to construct a nearly-complete model of the Dot/Icm T4SS accounting for seventeen protein components. We locate and provide insights into the structure and function of six new components including DotI, DotJ, DotU, IcmF, IcmT, and IcmX. We find that the cytosolic N-terminal domain of IcmF, a key protein forming a central hollow cylinder, interacts with DotU, providing insight into previously uncharacterized density. Furthermore, our model, in combination with analyses of compositional heterogeneity, explains how the cytoplasmic ATPase DotO is connected to the periplasmic complex via interactions with membrane-bound DotI/DotJ proteins. Coupled with in situ infection data, our model offers new insights into the T4SS-mediated secretion mechanism.
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Affiliation(s)
- Przemysław Dutka
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yuxi Liu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Stefano Maggi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Debnath Ghosal
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Present address: Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Jue Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Stephen D. Carter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Present address: MRC-University of Glasgow Centre for Virus Research, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Wei Zhao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Joseph P. Vogel
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Grant J. Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
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Shi Y, Liu H, Ma K, Luo ZQ, Qiu J. Legionella longbeachae effector protein RavZ inhibits autophagy and regulates phagosome ubiquitination during infection. PLoS One 2023; 18:e0281587. [PMID: 36758031 PMCID: PMC9910735 DOI: 10.1371/journal.pone.0281587] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Legionella organisms are ubiquitous environmental bacteria that are responsible for human Legionnaires' disease, a fatal form of severe pneumonia. These bacteria replicate intracellularly in a wide spectrum of host cells within a distinct compartment termed the Legionella-containing vacuole (LCV). Effector proteins translocated by the Dot/Icm apparatus extensively modulate host cellular functions to aid in the biogenesis of the LCV and intracellular proliferation. RavZ is an L. pneumophila effector that functions as a cysteine protease to hydrolyze lipidated LC3, thereby compromising the host autophagic response to bacterial infection. In this study, we characterized the RavZ (RavZLP) ortholog in L. longbeachae (RavZLLO), the second leading cause of Legionella infections in the world. RavZLLO and RavZLP share approximately 60% sequence identity and a conserved His-Asp-Cys catalytic triad. RavZLLO is recognized by the Dot/Icm systems of both L. pneumophila and L. longbeachae. Upon translocation into the host, it suppresses autophagy signaling in cells challenged with both species, indicating the functional redundancy of RavZLLO and RavZLP. Additionally, ectopic expression of RavZLLO but not RavZLP in mammalian cells reduces the levels of cellular polyubiquitinated and polyneddylated proteins. Consistent with this process, RavZLLO regulates the accumulation of polyubiquitinated species on the LCV during L. longbeachae infection.
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Affiliation(s)
- Yunjia Shi
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hongtao Liu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Kelong Ma
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail: (JQ); (ZQL)
| | - Jiazhang Qiu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
- * E-mail: (JQ); (ZQL)
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Complete genome sequence of marine Roseobacter lineage member Ruegeria sp. YS9 with five plasmids isolated from red algae. Mar Genomics 2023; 67:100997. [PMID: 36682852 DOI: 10.1016/j.margen.2022.100997] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022]
Abstract
Ruegeria sp. YS9, an aerobic and chemoheterotrophic bacterium belonging to marine Roseobacter lineage, was a putative new species isolated from red algae Eucheuma okamurai in the South China Sea (Beihai, Guangxi province). The complete genome sequence in strain YS9 comprised one circular chromosome with 3,244,635 bp and five circular plasmids ranging from 38,085 to 748,160 bp, with a total length of 4.30 Mb and average GC content of 58.39%. In total, 4129 CDSs, 52 tRNA genes and 9 rRNA genes were obtained. Genomic analysis of strain YS9 revealed that 85 CAZymes were organized in 147 PUL-associated CAZymes involved in polysaccharides metabolism, which were the highest among its two closely related Ruegeria strains. Numerous PULs related to degradation on the cell wall of algae, especially agar, indicated its major player role in the remineralization of algal-derived carbon. Further, the existence of multiple plasmids provided strain YS9 with distinct advantages to facilitate its rapid environmental adaptation, including polysaccharide metabolism, denitrification, resistance to heavy metal stresses such as copper and cobalt, type IV secretion systems and type IV toxin-antitoxin systems, which were obviously different from the two Ruegeria strains. This study provides evidence for polysaccharide metabolic capacity and functions of five plasmids in strain YS9, broadening our understanding of the ecological roles of bacteria in the environment around red algae and the function patterns of plasmids in marine Roseobacter lineage members for environmental adaptation.
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Ireton K, Gyanwali GC, Herath TUB, Lee N. Exploitation of the host exocyst complex by bacterial pathogens. Mol Microbiol 2023. [PMID: 36717381 DOI: 10.1111/mmi.15034] [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: 11/17/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/01/2023]
Abstract
Intracellular bacterial pathogens remodel the plasma membrane of eukaryotic cells in order to establish infection. A common and well-studied mechanism of plasma membrane remodelling involves bacterial stimulation of polymerization of the host actin cytoskeleton. Here, we discuss recent results showing that several bacterial pathogens also exploit the host vesicular trafficking pathway of 'polarized exocytosis' to expand and reshape specific regions in the plasma membrane during infection. Polarized exocytosis is mediated by an evolutionarily conserved octameric protein complex termed the exocyst. We describe examples in which the bacteria Listeria monocytogenes, Salmonella enterica serovar Typhimurium, and Shigella flexneri co-opt the exocyst to promote internalization into human cells or intercellular spread within host tissues. We also discuss results showing that Legionella pneumophila or S. flexneri manipulate exocyst components to modify membrane vacuoles to favour intracellular replication or motility of bacteria. Finally, we propose potential ways that pathogens manipulate exocyst function, discuss how polarized exocytosis might promote infection and highlight the importance of future studies to determine how actin polymerization and polarized exocytosis are coordinated to achieve optimal bacterial infection.
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Affiliation(s)
- Keith Ireton
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | | | - Thilina U B Herath
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Nicole Lee
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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Blasey N, Rehrmann D, Riebisch AK, Mühlen S. Targeting bacterial pathogenesis by inhibiting virulence-associated Type III and Type IV secretion systems. Front Cell Infect Microbiol 2023; 12:1065561. [PMID: 36704108 PMCID: PMC9872159 DOI: 10.3389/fcimb.2022.1065561] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
Infections caused by Gram-negative pathogens pose a major health burden. Both respiratory and gastrointestinal infections are commonly associated with these pathogens. With the increase in antimicrobial resistance (AMR) over the last decades, bacterial infections may soon become the threat they have been before the discovery of antibiotics. Many Gram-negative pathogens encode virulence-associated Type III and Type IV secretion systems, which they use to inject bacterial effector proteins across bacterial and host cell membranes into the host cell cytosol, where they subvert host cell functions in favor of bacterial replication and survival. These secretion systems are essential for the pathogens to cause disease, and secretion system mutants are commonly avirulent in infection models. Hence, these structures present attractive targets for anti-virulence therapies. Here, we review previously and recently identified inhibitors of virulence-associated bacterial secretions systems and discuss their potential as therapeutics.
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Backert S, Linz B, Tegtmeyer N. Helicobacter pylori-Induced Host Cell DNA Damage and Genetics of Gastric Cancer Development. Curr Top Microbiol Immunol 2023; 444:185-206. [PMID: 38231219 DOI: 10.1007/978-3-031-47331-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Gastric cancer is a very serious and deadly disease worldwide with about one million new cases every year. Most gastric cancer subtypes are associated with genetic and epigenetic aberrations caused by chromosome instability, microsatellite instability or Epstein-Barr virus infection. Another risk factor is an infection with Helicobacter pylori, which also triggers severe alterations in the host genome. This pathogen expresses an extraordinary repertoire of virulence determinants that take over control of important host cell signaling functions. In fact, H. pylori is a paradigm of persistent infection, chronic inflammation and cellular destruction. In particular, H. pylori profoundly induces chromosomal DNA damage by introducing double-strand breaks (DSBs) followed by genomic instability. DSBs appear in response to oxidative stress and pro-inflammatory transcription during the S-phase of the epithelial cell cycle, which mainly depends on the presence of the bacterial cag pathogenicity island (cagPAI)-encoded type IV secretion system (T4SS). This scenario is closely connected with the T4SS-mediated injection of ADP-glycero-β-D-manno-heptose (ADP-heptose) and oncoprotein CagA. While ADP-heptose links transcription factor NF-κB-induced innate immune signaling with RNA-loop-mediated DNA replication stress and introduction of DSBs, intracellular CagA targets the tumor suppressor BRCA1. The latter scenario promotes BRCAness, a disease characterized by the deficiency of effective DSB repair. In addition, genetic studies of patients demonstrated the presence of gastric cancer-associated single nucleotide polymorphisms (SNPs) in immune-regulatory and other genes as well as specific pathogenic germline variants in several crucial genes involved in homologous recombination and DNA repair, all of which are connected to H. pylori infection. Here we review the molecular mechanisms leading to chromosomal DNA damage and specific genetic aberrations in the presence or absence of H. pylori infection, and discuss their importance in gastric carcinogenesis.
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Affiliation(s)
- Steffen Backert
- Division of Microbiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany.
| | - Bodo Linz
- Division of Microbiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Nicole Tegtmeyer
- Division of Microbiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany.
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Guzmán-Herrador DL, Fernández-Gómez A, Llosa M. Recruitment of heterologous substrates by bacterial secretion systems for transkingdom translocation. Front Cell Infect Microbiol 2023; 13:1146000. [PMID: 36949816 PMCID: PMC10025392 DOI: 10.3389/fcimb.2023.1146000] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
Bacterial secretion systems mediate the selective exchange of macromolecules between bacteria and their environment, playing a pivotal role in processes such as horizontal gene transfer or virulence. Among the different families of secretion systems, Type III, IV and VI (T3SS, T4SS and T6SS) share the ability to inject their substrates into human cells, opening up the possibility of using them as customized injectors. For this to happen, it is necessary to understand how substrates are recruited and to be able to engineer secretion signals, so that the transmembrane machineries can recognize and translocate the desired substrates in place of their own. Other factors, such as recruiting proteins, chaperones, and the degree of unfolding required to cross through the secretion channel, may also affect transport. Advances in the knowledge of the secretion mechanism have allowed heterologous substrate engineering to accomplish translocation by T3SS, and to a lesser extent, T4SS and T6SS into human cells. In the case of T4SS, transport of nucleoprotein complexes adds a bonus to its biotechnological potential. Here, we review the current knowledge on substrate recognition by these secretion systems, the many examples of heterologous substrate translocation by engineering of secretion signals, and the current and future biotechnological and biomedical applications derived from this approach.
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