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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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5
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Bugaytsova JA, Moonens K, Piddubnyi A, Schmidt A, Edlund JO, Lisiutin G, Brännström K, Chernov YA, Thorel K, Tkachenko I, Sharova O, Vikhrova I, Butsyk A, Shubin P, Chyzhma R, Johansson DX, Marcotte H, Sjöström R, Shevtsova A, Bylund G, Rakhimova L, Lundquist A, Berhilevych O, Kasianchuk V, Loboda A, Ivanytsia V, Hultenby K, Persson MAA, Gomes J, Matos R, Gartner F, Reis CA, Whitmire JM, Merrell DS, Pan-Hammarström Q, Landström M, Oscarson S, D’Elios MM, Agreus L, Ronkainen J, Aro P, Engstrand L, Graham DY, Kachkovska V, Mukhopadhyay A, Chaudhuri S, Karmakar BC, Paul S, Kravets O, Camorlinga M, Torres J, Berg DE, Moskalenko R, Haas R, Remaut H, Hammarström L, Borén T. Helicobacter pylori attachment-blocking antibodies protect against duodenal ulcer disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542096. [PMID: 37292721 PMCID: PMC10245814 DOI: 10.1101/2023.05.24.542096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The majority of the world population carry the gastric pathogen Helicobacter pylori. Fortunately, most individuals experience only low-grade or no symptoms, but in many cases the chronic inflammatory infection develops into severe gastric disease, including duodenal ulcer disease and gastric cancer. Here we report on a protective mechanism where H. pylori attachment and accompanying chronic mucosal inflammation can be reduced by antibodies that are present in a vast majority of H. pylori carriers. These antibodies block binding of the H. pylori attachment protein BabA by mimicking BabA's binding to the ABO blood group glycans in the gastric mucosa. However, many individuals demonstrate low titers of BabA blocking antibodies, which is associated with an increased risk for duodenal ulceration, suggesting a role for these antibodies in preventing gastric disease.
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Affiliation(s)
- Jeanna A. Bugaytsova
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- SUMEYA, The Ukrainian-Swedish Research Center, Sumy State University, 40022 Sumy, Ukraine
| | - Kristof Moonens
- Structural and Molecular Microbiology, VIB Department of Structural Biology, VIB, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- Present address: Ablynx, a Sanofi Company, Technologiepark 21, 9052 Zwijnaarde, Belgium
| | - Artem Piddubnyi
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- SUMEYA, The Ukrainian-Swedish Research Center, Sumy State University, 40022 Sumy, Ukraine
- Department of Pathology, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Alexej Schmidt
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital, SE14186 Huddinge, Sweden
- Present address: Department of Medical Biosciences, Umeå University, SE90185 Umeå, Sweden
| | - Johan Olofsson Edlund
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- The Biochemical Imaging Center Umeå (BICU), Umeå University, SE90187 Umeå, Sweden
| | - Gennadii Lisiutin
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Department of Microbiology, Virology and Biotechnology, Odesa Mechnikov National University, 65082 Odesa, Ukraine
| | - Kristoffer Brännström
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- The Biochemical Imaging Center Umeå (BICU), Umeå University, SE90187 Umeå, Sweden
- Present address: Pfizer Worldwide R&D, BioMedicine Design, 10 555 Science Center Drive, San Diego CA, 92121 USA
| | - Yevgen A. Chernov
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
| | - Kaisa Thorel
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Iryna Tkachenko
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Department of Public Health, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Oleksandra Sharova
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Department of Pediatrics, Medical Institute, Sumy State University, 40018 Sumy, Ukraine
| | - Iryna Vikhrova
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Department of Pediatrics, Medical Institute, Sumy State University, 40018 Sumy, Ukraine
| | - Anna Butsyk
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Department of Public Health, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Pavlo Shubin
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Department of Public Health, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Ruslana Chyzhma
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- SUMEYA, The Ukrainian-Swedish Research Center, Sumy State University, 40022 Sumy, Ukraine
- Department of Pathology, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Daniel X. Johansson
- Department of Clinical Neuroscience, Karolinska Institutet at Center for Molecular Medicine, Karolinska University Hospital, Solna, SE17176 Stockholm, Sweden
| | - Harold Marcotte
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital, SE14186 Huddinge, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, SE14183, Huddinge, Sweden
| | - Rolf Sjöström
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
| | - Anna Shevtsova
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
| | - Göran Bylund
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
| | - Lena Rakhimova
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Present address: Department of Odontology, Umeå University, SE90187 Umeå, Sweden
| | - Anders Lundquist
- Department of Statistics, USBE, Umeå University, SE90187 Umeå, Sweden
- Umeå Center for Functional Brain Imaging, Umeå University, SE90187 Umeå, Sweden
| | - Oleksandra Berhilevych
- Department of Public Health, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Victoria Kasianchuk
- Department of Public Health, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Andrii Loboda
- Department of Pediatrics, Medical Institute, Sumy State University, 40018 Sumy, Ukraine
| | - Volodymyr Ivanytsia
- Department of Microbiology, Virology and Biotechnology, Odesa Mechnikov National University, 65082 Odesa, Ukraine
| | - Kjell Hultenby
- Departments of Laboratory Medicine, Division of Biomolecular and Cellular Medicine, Karolinska Institutet at Karolinska University Hospital, SE14186 Huddinge, Sweden
| | - Mats A. A. Persson
- Department of Clinical Neuroscience, Karolinska Institutet at Center for Molecular Medicine, Karolinska University Hospital, Solna, SE17176 Stockholm, Sweden
| | - Joana Gomes
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP – Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
| | - Rita Matos
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP – Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
| | - Fátima Gartner
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP – Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, University of Porto, 4050-313 Porto, Portugal
| | - Celso A. Reis
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP – Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | | | - D. Scott Merrell
- Department of Microbiology and Immunology, USUHS, Bethesda, MD 20814, USA
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, SE14183, Huddinge, Sweden
| | - Maréne Landström
- Present address: Department of Medical Biosciences, Umeå University, SE90185 Umeå, Sweden
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mario M. D’Elios
- Department of Experimental and Clinical Medicine, Largo Brambilla 3, 50134 Firenze, Italy
| | - Lars Agreus
- Division of Family Medicine and Primary Care, Karolinska Institutet, SE14183 Huddinge, Sweden
| | - Jukka Ronkainen
- University of Oulu, Center for Life Course Health Research and Primary Health Care Center, Tornio Finland
| | - Pertti Aro
- University of Oulu, Center for Life Course Health Research and Primary Health Care Center, Tornio Finland
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE17177 Stockholm, Sweden
- Present address: Science for Life Laboratory, SE17165, Solna, Sweden
| | - David Y. Graham
- Department of Medicine, Molecular Virology and Microbiology, Baylor College of Medicine, Michael E. DeBakey VAMC, 2002 Holcombe Blvd. Houston, TX, 77030 USA
| | - Vladyslava Kachkovska
- Department of Internal Medicine, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Asish Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases P 33, CIT Road, Scheme XM, Kolkata 700010, India
| | - Sujit Chaudhuri
- Department of Gastroenterology, AMRI Hospital, Salt Lake City. Kolkata, West Bengal 700098, India
| | - Bipul Chandra Karmakar
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases P 33, CIT Road, Scheme XM, Kolkata 700010, India
| | - Sangita Paul
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases P 33, CIT Road, Scheme XM, Kolkata 700010, India
| | - Oleksandr Kravets
- Department of Surgery, Traumatology, Orthopedics and Physiology, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Margarita Camorlinga
- Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, CMN SXXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Javier Torres
- Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, CMN SXXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Douglas E. Berg
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Roman Moskalenko
- SUMEYA, The Ukrainian-Swedish Research Center, Sumy State University, 40022 Sumy, Ukraine
- Department of Pathology, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Rainer Haas
- German Center for Infection Research (DZIF), Munich Site, 80336 Munich, Germany
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer-Institute, Faculty of Medicine, LMU Munich, Germany
| | - Han Remaut
- Structural and Molecular Microbiology, VIB Department of Structural Biology, VIB, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, SE14183, Huddinge, Sweden
| | - Thomas Borén
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- SUMEYA, The Ukrainian-Swedish Research Center, Sumy State University, 40022 Sumy, Ukraine
- Lead contact
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6
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Fu J, Shan J, Cui Y, Yan C, Wang Q, Han J, Cao G. Metabolic disorder and intestinal microflora dysbiosis in chronic inflammatory demyelinating polyradiculoneuropathy. Cell Biosci 2023; 13:6. [PMID: 36627678 PMCID: PMC9832664 DOI: 10.1186/s13578-023-00956-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVE Chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) is a rare acquired immune-mediated neuropathy. Although microbial infection is potentially a contributing factor, a causative link between CIDP and microbial infection remains unclear. There is also no definitive biomarker for CIDP diagnostics and therapies. The present study aimed to characterize the serum metabolic profile and gut microbiome structure in CIDP. METHODS Targeted metabolomics profiling of serum, using liquid chromatography-mass spectrometry, and metagenomics sequencing of stool samples from a cohort of CIDP and non-CIDP subjects were performed to evaluate serum metabolic profiles and gut microbiome structure in CIDP subjects relative to healthy controls. RESULTS Metabolome data revealed that the bile acids profile was perturbed in CIDP with bile acids and arachidonic acid enriched significantly in CIDP versus non-CIDP controls. Metagenome data revealed that opportunistic pathogens, such as Klebsiella pneumonia and Megamonas funiformis, and genes involved in bacterial infection were notably more abundant in CIDP subjects, while gut microbes related to biotransformation of secondary bile acids were abnormal in CIDP versus non-CIDP subjects. Correlation analysis revealed that changes in secondary bile acids were associated with altered gut microbes, including Bacteroides ovatus, Bacteroides caccae, and Ruminococcus gnavus. CONCLUSION Bile acids and arachidonic acid metabolism were disturbed in CIDP subjects and might be affected by the dysbiosis of gut microbial flora. These findings suggest that the combination of bile acids and arachidonic acid could be used as a CIDP biomarker and that modulation of gut microbiota might impact the clinical course of CIDP.
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Affiliation(s)
- Jiafang Fu
- grid.452422.70000 0004 0604 7301Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, First Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 China ,Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, 250117 China ,grid.410587.fNHC Key Laboratory of Biotechnology Drugs, Shandong Academy of Medical Sciences, Jinan, 250117 China
| | - Jingli Shan
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Yazhou Cui
- grid.452422.70000 0004 0604 7301Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, First Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 China ,Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, 250117 China ,grid.410587.fNHC Key Laboratory of Biotechnology Drugs, Shandong Academy of Medical Sciences, Jinan, 250117 China
| | - Chuanzhu Yan
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China ,Department of Central Laboratory and Mitochondrial Medicine Laboratory, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, 266035 China ,grid.27255.370000 0004 1761 1174Brain Science Research Institute, Shandong University, Jinan, 250012 China
| | - Qinzhou Wang
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Jinxiang Han
- grid.452422.70000 0004 0604 7301Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, First Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 China ,Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, 250117 China ,grid.410587.fNHC Key Laboratory of Biotechnology Drugs, Shandong Academy of Medical Sciences, Jinan, 250117 China
| | - Guangxiang Cao
- grid.452422.70000 0004 0604 7301Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, First Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 China ,Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, 250117 China ,grid.410587.fNHC Key Laboratory of Biotechnology Drugs, Shandong Academy of Medical Sciences, Jinan, 250117 China
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