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Ma X, Nugraha DK, Hiramatsu Y, Horiguchi Y. RpoN (sigma factor 54) contributes to bacterial fitness during tracheal colonization of Bordetella bronchiseptica. Microbiol Immunol 2024; 68:36-46. [PMID: 38105571 DOI: 10.1111/1348-0421.13109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/02/2023] [Accepted: 12/03/2023] [Indexed: 12/19/2023]
Abstract
The Gram-negative pathogenic bacterium Bordetella bronchiseptica is a respiratory pathogen closely related to Bordetella pertussis, the causative agent of whooping cough. Despite sharing homologous virulence factors, B. bronchiseptica infects a broad range of mammalian hosts, including some experimental animals, whereas B. pertussis is strictly adapted to humans. Therefore, B. bronchiseptica is often used as a representative model to explore the pathogenicity of Bordetella in infection experiments with laboratory animals. Although Bordetella virulence factors, including toxins and adhesins have been studied well, our recent study implied that unknown virulence factors are involved in tracheal colonization and infection. Here, we investigated bacterial genes contributing to tracheal colonization by high-throughput transposon sequencing (Tn-seq). After the screening, we picked up 151 candidate genes of various functions and found that a rpoN-deficient mutant strain was defective in tracheal colonization when co-inoculated with the wild-type strain. rpoN encodes σ54 , a sigma factor that regulates the transcription of various genes, implying its contribution to various bacterial activities. In fact, we found RpoN of B. bronchiseptica is involved in bacterial motility and initial biofilm formation. From these results, we propose that RpoN supports bacterial colonization by regulating various bacteriological functions.
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Affiliation(s)
- Xingyan Ma
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Dendi K Nugraha
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yukihiro Hiramatsu
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yasuhiko Horiguchi
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
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Saputri DS, Ismanto HS, Nugraha DK, Xu Z, Horiguchi Y, Sakakibara S, Standley DM. Deciphering the antigen specificities of antibodies by clustering their complementarity determining region sequences. mSystems 2023; 8:e0072223. [PMID: 37975681 PMCID: PMC10734444 DOI: 10.1128/msystems.00722-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Determining antigen and epitope specificity is an essential step in the discovery of therapeutic antibodies as well as in the analysis adaptive immune responses to disease or vaccination. Despite extensive efforts, deciphering antigen specificity solely from BCR amino acid sequence remains a challenging task, requiring a combination of experimental and computational approaches. Here, we describe and experimentally validate a simple and straightforward approach for grouping antibodies that share antigen and epitope specificities based on their CDR sequence similarity. This approach allows us to identify the specificities of a large number of antibodies whose antigen targets are unknown, using a small fraction of antibodies with well-annotated binding specificities.
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Affiliation(s)
- Dianita S. Saputri
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hendra S. Ismanto
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Dendi K. Nugraha
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Zichang Xu
- Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Yasuhiko Horiguchi
- Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
| | - Shuhei Sakakibara
- Immunology Frontier Research Center, Osaka University, Suita, Japan
- Graduate School of Medical Safety Management, Jikei University of Health Care Sciences, Osaka, Japan
| | - Daron M. Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Graduate School of Medicine, Osaka University, Suita, Japan
- Immunology Frontier Research Center, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
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Hiramatsu Y, Nishida T, Ota N, Tamaki Y, Nugraha DK, Horiguchi Y. DAT, deacylating autotransporter toxin, from Bordetella parapertussis demyristoylates Gα i GTPases and contributes to cough. Proc Natl Acad Sci U S A 2023; 120:e2308260120. [PMID: 37748060 PMCID: PMC10556565 DOI: 10.1073/pnas.2308260120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/28/2023] [Indexed: 09/27/2023] Open
Abstract
The pathogenic bacteria Bordetella pertussis and Bordetella parapertussis cause pertussis (whooping cough) and pertussis-like disease, respectively, both of which are characterized by paroxysmal coughing. We previously reported that pertussis toxin (PTx), which inactivates heterotrimeric GTPases of the Gi family through ADP-ribosylation of their α subunits, causes coughing in combination with Vag8 and lipid A in B. pertussis infection. In contrast, the mechanism of cough induced by B. parapertussis, which produces Vag8 and lipopolysaccharide (LPS) containing lipid A, but not PTx, remained to be elucidated. Here, we show that a toxin we named deacylating autotransporter toxin (DAT) of B. parapertussis inactivates heterotrimeric Gi GTPases through demyristoylation of their α subunits and contributes to cough production along with Vag8 and LPS. These results indicate that DAT plays a role in B. parapertussis infection in place of PTx.
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Affiliation(s)
- Yukihiro Hiramatsu
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka565-0871, Japan
| | - Takashi Nishida
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka565-0871, Japan
| | - Natsuko Ota
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka565-0871, Japan
| | - Yuki Tamaki
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka565-0871, Japan
| | - Dendi K. Nugraha
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka565-0871, Japan
| | - Yasuhiko Horiguchi
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka565-0871, Japan
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Ismanto HS, Xu Z, Saputri DS, Wilamowski J, Li S, Nugraha DK, Horiguchi Y, Okada M, Arase H, Standley DM. Landscape of infection enhancing antibodies in COVID-19 and healthy donors. Comput Struct Biotechnol J 2022; 20:6033-6040. [PMCID: PMC9635252 DOI: 10.1016/j.csbj.2022.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/01/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Hendra S. Ismanto
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Zichang Xu
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Dianita S. Saputri
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Jan Wilamowski
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Songling Li
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan
| | - Dendi K. Nugraha
- Deparment of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Yasuhiko Horiguchi
- Deparment of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan
| | - Masato Okada
- Deparment of Oncogene Research, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Department of Oncogene Research, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan
| | - Hisashi Arase
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Department of Immunochemistry, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan
| | - Daron M Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan
- Corresponding author at: Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan.
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