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MATSUMOTO Y, YAMASAKI S, HAYAMA K, IINO R, NOJI H, YAMAGUCHI A, NISHINO K. Changes in the expression of mexB, mexY, and oprD in clinical Pseudomonas aeruginosa isolates. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2024; 100:57-67. [PMID: 38199247 PMCID: PMC10864171 DOI: 10.2183/pjab.100.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/12/2023] [Indexed: 01/12/2024]
Abstract
Changes in expression levels of drug efflux pump genes, mexB and mexY, and porin gene oprD in Pseudomonas aeruginosa were investigated in this study. Fifty-five multidrug-resistant P. aeruginosa (MDRP) strains were compared with 26 drug-sensitive strains and 21 strains resistant to a single antibiotic. The effect of the efflux inhibitor Phe-Arg-β-naphthylamide on drug susceptibility was determined, and gene expression was quantified using real-time quantitative real-time reverse transcription polymerase chain reaction. In addition, the levels of metallo-β-lactamase (MBL) and 6'-N-aminoglycoside acetyltransferase [AAC(6')-Iae] were investigated. Efflux pump inhibitor treatment increased the sensitivity to ciprofloxacin, aztreonam, and imipenem in 71%, 73%, and 29% of MDRPs, respectively. MBL and AAC(6')-Iae were detected in 38 (69%) and 34 (62%) MDRP strains, respectively. Meanwhile, 76% of MDRP strains exhibited more than 8-fold higher mexY expression than the reference strain PAO1. Furthermore, 69% of MDRP strains expressed oprD at levels less than 0.01-fold of those in PAO1. These findings indicated that efflux pump inhibitors in combination with ciprofloxacin or aztreonam might aid in treating MDRP infections.
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Affiliation(s)
- Yoshimi MATSUMOTO
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, Japan
| | - Seiji YAMASAKI
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
- Institute for Advanced Co-Creation Studies, Osaka University, Osaka, Japan
| | - Kouhei HAYAMA
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, Japan
| | - Ryota IINO
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Graduate Institute for Advanced Studies, The Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa, Japan
| | - Hiroyuki NOJI
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Akihito YAMAGUCHI
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, Japan
| | - Kunihiko NISHINO
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
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Mosaic Evolution of Beta-Barrel-Porin-Encoding Genes in Escherichia coli. Appl Environ Microbiol 2022; 88:e0006022. [PMID: 35285711 DOI: 10.1128/aem.00060-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial porin-encoding genes are often found under positive selection. Local recombination has also been identified in a few of them to facilitate bacterial rapid adaptation, although it remains unknown whether it is a common evolutionary mechanism for the porins or outer membrane proteins in Gram-negative bacteria. In this study, we investigated the beta-barrel (β-barrel) porin-encoding genes in Escherichia coli that were reported under positive Darwinian selection. Besides fhuA that was found with ingenic local recombination previously, we identified four other genes, i.e., lamB, ompA, ompC, and ompF, all showing the similar mosaic evolution patterns. Comparative analysis of the protein sequences disclosed a list of highly variable regions in each family, which are mostly located in the convex of extracellular loops and coinciding with the binding sites of bacteriophages. For each of the porin families, mosaic recombination leads to unique combinations of the variable regions with different sequence patterns, generating diverse protein groups. Structural modeling indicated a conserved global topology among the different porins, with the extracellular surface varying a lot due to individual or combinatorial variable regions. The conservation of global tertiary structure would ensure the channel activity, while the wide diversity of variable regions may represent selection to avoid the invasion of phages, antibiotics or immune surveillance factors. Our study identified multiple bacterial porin genes with mosaic evolution. We hypothesize that this could be generalized strategy for outer membrane proteins to both maintain normal life processes and evade the attack of unfavored factors rapidly. IMPORTANCE Microevolution studies can disclose more elaborate evolutionary mechanisms of genes, appearing especially important for genes with multifaceted function such as those encoding outer membrane proteins. However, in most cases, the gene is considered as a whole unit, and the evolutionary patterns are disclosed. Here, we report that multiple bacterial porin proteins follow mosaic evolution, with local ingenic recombination combined with spontaneous mutations based on positive Darwinian selection, and conservation for most structural regions. This could represent a common mechanism for bacterial outer membrane proteins. The variable regions within each porin family showed large coincidence with the binding sites of bacteriophages, antibiotics, and immune factors and therefore would represent effective targets for the development of new antibacterial agents or vaccines.
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D'Arrigo I, Cardoso JGR, Rennig M, Sonnenschein N, Herrgård MJ, Long KS. Analysis of Pseudomonas putida growth on non-trivial carbon sources using transcriptomics and genome-scale modelling. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:87-97. [PMID: 30298597 DOI: 10.1111/1758-2229.12704] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 06/08/2023]
Abstract
Pseudomonas putida is characterized by a versatile metabolism and stress tolerance traits that allow the bacterium to cope with different environmental conditions. In this work, the mechanisms that allow P. putida KT2440 to grow in the presence of four sole carbon sources (glucose, citrate, ferulic acid, serine) were investigated by RNA sequencing (RNA-seq) and genome-scale metabolic modelling. Transcriptomic data identified uptake systems for the four carbon sources, and candidates were subjected to preliminary experimental characterization by mutant strain growth to test their involvement in substrate assimilation. The OpdH and BenF-like porins were involved in citrate and ferulic acid uptake respectively. The citrate transporter (encoded by PP_0147) and the TctABC system were important for supporting cell growth in citrate; PcaT and VanK were associated with ferulic acid uptake; and the ABC transporter AapJPQM was involved in serine transport. A genome-scale metabolic model of P. putida KT2440 was used to integrate and analyze the transcriptomic data, identifying and confirming the active catabolic pathways for each carbon source. This study reveals novel information about transporters that are essential for understanding bacterial adaptation to different environments.
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Affiliation(s)
- Isotta D'Arrigo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
| | - João G R Cardoso
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
| | - Maja Rennig
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
| | - Nikolaus Sonnenschein
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
| | - Katherine S Long
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
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Stenkova AM, Bystritskaya EP, Guzev KV, Rakin AV, Isaeva MP. Molecular Evolution of the Yersinia Major Outer Membrane Protein C (OmpC). Evol Bioinform Online 2016; 12:185-91. [PMID: 27578962 PMCID: PMC4993215 DOI: 10.4137/ebo.s40346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/21/2016] [Accepted: 07/25/2016] [Indexed: 01/06/2023] Open
Abstract
The genus Yersinia includes species with a wide range of eukaryotic hosts (from fish, insects, and plants to mammals and humans). One of the major outer membrane proteins, the porin OmpC, is preferentially expressed in the host gut, where osmotic pressure, temperature, and the concentrations of nutrients and toxic products are relatively high. We consider here the molecular evolution and phylogeny of Yersinia ompC. The maximum likelihood gene tree reflects the macroevolution processes occurring within the genus Yersinia. Positive selection and horizontal gene transfer are the key factors of ompC diversification, and intraspecies recombination was revealed in two Yersinia species. The impact of recombination on ompC evolution was different from that of another major porin gene, ompF, possibly due to the emergence of additional functions and conservation of the basic transport function. The predicted antigenic determinants of OmpC were located in rapidly evolving regions, which may indicate the evolutionary mechanisms of Yersinia adaptation to the host immune system.
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Affiliation(s)
- Anna M. Stenkova
- Far Eastern Federal University, Vladivostok, Russia
- Pacific Institute of Bioorganic Chemistry, Vladivostok, Russia
| | - Evgeniya P. Bystritskaya
- Far Eastern Federal University, Vladivostok, Russia
- Pacific Institute of Bioorganic Chemistry, Vladivostok, Russia
| | | | - Alexander V. Rakin
- Max von Pettenkofer Institute for Hygiene and Clinical Microbiology, Ludwig Maximilian University, Munich, Germany
| | - Marina P. Isaeva
- Far Eastern Federal University, Vladivostok, Russia
- Pacific Institute of Bioorganic Chemistry, Vladivostok, Russia
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Li H, Luo YF, Williams BJ, Blackwell TS, Xie CM. Structure and function of OprD protein in Pseudomonas aeruginosa: from antibiotic resistance to novel therapies. Int J Med Microbiol 2012; 302:63-8. [PMID: 22226846 DOI: 10.1016/j.ijmm.2011.10.001] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Revised: 10/06/2011] [Accepted: 10/16/2011] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is a common pathogen isolated from patients with nosocomial infections. Due to its intrinsic and acquired antimicrobial resistance, limited classes of antibiotics can be used for the treatment of infection with P. aeruginosa. Of these, the carbapenems are very important; however, the occurrence of carbapenem-resistant strains is gradually increasing over time. Deficiency of the outer membrane protein OprD confers P. aeruginosa a basal level of resistance to carbapenems, especially to imipenem. Functional studies have revealed that loops 2 and 3 in the OprD protein contain the entrance and/or binding sites for imipenem. Therefore, any mutation in loop 2 and/or loop 3 that causes conformational changes could result in carbapenem resistance. OprD is also a common channel for some amino acids and peptides, and competition with carbapenems through the channel may also occur. Furthermore, OprD is a highly regulated protein at transcriptional and post-transcriptional levels by some metals, small bioactive molecules, amino acids, and efflux pump regulators. Because of its hypermutability and highly regulated properties, OprD is thought to be the most prevalent mechanism for carbapenem resistance in P. aeruginosa. Developing new strategies to combat infection with carbapenem-resistant P. aeruginosa lacking OprD is an ongoing challenge.
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Affiliation(s)
- Hui Li
- Division of Respiratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
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Guyard-Nicodème M, Bazire A, Hémery G, Meylheuc T, Mollé D, Orange N, Fito-Boncompte L, Feuilloley M, Haras D, Dufour A, Chevalier S. Outer membrane Modifications of Pseudomonas fluorescens MF37 in Response to Hyperosmolarity. J Proteome Res 2008; 7:1218-25. [DOI: 10.1021/pr070539x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Muriel Guyard-Nicodème
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Alexis Bazire
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Gaëlle Hémery
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Thierry Meylheuc
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Daniel Mollé
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Nicole Orange
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Laurène Fito-Boncompte
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Marc Feuilloley
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Dominique Haras
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Alain Dufour
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Sylvie Chevalier
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
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