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Hota S, Kumar M. Unveiling the impact of Leptospira TolC efflux protein on host tissue adherence, complement evasion, and diagnostic potential. Infect Immun 2024:e0041924. [PMID: 39392312 DOI: 10.1128/iai.00419-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Accepted: 09/23/2024] [Indexed: 10/12/2024] Open
Abstract
The TolC family protein of Leptospira is a type I outer membrane efflux protein. Phylogenetic analysis revealed significant sequence conservation among pathogenic Leptospira species (83%-98% identity) compared with intermediate and saprophytic species. Structural modeling indicated a composition of six β-strands and 10 α-helices arranged in two repeats, resembling bacterial outer membrane efflux proteins. Recombinant TolC (rTolC), expressed in a heterologous host and purified via Ni-NTA chromatography, maintained its secondary structural integrity, as verified by circular dichroism spectroscopy. Polyclonal antibodies against rTolC detected native TolC expression in pathogenic Leptospira but not in nonpathogenic ones. Immunoassays and detergent fractionation assays indicated surface localization of TolC. The rTolC's recognition by sera from leptospirosis-infected hosts across species suggests its utility as a diagnostic marker. Notably, rTolC demonstrated binding affinity for various extracellular matrix components, including collagen and chondroitin sulfate A, as well as plasma proteins such as factor H, C3b, and plasminogen, indicating potential roles in tissue adhesion and immune evasion. Functional assays demonstrated that rTolC-bound FH retained cofactor activity for C3b cleavage, highlighting TolC's role in complement regulation. The rTolC protein inhibited both the alternative and the classical pathway-mediated membrane attack complex (MAC) deposition in vitro. Blocking surface-expressed TolC on leptospires using specific antibodies reduced FH acquisition by Leptospira and increased MAC deposition on the spirochete. These findings indicate that TolC contributes to leptospiral virulence by promoting host tissue colonization and evading the immune response, presenting it as a potential target for diagnostic and therapeutic strategies.
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Affiliation(s)
- Saswat Hota
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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2
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Bao X, Yang C, Li T, Wang Y, Cui A, Meng X, Huang Q, Li S. Efflux of TolC protein to different antimicrobials can be replaced by other outer membrane proteins with similar β-barrel structures in extraintestinal pathogenic Escherichia coli. J Appl Microbiol 2024; 135:lxae214. [PMID: 39217099 DOI: 10.1093/jambio/lxae214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 08/06/2024] [Accepted: 08/30/2024] [Indexed: 09/04/2024]
Abstract
AIM As a major efflux pump system in Gram-negative bacteria, AcrAB-TolC plays a key role in the transport of multiple drug substrates and is considered a potential target for the development of novel antimicrobials. Our previous study found that TolC inactivation compromised the resistance to different antimicrobials in porcine extraintestinal pathogenic Escherichia coli (ExPEC) strain PPECC042 (WT). This study was designed to investigate the functional substitution of TolC by other outer membrane proteins (OMPs) with similar β-barrel structures in pumping out different antimicrobials. METHODS AND RESULTS In this study, we found that over-expression of several OMPs with similar β-barrel structures, OmpX, OmpC, OmpN, OmpW, and PhoE, in the ΔtolC strain restored the resistance to macrolides, quinolones, or tetracyclines to the level of WT strain. However, the introduction of any one of the five OMPs did not affect the resistance of the strains ΔacrA, ΔacrB, and ΔacrAΔtolC. Further study revealed that the efflux activity was significantly reduced in the ΔtolC strain, but not in the WT strain and the ΔtolC strains over-expressing various OMPs. Additionally, Nile red dye test and ciprofloxacin accumulation test confirmed that the lost efflux activity and drug accumulation in bacterial periplasm by TolC inactivation was restored by the over-expression of each OMP, depending on the presence of genes acrA and acrB. CONCLUSION All five OMPs can replace the TolC protein to play the efflux role in pumping out the drugs from the periplasm to the extracellular space with the help of proteins AcrA and AcrB.
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Affiliation(s)
- Xue Bao
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Chenglong Yang
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Tian Li
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanlin Wang
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Ailian Cui
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xianrong Meng
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Huang
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Shaowen Li
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
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Beaud Benyahia B, Taib N, Beloin C, Gribaldo S. Terrabacteria: redefining bacterial envelope diversity, biogenesis and evolution. Nat Rev Microbiol 2024:10.1038/s41579-024-01088-0. [PMID: 39198708 DOI: 10.1038/s41579-024-01088-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2024] [Indexed: 09/01/2024]
Abstract
The bacterial envelope is one of the oldest and most essential cellular components and has been traditionally divided into Gram-positive (monoderm) and Gram-negative (diderm). Recent landmark studies have challenged a major paradigm in microbiology by inferring that the last bacterial common ancestor had a diderm envelope and that the outer membrane (OM) was lost repeatedly in evolution to give rise to monoderms. Intriguingly, OM losses appear to have occurred exclusively in the Terrabacteria, one of the two major clades of bacteria. In this Review, we present current knowledge about the Terrabacteria. We describe their diversity and phylogeny and then highlight the vast phenotypic diversity of the Terrabacteria cell envelopes, which display large deviations from the textbook examples of diderms and monoderms, challenging the classical Gram-positive-Gram-negative divide. We highlight the striking differences in the systems involved in OM biogenesis in Terrabacteria with respect to the classical diderm experimental models and how they provide novel insights into the diversity and biogenesis of the bacterial cell envelope. We also discuss the potential evolutionary steps that might have led to the multiple losses of the OM and speculate on how the very first OM might have emerged before the last bacterial common ancestor.
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Affiliation(s)
- Basile Beaud Benyahia
- Evolutionary Biology of the Microbial Cell Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
| | - Najwa Taib
- Evolutionary Biology of the Microbial Cell Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
| | - Christophe Beloin
- Genetics of Biofilms Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell Laboratory, Institut Pasteur, Université Paris Cité, Paris, France.
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4
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Burcham ZM. Comparative genomic analysis of an emerging Pseudomonadaceae member, Thiopseudomonas alkaliphila. Microbiol Spectr 2024; 12:e0415723. [PMID: 38934605 PMCID: PMC11302033 DOI: 10.1128/spectrum.04157-23] [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: 12/12/2023] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Thiopseudomonas alkaliphila, an organism recently classified within the Pseudomonadaceae family, has been detected in diverse sources such as human tissues, animal guts, industrial fermenters, and decomposition environments, suggesting a diverse ecological role. However, a large knowledge gap exists in how T. alkaliphila functions. In this comparative genomic analysis, adaptations indicative of habitat specificity among strains and genomic similarity to known opportunistic pathogens are revealed. Genomic investigation reveals a core metabolic utilization of multiple oxidative and non-oxidative catabolic pathways, suggesting adaptability to varied environments and carbon sources. The genomic repertoire of T. alkaliphila includes secondary metabolites, such as antimicrobials and siderophores, indicative of its involvement in microbial competition and resource acquisition. Additionally, the presence of transposases, prophages, plasmids, and Clustered Regularly Interspaced Short Palindromic Repeats-Cas systems in T. alkaliphila genomes suggests mechanisms for horizontal gene transfer and defense against viral predation. This comprehensive genomic analysis expands our understanding on the ecological functions, community interactions, and potential virulence of T. alkaliphila, while emphasizing its adaptability and diverse capabilities across environmental and host-associated ecosystems.IMPORTANCEAs the microbial world continues to be explored, new organisms will emerge with beneficial and/or pathogenetic impact. Thiopseudomonas alkaliphila is a species originally isolated from clinical human tissue and fluid samples but has not been attributed to disease. Since its classification, T. alkaliphila has been found in animal guts, animal waste, decomposing remains, and biogas fermentation reactors. This is the first study to provide an in-depth view of the metabolic potential of publicly available genomes belonging to this species through a comparative genomics and draft pangenome calculation approach. It was found that T. alkaliphila is metabolically versatile and likely adapts to diverse energy sources and environments, which may make it useful for bioremediation and in industrial settings. A range of virulence factors and antibiotic resistances were also detected, suggesting T. alkaliphila may operate as an undescribed opportunistic pathogen.
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Affiliation(s)
- Zachary M. Burcham
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
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5
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Burmeister AR, Tewatia H, Skinner C. A tradeoff between bacteriophage resistance and bacterial motility is mediated by the Rcs phosphorelay in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2024; 170. [PMID: 39194382 DOI: 10.1099/mic.0.001491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Across the tree of life, pleiotropy is thought to constrain adaptation through evolutionary tradeoffs. However, few examples of pleiotropy exist that are well explained at the genetic level, especially for pleiotropy that is mediated by multiple genes. Here, we describe a set of pleiotropic mutations that mediate two key fitness components in bacteria: parasite resistance and motility. We subjected Escherichia coli to strong selection by phage U136B to obtain 27 independent mucoid mutants. Mucoidy is a phenotype that results from excess exopolysaccharide and can act as a barrier against viral infection but can also interfere with other cellular functions. We quantified the mutants' phage resistance using efficiency of plaquing assays and swimming motility using swim agar plates, and we sequenced the complete genomes of all mutants to identify mucoid-causing mutations. Increased phage resistance co-occurred with decreased motility. This relationship was mediated by highly parallel (27/27) mutations to the Rcs phosphorelay pathway, which senses membrane stress to regulate exopolysaccharide production. Together, these results provide an empirical example of a pleiotropic relationship between two traits with intermediate genetic complexity.
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Affiliation(s)
- Alita R Burmeister
- Department of Biological Sciences, University of Wisconsin Milwaukee, Milwaukee, WI, USA
| | - Harleen Tewatia
- Department of Biological Sciences, University of Wisconsin Milwaukee, Milwaukee, WI, USA
| | - Chloé Skinner
- Department of Biological Sciences, University of Wisconsin Milwaukee, Milwaukee, WI, USA
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6
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Kherroubi L, Bacon J, Rahman KM. Navigating fluoroquinolone resistance in Gram-negative bacteria: a comprehensive evaluation. JAC Antimicrob Resist 2024; 6:dlae127. [PMID: 39144447 PMCID: PMC11323783 DOI: 10.1093/jacamr/dlae127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 07/04/2024] [Indexed: 08/16/2024] Open
Abstract
Since the introduction of quinolone and fluoroquinolone antibiotics to treat bacterial infections in the 1960s, there has been a pronounced increase in the number of bacterial species that have developed resistance to fluoroquinolone treatment. In 2017, the World Health Organization established a priority list of the most critical Gram-negative resistant pathogens. These included Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli. In the last three decades, investigations into the mechanisms of fluoroquinolone resistance have revealed that mutations in the target enzymes of fluoroquinolones, DNA gyrase or topoisomerase IV, are the most prevalent mechanism conferring high levels of resistance. Alterations to porins and efflux pumps that facilitate fluoroquinolone permeation and extrusion across the bacterial cell membrane also contribute to the development of resistance. However, there is a growing observation of novel mutants with newer generations of fluoroquinolones, highlighting the need for novel treatments. Currently, steady progress has been made in the development of novel antimicrobial agents that target DNA gyrase or topoisomerase IV through different avenues than current fluoroquinolones to prevent target-mediated resistance. Therefore, an updated review of the current understanding of fluoroquinolone resistance within the literature is imperative to aid in future investigations.
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Affiliation(s)
- Linda Kherroubi
- School of Cancer and Pharmaceutical Science, King’s College London, London SE1 9NH, UK
| | - Joanna Bacon
- Discovery Group, Vaccine Development and Evaluation Centre, UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
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Tajer L, Paillart JC, Dib H, Sabatier JM, Fajloun Z, Abi Khattar Z. Molecular Mechanisms of Bacterial Resistance to Antimicrobial Peptides in the Modern Era: An Updated Review. Microorganisms 2024; 12:1259. [PMID: 39065030 PMCID: PMC11279074 DOI: 10.3390/microorganisms12071259] [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: 05/08/2024] [Revised: 06/10/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
Antimicrobial resistance (AMR) poses a serious global health concern, resulting in a significant number of deaths annually due to infections that are resistant to treatment. Amidst this crisis, antimicrobial peptides (AMPs) have emerged as promising alternatives to conventional antibiotics (ATBs). These cationic peptides, naturally produced by all kingdoms of life, play a crucial role in the innate immune system of multicellular organisms and in bacterial interspecies competition by exhibiting broad-spectrum activity against bacteria, fungi, viruses, and parasites. AMPs target bacterial pathogens through multiple mechanisms, most importantly by disrupting their membranes, leading to cell lysis. However, bacterial resistance to host AMPs has emerged due to a slow co-evolutionary process between microorganisms and their hosts. Alarmingly, the development of resistance to last-resort AMPs in the treatment of MDR infections, such as colistin, is attributed to the misuse of this peptide and the high rate of horizontal genetic transfer of the corresponding resistance genes. AMP-resistant bacteria employ diverse mechanisms, including but not limited to proteolytic degradation, extracellular trapping and inactivation, active efflux, as well as complex modifications in bacterial cell wall and membrane structures. This review comprehensively examines all constitutive and inducible molecular resistance mechanisms to AMPs supported by experimental evidence described to date in bacterial pathogens. We also explore the specificity of these mechanisms toward structurally diverse AMPs to broaden and enhance their potential in developing and applying them as therapeutics for MDR bacteria. Additionally, we provide insights into the significance of AMP resistance within the context of host-pathogen interactions.
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Affiliation(s)
- Layla Tajer
- Laboratory of Applied Biotechnology (LBA3B), Azm Center for Research in Biotechnology and Its Applications, Department of Cell Culture, EDST, Lebanese University, Tripoli 1300, Lebanon; (L.T.); (Z.F.)
| | - Jean-Christophe Paillart
- CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Université de Strasbourg, 2 Allée Konrad Roentgen, F-67000 Strasbourg, France;
| | - Hanna Dib
- College of Engineering and Technology, American University of the Middle East, Egaila 54200, Kuwait;
| | - Jean-Marc Sabatier
- CNRS, INP, Inst Neurophysiopathol, Aix-Marseille Université, 13385 Marseille, France
| | - Ziad Fajloun
- Laboratory of Applied Biotechnology (LBA3B), Azm Center for Research in Biotechnology and Its Applications, Department of Cell Culture, EDST, Lebanese University, Tripoli 1300, Lebanon; (L.T.); (Z.F.)
- Department of Biology, Faculty of Sciences 3, Lebanese University, Campus Michel Slayman Ras Maska, Tripoli 1352, Lebanon
| | - Ziad Abi Khattar
- Faculty of Medicine and Medical Sciences, University of Balamand, Kalhat, P.O. Box 100, Tripoli, Lebanon
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8
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Zhu S, Alexander MK, Paiva TO, Rachwalski K, Miu A, Xu Y, Verma V, Reichelt M, Dufrêne YF, Brown ED, Cox G. The inactivation of tolC sensitizes Escherichia coli to perturbations in lipopolysaccharide transport. iScience 2024; 27:109592. [PMID: 38628966 PMCID: PMC11019271 DOI: 10.1016/j.isci.2024.109592] [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: 12/01/2023] [Revised: 02/02/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
The Escherichia coli outer membrane channel TolC complexes with several inner membrane efflux pumps to export compounds across the cell envelope. All components of these complexes are essential for robust efflux activity, yet E. coli is more sensitive to antimicrobial compounds when tolC is inactivated compared to the inactivation of genes encoding the inner membrane drug efflux pumps. While investigating these susceptibility differences, we identified a distinct class of inhibitors targeting the core-lipopolysaccharide translocase, MsbA. We show that tolC null mutants are sensitized to structurally unrelated MsbA inhibitors and msbA knockdown, highlighting a synthetic-sick interaction. Phenotypic profiling revealed that tolC inactivation induced cell envelope softening and increased outer membrane permeability. Overall, this work identified a chemical probe of MsbA, revealed that tolC is associated with cell envelope mechanics and integrity, and highlighted that these findings should be considered when using tolC null mutants to study efflux deficiency.
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Affiliation(s)
- Shawna Zhu
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada
| | | | - Telmo O. Paiva
- Institute of Life Sciences, UCLouvain, Croix du Sud, 4-5, bte L7.07.06, B-1348 Louvain-la-Neuve, Belgium
| | - Kenneth Rachwalski
- Biochemistry and Biomedical Sciences and Degroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Anh Miu
- Genentech Inc, Biochemical and Cellular Pharmacology, South San Francisco, CA, USA
| | - Yiming Xu
- Genentech Inc, Infectious Diseases, South San Francisco, CA, USA
| | - Vishal Verma
- Genentech Inc, Discovery Chemistry, South San Francisco, CA, USA
| | - Mike Reichelt
- Genentech Inc, Pathology, South San Francisco, CA, USA
| | - Yves F. Dufrêne
- Institute of Life Sciences, UCLouvain, Croix du Sud, 4-5, bte L7.07.06, B-1348 Louvain-la-Neuve, Belgium
| | - Eric D. Brown
- Biochemistry and Biomedical Sciences and Degroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Georgina Cox
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada
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Zheng S, Tang X, Yang Q, Zhou X, Li Y, Wu Z. Aeromonas veronii tolC modulates its virulence and the immune response of freshwater pearl mussels, Hyriopsis cumingii. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 153:105137. [PMID: 38224762 DOI: 10.1016/j.dci.2024.105137] [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: 10/18/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 01/17/2024]
Abstract
Aeromonas veronii is an opportunistic pathogen that causes diseases in aquatic animals, but its key virulence factors remain unclear. We screened the gene tolC with significantly different expression levels in the two isolates, A. veronii GL2 (higher virulence) and A. veronii FO1 (lower virulence). Therefore, we constructed mutant strain ΔtolC and analyzed its immunological properties. ΔtolC exhibited the reduced ability of biofilms formation, inhibited envelope stress response mediated by several antibiotics except cefuroxime, implying the ability to evade host immunity might be restrained. Challenge tests showed that the LD50 of ΔtolC was 10.89-fold than that of GL2. Enzymatic activities of ΔtolC group were significantly lower and peak time was delayed to 12 h, as demonstrated by qRT-PCR results. Histopathological examination displayed that the degree of tissue damage in ΔtolC group was alleviated. The results show that tolC is an important virulence factor of A. veronii, which provides references for live-attenuated vaccine.
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Affiliation(s)
- Sichun Zheng
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), and Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing, 400715, China
| | - Xiaoqi Tang
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), and Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing, 400715, China
| | - Qinglin Yang
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), and Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing, 400715, China
| | - Xicheng Zhou
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), and Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing, 400715, China
| | - Yanhong Li
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), and Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing, 400715, China
| | - Zhengli Wu
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), and Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing, 400715, China.
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Bouillet S, Bauer TS, Gottesman S. RpoS and the bacterial general stress response. Microbiol Mol Biol Rev 2024; 88:e0015122. [PMID: 38411096 PMCID: PMC10966952 DOI: 10.1128/mmbr.00151-22] [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] [Indexed: 02/28/2024] Open
Abstract
SUMMARYThe general stress response (GSR) is a widespread strategy developed by bacteria to adapt and respond to their changing environments. The GSR is induced by one or multiple simultaneous stresses, as well as during entry into stationary phase and leads to a global response that protects cells against multiple stresses. The alternative sigma factor RpoS is the central GSR regulator in E. coli and conserved in most γ-proteobacteria. In E. coli, RpoS is induced under conditions of nutrient deprivation and other stresses, primarily via the activation of RpoS translation and inhibition of RpoS proteolysis. This review includes recent advances in our understanding of how stresses lead to RpoS induction and a summary of the recent studies attempting to define RpoS-dependent genes and pathways.
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Affiliation(s)
- Sophie Bouillet
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Taran S. Bauer
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
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11
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Lories B, Belpaire TER, Smeets B, Steenackers HP. Competition quenching strategies reduce antibiotic tolerance in polymicrobial biofilms. NPJ Biofilms Microbiomes 2024; 10:23. [PMID: 38503782 PMCID: PMC10951329 DOI: 10.1038/s41522-024-00489-6] [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: 10/20/2022] [Accepted: 02/20/2024] [Indexed: 03/21/2024] Open
Abstract
Bacteria typically live in dense communities where they are surrounded by other species and compete for a limited amount of resources. These competitive interactions can induce defensive responses that also protect against antimicrobials, potentially complicating the antimicrobial treatment of pathogens residing in polymicrobial consortia. Therefore, we evaluate the potential of alternative antivirulence strategies that quench this response to competition. We test three competition quenching approaches: (i) interference with the attack mechanism of surrounding competitors, (ii) inhibition of the stress response systems that detect competition, and (iii) reduction of the overall level of competition in the community by lowering the population density. We show that either strategy can prevent the induction of antimicrobial tolerance of Salmonella Typhimurium in response to competitors. Competition quenching strategies can thus reduce tolerance of pathogens residing in polymicrobial communities and could contribute to the improved eradication of these pathogens via traditional methods.
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Affiliation(s)
- Bram Lories
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
| | - Tom E R Belpaire
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Division of Mechatronics, Biostatistics, and Sensors (MeBioS), Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Bart Smeets
- Division of Mechatronics, Biostatistics, and Sensors (MeBioS), Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Hans P Steenackers
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium.
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12
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Veisi R, Nazarian S, Fathi J, Hadi N. Expression and purification of TolC as a recombinant protein vaccine against Shigella flexneri and evaluation of immunogenic response in mice. Microb Pathog 2024; 188:106539. [PMID: 38211835 DOI: 10.1016/j.micpath.2024.106539] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/30/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND Shigella is one of the major causes of dysenteric diarrhea, which is known shigelosis. Shigelosis causes 160,000 deaths annually of diarrheal disease in the global scale especially children less than 5 years old. No licensed vaccine is available against shigelosis, therefore, efforts for develop an effective and safe vaccine against Shigella as before needed. The reverse vaccinology (RV) is a novel strategy that evaluate genome or proteome of the organism to find a new promising vaccine candidate. In this study, immunogenicity of a designed-recombinant antigen is evaluated through the in silico studies and animal experiments to predict a new immunogenic candidate against Shigella. METHODS In the first step, proteome of Shigella flexneri was obtained from UniProtKB and then the outer membrane and extracellular proteins were predicted. In this study TolC as an outer membrane protein was selected and confirmed among candidates. In next steps, pre-selected protein was evaluated for transmembrane domains, homology, conservation, antigenicity, solubility, and B- and T-cell prediction by different online servers. RESULT TolC as a conserved outer membrane protein, using different immune-informatics tools had acceptable scores and was selected as the immunogenic antigen for animal experiment studies. Recombinant TolC protein after expression and purification, was administered to BALB/c mice over three intraperitoneal routes. The sera of mice was used to evaluate the IgG1 production assay by indirect-ELISA. The immunized mice depicted effective protection against 2LD50 of Shigella. Flexneri ATCC12022 (challenge study). CONCLUSION Therefore, the reverse vaccinology approach and experimental test results demonstrated that TolC as a novel effective and immunogenic antigen is capable for protection against shigellosis.
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Affiliation(s)
- Razieh Veisi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shahram Nazarian
- Department of Biological Sciences, Faculty of Science, Imam Hossein University, Tehran, Iran
| | - Javad Fathi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nahal Hadi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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13
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Hadi N, Nazarian S, Rouhi S, Hosseini SE, Fathi J. Production of egg yolk antibody (IgY) against a chimeric protein containing IpaD, StxB, and TolC antigens from Shigella: An investigation of its prophylactic effects against Shiga toxin (Stx) and Shigella dysenteriae in vitro and in vivo. Heliyon 2024; 10:e26361. [PMID: 38404796 PMCID: PMC10884852 DOI: 10.1016/j.heliyon.2024.e26361] [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: 12/05/2023] [Revised: 02/10/2024] [Accepted: 02/12/2024] [Indexed: 02/27/2024] Open
Abstract
Shigella is a major problem in developing countries. Immunoglobulin Y (IgY) can be used for prophylaxis and neutralize bacteria. The aim of this study was to produce IgY against the chimeric protein containing IpaD, StxB, and TolC antigens from Shigella, investigate its prophylactic and neutralizing effects against Stx and Shigella dysenteriae. The nucleotide sequence corresponding to the chimeric protein was cloned into pET28a plasmid and expressed in E. coli BL21 (DE3). Protein expression was confirmed by SDS-PAGE and the recombinant protein was purified by Ni-NTA affinity chromatography. The 150 μg of chimeric protein was mixed with Freund's adjutant and injected into laying hens (Leghorn). IgY was purified using PEG6000 precipitation. Antibody titer in the serum and egg yolk was evaluated by ELISA. IgY challenge against 1,10 and 50 LD50 of Stx and S. dysenteriae was investigated. A 60.6 kDa recombinant protein was confirmed by SDS-PAGE. ELISA showed that the antibody titer was significantly increased. MTT assay [3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide] showed that at 16 μmol/L, IgY protected HeLa cells against Stx. Treatment of mice with 1000 and 1500 μg IgY leads to complete survival of the mice against 1LD50 toxin and 4000 μg of IgY led to complete survival against 1LD50, also 70% and 30% survival against 10 and 50 LD50S. dysenteriae. This study showed that IgY produced against Stx and Shigella virulence factors could cause high protective effects against bacteria and toxins.
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Affiliation(s)
- Nahal Hadi
- Department of Bacteriology and Virology, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shahram Nazarian
- Department of Biology, Faculty of Basic Science, Imam Hossein University, Tehran, Iran
| | - Saber Rouhi
- Resident of Large Animal Internal Medicine, Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Iran
| | - Seyed Edris Hosseini
- Resident of Large Animal Internal Medicine, Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Iran
| | - Javad Fathi
- Department of Bacteriology and Virology, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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14
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Johnson RM, Li K, Chen X, Morgan GL, Aubé J, Li B. The Hybrid Antibiotic Thiomarinol A Overcomes Intrinsic Resistance in Escherichia coli Using a Privileged Dithiolopyrrolone Moiety. ACS Infect Dis 2024; 10:582-593. [PMID: 38226592 PMCID: PMC11235417 DOI: 10.1021/acsinfecdis.3c00504] [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] [Indexed: 01/17/2024]
Abstract
An impermeable outer membrane and multidrug efflux pumps work in concert to provide Gram-negative bacteria with intrinsic resistance against many antibiotics. These resistance mechanisms reduce the intracellular concentrations of antibiotics and render them ineffective. The natural product thiomarinol A combines holothin, a dithiolopyrrolone antibiotic, with marinolic acid A, a close analogue of mupirocin. The hybridity of thiomarinol A converts the mupirocin scaffold from inhibiting Gram-positive bacteria to inhibiting both Gram-positive and -negative bacteria. We found that thiomarinol A accumulates significantly more than mupirocin within the Gram-negative bacterium Escherichia coli, likely contributing to its broad-spectrum activity. Antibiotic susceptibility testing of E. coli mutants reveals that thiomarinol A overcomes the intrinsic resistance mechanisms that render mupirocin inactive. Structure-activity relationship studies suggest that the dithiolopyrrolone is a privileged moiety for improving the accumulation and antibiotic activity of the mupirocin scaffold without compromising binding to isoleucyl-tRNA synthetase. These studies also highlight that accumulation is required but not sufficient for antibiotic activity. Our work reveals a role of the dithiolopyrrolone moiety in overcoming intrinsic mupirocin resistance in E. coli and provides a starting point for designing dual-acting and high-accumulating hybrid antibiotics.
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Affiliation(s)
- Rachel M Johnson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Xiaoyan Chen
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Gina L Morgan
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Bo Li
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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15
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Bina XR, Weng Y, Budnick J, Van Allen ME, Bina JE. Klebsiella pneumoniae TolC contributes to antimicrobial resistance, exopolysaccharide production, and virulence. Infect Immun 2023; 91:e0030323. [PMID: 37982617 PMCID: PMC10715176 DOI: 10.1128/iai.00303-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/26/2023] [Indexed: 11/21/2023] Open
Abstract
Klebsiella pneumoniae is a Gram-negative bacterium that causes a variety of human diseases, ranging from pneumonia to urinary tract infections and invasive diseases. The emergence of K. pneumoniae strains that are resistant to multiple antibiotics has made treatment more complex and led to K. pneumoniae becoming a global health threat. Addressing this threat necessitates the development of new therapeutic strategies to combat this pathogen, including strategies to overcome antimicrobial resistance and therapeutics for novel targets such as antivirulence. Here, we investigated the function of TolC, an outer membrane protein essential for the function of tripartite transporters, in K. pneumoniae. Mutation of tolC rendered K. pneumoniae hypersensitive to multiple antibiotics. Moreover, the tolC mutation impaired capsule production and affected the expression of key capsule biosynthetic genes, indicating a regulatory role for TolC in capsule biosynthesis. Additionally, TolC was essential for growth under iron-limiting conditions, suggesting its involvement in iron acquisition. The tolC mutant exhibited increased adherence to human enterocytes and enhanced serum sensitivity. In the Galleria mellonella infection model, the tolC mutant displayed reduced virulence compared to the wild type. Our findings highlight the pleiotropic role of TolC in K. pneumoniae pathobiology, influencing antimicrobial resistance, capsule production, iron homeostasis, adherence to host cells, and virulence. Understanding the multifaceted role of TolC in K. pneumoniae may guide the development of new therapeutic strategies against this pathogen. .
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Affiliation(s)
- X. Renee Bina
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yuding Weng
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - James Budnick
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mia E. Van Allen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - James E. Bina
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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16
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Ding Y, Hao J, Xiao W, Ye C, Xiao X, Jian C, Tang M, Li G, Liu J, Zeng Z. Role of efflux pumps, their inhibitors, and regulators in colistin resistance. Front Microbiol 2023; 14:1207441. [PMID: 37601369 PMCID: PMC10436536 DOI: 10.3389/fmicb.2023.1207441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/13/2023] [Indexed: 08/22/2023] Open
Abstract
Colistin is highly promising against multidrug-resistant and extensively drug-resistant bacteria clinically. Bacteria are resistant to colistin mainly through mcr and chromosome-mediated lipopolysaccharide (LPS) synthesis-related locus variation. However, the current understanding cannot fully explain the resistance mechanism in mcr-negative colistin-resistant strains. Significantly, the contribution of efflux pumps to colistin resistance remains to be clarified. This review aims to discuss the contribution of efflux pumps and their related transcriptional regulators to colistin resistance in various bacteria and the reversal effect of efflux pump inhibitors on colistin resistance. Previous studies suggested a complex regulatory relationship between the efflux pumps and their transcriptional regulators and LPS synthesis, transport, and modification. Carbonyl cyanide 3-chlorophenylhydrazone (CCCP), 1-(1-naphthylmethyl)-piperazine (NMP), and Phe-Arg-β-naphthylamide (PAβN) all achieved the reversal of colistin resistance, highlighting the role of efflux pumps in colistin resistance and their potential for adjuvant development. The contribution of the efflux pumps to colistin resistance might also be related to specific genetic backgrounds. They can participate in colistin tolerance and heterogeneous resistance to affect the treatment efficacy of colistin. These findings help understand the development of resistance in mcr-negative colistin-resistant strains.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jinbo Liu
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zhangrui Zeng
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
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17
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Szal T, Chauhan SS, Lewe P, Rachad FZ, Madre M, Paunina L, Witt S, Parthasarathi R, Windshügel B. Efflux Pump-Binding 4(3-Aminocyclobutyl)Pyrimidin-2-Amines Are Colloidal Aggregators. Biomolecules 2023; 13:1000. [PMID: 37371580 PMCID: PMC10296211 DOI: 10.3390/biom13061000] [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: 02/14/2023] [Revised: 06/02/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Efflux pumps are a relevant factor in antimicrobial resistance. In E. coli, the tripartite efflux pump AcrAB-TolC removes a chemically diverse set of antibiotics from the bacterium. Therefore, small molecules interfering with efflux pump function are considered adjuvants for improving antimicrobial therapies. Several compounds targeting the periplasmic adapter protein AcrA and the efflux pump AcrB have been identified to act synergistically with different antibiotics. Among those, several 4(3-aminocyclobutyl)pyrimidin-2-amines have been shown to bind to both proteins. In this study, we intended to identify analogs of these substances with improved binding affinity to AcrA using virtual screening followed by experimental validation. While we succeeded in identifying several compounds showing a synergistic effect with erythromycin on E. coli, biophysical studies suggested that 4(3-aminocyclobutyl)pyrimidin-2-amines form colloidal aggregates that do not bind specifically to AcrA. Therefore, these substances are not suited for further development. Our study emphasizes the importance of implementing additional control experiments to identify aggregators among bioactive compounds.
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Affiliation(s)
- Tania Szal
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, 22525 Hamburg, Germany; (T.S.); (F.-Z.R.)
- School of Science, Constructor University, 28759 Bremen, Germany
| | - Shweta Singh Chauhan
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; (S.S.C.); (R.P.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Philipp Lewe
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), 22607 Hamburg, Germany; (P.L.); (S.W.)
| | - Fatima-Zahra Rachad
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, 22525 Hamburg, Germany; (T.S.); (F.-Z.R.)
| | - Marina Madre
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia; (M.M.); (L.P.)
| | - Laura Paunina
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia; (M.M.); (L.P.)
| | - Susanne Witt
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), 22607 Hamburg, Germany; (P.L.); (S.W.)
| | - Ramakrishnan Parthasarathi
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; (S.S.C.); (R.P.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Björn Windshügel
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, 22525 Hamburg, Germany; (T.S.); (F.-Z.R.)
- School of Science, Constructor University, 28759 Bremen, Germany
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18
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Jang S. AcrAB-TolC, a major efflux pump in Gram negative bacteria: toward understanding its operation mechanism. BMB Rep 2023; 56:326-334. [PMID: 37254571 PMCID: PMC10315565 DOI: 10.5483/bmbrep.2023-0070] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/18/2023] [Accepted: 05/30/2023] [Indexed: 08/27/2023] Open
Abstract
Antibiotic resistance (AR) is a silent pandemic that kills millions worldwide. Although the development of new therapeutic agents against antibiotic resistance is in urgent demand, this has presented a great challenge, especially for Gram-negative bacteria that have inherent drug-resistance mediated by impermeable outer membranes and multidrug efflux pumps that actively extrude various drugs from the bacteria. For the last two decades, multidrug efflux pumps, including AcrAB-TolC, the most clinically important efflux pump in Gram-negative bacteria, have drawn great attention as strategic targets for re-sensitizing bacteria to the existing antibiotics. This article aims to provide a concise overview of the AcrAB-TolC operational mechanism, reviewing its architecture and substrate specificity, as well as the recent development of AcrAB-TolC inhibitors. [BMB Reports 2023; 56(6): 326-334].
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Affiliation(s)
- Soojin Jang
- Department of Discovery Biology, Antibacterial Resistance Laboratory, Institut Pasteur Korea, Seongnam 13488, Korea
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19
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Burmeister AR, Tzintzun-Tapia E, Roush C, Mangal I, Barahman R, Bjornson RD, Turner PE. Experimental Evolution of the TolC-Receptor Phage U136B Functionally Identifies a Tail Fiber Protein Involved in Adsorption through Strong Parallel Adaptation. Appl Environ Microbiol 2023:e0007923. [PMID: 37191555 DOI: 10.1128/aem.00079-23] [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] [Indexed: 05/17/2023] Open
Abstract
Bacteriophages have received recent attention for their therapeutic potential to treat antibiotic-resistant bacterial infections. One particular idea in phage therapy is to use phages that not only directly kill their bacterial hosts but also rely on particular bacterial receptors, such as proteins involved in virulence or antibiotic resistance. In such cases, the evolution of phage resistance would correspond to the loss of those receptors, an approach termed evolutionary steering. We previously found that during experimental evolution, phage U136B can exert selection pressure on Escherichia coli to lose or modify its receptor, the antibiotic efflux protein TolC, often resulting in reduced antibiotic resistance. However, for TolC-reliant phages like U136B to be used therapeutically, we also need to study their own evolutionary potential. Understanding phage evolution is critical for the development of improved phage therapies as well as the tracking of phage populations during infection. Here, we characterized phage U136B evolution in 10 replicate experimental populations. We quantified phage dynamics that resulted in five surviving phage populations at the end of the 10-day experiment. We found that phages from all five surviving populations had evolved higher rates of adsorption on either ancestral or coevolved E. coli hosts. Using whole-genome and whole-population sequencing, we established that these higher rates of adsorption were associated with parallel molecular evolution in phage tail protein genes. These findings will be useful in future studies to predict how key phage genotypes and phenotypes influence phage efficacy and survival despite the evolution of host resistance. IMPORTANCE Antibiotic resistance is a persistent problem in health care and a factor that may help maintain bacterial diversity in natural environments. Bacteriophages ("phages") are viruses that specifically infect bacteria. We previously discovered and characterized a phage called U136B, which infects bacteria through TolC. TolC is an antibiotic resistance protein that helps bacteria pump antibiotics out of the cell. Over short timescales, phage U136B can be used to evolutionarily "steer" bacterial populations to lose or modify the TolC protein, sometimes reducing antibiotic resistance. In this study, we investigate whether U136B itself evolves to better infect bacterial cells. We discovered that the phage can readily evolve specific mutations that increase its infection rate. This work will be useful for understanding how phages can be used to treat bacterial infections.
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Affiliation(s)
- Alita R Burmeister
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
- Department of Biological Sciences, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA
| | - Eddy Tzintzun-Tapia
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
| | - Carli Roush
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
| | - Ivan Mangal
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
| | - Roxanna Barahman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
| | | | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
- Microbiology Program, Yale School of Medicine, New Haven, Connecticut, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, Connecticut, USA
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20
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LaGree TJ, Byrd BA, Quelle RM, Schofield SL, Mok WWK. Stimulating Transcription in Antibiotic-Tolerant Escherichia coli Sensitizes It to Fluoroquinolone and Nonfluoroquinolone Topoisomerase Inhibitors. Antimicrob Agents Chemother 2023; 67:e0163922. [PMID: 36951560 PMCID: PMC10112259 DOI: 10.1128/aac.01639-22] [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: 12/08/2022] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
Antibiotic tolerant bacteria and persistent cells that remain alive after a course of antibiotic treatment can foster the chronicity of infections and the development of antibiotic resistance. Elucidating how bacteria overcome antibiotic action and devising strategies to bolster a new drug's activity can allow us to preserve our antibiotic arsenal. Here, we investigate strategies to potentiate the activities of topoisomerase inhibitors against nongrowing Escherichia coli that are often recalcitrant to existing antibiotics. We focus on sensitizing bacteria to the fluoroquinolone (FQ) levofloxacin (Levo) and to the spiropyrimidinetrione zoliflodacin (Zoli)-the first antibiotic in its class of compounds in clinical development. We found that metabolic stimulation either alone or in combination with inhibiting the AcrAB-TolC efflux pump sensitized stationary-phase E. coli to Levo and Zoli. We demonstrate that the added metabolites increased proton motive force generation and ATP production in stationary-phase cultures without restarting growth. Instead, the stimulated bacteria increased transcription and translation, which rendered the populations more susceptible to topoisomerase inhibitors. Our findings illuminate potential vulnerabilities of antibiotic-tolerant bacteria that can be leveraged to sensitize them to new and existing classes of topoisomerase inhibitors. These approaches enable us to stay one step ahead of adaptive bacteria and safeguard the efficacy of our existing antibiotics.
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Affiliation(s)
- Travis J. LaGree
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Brandon A. Byrd
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, Connecticut, USA
- School of Medicine, University of Connecticut, Farmington, Connecticut, USA
| | - Ryan M. Quelle
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Stephanie L. Schofield
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, Connecticut, USA
- Department of Molecular & Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Wendy W. K. Mok
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, Connecticut, USA
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21
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Dual-Uptake Mode of the Antibiotic Phazolicin Prevents Resistance Acquisition by Gram-Negative Bacteria. mBio 2023; 14:e0021723. [PMID: 36802165 PMCID: PMC10128002 DOI: 10.1128/mbio.00217-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Phazolicin (PHZ) is a peptide antibiotic exhibiting narrow-spectrum activity against rhizobia closely related to its producer, Rhizobium sp. strain Pop5. Here, we show that the frequency of spontaneous PHZ-resistant mutants in Sinorhizobium meliloti is below the detection limit. We find that PHZ can enter S. meliloti cells through two distinct promiscuous peptide transporters, BacA and YejABEF, which belong to the SLiPT (SbmA-like peptide transporter) and ABC (ATP-binding cassette) transporter families, respectively. The dual-uptake mode explains the lack of observed resistance acquisition because the simultaneous inactivation of both transporters is necessary for resistance to PHZ. Since both BacA and YejABEF are essential for the development of functional symbiosis of S. meliloti with leguminous plants, the unlikely acquisition of PHZ resistance via the inactivation of these transporters is further disfavored. A whole-genome transposon sequencing screen did not reveal additional genes that can provide strong PHZ resistance when inactivated. However, it was found that the capsular polysaccharide KPS, the novel putative envelope polysaccharide PPP (PHZ-protecting polysaccharide), as well as the peptidoglycan layer jointly contribute to the sensitivity of S. meliloti to PHZ, most likely serving as barriers that reduce the amount of PHZ transported inside the cell. IMPORTANCE Many bacteria produce antimicrobial peptides to eliminate competitors and create an exclusive niche. These peptides act either by membrane disruption or by inhibiting essential intracellular processes. The Achilles' heel of the latter type of antimicrobials is their dependence on transporters to enter susceptible cells. Transporter inactivation results in resistance. Here, we show that a rhizobial ribosome-targeting peptide, phazolicin (PHZ), uses two different transporters, BacA and YejABEF, to enter the cells of a symbiotic bacterium, Sinorhizobium meliloti. This dual-entry mode dramatically reduces the probability of the appearance of PHZ-resistant mutants. Since these transporters are also crucial for S. meliloti symbiotic associations with host plants, their inactivation in natural settings is strongly disfavored, making PHZ an attractive lead for the development of biocontrol agents for agriculture.
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22
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Das Q, Hasted TL, Lepp D, Yin X, Tang J, Chalmers G, Ross K, Boerlin P, Diarra MS. Transcriptional profiling of extraintestinal Escherichia coli exposed to cranberry pomace extracts alone or in combination with ceftriaxone. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2022.957099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) includes several serotypes that have been associated with colibacillosis in poultry, as well as urinary tract infections and newborn meningitis in humans. This study investigated the antimicrobial activities of ceftriaxone (AXO) and cranberry pomace extracts (CRAN) alone or in combination (CC) against multidrug-resistant (MDR) ExPEC from broiler. The growth-inhibitory activity of CRAN and synergy tests by a checkerboard method were determined in cation-adjusted Mueller–Hinton broth (CAMHB). The transcriptomic profile of the MDR E. coli O7:H18 (ST38) grown in CAMHB supplemented with sub-inhibitory concertation of CRAN and AXO alone or in combination was obtained by RNA-seq. The MIC of CRAN for all isolates was 16 mg/mL. An additive activity was observed between 4 mg/mL of CRAN and 4 μg/mL of AXO. Compared to the control, the transcriptomic analysis revealed that 4 mg/ml of (1/4MIC) CRAN and its combination with 4 μg/mL of (1/8MIC) AXO (CC) exposures resulted in 727 and 712 differentially expressed genes, respectively (false discovery rate < 0.001 and log2-fold change > 2), in the studied E. coli. Major virulence genes including adhesins (fim, flg, csg, and yad), protectins (omp, tra, waa, and hly), secretion systems (hof, pho, and vir), and quorum sensing (lsr), which are energetically expensive for bacteria, were downregulated. Most importantly, 1/4MIC of CRAN or CC downregulated the β-lactamase blaCMY-2 and efflux pump including tolC, mdtEIJ, gadEW, and their regulator gene evgS, while upregulating the cysteine biosynthesis and oxidative stress-related regulatory genes including cys, dmlA, sbp, nrdGHI, soxSR, and rpoH. Downregulation of multiple enzymes involved in TCA cycles and upregulation of Fe–S cluster coordinated by Cys and Isc proteins reflect the regulation of energy metabolism of the studied E. coli upon CRAN or CC exposure. The downregulation of outer membrane protein genes that control permeability barriers, along with different antimicrobial resistance genes, demonstrates that CRAN may have the unique potential to enhance the antimicrobial activities of third-generation cephalosporins such as AXO against MDR E. coli.
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23
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Yang C, Diarra MS, Attiq Rehman M, Li L, Yu H, Yin X, Aslam M, Carrillo CD, Yang C, Gong J. Virulence potential of antimicrobial-resistant extraintestinal pathogenic Escherichia coli from retail poultry meat in a Caenorhabditis elegans model. J Food Prot 2023; 86:100008. [PMID: 36916583 DOI: 10.1016/j.jfp.2022.11.001] [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: 03/09/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 12/23/2022]
Abstract
Healthy poultry can be a reservoir for extraintestinal pathogenic Escherichia coli (ExPEC), some of which could be multidrug resistant to antimicrobials. These ExPEC strains could contaminate the environment and/or food chain representing thus, food safety and human health risk. However, few studies have shown the virulence of poultry-source antimicrobial-resistant (AMR) ExPEC in humans. This study characterized AMR ExPEC and investigated the virulence potential of some of their isolates in a Caenorhabditis elegans infection model. A total of 46 E. coli isolates from poultry (chicken, n = 29; turkey, n = 12) retail meats and chicken feces (n = 4), or humans (n = 1) were sequenced and identified as ExPEC. Except eight, all remaining 38 ExPEC isolates were resistant to at least one antibiotic and carried corresponding antimicrobial resistance genes (ARGs). About 27 of the 46 ExPEC isolates were multidrug-resistant (≥3 antibiotic classes). Seven ExPEC isolates from chicken or turkey meats were of serotype O25:H4 and sequence type (ST) 131 which clustered with an isolate from a human urinary tract infection (UTI) case having the same serotype and ST. The C. elegans challenge model using eight of studied ExPEC isolates harboring various ARGs and virulence genes (VGs) showed that regardless of their ARG or VG numbers in tested poultry meat and feces, ExPEC significantly reduced the life span of the nematode (P < 0.05) similarly to a human UTI isolate. This study indicated the pathogenic potential of AMR ExPEC from retail poultry meat or feces, but more studies are warranted to establish their virulence in poultry and human. Furthermore, relationships between specific resistance profiles and/or VGs in these E. coli isolates for their pathogenicity deserve investigations.
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Affiliation(s)
- Chongwu Yang
- Guelph Research and Development Centre, Agriculture Agri-Food Canada (AAFC), Guelph, Ontario, Canada N1G 5C9; Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Moussa S Diarra
- Guelph Research and Development Centre, Agriculture Agri-Food Canada (AAFC), Guelph, Ontario, Canada N1G 5C9.
| | - Muhammad Attiq Rehman
- Guelph Research and Development Centre, Agriculture Agri-Food Canada (AAFC), Guelph, Ontario, Canada N1G 5C9
| | - Linyan Li
- Guelph Research and Development Centre, Agriculture Agri-Food Canada (AAFC), Guelph, Ontario, Canada N1G 5C9; State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Hai Yu
- Guelph Research and Development Centre, Agriculture Agri-Food Canada (AAFC), Guelph, Ontario, Canada N1G 5C9
| | - Xianhua Yin
- Guelph Research and Development Centre, Agriculture Agri-Food Canada (AAFC), Guelph, Ontario, Canada N1G 5C9
| | - Mueen Aslam
- Lacombe Research Centre, AAFC, Lacombe, Alberta, Canada T4L1W1
| | - Catherine D Carrillo
- Canadian Food Inspection Agency (CFIA), Ottawa Laboratory (Carling), Ottawa, Ontario, Canada K1Y 4K7
| | - Chengbo Yang
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Joshua Gong
- Guelph Research and Development Centre, Agriculture Agri-Food Canada (AAFC), Guelph, Ontario, Canada N1G 5C9.
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Yamasaki S, Yoneda T, Ikawa S, Hayashi-Nishino M, Nishino K. Investigating multidrug efflux pumps associated with fatty acid salt resistance in Escherichia coli. Front Microbiol 2023; 14:954304. [PMID: 36896427 PMCID: PMC9989013 DOI: 10.3389/fmicb.2023.954304] [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: 05/27/2022] [Accepted: 01/24/2023] [Indexed: 02/25/2023] Open
Abstract
Fatty acids salts exert bactericidal and bacteriostatic effects that inhibit bacterial growth and survival. However, bacteria can overcome these effects and adapt to their environment. Bacterial efflux systems are associated with resistance to different toxic compounds. Here, several bacterial efflux systems were examined to determine their influence on fatty acid salt resistance in Escherichia coli. Both acrAB and tolC E. coli deletion strains were susceptible to fatty acid salts, while plasmids carrying acrAB, acrEF, mdtABC, or emrAB conferred drug resistance to the ΔacrAB mutant, which indicated complementary roles for these multidrug efflux pumps. Our data exemplify the importance of bacterial efflux systems in E. coli resistance to fatty acid salts.
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Affiliation(s)
- Seiji Yamasaki
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan.,Institute for Advanced Co-Creation Studies, Osaka University, Osaka, Japan
| | - Tomohiro Yoneda
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Sota Ikawa
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Mitsuko Hayashi-Nishino
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Kunihiko Nishino
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan.,Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
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25
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The Multidrug Efflux Regulator AcrR of Escherichia coli Responds to Exogenous and Endogenous Ligands To Regulate Efflux and Detoxification. mSphere 2022; 7:e0047422. [PMID: 36416552 PMCID: PMC9769551 DOI: 10.1128/msphere.00474-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The transcriptional repressor AcrR is the main regulator of the multidrug efflux pump AcrAB-TolC, which plays a major role in antibiotic resistance and cell physiology in Escherichia coli and other Enterobacteriaceae. However, it remains unknown which ligands control the function of AcrR. To address this gap in knowledge, this study tested whether exogenous and/or endogenous molecules identified as potential AcrR ligands regulate the activity of AcrR. Using electrophoretic mobility shift assays (EMSAs) with purified AcrR and the acrAB promoter and in vivo gene expression experiments, we found that AcrR responds to both exogenous molecules and cellular metabolites produced by E. coli. In total, we identified four functional ligands of AcrR, ethidium bromide (EtBr), an exogenous antimicrobial known to be effluxed by the AcrAB-TolC pump and previously shown to bind to AcrR, and three polyamines produced by E. coli, namely, putrescine, cadaverine, and spermidine. We found that EtBr and polyamines bind to AcrR both in vitro and in vivo, which prevents the binding of AcrR to the acrAB promoter and, ultimately, induces the expression of acrAB. Finally, we also found that AcrR contributes to mitigating the toxicity produced by excess polyamines by directly regulating the expression of AcrAB-TolC and two previously unknown AcrR targets, the MdtJI spermidine efflux pump and the putrescine degradation enzyme PuuA. Overall, these findings significantly expand our understanding of the function of AcrR by revealing that this regulator responds to different exogenous and endogenous ligands to regulate the expression of multiple genes involved in efflux and detoxification. IMPORTANCE Multidrug efflux pumps can remove antibiotics and other toxic molecules from cells and are major contributors to antibiotic resistance and bacterial physiology. Therefore, it is essential to better understand their function and regulation. AcrAB-TolC is the main multidrug efflux pump in the Enterobacteriaceae family, and AcrR is its major transcriptional regulator. However, little is known about which ligands control the function of AcrR or which other genes are controlled by this regulator. This study contributes to addressing these gaps in knowledge by showing that (i) the activity of AcrR is controlled by the antimicrobial ethidium bromide and by polyamines produced by E. coli, and (ii) AcrR directly regulates the expression of AcrAB-TolC and genes involved in detoxification and efflux of excess polyamines. These findings significantly advance our understanding of the biological role of AcrR by identifying four ligands that control its function and two novel targets of this regulator.
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Hou B, Wang CY, Li SW, Zhou LJ, Che YL, Chen QY. Effects of Toxin-Antitoxin System HicAB on Biofilm Formation by Extraintestinal Pathogenic E. coli. Curr Microbiol 2022; 80:50. [PMID: 36542185 DOI: 10.1007/s00284-022-03138-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022]
Abstract
The type II toxin-antitoxin (T-A) HicAB system is abundant in several bacteria and archaea, such as Escherichia coli, Burkholderia Pseudomallei, Yersinia pestis, Pseudomonas aeruginosa, and Streptococcus pneumoniae. This system engages in stress response, virulence, and bacterial persistence. This study showed that the biofilm-forming ability of the hicAB deletion mutant was significantly decreased to moderate ability compared to the extra-intestinal pathogenic Escherichia coli (ExPEC) parent strain and the complemented strain, which are strong biofilm producers. Congo red assay showed that the hicAB mutant maintained the ability to form curli fimbriae. Using RNA-seq and comparative real-time quantitative RT-PCR, we observed the difference in gene expression between the hicAB mutant and the parent strain, which was associated with biofilm formation. Our data indicate that the HicAB type II T-A system has a key role in biofilm formation by ExPEC, which may be associated with outer membrane protein (OMP) gene expression. Collectively, our results indicate that the hicAB type II T-A system is involved in ExPEC biofilm formation.
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Affiliation(s)
- Bo Hou
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Animal Disease Control Technology Development Center, Fujian Academy of Agricultural Sciences, No. 104 Xindian Town, Fuzhou, 350013, Fujian, China.
| | - Chen-Yan Wang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Animal Disease Control Technology Development Center, Fujian Academy of Agricultural Sciences, No. 104 Xindian Town, Fuzhou, 350013, Fujian, China
| | - Shao-Wen Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Lun-Jiang Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Animal Disease Control Technology Development Center, Fujian Academy of Agricultural Sciences, No. 104 Xindian Town, Fuzhou, 350013, Fujian, China.
| | - Yong-Liang Che
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Animal Disease Control Technology Development Center, Fujian Academy of Agricultural Sciences, No. 104 Xindian Town, Fuzhou, 350013, Fujian, China
| | - Qiu-Yong Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Animal Disease Control Technology Development Center, Fujian Academy of Agricultural Sciences, No. 104 Xindian Town, Fuzhou, 350013, Fujian, China
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27
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Guardia AE, Wagner A, Busalmen JP, Di Capua C, Cortéz N, Beligni MV. The draft genome of Andean Rhodopseudomonas sp. strain AZUL predicts genome plasticity and adaptation to chemical homeostasis. BMC Microbiol 2022; 22:297. [PMID: 36494611 PMCID: PMC9733117 DOI: 10.1186/s12866-022-02685-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/29/2022] [Indexed: 12/13/2022] Open
Abstract
The genus Rhodopseudomonas comprises purple non-sulfur bacteria with extremely versatile metabolisms. Characterization of several strains revealed that each is a distinct ecotype highly adapted to its specific micro-habitat. Here we present the sequencing, genomic comparison and functional annotation of AZUL, a Rhodopseudomonas strain isolated from a high altitude Andean lagoon dominated by extreme conditions and fluctuating levels of chemicals. Average nucleotide identity (ANI) analysis of 39 strains of this genus showed that the genome of AZUL is 96.2% identical to that of strain AAP120, which suggests that they belong to the same species. ANI values also show clear separation at the species level with the rest of the strains, being more closely related to R. palustris. Pangenomic analyses revealed that the genus Rhodopseudomonas has an open pangenome and that its core genome represents roughly 5 to 12% of the total gene repertoire of the genus. Functional annotation showed that AZUL has genes that participate in conferring genome plasticity and that, in addition to sharing the basal metabolic complexity of the genus, it is also specialized in metal and multidrug resistance and in responding to nutrient limitation. Our results also indicate that AZUL might have evolved to use some of the mechanisms involved in resistance as redox reactions for bioenergetic purposes. Most of those features are shared with strain AAP120, and mainly involve the presence of additional orthologs responsible for the mentioned processes. Altogether, our results suggest that AZUL, one of the few bacteria from its habitat with a sequenced genome, is highly adapted to the extreme and changing conditions that constitute its niche.
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Affiliation(s)
- Aisha E. Guardia
- grid.473319.b0000 0004 0461 9871Ingeniería de Interfases y Bioprocesos, Instituto de Tecnología de Materiales (INTEMA-CONICET-UNMdP), Mar del Plata, Argentina
| | - Agustín Wagner
- grid.10814.3c0000 0001 2097 3211Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Juan P. Busalmen
- grid.473319.b0000 0004 0461 9871Ingeniería de Interfases y Bioprocesos, Instituto de Tecnología de Materiales (INTEMA-CONICET-UNMdP), Mar del Plata, Argentina
| | - Cecilia Di Capua
- grid.501777.30000 0004 0638 1836Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Universidad Nacional de Rosario, Rosario, Argentina
| | - Néstor Cortéz
- grid.501777.30000 0004 0638 1836Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Universidad Nacional de Rosario, Rosario, Argentina
| | - María V. Beligni
- grid.412221.60000 0000 9969 0902Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
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28
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Rajput A, Tsunemoto H, Sastry AV, Szubin R, Rychel K, Chauhan SM, Pogliano J, Palsson BO. Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa. Nucleic Acids Res 2022; 50:9675-9688. [PMID: 36095122 PMCID: PMC9508857 DOI: 10.1093/nar/gkac743] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/06/2022] [Accepted: 09/06/2022] [Indexed: 11/14/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen and major cause of hospital-acquired infections. The virulence of P. aeruginosa is largely determined by its transcriptional regulatory network (TRN). We used 411 transcription profiles of P. aeruginosa from diverse growth conditions to construct a quantitative TRN by identifying independently modulated sets of genes (called iModulons) and their condition-specific activity levels. The current study focused on the use of iModulons to analyze the biofilm production and antibiotic resistance of P. aeruginosa. Our analysis revealed: (i) 116 iModulons, 81 of which show strong association with known regulators; (ii) novel roles of regulators in modulating antibiotics efflux pumps; (iii) substrate-efflux pump associations; (iv) differential iModulon activity in response to beta-lactam antibiotics in bacteriological and physiological media; (v) differential activation of 'Cell Division' iModulon resulting from exposure to different beta-lactam antibiotics and (vi) a role of the PprB iModulon in the stress-induced transition from planktonic to biofilm lifestyle. In light of these results, the construction of an iModulon-based TRN provides a transcriptional regulatory basis for key aspects of P. aeruginosa infection, such as antibiotic stress responses and biofilm formation. Taken together, our results offer a novel mechanistic understanding of P. aeruginosa virulence.
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Affiliation(s)
- Akanksha Rajput
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Hannah Tsunemoto
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Anand V Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Siddharth M Chauhan
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Joe Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
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29
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A genetic platform to investigate the functions of bacterial drug efflux pumps. Nat Chem Biol 2022; 18:1399-1409. [PMID: 36065018 DOI: 10.1038/s41589-022-01119-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 07/21/2022] [Indexed: 11/08/2022]
Abstract
Efflux pumps are a serious challenge for the development of antibacterial agents. Overcoming efflux requires an in-depth understanding of efflux pump functions, specificities and the development of inhibitors. However, the complexities of efflux networks have limited such studies. To address these challenges, we generated Efflux KnockOut-35 (EKO-35), a highly susceptible Escherichia coli strain lacking 35 efflux pumps. We demonstrate the use of this strain by constructing an efflux platform comprising EKO-35 strains individually producing efflux pumps forming tripartite complexes with TolC. This platform was profiled against a curated diverse compound collection, which enabled us to define physicochemical properties that contribute to transport. We also show the E. coli drug efflux network is conditionally essential for growth, and that the platform can be used to investigate efflux pump inhibitor specificities and efflux pump interplay. We believe EKO-35 and the efflux platform will have widespread application for the study of drug efflux.
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30
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New C-6 functionalized quinoline NorA inhibitors strongly synergize with ciprofloxacin against planktonic and biofilm growing resistant Staphylococcus aureus strains. Eur J Med Chem 2022; 241:114656. [DOI: 10.1016/j.ejmech.2022.114656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/22/2022] [Accepted: 08/01/2022] [Indexed: 11/17/2022]
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31
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Álvarez B, Muñoz-Abad V, Asensio-Calavia A, Fernández LÁ. Enhanced protein translocation to mammalian cells by expression of EtgA transglycosylase in a synthetic injector E. coli strain. Microb Cell Fact 2022; 21:133. [PMID: 35780105 PMCID: PMC9250224 DOI: 10.1186/s12934-022-01860-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/23/2022] [Indexed: 12/29/2022] Open
Abstract
Background Bacterial type III secretion systems (T3SSs) assemble a multiprotein complex termed the injectisome, which acts as a molecular syringe for translocation of specific effector proteins into the cytoplasm of host cells. The use of injectisomes for delivery of therapeutic proteins into mammalian cells is attractive for biomedical applications. With that aim, we previously generated a non-pathogenic Escherichia coli strain, called Synthetic Injector E. coli (SIEC), which assembles functional injectisomes from enteropathogenic E. coli (EPEC). The assembly of injectisomes in EPEC is assisted by the lytic transglycosylase EtgA, which degrades the peptidoglycan layer. As SIEC lacks EtgA, we investigated whether expression of this transglycosylase enhances the protein translocation capacity of the engineered bacterium. Results The etgA gene from EPEC was integrated into the SIEC chromosome under the control of the inducible tac promoter, generating the strain SIEC-eEtgA. The controlled expression of EtgA had no effect on the growth or viability of bacteria. Upon induction, injectisome assembly was ~ 30% greater in SIEC-eEtgA than in the parental strain, as determined by the level of T3SS translocon proteins, the hemolytic activity of the bacterial strain, and the impairment in flagellar motility. The functionality of SIEC-eEtgA injectisomes was evaluated in a derivative strain carrying a synthetic operon (eLEE5), which was capable of delivering Tir effector protein into the cytoplasm of HeLa cells triggering F-actin polymerization beneath the attached bacterium. Lastly, using β-lactamase as a reporter of T3SS-protein injection, we determined that the protein translocation capacity was ~ 65% higher in the SIEC-EtgA strain than in the parental SIEC strain. Conclusions We demonstrate that EtgA enhances the assembly of functional injectisomes in a synthetic injector E. coli strain, enabling the translocation of greater amounts of proteins into the cytoplasm of mammalian cells. Accordingly, EtgA expression may boost the protein translocation of SIEC strains programmed as living biotherapeutics.
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Affiliation(s)
- Beatriz Álvarez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus Cantoblanco, 28049, Madrid, Spain
| | - Víctor Muñoz-Abad
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus Cantoblanco, 28049, Madrid, Spain.,Programa de Doctorado en Biociencias Moleculares, Universidad Autónoma de Madrid (UAM), Campus Cantoblanco, 28049, Madrid, Spain.,Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid), Nicolas Cabrera 1, Campus Cantoblanco, 28049, Madrid, Spain
| | - Alejandro Asensio-Calavia
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus Cantoblanco, 28049, Madrid, Spain.,Programa de Doctorado en Biociencias Moleculares, Universidad Autónoma de Madrid (UAM), Campus Cantoblanco, 28049, Madrid, Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus Cantoblanco, 28049, Madrid, Spain.
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García-Descalzo L, García-López E, Cid C. Comparative Proteomic Analysis of Psychrophilic vs. Mesophilic Bacterial Species Reveals Different Strategies to Achieve Temperature Adaptation. Front Microbiol 2022; 13:841359. [PMID: 35591995 PMCID: PMC9111180 DOI: 10.3389/fmicb.2022.841359] [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: 12/22/2021] [Accepted: 03/08/2022] [Indexed: 11/16/2022] Open
Abstract
The old debate of nature (genes) vs. nurture (environmental variables) is once again topical concerning the effect of climate change on environmental microorganisms. Specifically, the Polar Regions are experiencing a drastic increase in temperature caused by the rise in greenhouse gas emissions. This study, in an attempt to mimic the molecular adaptation of polar microorganisms, combines proteomic approaches with a classical microbiological analysis in three bacterial species Shewanella oneidensis, Shewanella frigidimarina, and Psychrobacter frigidicola. Both shewanellas are members of the same genus but they live in different environments. On the other hand, Shewanella frigidimarina and Psychrobacter frigidicola share the same natural environment but belong to a different genus. The comparison of the strategies employed by each bacterial species estimates the contribution of genome vs. environmental variables in the adaptation to temperature. The results show a greater versatility of acclimatization for the genus Shewanella with respect to Psychrobacter. Besides, S. frigidimarina was the best-adapted species to thermal variations in the temperature range 4–30°C and displayed several adaptation mechanisms common with the other two species. Regarding the molecular machinery used by these bacteria to face the consequences of temperature changes, chaperones have a pivoting role. They form complexes with other proteins in the response to the environment, establishing cooperation with transmembrane proteins, elongation factors, and proteins for protection against oxidative damage.
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Affiliation(s)
- Laura García-Descalzo
- Centro de Astrobiología, Department of Planetology and Habitability, CSIC-INTA, Madrid, Spain
| | - Eva García-López
- Centro de Astrobiología, Department of Molecular Ecology, CSIC-INTA, Madrid, Spain
| | - Cristina Cid
- Centro de Astrobiología, Department of Molecular Ecology, CSIC-INTA, Madrid, Spain
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Abstract
SignificanceOuter membrane porins play a crucial role in processes as varied as energy production, photosynthesis, and nutrient transport. They act as the gatekeepers between a gram-negative bacterium and its environment. Understanding how these proteins fold and function is important in improving our understanding and control of these processes. Here we use single-molecule methods to help resolve the apparent differences between the fast folding expected on a molecular scale and the slow kinetics observed in ensemble measurements in the laboratory.
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Distinct Potentially Adaptive Accumulation of Truncation Mutations in Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi A. Microbiol Spectr 2022; 10:e0196921. [PMID: 35467366 PMCID: PMC9241588 DOI: 10.1128/spectrum.01969-21] [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] [Indexed: 11/20/2022] Open
Abstract
Gene inactivation through the accumulation of truncation (or premature stop codon) mutations is a common mode of evolution in bacteria. It is frequently believed to result from reductive evolutionary processes allowing purging of superfluous traits. However, several works have demonstrated that, similar to the occurrences of inactivating nonsynonymous (i.e., amino acid replacement) mutations under positive selection pressures, truncation mutations can also be adaptive where specific traits deleterious in particular environmental conditions need to be inactivated for survival. Here, we performed a comparative analysis of genome-wide accumulation of truncation mutations in Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi A. Considering the known convergent evolutionary trajectories in these two serovars, we expected a strong overlap of truncated genes in S. Typhi and S. Paratyphi A, emerging through either reductive or adaptive dynamics. However, we detected a distinct set of core truncated genes encoding different overrepresented functional clusters in each serovar. In 54% and 28% truncated genes in S. Typhi and S. Paratyphi A, respectively, inactivating mutations were acquired by only different subsets of isolates, instead of all isolates analyzed for that serovar. Importantly, 62% truncated genes (P < 0.001) in S. Typhi and S. Paratyphi A were also targeted by convergent amino acid mutations in different serovars, suggesting those genes to be under selection pressures. Our findings indicate significant presence of potentially adaptive truncation mutations in conjunction with the ones emerging due to reductive evolution. Further experimental and large-scale bioinformatic studies are necessary to better explore the impact of such adaptive footprints of truncation mutations in the evolution of bacterial virulence. IMPORTANCE Detecting the adaptive mutations leading to gene inactivation or loss of function is crucial for understanding their contribution in the evolution of bacterial virulence and antibiotic resistance. Such inactivating mutations, apart from being of nonsynonymous (i.e., amino acid replacement) nature, can also be truncation mutations, abruptly trimming the length of encoded proteins. Importantly, the notion of reductive evolutionary dynamics is primarily accepted toward the accumulation of truncation mutations. However, our case study on S. Typhi and S. Paratyphi A, two human-restricted systemically invasive pathogens exerting similar clinical manifestations, indicated that a significant proportion of truncation mutations emerge from positive selection pressures. The candidate genes from our study will enable directed functional assays for deciphering the adaptive role of truncation mutations in S. Typhi and S. Paratyphi A pathogenesis. Also, our genome-level analytical approach will pave the way to understand the contribution of truncation mutations in the adaptive evolution of other bacterial pathogens.
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Detection of Antimicrobial Resistance, Pathogenicity, and Virulence Potentials of Non-Typhoidal Salmonella Isolates at the Yaounde Abattoir Using Whole-Genome Sequencing Technique. Pathogens 2022; 11:pathogens11050502. [PMID: 35631023 PMCID: PMC9148033 DOI: 10.3390/pathogens11050502] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
One of the crucial public health problems today is the emerging and re-emerging of multidrug-resistant (MDR) bacteria coupled with a decline in the development of new antimicrobials. Non-typhoidal Salmonella (NTS) is classified among the MDR pathogens of international concern. To predict their MDR potentials, 23 assembled genomes of NTS from live cattle (n = 1), beef carcass (n = 19), butchers’ hands (n = 1) and beef processing environments (n = 2) isolated from 830 wet swabs at the Yaounde abattoir between December 2014 and November 2015 were explored using whole-genome sequencing. Phenotypically, while 22% (n = 5) of Salmonella isolates were streptomycin-resistant, 13% (n = 3) were MDR. Genotypically, all the Salmonella isolates possessed high MDR potentials against several classes of antibiotics including critically important drugs (carbapenems, third-generation cephalosporin and fluoroquinolone). Moreover, >31% of NTS exhibited resistance potentials to polymyxin, considered as the last resort drug. Additionally, ≤80% of isolates harbored “silent resistant genes” as a potential reservoir of drug resistance. Our isolates showed a high degree of pathogenicity and possessed key virulence factors to establish infection even in humans. Whole-genome sequencing unveiled both broader antimicrobial resistance (AMR) profiles and inference of pathogen characteristics. This study calls for the prudent use of antibiotics and constant monitoring of AMR of NTS.
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36
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Lozano C, Kielbasa M, Gaillard JC, Miotello G, Pible O, Armengaud J. Identification and Characterization of Marine Microorganisms by Tandem Mass Spectrometry Proteotyping. Microorganisms 2022; 10:microorganisms10040719. [PMID: 35456770 PMCID: PMC9027524 DOI: 10.3390/microorganisms10040719] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 02/01/2023] Open
Abstract
The vast majority of marine microorganisms and their functions are yet to be explored. The considerable diversity they encompass is an endless source of knowledge and wealth that can be valued on an industrial scale, emphasizing the need to develop rapid and efficient identification and characterization techniques. In this study, we identified 26 microbial isolates from coastal water of the NW Mediterranean Sea, using phylopeptidomics, a cutting-edge tandem mass spectrometry proteotyping technique. Taxonomical identification at the species level was successfully conducted for all isolates. The presence of strains belonging to the newly described Balneolaeota phylum, yet uncharacterized at the proteomics scale, was noted. The very first proteomics-based investigation of a representative of the Balneolaeota phylum, Balneola vulgaris, is proposed, demonstrating the use of our proteotyping workflow for the rapid identification and in-depth molecular characterization, in a single MS/MS analytical run. Tandem mass spectrometry proteotyping is a valuable asset for culturomic programs as the methodology is able to quickly classify the most atypical isolates.
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Lo HH, Chang HC, Liao CT, Hsiao YM. Expression and function of clpS and clpA in Xanthomonas campestris pv. campestris. Antonie van Leeuwenhoek 2022; 115:589-607. [PMID: 35322326 DOI: 10.1007/s10482-022-01725-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
Abstract
ATP-dependent proteases (FtsH, Lon, and Clp family proteins) are ubiquitous in bacteria and play essential roles in numerous regulatory cell processes. Xanthomonas campestris pv. campestris is a Gram-negative pathogen that can cause black rot diseases in crucifers. The genome of X. campestris pv. campestris has several clp genes, namely, clpS, clpA, clpX, clpP, clpQ, and clpY. Among these genes, only clpX and clpP is known to be required for pathogenicity. Here, we focused on two uncharacterized clp genes (clpS and clpA) that encode the adaptor (ClpS) and ATPase subunit (ClpA) of the ClpAP protease complex. Transcriptional analysis revealed that the expression of clpS and clpA was growth phase-dependent and affected by the growth temperature. The inactivation of clpA, but not of clpS, resulted in susceptibility to high temperature and attenuated virulence in the host plant. The altered phenotypes of the clpA mutant could be complemented in trans. Site-directed mutagenesis revealed that K223 and K504 were the amino acid residues critical for ClpA function in heat tolerance. The protein expression profile shown by the clpA mutant in response to heat stress was different from that exhibited by the wild type. In summary, we characterized two clp genes (clpS and clpA) by examining their expression profiles and functions in different processes, including stress tolerance and pathogenicity. We demonstrated that clpS and clpA were expressed in a temperature-dependent manner and that clpA was required for the survival at high temperature and full virulence of X. campestris pv. campestris. This work represents the first time that clpS and clpA were characterized in Xanthomonas.
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Affiliation(s)
- Hsueh-Hsia Lo
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 40601, Taiwan
| | - Hsiao-Ching Chang
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 40601, Taiwan
| | - Chao-Tsai Liao
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 40601, Taiwan
| | - Yi-Min Hsiao
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 40601, Taiwan.
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38
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Yang L, Pandeya A, Li L, Ojo I, Li Z, Wei Y. Transport Across Two Membrane Bilayers in E. coli by Efflux Pumps of Different Dimensions. J Mol Biol 2022; 434:167376. [PMID: 34838522 DOI: 10.1016/j.jmb.2021.167376] [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: 06/30/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 11/30/2022]
Abstract
AcrAB-TolC and CusBAC are two of the most well-studied Resistance-Nodulation-Division (RND) family tripartite efflux pumps in E. coli. AcrAB-TolC is a multidrug efflux system, while CusBAC transports Cu(I), Cu(II) and Ag(I). The RND pump complexes span both the inner membrane (IM) and the outer membrane (OM). The long axis dimension of the fully assembled AcrAB-TolC is ∼3 nm longer than that of CusBAC. To probe if these two efflux systems with different dimensions affect each other when they need to work simultaneously in the same cell, two real-time assays were used to monitor the efflux activities of these two pumps and their impact on each other. The results showed that the presence of AcrAB-TolC substrates accelerated the accumulation of Cu(I) in BW25113 but not in BW25113ΔcusBA or BW25113ΔtolC strains. Similarly, the presence of Ag(I) slowed down the Nile red efflux in the parent strain more significantly than in the CusBA deficient mutant. To further investigate the impact of the OM/IM distance on the function of these tripartite complexes, we experimented with strains lacking the lipoprotein Lpp or containing Lpp mutant of different lengths. Data from efflux/accumulation assays and susceptibility tests revealed that mutation of Lpp resulted in functional deficiency of both AcrAB-TolC and CusBAC. In conclusion, this study demonstrated that when AcrAB-TolC and CusBAC functioned simultaneously, it took the cell a few minutes to adjust. Furthermore, the presence of Lpp of proper length is important to support full efflux activity of transporters spanning both membrane layers in E. coli.
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Affiliation(s)
- Ling Yang
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | - Ankit Pandeya
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | - Lan Li
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | - Isoiza Ojo
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | - Zhenyu Li
- Saha Cardiovascular Research Center, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Yinan Wei
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA.
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Kerr R, Jabbari S, Blair JMA, Johnston IG. Dynamic Boolean modelling reveals the influence of energy supply on bacterial efflux pump expression. J R Soc Interface 2022; 19:20210771. [PMID: 35078338 PMCID: PMC8790346 DOI: 10.1098/rsif.2021.0771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global health issue. One key factor contributing to AMR is the ability of bacteria to export drugs through efflux pumps, which relies on the ATP-dependent expression and interaction of several controlling genes. Recent studies have shown that significant cell-to-cell ATP variability exists within clonal bacterial populations, but the contribution of intrinsic cell-to-cell ATP heterogeneity is generally overlooked in understanding efflux pumps. Here, we consider how ATP variability influences gene regulatory networks controlling expression of efflux pump genes in two bacterial species. We develop and apply a generalizable Boolean modelling framework, developed to incorporate the dependence of gene expression dynamics on available cellular energy supply. Theoretical results show that differences in energy availability can cause pronounced downstream heterogeneity in efflux gene expression. Cells with higher energy availability have a superior response to stressors. Furthermore, in the absence of stress, model bacteria develop heterogeneous pulses of efflux pump gene expression which contribute to a sustained sub-population of cells with increased efflux expression activity, potentially conferring a continuous pool of intrinsically resistant bacteria. This modelling approach thus reveals an important source of heterogeneity in cell responses to antimicrobials and sheds light on potentially targetable aspects of efflux pump-related antimicrobial resistance.
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Affiliation(s)
- Ryan Kerr
- School of Mathematics, University of Birmingham, Birmingham, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Sara Jabbari
- School of Mathematics, University of Birmingham, Birmingham, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Jessica M A Blair
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Iain G Johnston
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway.,Computational Biology Unit, University of Bergen, Bergen, Norway.,CAMRIA Centre for Antimicrobial Resistance, Vestland, Norway
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40
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Webber A, Ratnaweera M, Harris A, Luisi BF, Ntsogo Enguéné VY. A Model for Allosteric Communication in Drug Transport by the AcrAB-TolC Tripartite Efflux Pump. Antibiotics (Basel) 2022; 11:52. [PMID: 35052929 PMCID: PMC8773123 DOI: 10.3390/antibiotics11010052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 01/30/2023] Open
Abstract
RND family efflux pumps are complex macromolecular machines involved in multidrug resistance by extruding antibiotics from the cell. While structural studies and molecular dynamics simulations have provided insights into the architecture and conformational states of the pumps, the path followed by conformational changes from the inner membrane protein (IMP) to the periplasmic membrane fusion protein (MFP) and to the outer membrane protein (OMP) in tripartite efflux assemblies is not fully understood. Here, we investigated AcrAB-TolC efflux pump's allostery by comparing resting and transport states using difference distance matrices supplemented with evolutionary couplings data and buried surface area measurements. Our analysis indicated that substrate binding by the IMP triggers quaternary level conformational changes in the MFP, which induce OMP to switch from the closed state to the open state, accompanied by a considerable increase in the interface area between the MFP subunits and between the OMPs and MFPs. This suggests that the pump's transport-ready state is at a more favourable energy level than the resting state, but raises the puzzle of how the pump does not become stably trapped in a transport-intermediate state. We propose a model for pump allostery that includes a downhill energetic transition process from a proposed 'activated' transport state back to the resting pump.
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Affiliation(s)
- Anya Webber
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK; (A.W.); (A.H.)
| | - Malitha Ratnaweera
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK;
| | - Andrzej Harris
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK; (A.W.); (A.H.)
| | - Ben F. Luisi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK; (A.W.); (A.H.)
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41
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Chen H, Yang N, Yang Y, Zheng Y, Xu M, Zhang H, Liu Y, Shen W, Li J. Doxofylline Protects Gram-Negative Pathogens against Antibiotic-Mediated Killing. ACS Infect Dis 2021; 7:3241-3253. [PMID: 34851627 DOI: 10.1021/acsinfecdis.1c00417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Given the growing rate of Gram-negative bacterial infections, antibiotics are now frequently prescribed for various respiratory diseases. Doxofylline is a newer generation xanthine with both bronchodilating and anti-inflammatory activities, but its influence on antibiotics remains poorly understood. Here, we first report the discovery of doxofylline-induced high minimum inhibitory concentrations of antibiotics. We also showed that doxofylline blocked antimicrobial-mediated killing for Gram-negative pathogens in vitro and in murine lung infection models in vivo. By combining efflux pump inhibition tests, gene expression analyses, and using the gene tolC knockout strain, we found that doxofylline positively regulated gene expression of the AcrAB-TolC efflux pump and attenuated the effect of doxofylline on antibacterial activities in ΔtolC mutants. Notably, doxofylline-mediated protection correlated with decreased reactive oxygen species (ROS) production. Collectively, our study indicates that doxofylline protects Gram-negative bacteria from antimicrobial lethality by regulating the AcrAB-TolC efflux pump in a TolC-dependent manner and suppressing antibiotic-induced ROS accumulation. These results suggest caution when using antibiotics alongside doxofylline in clinical treatment.
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Affiliation(s)
- Haoran Chen
- Department of Infectious Disease, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Ning Yang
- Department of Infectious Disease, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Yi Yang
- Department of Infectious Disease, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Yahong Zheng
- Department of Infectious Disease, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Mengran Xu
- Department of Infectious Disease, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Hui Zhang
- Department of Infectious Disease, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Yanyan Liu
- Department of Infectious Disease, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
- Anhui Center for Surveillance of Bacterial Resistance, Hefei, Anhui 230022, China
- Institute of Bacterial Resistance, Anhui Medical University, Hefei, Anhui 230022, China
| | - Weihua Shen
- Department of Special Clinic, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Jiabin Li
- Department of Infectious Disease, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
- Department of Molecular Biology, Anhui Center for Surveillance of Bacterial Resistance, Hefei, Anhui 230022, China
- Anhui Center for Surveillance of Bacterial Resistance, Hefei, Anhui 230022, China
- Institute of Bacterial Resistance, Anhui Medical University, Hefei, Anhui 230022, China
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Haseena, Khan A, Ghaffar I, Baty RS, Abdel-Daim MM, Habib SM, Kanwal T, Shah MR. Synthesis of Ribose-Coated Copper-Based Metal-Organic Framework for Enhanced Antibacterial Potential of Chloramphenicol against Multi-Drug Resistant Bacteria. Antibiotics (Basel) 2021; 10:1469. [PMID: 34943681 PMCID: PMC8698127 DOI: 10.3390/antibiotics10121469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/28/2021] [Accepted: 11/11/2021] [Indexed: 01/21/2023] Open
Abstract
The rise in bacterial resistance to currently used antibiotics is the main focus of medical researchers. Bacterial multidrug resistance (MDR) is a major threat to humans, as it is linked to greater rates of chronic disease and mortality. Hence, there is an urgent need for developing effective strategies to overcome the bacterial MDR. Metal-organic frameworks (MOFs) are a new class of porous crystalline materials made up of metal ions and organic ligands that can vary their pore size and structure to better encapsulate drug candidates. This study reports the synthesis of ribose-coated Cu-MOFs for enhanced bactericidal activity of chloramphenicol (CHL) against Escherichia coli (resistant and sensitive) and MDR Pseudomonas aeruginosa. The synthesized Cu-MOFs were characterized with DLS, FT-IR, powder X-ray diffraction, scanning electron microscope, and atomic force microscope. They were further investigated for their efficacy against selected bacterial strains. The synthesized ribose-coated Cu-MOFs were observed as spherical shape structure with the particle size of 562.84 ± 13.42 nm. CHL caused the increased inhibition of E. coli and MDR P. aeruginosa with significantly reduced MIC and MBIC values after being encapsulated in ribose-coated Cu-MOFs. The morphological analysis of the bacterial strains treated with ribose-coated CHL-Cu-MOFs showed the complete morphological distortion of both E. coli and MDR P. aeruginosa. Based on the results of the study, it can be suggested that ribose-coated Cu-MOFs may be an effective alternate candidate to overcome the MDR and provide new perspective for the treatment of MDR bacterial infections.
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Affiliation(s)
- Haseena
- Institute of Chemical Sciences, University of Peshawar, Peshawar 25120, Pakistan; (H.); (A.K.)
| | - Adnan Khan
- Institute of Chemical Sciences, University of Peshawar, Peshawar 25120, Pakistan; (H.); (A.K.)
| | - Iqra Ghaffar
- International Centre for Chemical and Biological Sciences, Research Institute of Chemistry, University of Karachi, Karachi 74200, Pakistan; (I.G.); (S.M.H.); (T.K.)
| | - Roua S. Baty
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Mohamed M. Abdel-Daim
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt;
| | - Shahida M. Habib
- International Centre for Chemical and Biological Sciences, Research Institute of Chemistry, University of Karachi, Karachi 74200, Pakistan; (I.G.); (S.M.H.); (T.K.)
| | - Tasmina Kanwal
- International Centre for Chemical and Biological Sciences, Research Institute of Chemistry, University of Karachi, Karachi 74200, Pakistan; (I.G.); (S.M.H.); (T.K.)
| | - Muhammad Raza Shah
- International Centre for Chemical and Biological Sciences, Research Institute of Chemistry, University of Karachi, Karachi 74200, Pakistan; (I.G.); (S.M.H.); (T.K.)
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43
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Sette-de-Souza PH, Silva Bezerra WMD, Gomes Dantas MK, Santos Moura LM, Donato Duarte Filho ES, Lopes DS. Identification of docosahexaenoic and eicosapentaenoic acids multiple targets facing periodontopathogens. Microb Pathog 2021; 161:105266. [PMID: 34699926 DOI: 10.1016/j.micpath.2021.105266] [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: 05/24/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/01/2022]
Abstract
The eicosapentaenoic (EPA) and docosahexaenoic acid (DHA) play a substantial role in Periodontal Disease (PD) due to their antimicrobial and immunomodulatory actions. However, their antimicrobial mechanism of action against bacteria involved in PD remains unclear. We aimed to estimate the probable targets of EPA and DHA against the seven periodontopathogens. Through in silico analyses, the protein-acids interactions, protein characterization, and molecular docking were performed. We identified 165 proteins from periodontopathogens that may interact with EPA and DHA. Fusobacterium nucleatum has the highest number of predicted proteins among analyzed bacteria (n = 43, 26.06%). The EPA shows more interactions than DHA. The EPA and DHA interact mainly with proteins involved in the metabolism (n = 69, 41.81%). Also, the EPA and DHA interact with proteins located in any subcellular location. The affinities between acids and pathogenic proteins were moderate (binding energy was lower than -4.0 kcal/mol). The interactions between EPA and DHA and periodontopathogens occur in multiples proteins. There is not a predilection about the functional class of pathogenic proteins targeting EPA and DHA. However, there are moderate binding affinities between EPA or DHA and essential pathogenic proteins (TolC, CRISPR, FusA).
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Affiliation(s)
- Pedro Henrique Sette-de-Souza
- School of Dentistry, Universidade de Pernambuco, Campus Arcoverde, Arcoverde, Pernambuco, Brazil; Graduate Program in Health and Socioambiental Development, Universidade de Pernambuco, Campus Garanhuns, Garanhuns, Pernambuco, Brazil.
| | | | | | | | | | - Daniela Siqueira Lopes
- School of Dentistry, Universidade de Pernambuco, Campus Arcoverde, Arcoverde, Pernambuco, Brazil
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Rapacka-Zdonczyk A, Wozniak A, Kruszewska B, Waleron K, Grinholc M. Can Gram-Negative Bacteria Develop Resistance to Antimicrobial Blue Light Treatment? Int J Mol Sci 2021; 22:ijms222111579. [PMID: 34769009 PMCID: PMC8583887 DOI: 10.3390/ijms222111579] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/18/2021] [Accepted: 10/24/2021] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial blue light (aBL) treatment is considered low risk for the development of bacterial resistance and tolerance due to its multitarget mode of action. The aim of the current study was to demonstrate whether tolerance development occurs in Gram-negative bacteria. We evaluated the potential of tolerance/resistance development in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa and demonstrated that representative Gram-negative bacteria may develop tolerance to aBL. The observed adaption was a stable feature. Assays involving E. coli K-12 tolC-, tolA-, umuD-, and recA-deficient mutants revealed some possible mechanisms for aBL tolerance development.
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Affiliation(s)
- Aleksandra Rapacka-Zdonczyk
- Department of Pharmaceutical Microbiology, The Faculty of Pharmacy, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland; (B.K.); (K.W.)
- Correspondence:
| | - Agata Wozniak
- Laboratory of Photobiology and Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (A.W.); (M.G.)
| | - Beata Kruszewska
- Department of Pharmaceutical Microbiology, The Faculty of Pharmacy, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland; (B.K.); (K.W.)
- Laboratory of Photobiology and Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (A.W.); (M.G.)
| | - Krzysztof Waleron
- Department of Pharmaceutical Microbiology, The Faculty of Pharmacy, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland; (B.K.); (K.W.)
| | - Mariusz Grinholc
- Laboratory of Photobiology and Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (A.W.); (M.G.)
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Gumbart JC, Ferreira JL, Hwang H, Hazel AJ, Cooper CJ, Parks JM, Smith JC, Zgurskaya HI, Beeby M. Lpp positions peptidoglycan at the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump. Biophys J 2021; 120:3973-3982. [PMID: 34411576 DOI: 10.1016/j.bpj.2021.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 07/02/2021] [Accepted: 08/11/2021] [Indexed: 01/07/2023] Open
Abstract
The multidrug efflux pumps of Gram-negative bacteria are a class of complexes that span the periplasm, coupling both the inner and outer membranes to expel toxic molecules. The best-characterized example of these tripartite pumps is the AcrAB-TolC complex of Escherichia coli. However, how the complex interacts with the peptidoglycan (PG) cell wall, which is anchored to the outer membrane (OM) by Braun's lipoprotein (Lpp), is still largely unknown. In this work, we present molecular dynamics simulations of a complete, atomistic model of the AcrAB-TolC complex with the inner membrane, OM, and PG layers all present. We find that the PG localizes to the junction of AcrA and TolC, in agreement with recent cryo-tomography data. Free-energy calculations reveal that the positioning of PG is determined by the length and conformation of multiple Lpp copies anchoring it to the OM. The distance between the PG and OM measured in cryo-electron microscopy images of wild-type E. coli also agrees with the simulation-derived spacing. Sequence analysis of AcrA suggests a conserved role for interactions with PG in the assembly and stabilization of efflux pumps, one that may extend to other trans-envelope complexes as well.
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Affiliation(s)
- James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia.
| | - Josie L Ferreira
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Anthony J Hazel
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Connor J Cooper
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
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Ma X, Zheng B, Wang J, Li G, Cao S, Wen Y, Huang X, Zuo Z, Zhong Z, Gu Y. Quinolone Resistance of Actinobacillus pleuropneumoniae Revealed through Genome and Transcriptome Analyses. Int J Mol Sci 2021; 22:ijms221810036. [PMID: 34576206 PMCID: PMC8472844 DOI: 10.3390/ijms221810036] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/16/2022] Open
Abstract
Actinobacillus pleuropneumoniae is a pathogen that infects pigs and poses a serious threat to the pig industry. The emergence of quinolone-resistant strains of A.pleuropneumoniae further limits the choice of treatment. However, the mechanisms behind quinolone resistance in A.pleuropneumoniae remain unclear. The genomes of a ciprofloxacin-resistant strain, A. pleuropneumoniae SC1810 and its isogenic drug-sensitive counterpart were sequenced and analyzed using various bioinformatics tools, revealing 559 differentially expressed genes. The biological membrane, plasmid-mediated quinolone resistance genes and quinolone resistance-determining region were detected. Upregulated expression of efflux pump genes led to ciprofloxacin resistance. The expression of two porins, OmpP2B and LamB, was significantly downregulated in the mutant. Three nonsynonymous mutations in the mutant strain disrupted the water–metal ion bridge, subsequently reducing the affinity of the quinolone–enzyme complex for metal ions and leading to cross-resistance to multiple quinolones. The mechanism of quinolone resistance in A. pleuropneumoniae may involve inhibition of expression of the outer membrane protein genes ompP2B and lamB to decrease drug influx, overexpression of AcrB in the efflux pump to enhance its drug-pumping ability, and mutation in the quinolone resistance-determining region to weaken the binding of the remaining drugs. These findings will provide new potential targets for treatment.
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Affiliation(s)
- Xiaoping Ma
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (X.M.); (B.Z.); (J.W.); (G.L.); (Z.Z.); (Z.Z.)
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.H.)
| | - Bowen Zheng
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (X.M.); (B.Z.); (J.W.); (G.L.); (Z.Z.); (Z.Z.)
| | - Jiafan Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (X.M.); (B.Z.); (J.W.); (G.L.); (Z.Z.); (Z.Z.)
| | - Gen Li
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (X.M.); (B.Z.); (J.W.); (G.L.); (Z.Z.); (Z.Z.)
- Bioengineering Department, Sichuan Water Conservancy Vocational College, Chengdu 611231, China
| | - Sanjie Cao
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.H.)
- Correspondence: (S.C.); (Y.G.)
| | - Yiping Wen
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.H.)
| | - Xiaobo Huang
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.H.)
| | - Zhicai Zuo
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (X.M.); (B.Z.); (J.W.); (G.L.); (Z.Z.); (Z.Z.)
| | - Zhijun Zhong
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (X.M.); (B.Z.); (J.W.); (G.L.); (Z.Z.); (Z.Z.)
| | - Yu Gu
- College of Life Sciences, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (S.C.); (Y.G.)
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Thompson DK, Sharkady SM. Genomic Insights into Drug Resistance Determinants in Cedecea neteri, A Rare Opportunistic Pathogen. Microorganisms 2021; 9:microorganisms9081741. [PMID: 34442820 PMCID: PMC8401664 DOI: 10.3390/microorganisms9081741] [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: 07/22/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 11/16/2022] Open
Abstract
Cedecea, a genus in the Enterobacteriaceae family, includes several opportunistic pathogens reported to cause an array of sporadic acute infections, most notably of the lung and bloodstream. One species, Cedecea neteri, is associated with cases of bacteremia in immunocompromised hosts and has documented resistance to different antibiotics, including β-lactams and colistin. Despite the potential to inflict serious infections, knowledge about drug resistance determinants in Cedecea is limited. In this study, we utilized whole-genome sequence data available for three environmental strains (SSMD04, M006, ND14a) of C. neteri and various bioinformatics tools to analyze drug resistance genes in this bacterium. All three genomes harbor multiple chromosome-encoded β-lactamase genes. A deeper analysis of β-lactamase genes in SSMD04 revealed four metallo-β-lactamases, a novel variant, and a CMY/ACT-type AmpC putatively regulated by a divergently transcribed AmpR. Homologs of known resistance-nodulation-cell division (RND)-type multidrug efflux pumps such as OqxB, AcrB, AcrD, and MdtBC were also identified. Genomic island prediction for SSMD04 indicated that tolC, involved in drug and toxin export across the outer membrane of Gram-negative bacteria, was acquired by a transposase-mediated genetic transfer mechanism. Our study provides new insights into drug resistance mechanisms of an environmental microorganism capable of behaving as a clinically relevant opportunistic pathogen.
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Abstract
Vibrio cholerae is a Gram-negative bacterium that causes the enteric disease cholera. V. cholerae colonization of the human intestine is dependent on the expression of both virulence genes and environmental adaptation genes involved in antimicrobial resistance. The expression of virulence genes, including the genes encoding for the main virulence factors cholera toxin (CT) and the toxin coregulated pilus (TCP), are coordinately regulated by the ToxR regulon. Tripartite transport systems belonging to the ATP binding cassette, major facilitator, and Resistance-Nodulation-Division families are critical for V. cholerae pathogenesis. Transport systems belonging to these families contribute to myriad phenotypes including protein secretion, antimicrobial resistance and virulence. TolC plays a central role in bacterial physiology by functioning as the outer membrane pore protein for tripartite transport systems. Consistent with this, V. cholerae tolC was previously found to be required for MARTX toxin secretion and antimicrobial resistance. Herein we investigated the contribution of TolC to V. cholerae virulence. We documented that tolC was required for CT and TCP production in O1 El Tor V. cholerae. This phenotype was linked to repression of the critical ToxR regulon transcription factor aphA. Decreased aphA transcription correlated with increased expression of the LysR-family transcription factor leuO. Deletion of leuO restored aphA expression, and CT and TCP production, in a tolC mutant. The collective results document that tolC is required for ToxR regulon expression and further suggest that tolC may participate in a efflux-dependent feedback circuit to regulate virulence gene expression.
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Wang X, Wang Y, Ling N, Shen Y, Zhang D, Liu D, Ou D, Wu Q, Ye Y. Effects of tolC on tolerance to bile salts and biofilm formation in Cronobacter malonaticus. J Dairy Sci 2021; 104:9521-9531. [PMID: 34099300 DOI: 10.3168/jds.2021-20128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/29/2021] [Indexed: 12/21/2022]
Abstract
Bile salts is one of essential components of bile secreted into the intestine to confer antibacterial protection. Cronobacter species are associated with necrotizing enterocolitis in newborns and show a strong tolerance to bile salts. However, little attempt has been made to focus on the molecular basis of the tolerance to bile salts. In this study, we investigated the roles of tolC on growth, cell morphology, motility, and biofilm formation ability in Cronobacter malonaticus under bile salt stress. The results indicated that the absence of tolC significantly affected the colony morphology and outer membrane structure in a normal situation, compared with those of the wild type strain. The deletion of tolC caused the decline in resistance to bile salt stress, inhibition of growth, and observable reduction in relative growth rate and motility. Moreover, the bacterial stress response promoted the biofilm formation ability of the mutant strain. The expression of the AcrAB-TolC system (acrA, acrB, and tolC) was effectively upregulated compared with the control sample when exposed to different bile salt concentrations. The findings provide valuable information for deeply understanding molecular mechanisms about the roles of tolC under bile salt stress and the prevention and control of C. malonaticus.
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Affiliation(s)
- Xin Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Yaping Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Na Ling
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Yizhong Shen
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Danfeng Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Dengyu Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Dexin Ou
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Yingwang Ye
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China.
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Kocak E, Nemutlu E, Kır S, Sagıroglu M, Özkul C. Integrative proteomics and metabolomics approach to elucidate the antimicrobial effect of simvastatin on Escherichia coli. Biomed Chromatogr 2021; 35:e5180. [PMID: 34043824 DOI: 10.1002/bmc.5180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 11/07/2022]
Abstract
Globally, simvastatin is one of the most commonly used statin drugs. Its antimicrobial properties have been investigated against various pathogens. However, its effect on biological processes in bacteria has been unclear. This study focused on altered biological and metabolic processes at protein and metabolite levels induced by simvastatin. MS-based proteomics and metabolomics were used to investigate the altered proteins and metabolites between experimental groups. Proteomics results showed that simvastatin induced various antimicrobial targets such as chaperon protein DnaK and cell division protein FtsZ. Metabolomics results revealed phenotypic changes in cells under simvastatin stress. Integrated proteomics and metabolomics result indicated that various metabolic processes were altered to adapt to stress conditions. Energy metabolism (glycolysis, tricarboxylic acid cycle, etc.), amino acid synthesis and ribosomal proteins, and purine and pyrimidine synthesis were induced by the effect of simvastatin. This study will contribute to the understanding of antimicrobial properties of statin drugs.
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Affiliation(s)
- Engin Kocak
- Department of Analytical Chemistry, Faculty of Gulhane Pharmacy, Health Sciences University, Ankara, Turkey
| | - Emirhan Nemutlu
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Sedef Kır
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Meral Sagıroglu
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Ceren Özkul
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
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