1
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Smith DR, Kearns DB, Burton BM. ComI inhibits transformation in Bacillus subtilis by selectively killing competent cells. J Bacteriol 2024:e0041323. [PMID: 38874341 DOI: 10.1128/jb.00413-23] [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: 01/31/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024] Open
Abstract
Many bacteria build elaborate molecular machines to import DNA via natural competence, yet this activity is often not identified until strains have been handled and domesticated in laboratory settings. For example, one of the best studied Gram-positive model organisms, Bacillus subtilis, has a poorly transformable ancestor. Transformation in the ancestral strain is inhibited by a transmembrane peptide, ComI, which is encoded on an extrachromosomal plasmid. Although ComI was shown to be necessary and sufficient to inhibit transformation when produced at high levels under an inducible promoter, the mechanism by which ComI inhibits transformation is unknown. Here, we examine the native regulation and mechanism of transformation inhibition by ComI. We find that under native regulation, ComI expression is restricted in the absence of the plasmid. In the presence of the plasmid, we find that ComI is expressed at higher levels in cells that are differentiating into a competent state. The subcellular localization of ComI, however, does not depend on any other competence proteins, and permeabilization activity is concentration-dependent. Time-lapse microscopy reveals that competent cells producing ComI are first permeabilized and then die. Based on these observations, we propose a new model for the mechanism of ComI in which response to competence activation leads to selective elimination of the competent subpopulation. IMPORTANCE Natural transformation mechanisms have been studied across several bacterial systems, but few examples of inhibition exist. This work investigates the mechanism of action of a plasmid-encoded transmembrane inhibitor of natural transformation. The data reveal that the peptide can cause cell permeabilization. Permeabilization is synergistic with entry of Bacillus subtilis into the "competent" state, such that cells with the ability to be transformed are preferentially killed. These findings reveal a self-preservation mechanism coupled to the physiological state of the cells that ensures that the population can maintain an unaltered plasmid and its predicted prophage.
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Affiliation(s)
- Dominique R Smith
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
| | - Daniel B Kearns
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Briana M Burton
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
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2
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Aziz S, Rasheed F, Akhter TS, Zahra R, König S. Microbial Proteins in Stomach Biopsies Associated with Gastritis, Ulcer, and Gastric Cancer. Molecules 2022; 27:molecules27175410. [PMID: 36080177 PMCID: PMC9458002 DOI: 10.3390/molecules27175410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/12/2022] [Accepted: 08/20/2022] [Indexed: 11/24/2022] Open
Abstract
(1) Background: Gastric cancer (GC) is the fourth leading cause of cancer-related deaths worldwide. Helicobacter pylori infection is a major risk factor, but other microbial species may also be involved. In the context of an earlier proteomics study of serum and biopsies of patients with gastroduodenal diseases, we explored here a simplified microbiome in these biopsies (H. pylori, Acinetobacter baumannii, Escherichia coli, Fusobacterium nucleatum, Bacteroides fragilis) on the protein level. (2) Methods: A cohort of 75 patients was divided into groups with respect to the findings of the normal gastric mucosa (NGM) and gastroduodenal disorders such as gastritis, ulcer, and gastric cancer (GC). The H. pylori infection status was determined. The protein expression analysis of the biopsy samples was carried out using high-definition mass spectrometry of the tryptic digest (label-free data-independent quantification and statistical analysis). (3) Results: The total of 304 bacterial protein matches were detected based on two or more peptide hits. Significantly regulated microbial proteins like virulence factor type IV secretion system protein CagE from H. pylori were found with more abundance in gastritis than in GC or NGM. This finding could reflect the increased microbial involvement in mucosa inflammation in line with current hypotheses. Abundant proteins across species were heat shock proteins and elongation factors. (4) Conclusions: Next to the bulk of human proteins, a number of species-specific bacterial proteins were detected in stomach biopsies of patients with gastroduodenal diseases, some of which, like those expressed by the cag pathogenicity island, may provide gateways to disease prevention without antibacterial intervention in order to reduce antibiotic resistance.
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Affiliation(s)
- Shahid Aziz
- Patients Diagnostic Lab, Isotope Application Division, Pakistan Institute of Nuclear Science and Technology (PINSTECH), Islamabad 44000, Pakistan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
- Correspondence: or
| | - Faisal Rasheed
- Patients Diagnostic Lab, Isotope Application Division, Pakistan Institute of Nuclear Science and Technology (PINSTECH), Islamabad 44000, Pakistan
| | - Tayyab Saeed Akhter
- The Centre for Liver and Digestive Diseases, Holy Family Hospital, Rawalpindi 46300, Pakistan
| | - Rabaab Zahra
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Simone König
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
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3
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Eisenreich W, Rudel T, Heesemann J, Goebel W. Link Between Antibiotic Persistence and Antibiotic Resistance in Bacterial Pathogens. Front Cell Infect Microbiol 2022; 12:900848. [PMID: 35928205 PMCID: PMC9343593 DOI: 10.3389/fcimb.2022.900848] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022] Open
Abstract
Both, antibiotic persistence and antibiotic resistance characterize phenotypes of survival in which a bacterial cell becomes insensitive to one (or even) more antibiotic(s). However, the molecular basis for these two antibiotic-tolerant phenotypes is fundamentally different. Whereas antibiotic resistance is genetically determined and hence represents a rather stable phenotype, antibiotic persistence marks a transient physiological state triggered by various stress-inducing conditions that switches back to the original antibiotic sensitive state once the environmental situation improves. The molecular basics of antibiotic resistance are in principle well understood. This is not the case for antibiotic persistence. Under all culture conditions, there is a stochastically formed, subpopulation of persister cells in bacterial populations, the size of which depends on the culture conditions. The proportion of persisters in a bacterial population increases under different stress conditions, including treatment with bactericidal antibiotics (BCAs). Various models have been proposed to explain the formation of persistence in bacteria. We recently hypothesized that all physiological culture conditions leading to persistence converge in the inability of the bacteria to re-initiate a new round of DNA replication caused by an insufficient level of the initiator complex ATP-DnaA and hence by the lack of formation of a functional orisome. Here, we extend this hypothesis by proposing that in this persistence state the bacteria become more susceptible to mutation-based antibiotic resistance provided they are equipped with error-prone DNA repair functions. This is - in our opinion - in particular the case when such bacterial populations are exposed to BCAs.
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Affiliation(s)
- Wolfgang Eisenreich
- Bavarian NMR Center – Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
- *Correspondence: Wolfgang Eisenreich,
| | - Thomas Rudel
- Chair of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jürgen Heesemann
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
| | - Werner Goebel
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
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4
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Richard D, Roumagnac P, Pruvost O, Lefeuvre P. A network approach to decipher the dynamics of Lysobacteraceae plasmid gene sharing. Mol Ecol 2022; 32:2660-2673. [PMID: 35593155 DOI: 10.1111/mec.16536] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 04/21/2022] [Accepted: 05/05/2022] [Indexed: 11/27/2022]
Abstract
Plasmids provide an efficient vehicle for gene sharing among bacterial populations, playing a key role in bacterial evolution. Network approaches are particularly suitable to represent multipartite relationships and are useful tools to characterize plasmid-mediated gene sharing events. The Lysobacteraceae bacterial family gathers plant commensal, plant pathogenic and opportunistic human pathogens for which plasmid mediated adaptation was reported. We searched for homologues of plasmid gene sequences from this family in all the diversity of available bacterial genome sequences and built a network of plasmid gene sharing from the results. While plasmid genes are openly shared between the bacteria of the Lysobacteraceae family, taxonomy strongly defined the boundaries of these exchanges, that only barely reached other families. Most inferred plasmid gene sharing events involved a few genes only, and evidence of full plasmid transfers were restricted to taxonomically close taxon. We detected multiple plasmid-chromosome gene transfers, among which the otherwise known sharing of a heavy metal resistance transposon. In the network, bacterial lifestyles shaped sub-structures of isolates colonizing specific ecological niches and harboring specific types of resistance genes. Genes associated to pathogenicity or antibiotic and metal resistance were among those that most importantly structured the network, highlighting the imprints of human-mediated selective pressure on pathogenic populations. A massive sequencing effort on environmental Lysobacteraceae is therefore required to refine our understanding on how this reservoir fuels the emergence and the spread of genes amongst this family and its potential impact on plant, animal and human health.
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Affiliation(s)
- D Richard
- Cirad, UMR PVBMT, F-97410 St Pierre, Réunion, France.,ANSES, Plant Health Laboratory, F-97410 St Pierre, Réunion, France.,Université de La Réunion, La Réunion, France
| | - P Roumagnac
- Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - O Pruvost
- Cirad, UMR PVBMT, F-97410 St Pierre, Réunion, France
| | - P Lefeuvre
- Cirad, UMR PVBMT, F-97410 St Pierre, Réunion, France
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5
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Liu Y, Yang F, Wang S, Chi W, Ding L, Liu T, Zhu F, Ji D, Zhou J, Fang Y, Zhang J, Xiang P, Zhang Y, Zhao H. HopE and HopD Porin-Mediated Drug Influx Contributes to Intrinsic Antimicrobial Susceptibility and Inhibits Streptomycin Resistance Acquisition by Natural Transformation in Helicobacter pylori. Microbiol Spectr 2022; 10:e0198721. [PMID: 35234510 PMCID: PMC9045298 DOI: 10.1128/spectrum.01987-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/21/2022] [Indexed: 12/14/2022] Open
Abstract
Helicobacter pylori is a human pathogen competent for natural transformation. Intrinsic and acquired antibiotic resistance contribute to the survival and multiplication of H. pylori under antibiotics. While drug-resistance dissemination by natural transformation (NT)-mediated horizontal gene transfer remains poorly understood in H. pylori. The purpose of the study was to investigate the role of H. pylori porins (HopA, HopB, HopC, HopD, and HopE) in the intrinsic antibiotic resistance and to preliminarily reveal the potential effect of HopE and HopD porins in streptomycin resistance acquisition after NT in the presence of antibiotics. Using traditional antibiotic susceptibility tests and growth curve analysis, we found the MIC values of metronidazole, clarithromycin, levofloxacin, tetracycline, rifampin, and streptomycin in mutants lacking HopE and/or HopD were significantly elevated compare to those in wild-type strain. The quantitative analysis of the tetramethyl rhodamine isothiocyanate (TRITC)-labeled streptomycin accumulation at the single-cell level showed reduced streptomycin intracellular fluorescence in ΔhopE and ΔhopD mutant cells. Furthermore, in the presence of translation-inhibiting antibiotic streptomycin, the resistance acquisition frequency was decreased in the wild-type strain, which could be reversed by mutants lacking HopE and HopD that restored relatively high resistance acquisition frequencies. By transforming a pUC19-rpsLmut-sfgfp linear plasmid carrying a streptomycin conferring mutation, we observed that the impaired ability of rpsLmut synthesis in the wild-type strain was restored in the ΔhopE and ΔhopD mutant transformants. Our study revealed that in the presence of streptomycin, resistance acquisition at least partially relied on the deletion of the hopE and hopD genes, because their loss reduced streptomycin concentration in the cell and thus restored the expression of the resistance-conferring gene, which was inhibited by streptomycin in wild-type strain. The loss of HopE and HopD influx activity may also preserve resistance acquisition by transformation in the presence of antibiotics with other modes of action. IMPORTANCE Helicobacter pylori is constitutively competent for natural transformation (NT) and possesses an efficient system for homologous recombination, which could be utilized to study the NT-mediated horizontal gene transfer induced antibiotic resistance acquisition. Bacterial porins have drawn renewed attention because of their crucial role in antibiotic susceptibility. From the perspective of porin-mediated influx in H. pylori, our study preliminarily revealed the important role of HopE and HopD porins not only in preserving the intrinsic susceptibility to specific antibiotic but also in evading acquired antibiotic resistance by NT in the presence of translation-inhibiting antimicrobial. Therefore, the loss of HopE or HopD porin in H. pylori genomes, combined with the large number of secreted or cell-free genetic elements carrying mutations conferring antibiotic resistance, may raise the possibility that this mechanism plays a potential role in the propagation of antibiotic resistance within H. pylori communities.
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Affiliation(s)
- Yixin Liu
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Feng Yang
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Su Wang
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Wenjing Chi
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Li Ding
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Tao Liu
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Feng Zhu
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Danian Ji
- Department of Endoscopy, Huadong Hospital, Fudan University, Shanghai, China
| | - Jun Zhou
- Department of Endoscopy, Huadong Hospital, Fudan University, Shanghai, China
| | - Yi Fang
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Jinghao Zhang
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Ping Xiang
- Department of Endoscopy, Huadong Hospital, Fudan University, Shanghai, China
| | - Yanmei Zhang
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Hu Zhao
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
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6
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Liu G, Thomsen LE, Olsen JE. Antimicrobial-induced horizontal transfer of antimicrobial resistance genes in bacteria: a mini-review. J Antimicrob Chemother 2021; 77:556-567. [PMID: 34894259 DOI: 10.1093/jac/dkab450] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The emergence and spread of antimicrobial resistance (AMR) among pathogenic bacteria constitute an accelerating crisis for public health. The selective pressures caused by increased use and misuse of antimicrobials in medicine and livestock production have accelerated the overall selection of resistant bacteria. In addition, horizontal gene transfer (HGT) plays an important role in the spread of resistance genes, for example mobilizing reservoirs of AMR from commensal bacteria into pathogenic ones. Antimicrobials, besides antibacterial function, also result in undesirable effects in the microbial populations, including the stimulation of HGT. The main aim of this narrative review was to present an overview of the current knowledge of the impact of antimicrobials on HGT in bacteria, including the effects of transformation, transduction and conjugation, as well as other less well-studied mechanisms of HGT. It is widely accepted that conjugation plays a major role in the spread of AMR in bacteria, and the focus of this review is therefore mainly on the evidence provided that antimicrobial treatment affects this process. Other mechanisms of HGT have so far been deemed less important in this respect; however, recent discoveries suggest their role may be larger than previously thought, and the review provides an update on the rather limited knowledge currently available regarding the impact of antimicrobial treatment on these processes as well. A conclusion from the review is that there is an urgent need to investigate the mechanisms of antimicrobial-induced HGT, since this will be critical for developing new strategies to combat the spread of AMR.
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Affiliation(s)
- Gang Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China.,Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - Line Elnif Thomsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
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7
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Huang M, Liu M, Huang L, Wang M, Jia R, Zhu D, Chen S, Zhao X, Zhang S, Gao Q, Zhang L, Cheng A. The activation and limitation of the bacterial natural transformation system: The function in genome evolution and stability. Microbiol Res 2021; 252:126856. [PMID: 34454311 DOI: 10.1016/j.micres.2021.126856] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/19/2021] [Accepted: 08/22/2021] [Indexed: 12/26/2022]
Abstract
Bacteria can take up exogenous naked DNA and integrate it into their genomes, which has been regarded as a main contributor to bacterial evolution. The competent status of bacteria is influenced by environmental cues and by the immune systems of bacteria. Here, we review recent advances in understanding the working mechanisms underlying activation of the natural transformation system and limitations thereof. Environmental stresses including the presence of antimicrobials can activate the natural transformation system. However, bacterial enzymes (nucleases), non-coding RNAs, specific DNA sequences, the restriction-modification (R-M) systems, CRISPR-Cas systems and prokaryotic Argonaute proteins (Agos) are have been found to be involved in the limitation of the natural transformation system. Together, this review represents an opportunity to gain insight into bacterial genome stability and evolution.
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Affiliation(s)
- Mi Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Li Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Dekang Zhu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China.
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8
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Zhang L, Huang L, Huang M, Wang M, Zhu D, Wang M, Jia R, Chen S, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Mao S, Gao Q, Tian B, Cheng A, Liu M. Effect of Nutritional Determinants and TonB on the Natural Transformation of Riemerella anatipestifer. Front Microbiol 2021; 12:644868. [PMID: 34447355 PMCID: PMC8383284 DOI: 10.3389/fmicb.2021.644868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 07/13/2021] [Indexed: 11/27/2022] Open
Abstract
Riemerella anatipestifer is a gram-negative bacterium that is the first naturally competent bacterium identified in the family Flavobacteriaceae. However, the determinants that influence the natural transformation and the underlying mechanism remain unknown. In this study, we evaluated the effects of various nutritional factors of the GCB medium [glucose, L-glutamine, vitamin B1, Fe (NO3)3, NaCl, phosphate, and peptone], on the natural transformation of R. anatipestifer ATCC 11845. Among the assayed nutrients, peptone and phosphate affected the natural transformation of R. anatipestifer ATCC 11845, and the transformation frequency was significantly decreased when phosphate or peptone was removed from the GCB medium. When the iron chelator 2,2′-dipyridyl (Dip) was added, the transformation frequency was decreased by approximately 100-fold and restored gradually when Fe (NO3)3 was added, suggesting that the natural transformation of R. anatipestifer ATCC 11845 requires iron. Given the importance of TonB in nutrient transportation, we further identified whether TonB is involved in the natural transformation of R. anatipestifer ATCC 11845. Mutation of tonBA or tonBB, but not tbfA, was shown to inhibit the natural transformation of R. anatipestifer ATCC 11845 in the GCB medium. In parallel, it was shown that the tonBB mutant, but not the tonBA mutant, decreased iron acquisition in the GCB medium. This result suggested that the tonBB mutant affects the natural transformation frequency due to the deficiency of iron utilization.
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Affiliation(s)
- Li Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Li Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mi Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mengying Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Dekang Zhu
- Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
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9
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Ailloud F, Estibariz I, Suerbaum S. Evolved to vary: genome and epigenome variation in the human pathogen Helicobacter pylori. FEMS Microbiol Rev 2021; 45:5900976. [PMID: 32880636 DOI: 10.1093/femsre/fuaa042] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/31/2020] [Indexed: 12/24/2022] Open
Abstract
Helicobacter pylori is a Gram-negative, spiral shaped bacterium that selectively and chronically infects the gastric mucosa of humans. The clinical course of this infection can range from lifelong asymptomatic infection to severe disease, including peptic ulcers or gastric cancer. The high mutation rate and natural competence typical of this species are responsible for massive inter-strain genetic variation exceeding that observed in all other bacterial human pathogens. The adaptive value of such a plastic genome is thought to derive from a rapid exploration of the fitness landscape resulting in fast adaptation to the changing conditions of the gastric environment. Nevertheless, diversity is also lost through recurrent bottlenecks and H. pylori's lifestyle is thus a perpetual race to maintain an appropriate pool of standing genetic variation able to withstand selection events. Another aspect of H. pylori's diversity is a large and variable repertoire of restriction-modification systems. While not yet completely understood, methylome evolution could generate enough transcriptomic variation to provide another intricate layer of adaptive potential. This review provides an up to date synopsis of this rapidly emerging area of H. pylori research that has been enabled by the ever-increasing throughput of Omics technologies and a multitude of other technological advances.
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Affiliation(s)
- Florent Ailloud
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany
| | - Iratxe Estibariz
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany
| | - Sebastian Suerbaum
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany.,DZIF Deutsches Zentrum für Infektionsforschung, Partner Site Munich, Pettenkoferstr. 9a, 80336 München, Germany.,National Reference Center for Helicobacter pylori, Pettenkoferstr. 9a, 80336 München, Germany
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10
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Li Y, Lu L, Wu X, Li Q, Zhao Y, Du F, Chen Y, Shen J, Xiao Z, Wu Z, Hu W, Cho CH, Li M. The Multifaceted Role of Long Non-Coding RNA in Gastric Cancer: Current Status and Future Perspectives. Int J Biol Sci 2021; 17:2737-2755. [PMID: 34345204 PMCID: PMC8326121 DOI: 10.7150/ijbs.61410] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/08/2021] [Indexed: 12/22/2022] Open
Abstract
Gastric cancer (GC) is one of the major public health concerns. Long non-coding RNAs (lncRNAs) have been increasingly demonstrated to possess a strong correlation with GC and play a critical role in GC occurrence, progression, metastasis and drug resistance. Many studies have shed light on the understanding of the underlying mechanisms of lncRNAs in GC. In this review, we summarized the updated research about lncRNAs in GC, focusing on their roles in Helicobacter pylori infection, GC metastasis, tumor microenvironment regulation, drug resistance and associated signaling pathways. LncRNAs may serve as novel biomarkers for diagnosis and prognosis of GC and potential therapeutic targets. The research gaps and future directions were also discussed.
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Affiliation(s)
- Yifan Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China.,South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China
| | - Lan Lu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province,Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu 610106, Sichuan, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China.,South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China
| | - Qianxiu Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China.,South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China.,South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China
| | - Yu Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China.,South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China.,South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China.,South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China
| | - Zhigui Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China.,South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China.,Department of Pharmacy, the Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Wei Hu
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen 518000, Guangzhou, China
| | - Chi Hin Cho
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China.,South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China.,South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China
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11
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Kin discrimination promotes horizontal gene transfer between unrelated strains in Bacillus subtilis. Nat Commun 2021; 12:3457. [PMID: 34103505 PMCID: PMC8187645 DOI: 10.1038/s41467-021-23685-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 05/07/2021] [Indexed: 11/08/2022] Open
Abstract
Bacillus subtilis is a soil bacterium that is competent for natural transformation. Genetically distinct B. subtilis swarms form a boundary upon encounter, resulting in killing of one of the strains. This process is mediated by a fast-evolving kin discrimination (KD) system consisting of cellular attack and defence mechanisms. Here, we show that these swarm antagonisms promote transformation-mediated horizontal gene transfer between strains of low relatedness. Gene transfer between interacting non-kin strains is largely unidirectional, from killed cells of the donor strain to surviving cells of the recipient strain. It is associated with activation of a stress response mediated by sigma factor SigW in the donor cells, and induction of competence in the recipient strain. More closely related strains, which in theory would experience more efficient recombination due to increased sequence homology, do not upregulate transformation upon encounter. This result indicates that social interactions can override mechanistic barriers to horizontal gene transfer. We hypothesize that KD-mediated competence in response to the encounter of distinct neighbouring strains could maximize the probability of efficient incorporation of novel alleles and genes that have proved to function in a genomically and ecologically similar context.
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12
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Tagoe EA, Awandare GA, Quaye O, Asmah RH, Archampong TN, Osman MA, Brown CA. Helicobacter Pylori Variants with ABC-Type Tyrosine Phosphorylation Motif in Gastric Biopsies of Ghanaian Patients. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6616059. [PMID: 33860041 PMCID: PMC8026283 DOI: 10.1155/2021/6616059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Helicobacter pylori pathogenicity and disease severity are determined by the tyrosine phosphorylation motifs of CagA protein. This study is aimed at detecting the presence of H. pylori and identifying the CagA tyrosine phosphorylation motifs in Ghanaian patients. Material and Methods. A total of 94 archival genomic DNA samples from gastric biopsies were used for the study, and H. pylori was detected by amplifying the 16S rRNA gene. The 3'-end variable region of the cagA gene was amplified, and the entire 3'-end was sequenced and translated into amino acids. RESULTS H. pylori was detected in 53.2% (50/94) of the samples, and all the detected bacteria harboured the cagA gene. Two variants of the bacteria were identified based on the size of the amplified cagA gene: 207 bp and 285 bp. The 207 bp and 285 bp variants accounted for 74% and 22%, respectively, and 4% showed both fragments. Translated amino acid sequence of the cagA gene showed EPIYA-A, EPIYA-B, and EPIYA-C (ABC type) motifs, indicating the Western variant. The CagA protein C-terminal showed insertion of amino acids in the sequence flanking the EPIYA-A motif at the N-terminal and a complete deletion of the EPIYA-CC and EPIYA-CCC motifs together with the flanking sequences. CONCLUSIONS H. pylori identified were Western variant (ABC type) with unique amino acid insertions, suggesting unique variants in Ghanaian patients. Further investigation is however required to understand the role of the molecular diversity of the variant in gastric disease outcome.
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Affiliation(s)
- Emmanuel A. Tagoe
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP)/Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
- Department of Medical Laboratory Sciences, University of Ghana, Korle Bu, Accra, Ghana
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP)/Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP)/Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Richard H. Asmah
- Department of Medical Laboratory Sciences, University of Ghana, Korle Bu, Accra, Ghana
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Allied Health Sciences, Ho, Ghana
| | - Timothy N. Archampong
- Department of Medicine, University of Ghana Medical School, University of Ghana, Korle Bu, Accra, Ghana
| | - Mahasin A. Osman
- Departments of Medicine, College of Medicine and Life Sciences, University of Toledo, OH 34614, USA
| | - Charles A. Brown
- Department of Medical Laboratory Sciences, University of Ghana, Korle Bu, Accra, Ghana
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13
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Huang L, Liu M, Zhu D, Xie L, Huang M, Xiang C, Biville F, Jia R, Chen S, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, Wang M, Cheng A. Natural Transformation of Riemerella columbina and Its Determinants. Front Microbiol 2021; 12:634895. [PMID: 33746928 PMCID: PMC7965970 DOI: 10.3389/fmicb.2021.634895] [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: 11/29/2020] [Accepted: 02/12/2021] [Indexed: 12/17/2022] Open
Abstract
In a previous study, it was shown that Riemerella anatipestifer, a member of Flavobacteriaceae, is naturally competent. However, whether natural competence is universal in Flavobacteriaceae remains unknown. In this study, it was shown for the first time that Riemerella columbina was naturally competent in the laboratory condition; however, Flavobacterium johnsoniae was not naturally competent under the same conditions. The competence of R. columbina was maintained throughout the growth phases, and the transformation frequency was highest during the logarithmic phase. A competition assay revealed that R. columbina preferentially took up its own genomic DNA over heterologous DNA. The natural transformation frequency of R. columbina was significantly increased in GCB medium without peptone or phosphate. Furthermore, natural transformation of R. columbina was inhibited by 0.5 mM EDTA, but could be restored by the addition of CaCl2, MgCl2, ZnCl2, and MnCl2, suggesting that these divalent cations promote the natural transformation of R. columbina. Overall, this study revealed that natural competence is not universal in Flavobacteriaceae members and triggering of competence differs from species to species.
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Affiliation(s)
- Li Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Dekang Zhu
- Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Li Xie
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mi Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Chen Xiang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Francis Biville
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
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14
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Han T, Jing X, Bao J, Zhao L, Zhang A, Miao R, Guo H, Zhou B, Zhang S, Sun J, Shi J. H. pylori infection alters repair of DNA double-strand breaks via SNHG17. J Clin Invest 2021; 130:3901-3918. [PMID: 32538894 DOI: 10.1172/jci125581] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 04/14/2020] [Indexed: 12/15/2022] Open
Abstract
Chronic infections can lead to carcinogenesis through inflammation-related mechanisms. Chronic infection of the human gastric mucosa with Helicobacter pylori is a well-known risk factor for gastric cancer. However, the mechanisms underlying H. pylori-induced gastric carcinogenesis are incompletely defined. We aimed to screen and clarify the functions of long noncoding RNAs (lncRNAs) that are differentially expressed in H. pylori-related gastric cancer. We found that lncRNA SNHG17 was upregulated by H. pylori infection and markedly increased the levels of double-strand breaks (DSBs). SNHG17 overexpression correlated with poor overall survival in patients with gastric cancer. The recruitment of NONO by overabundant nuclear SNHG17, along with the role of cytoplasmic SNHG17 as a decoy for miR-3909, which regulates Rad51 expression, shifted the DSB repair balance from homologous recombination toward nonhomologous end joining. Notably, during chronic H. pylori infection, SNHG17 knockdown inhibited chromosomal aberrations. Our findings suggest that spatially independent deregulation of the SNHG17/NONO and SNHG17/miR-3909/RING1/Rad51 pathways upon H. pylori infection promotes tumorigenesis in gastric cancer by altering the DNA repair system, which is critical for the maintenance of genomic stability. Upregulation of SNHG17 by H. pylori infection might be an undefined link between cancer and inflammation.
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Affiliation(s)
- Taotao Han
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaohui Jing
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiayu Bao
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lianmei Zhao
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Research Center, Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, China
| | - Aidong Zhang
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Renling Miao
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui Guo
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Baoguo Zhou
- Department of General Surgery, First Affiliated Hospital of Harbin Medical University, Heilongjiang, China
| | - Shang Zhang
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiazeng Sun
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Juan Shi
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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15
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Samarth DP, Kwon YM. Horizontal genetic exchange of chromosomally encoded markers between Campylobacter jejuni cells. PLoS One 2020; 15:e0241058. [PMID: 33104745 PMCID: PMC7588059 DOI: 10.1371/journal.pone.0241058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 10/07/2020] [Indexed: 11/18/2022] Open
Abstract
Many epidemiological studies provide us with the evidence of horizontal gene transfer (HGT) contributing to the bacterial genomic diversity that benefits the bacterial populations with increased ability to adapt to the dynamic environments. Campylobacter jejuni, a major cause of acute enteritis in the U.S., often linked with severe post-infection neuropathies, has been reported to exhibit a non-clonal population structure and comparatively higher strain-level genetic variation. In this study, we provide evidence of the HGT of chromosomally encoded genetic markers between C. jejuni cells in the biphasic MH medium. We used two C. jejuni NCTC-11168 mutants harbouring distinct antibiotic-resistance genes [chloramphenicol (Cm) and kanamycin (Km)] present at two different neutral genomic loci. Cultures of both marker strains were mixed together and incubated for 5 hrs, then plated on MH agar plates supplemented with both antibiotics. The recombinant cells with double antibiotic markers were generated at the frequency of 0.02811 ± 0.0035% of the parental strains. PCR assays using locus-specific primers confirmed that transfer of the antibiotic-resistance genes was through homologous recombination. Also, the addition of chicken cecal content increased the recombination efficiency approximately up to 10-fold as compared to the biphasic MH medium (control) at P < 0.05. Furthermore, treating the co-culture with DNase I decreased the available DNA, which in turn significantly reduced recombination efficiency by 99.92% (P < 0.05). We used the cell-free supernatant of 16 hrs-culture of Wild-type C. jejuni as a template for PCR and found DNA sequences from six different genomic regions were easily amplified, indicating the presence of released chromosomal DNA in the culture supernatant. Our findings suggest that HGT in C. jejuni is facilitated in the chicken gut environment contributing to in vivo genomic diversity. Additionally, C. jejuni might have an active mechanism to release its chromosomal DNA into the extracellular environment, further expediting HGT in C. jejuni populations.
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Affiliation(s)
- Deepti Pranay Samarth
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States of America
- * E-mail:
| | - Young Min Kwon
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States of America
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States of America
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16
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Schirmacher AM, Hanamghar SS, Zedler JAZ. Function and Benefits of Natural Competence in Cyanobacteria: From Ecology to Targeted Manipulation. Life (Basel) 2020; 10:E249. [PMID: 33105681 PMCID: PMC7690421 DOI: 10.3390/life10110249] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 02/03/2023] Open
Abstract
Natural competence is the ability of a cell to actively take up and incorporate foreign DNA in its own genome. This trait is widespread and ecologically significant within the prokaryotic kingdom. Here we look at natural competence in cyanobacteria, a group of globally distributed oxygenic photosynthetic bacteria. Many cyanobacterial species appear to have the genetic potential to be naturally competent, however, this ability has only been demonstrated in a few species. Reasons for this might be due to a high variety of largely uncharacterised competence inducers and a lack of understanding the ecological context of natural competence in cyanobacteria. To shed light on these questions, we describe what is known about the molecular mechanisms of natural competence in cyanobacteria and analyse how widespread this trait might be based on available genomic datasets. Potential regulators of natural competence and what benefits or drawbacks may derive from taking up foreign DNA are discussed. Overall, many unknowns about natural competence in cyanobacteria remain to be unravelled. A better understanding of underlying mechanisms and how to manipulate these, can aid the implementation of cyanobacteria as sustainable production chassis.
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Affiliation(s)
| | | | - Julie A. Z. Zedler
- Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (A.M.S.); (S.S.H.)
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17
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Horizontal gene transfer potentiates adaptation by reducing selective constraints on the spread of genetic variation. Proc Natl Acad Sci U S A 2020; 117:26868-26875. [PMID: 33055207 DOI: 10.1073/pnas.2005331117] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Horizontal gene transfer (HGT) confers the rapid acquisition of novel traits and is pervasive throughout microbial evolution. Despite the central role of HGT, the evolutionary forces that drive the dynamics of HGT alleles in evolving populations are poorly understood. Here, we show that HGT alters the evolutionary dynamics of genetic variation, so that deleterious genetic variants, including antibiotic resistance genes, can establish in populations without selection. We evolve antibiotic-sensitive populations of the human pathogen Helicobacter pylori in an environment without antibiotic but with HGT from an antibiotic-resistant isolate of H. pylori We find that HGT increases the rate of adaptation, with most horizontally transferred genetic variants establishing at a low frequency in the population. When challenged with antibiotic, this low-level variation potentiates adaptation, with HGT populations flourishing in conditions where nonpotentiated populations go extinct. By extending previous models of evolution under HGT, we evaluated the conditions for the establishment and spread of HGT-acquired alleles into recipient populations. We then used our model to estimate parameters of HGT and selection from our experimental evolution data. Together, our findings show how HGT can act as an evolutionary force that facilitates the spread of nonselected genetic variation and expands the adaptive potential of microbial populations.
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18
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Goneau LW, Delport J, Langlois L, Poutanen SM, Razvi H, Reid G, Burton JP. Issues beyond resistance: inadequate antibiotic therapy and bacterial hypervirulence. FEMS MICROBES 2020; 1:xtaa004. [PMID: 37333955 PMCID: PMC10117437 DOI: 10.1093/femsmc/xtaa004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/15/2020] [Indexed: 10/15/2023] Open
Abstract
The administration of antibiotics while critical for treatment, can be accompanied by potentially severe complications. These include toxicities associated with the drugs themselves, the selection of resistant organisms and depletion of endogenous host microbiota. In addition, antibiotics may be associated with less well-recognized complications arising through changes in the pathogens themselves. Growing evidence suggests that organisms exposed to antibiotics can respond by altering the expression of toxins, invasins and adhesins, as well as biofilm, resistance and persistence factors. The clinical significance of these changes continues to be explored; however, it is possible that treatment with antibiotics may inadvertently precipitate a worsening of the clinical course of disease. Efforts are needed to adjust or augment antibiotic therapy to prevent the transition of pathogens to hypervirulent states. Better understanding the role of antibiotic-microbe interactions and how these can influence disease course is critical given the implications on prescription guidelines and antimicrobial stewardship policies.
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Affiliation(s)
- Lee W Goneau
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
- Lawson Health Research Institute, 268 Grosvenor St, London, Ontario, N6A 4V2 Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto,1 King's College Cir, Toronto, ON M5S 1A8 Ontario, Canada
| | - Johannes Delport
- Department of Pathology, London Health Sciences Center - Victoria Hospital, 800 Commissioners Rd E, London, Ontario, Canada N6A 5W9
| | - Luana Langlois
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
| | - Susan M Poutanen
- Department of Laboratory Medicine and Pathobiology, University of Toronto,1 King's College Cir, Toronto, ON M5S 1A8 Ontario, Canada
- Department of Medicine, University of Toronto, 1 King's College Cir, Toronto, ON M5S 1A8 Toronto, Ontario, Canada
- Department of Microbiology, University Health Network and Sinai Health, 190 Elizabeth St. Toronto, ON M5G 2C4, Ontario, Canada
| | - Hassan Razvi
- Lawson Health Research Institute, 268 Grosvenor St, London, Ontario, N6A 4V2 Canada
- Division of Urology, Department of Surgery, Western University, 1151 Richmond St, London, Ontario, N6A 3K7 Canada
| | - Gregor Reid
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
- Lawson Health Research Institute, 268 Grosvenor St, London, Ontario, N6A 4V2 Canada
- Division of Urology, Department of Surgery, Western University, 1151 Richmond St, London, Ontario, N6A 3K7 Canada
| | - Jeremy P Burton
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
- Lawson Health Research Institute, 268 Grosvenor St, London, Ontario, N6A 4V2 Canada
- Division of Urology, Department of Surgery, Western University, 1151 Richmond St, London, Ontario, N6A 3K7 Canada
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Abstract
The ancestral strain of Bacillus subtilis NCIB3610 (3610) bears a large, low-copy-number plasmid, called pBS32, that was lost during the domestication of laboratory strain derivatives. Selection against pBS32 may have been because it encodes a potent inhibitor of natural genetic competence (ComI), as laboratory strains were selected for high-frequency transformation. Previous studies have shown that pBS32 and its sibling, pLS32 in Bacillus subtilis subsp. natto, encode a replication initiation protein (RepN), a plasmid partitioning system (AlfAB), a biofilm inhibitor (RapP), and an alternative sigma factor (SigN) that can induce plasmid-mediated cell death in response to DNA damage. Here, we review the literature on pBS32/pLS32, the genes found on it, and their associated phenotypes.
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20
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Wang Y, Lu J, Engelstädter J, Zhang S, Ding P, Mao L, Yuan Z, Bond PL, Guo J. Non-antibiotic pharmaceuticals enhance the transmission of exogenous antibiotic resistance genes through bacterial transformation. THE ISME JOURNAL 2020; 14:2179-2196. [PMID: 32424247 PMCID: PMC7367833 DOI: 10.1038/s41396-020-0679-2] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 12/19/2022]
Abstract
Antibiotic resistance is a serious global threat for public health. Considering the high abundance of cell-free DNA encoding antibiotic resistance genes (ARGs) in both clinical and environmental settings, natural transformation is an important horizontal gene transfer pathway to transmit antibiotic resistance. It is acknowledged that antibiotics are key drivers for disseminating antibiotic resistance, yet the contributions of non-antibiotic pharmaceuticals on transformation of ARGs are overlooked. In this study, we report that some commonly consumed non-antibiotic pharmaceuticals, at clinically and environmentally relevant concentrations, significantly facilitated the spread of antibiotic resistance through the uptake of exogenous ARGs. This included nonsteroidal anti-inflammatories, ibuprofen, naproxen, diclofenac, the lipid-lowering drug, gemfibrozil, and the β-blocker propranolol. Based on the results of flow cytometry, whole-genome RNA sequencing and proteomic analysis, the enhanced transformation of ARGs was affiliated with promoted bacterial competence, enhanced stress levels, over-produced reactive oxygen species and increased cell membrane permeability. In addition, a mathematical model was proposed and calibrated to predict the dynamics of transformation during exposure to non-antibiotic pharmaceuticals. Given the high consumption of non-antibiotic pharmaceuticals, these findings reveal new concerns regarding antibiotic resistance dissemination exacerbated by non-antibiotic pharmaceuticals.
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Affiliation(s)
- Yue Wang
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ji Lu
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Shuai Zhang
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Pengbo Ding
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Likai Mao
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia.
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21
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Hyun JC, Kavvas ES, Monk JM, Palsson BO. Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens. PLoS Comput Biol 2020; 16:e1007608. [PMID: 32119670 PMCID: PMC7067475 DOI: 10.1371/journal.pcbi.1007608] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/12/2020] [Accepted: 12/16/2019] [Indexed: 12/29/2022] Open
Abstract
The evolution of antimicrobial resistance (AMR) poses a persistent threat to global public health. Sequencing efforts have already yielded genome sequences for thousands of resistant microbial isolates and require robust computational tools to systematically elucidate the genetic basis for AMR. Here, we present a generalizable machine learning workflow for identifying genetic features driving AMR based on constructing reference strain-agnostic pan-genomes and training random subspace ensembles (RSEs). This workflow was applied to the resistance profiles of 14 antimicrobials across three urgent threat pathogens encompassing 288 Staphylococcus aureus, 456 Pseudomonas aeruginosa, and 1588 Escherichia coli genomes. We find that feature selection by RSE detects known AMR associations more reliably than common statistical tests and previous ensemble approaches, identifying a total of 45 known AMR-conferring genes and alleles across the three organisms, as well as 25 candidate associations backed by domain-level annotations. Furthermore, we find that results from the RSE approach are consistent with existing understanding of fluoroquinolone (FQ) resistance due to mutations in the main drug targets, gyrA and parC, in all three organisms, and suggest the mutational landscape of those genes with respect to FQ resistance is simple. As larger datasets become available, we expect this approach to more reliably predict AMR determinants for a wider range of microbial pathogens.
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Affiliation(s)
- Jason C. Hyun
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, California, United States of America
| | - Erol S. Kavvas
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Jonathan M. Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
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22
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Stingl K, Koraimann G. Prokaryotic Information Games: How and When to Take up and Secrete DNA. Curr Top Microbiol Immunol 2019. [PMID: 29536355 DOI: 10.1007/978-3-319-75241-9_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Besides transduction via bacteriophages natural transformation and bacterial conjugation are the most important mechanisms driving bacterial evolution and horizontal gene spread. Conjugation systems have evolved in eubacteria and archaea. In Gram-positive and Gram-negative bacteria, cell-to-cell DNA transport is typically facilitated by a type IV secretion system (T4SS). T4SSs also mediate uptake of free DNA in Helicobacter pylori, while most transformable bacteria use a type II secretion/type IV pilus system. In this chapter, we focus on how and when bacteria "decide" that such a DNA transport apparatus is to be expressed and assembled in a cell that becomes competent. Development of DNA uptake competence and DNA transfer competence is driven by a variety of stimuli and often involves intricate regulatory networks leading to dramatic changes in gene expression patterns and bacterial physiology. In both cases, genetically homogeneous populations generate a distinct subpopulation that is competent for DNA uptake or DNA transfer or might uniformly switch into competent state. Phenotypic conversion from one state to the other can rely on bistable genetic networks that are activated stochastically with the integration of external signaling molecules. In addition, we discuss principles of DNA uptake processes in naturally transformable bacteria and intend to understand the exceptional use of a T4SS for DNA import in the gastric pathogen H. pylori. Realizing the events that trigger developmental transformation into competence within a bacterial population will eventually help to create novel and effective therapies against the transmission of antibiotic resistances among pathogens.
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Affiliation(s)
- Kerstin Stingl
- National Reference Laboratory for Campylobacter, Department Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, 12277, Berlin, Germany.
| | - Günther Koraimann
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria.
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23
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α-Difluoromethylornithine reduces gastric carcinogenesis by causing mutations in Helicobacter pylori cagY. Proc Natl Acad Sci U S A 2019; 116:5077-5085. [PMID: 30804204 DOI: 10.1073/pnas.1814497116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Infection by Helicobacter pylori is the primary cause of gastric adenocarcinoma. The most potent H. pylori virulence factor is cytotoxin-associated gene A (CagA), which is translocated by a type 4 secretion system (T4SS) into gastric epithelial cells and activates oncogenic signaling pathways. The gene cagY encodes for a key component of the T4SS and can undergo gene rearrangements. We have shown that the cancer chemopreventive agent α-difluoromethylornithine (DFMO), known to inhibit the enzyme ornithine decarboxylase, reduces H. pylori-mediated gastric cancer incidence in Mongolian gerbils. In the present study, we questioned whether DFMO might directly affect H. pylori pathogenicity. We show that H. pylori output strains isolated from gerbils treated with DFMO exhibit reduced ability to translocate CagA in gastric epithelial cells. Further, we frequently detected genomic modifications in the middle repeat region of the cagY gene of output strains from DFMO-treated animals, which were associated with alterations in the CagY protein. Gerbils did not develop carcinoma when infected with a DFMO output strain containing rearranged cagY or the parental strain in which the wild-type cagY was replaced by cagY with DFMO-induced rearrangements. Lastly, we demonstrate that in vitro treatment of H. pylori by DFMO induces oxidative DNA damage, expression of the DNA repair enzyme MutS2, and mutations in cagY, demonstrating that DFMO directly affects genomic stability. Deletion of mutS2 abrogated the ability of DFMO to induce cagY rearrangements directly. In conclusion, DFMO-induced oxidative stress in H. pylori leads to genomic alterations and attenuates virulence.
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24
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Fluorescence-Based Detection of Natural Transformation in Drug-Resistant Acinetobacter baumannii. J Bacteriol 2018; 200:JB.00181-18. [PMID: 30012729 PMCID: PMC6148472 DOI: 10.1128/jb.00181-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/27/2018] [Indexed: 01/05/2023] Open
Abstract
Acinetobacter baumannii is a nosocomial agent with a high propensity for developing resistance to antibiotics. This ability relies on horizontal gene transfer mechanisms occurring in the Acinetobacter genus, including natural transformation. To study natural transformation in bacteria, the most prevalent method uses selection for the acquisition of an antibiotic resistance marker in a target chromosomal locus by the recipient cell. Most clinical isolates of A. baumannii are resistant to multiple antibiotics, limiting the use of such selection-based methods. Here, we report the development of a phenotypic and selection-free method based on flow cytometry to detect transformation events in multidrug-resistant (MDR) clinical A. baumannii isolates. To this end, we engineered a translational fusion between the abundant and conserved A. baumannii nucleoprotein (HU) and the superfolder green fluorescent protein (sfGFP). The new method was benchmarked against the conventional antibiotic selection-based method. Using this new method, we investigated several parameters affecting transformation efficiencies and identified conditions of transformability one hundred times higher than those previously reported. Using optimized transformation conditions, we probed natural transformation in a set of MDR clinical and nonclinical animal A. baumannii isolates. Regardless of their origin, the majority of the isolates displayed natural transformability, indicative of a conserved trait in the species. Overall, this new method and optimized protocol will greatly facilitate the study of natural transformation in the opportunistic pathogen A. baumannii IMPORTANCE Antibiotic resistance is a pressing global health concern with the rise of multiple and panresistant pathogens. The rapid and unfailing resistance to multiple antibiotics of the nosocomial agent Acinetobacter baumannii, notably to carbapenems, prompt to understand the mechanisms behind acquisition of new antibiotic resistance genes. Natural transformation, one of the horizontal gene transfer mechanisms in bacteria, was only recently described in A. baumannii and could explain its ability to acquire resistance genes. We developed a reliable method to probe and study natural transformation mechanism in A. baumannii More broadly, this new method based on flow cytometry will allow experimental detection and quantification of horizontal gene transfer events in multidrug-resistant A. baumannii.
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25
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Dai K, He L, Chang YF, Cao S, Zhao Q, Huang X, Wu R, Huang Y, Yan Q, Han X, Ma X, Wen X, Wen Y. Basic Characterization of Natural Transformation in a Highly Transformable Haemophilus parasuis Strain SC1401. Front Cell Infect Microbiol 2018; 8:32. [PMID: 29473023 PMCID: PMC5809987 DOI: 10.3389/fcimb.2018.00032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/25/2018] [Indexed: 11/13/2022] Open
Abstract
Haemophilus parasuis causes Glässer's disease and pneumonia, incurring serious economic losses in the porcine industry. In this study, natural competence was investigated in H. parasuis. We found competence genes in H. parasuis homologous to ones in Haemophilus influenzae and a high consensus battery of Sxy-dependent cyclic AMP (cAMP) receptor protein (CRP-S) regulons using bioinformatics. High rates of natural competence were found from the onset of stationary-phase growth condition to mid-stationary phase (OD600 from 0.29 to 1.735); this rapidly dropped off as cells reached mid-stationary phase (OD600 from 1.735 to 1.625). As a whole, bacteria cultured in liquid media were observed to have lower competence levels than those grown on solid media plates. We also revealed that natural transformation in this species is stable after 200 passages and is largely dependent on DNA concentration. Transformation competition experiments showed that heterogeneous DNA cannot outcompete intraspecific natural transformation, suggesting an endogenous uptake sequence or other molecular markers may be important in differentiating heterogeneous DNA. We performed qRT-PCR targeting multiple putative competence genes in an effort to compare bacteria pre-cultured in TSB++ vs. TSA++ and SC1401 vs. SH0165 to determine expression profiles of the homologs of competence-genes in H. influenzae. Taken together, this study is the first to investigate natural transformation in H. parasuis based on a highly naturally transformable strain SC1401.
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Affiliation(s)
- Ke Dai
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lvqin He
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Sanjie Cao
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Sichuan Science-Observation Experimental Station of Veterinary Drugs and Veterinary Diagnostic Technology, Ministry of Agriculture, Chengdu, China
| | - Qin Zhao
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaobo Huang
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Rui Wu
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yong Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qigui Yan
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinfeng Han
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaoping Ma
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xintian Wen
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yiping Wen
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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26
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Bernstein H, Bernstein C, Michod RE. Sex in microbial pathogens. INFECTION GENETICS AND EVOLUTION 2018; 57:8-25. [DOI: 10.1016/j.meegid.2017.10.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/25/2017] [Accepted: 10/26/2017] [Indexed: 10/18/2022]
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27
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Ambur OH, Engelstädter J, Johnsen PJ, Miller EL, Rozen DE. Steady at the wheel: conservative sex and the benefits of bacterial transformation. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0528. [PMID: 27619692 PMCID: PMC5031613 DOI: 10.1098/rstb.2015.0528] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2016] [Indexed: 12/25/2022] Open
Abstract
Many bacteria are highly sexual, but the reasons for their promiscuity remain obscure. Did bacterial sex evolve to maximize diversity and facilitate adaptation in a changing world, or does it instead help to retain the bacterial functions that work right now? In other words, is bacterial sex innovative or conservative? Our aim in this review is to integrate experimental, bioinformatic and theoretical studies to critically evaluate these alternatives, with a main focus on natural genetic transformation, the bacterial equivalent of eukaryotic sexual reproduction. First, we provide a general overview of several hypotheses that have been put forward to explain the evolution of transformation. Next, we synthesize a large body of evidence highlighting the numerous passive and active barriers to transformation that have evolved to protect bacteria from foreign DNA, thereby increasing the likelihood that transformation takes place among clonemates. Our critical review of the existing literature provides support for the view that bacterial transformation is maintained as a means of genomic conservation that provides direct benefits to both individual bacterial cells and to transformable bacterial populations. We examine the generality of this view across bacteria and contrast this explanation with the different evolutionary roles proposed to maintain sex in eukaryotes. This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.
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Affiliation(s)
- Ole Herman Ambur
- Department of Life Sciences and Health, Oslo and Akershus University College of Applied Sciences, 1478 Oslo, Norway
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Pål J Johnsen
- Faculty of Health Sciences, Department of Pharmacy, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Eric L Miller
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Daniel E Rozen
- Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
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28
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29
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Molecular basis for the functions of a bacterial MutS2 in DNA repair and recombination. DNA Repair (Amst) 2017; 57:161-170. [PMID: 28800560 DOI: 10.1016/j.dnarep.2017.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 06/08/2017] [Accepted: 07/11/2017] [Indexed: 02/06/2023]
Abstract
Bacterial MutS2 proteins, consisting of functional domains for ATPase, DNA-binding, and nuclease activities, play roles in DNA recombination and repair. Here we observe a mechanism for generating MutS2 expression diversity in the human pathogen Helicobacter pylori, and identify a unique MutS2 domain responsible for specific DNA-binding. H. pylori strains differ in mutS2 expression due to variations in the DNA upstream sequence containing short sequence repeats. Based on Western blots, mutS2 in some strains appears to be co-translated with the upstream gene, but in other strains (e.g. UA948) such translational coupling does not occur. Accordingly, strain UA948 had phenotypes similar to its ΔmutS2 derivative, whereas expression of MutS2 at a separate locus in UA948 (the genetically complemented strain) displayed a lower mutation rate and lower transformation frequency than did ΔmutS2. A series of truncated HpMutS2 proteins were purified and tested for their specific abilities to bind 8-oxoG-containing DNA (GO:C) and Holiday Junction structures (HJ). The specific DNA binding domain was localized to an area adjacent to the Smr nuclease domain, and it encompasses 30-amino-acid-residues containing a "KPPKNKFKPPK" motif. Gel shift assays and competition assays supported that a truncated version of HpMutS2-C12 (∼12kDa protein containing the specific DNA-binding domain) has much greater capacity to bind to HJ or GO:C DNA than to normal double stranded DNA. By studying the in vivo roles of the separate domains of HpMutS2, we observed that the truncated versions were unable to complement the ΔmutS2 strain, suggesting the requirement for coordinated function of all the domains in vivo.
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30
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Kandel PP, Almeida RPP, Cobine PA, De La Fuente L. Natural Competence Rates Are Variable Among Xylella fastidiosa Strains and Homologous Recombination Occurs In Vitro Between Subspecies fastidiosa and multiplex. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:589-600. [PMID: 28459171 DOI: 10.1094/mpmi-02-17-0053-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Xylella fastidiosa, an etiological agent of emerging crop diseases around the world, is naturally competent for the uptake of DNA from the environment that is incorporated into its genome by homologous recombination. Homologous recombination between subspecies of X. fastidiosa was inferred by in silico studies and was hypothesized to cause disease emergence. However, no experimental data are available on the degree to which X. fastidiosa strains are capable of competence and whether recombination can be experimentally demonstrated between subspecies. Here, using X. fastidiosa strains from different subspecies, natural competence in 11 of 13 strains was confirmed with plasmids containing antibiotic markers flanked by homologous regions and, in three of five strains, with dead bacterial cells used as source of donor DNA. Recombination frequency differed among strains and was correlated to growth rate and twitching motility. Moreover, intersubspecific recombination occurred readily between strains of subsp. fastidiosa and multiplex, as demonstrated by movement of antibiotic resistance and green fluorescent protein from donor to recipient cells and confirmed by DNA sequencing of the flanking arms of recombinant strains. Results demonstrate that natural competence is widespread among X. fastidiosa strains and could have an impact in pathogen adaptation and disease development.
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Affiliation(s)
- Prem P Kandel
- 1 Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, U.S.A
| | - Rodrigo P P Almeida
- 2 Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, U.S.A.; and
| | - Paul A Cobine
- 3 Department of Biological Sciences, Auburn University
| | - Leonardo De La Fuente
- 1 Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, U.S.A
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31
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Blokesch M. In and out-contribution of natural transformation to the shuffling of large genomic regions. Curr Opin Microbiol 2017; 38:22-29. [PMID: 28458094 DOI: 10.1016/j.mib.2017.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/01/2017] [Accepted: 04/06/2017] [Indexed: 01/28/2023]
Abstract
Naturally competent bacteria can pull free DNA from their surroundings. This incoming DNA can serve various purposes, ranging from acting as a source of nutrients or DNA stretches for repair to the acquisition of novel genetic information. The latter process defines the natural competence for transformation as a mode of horizontal gene transfer (HGT) and led to its discovery almost a century ago. However, although it is widely accepted that natural competence can contribute to the spread of genetic material among prokaryotes, the question remains whether this mode of HGT can foster the transfer of larger DNA regions or only transfers shorter fragments, given that extracellular DNA is often heavily fragmented. Here, I outline examples of competence-mediated movement of large genomic segments. Moreover, I discuss a recent proposition that transformation is used to cure bacteria of selfish mobile genetic elements. Such a transformation-mediated genome maintenance mechanism could indeed be an important and underappreciated function of natural competence.
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Affiliation(s)
- Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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32
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Pinos S, Pontarotti P, Raoult D, Merhej V. Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum. BMC Evol Biol 2017; 17:75. [PMID: 28274202 PMCID: PMC5343374 DOI: 10.1186/s12862-017-0921-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Horizontal transfer plays an important role in the evolution of bacterial genomes, yet it obeys several constraints, including the ecological opportunity to meet other organisms, the presence of transfer systems, and the fitness of the transferred genes. Bacteria from the Planctomyctetes, Verrumicrobia, Chlamydiae (PVC) super-phylum have a compartmentalized cell plan delimited by an intracytoplasmic membrane that might constitute an additional constraint with particular impact on bacterial evolution. In this investigation, we studied the evolution of 33 genomes from PVC species and focused on the rate and the nature of horizontally transferred sequences in relation to their habitat and their cell plan. RESULTS Using a comparative phylogenomic approach, we showed that habitat influences the evolution of the bacterial genome's content and the flux of horizontal transfer of DNA (HT). Thus bacteria from soil, from insects and ubiquitous bacteria presented the highest average of horizontal transfer compared to bacteria living in water, extracellular bacteria in vertebrates, bacteria from amoeba and intracellular bacteria in vertebrates (with a mean of 379 versus 110 events per species, respectively and 7.6% of each genomes due to HT against 4.8%). The partners of these transfers were mainly bacterial organisms (94.9%); they allowed us to differentiate environmental bacteria, which exchanged more with Proteobacteria, and bacteria from vertebrates, which exchanged more with Firmicutes. The functional analysis of the horizontal transfers revealed a convergent evolution, with an over-representation of genes encoding for membrane biogenesis and lipid metabolism, among compartmentalized bacteria in the different habitats. CONCLUSIONS The presence of an intracytoplasmic membrane in PVC species seems to affect the genome's evolution through the selection of transferred DNA, according to their encoded functions.
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Affiliation(s)
- Sandrine Pinos
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Evolution Biologique et Modélisation, 3 place Victor Hugo, Marseille, 13331 France
- Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM URMITE, IHU -Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, 13005 France
| | - Pierre Pontarotti
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Evolution Biologique et Modélisation, 3 place Victor Hugo, Marseille, 13331 France
| | - Didier Raoult
- Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM URMITE, IHU -Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, 13005 France
| | - Vicky Merhej
- Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM URMITE, IHU -Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, 13005 France
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33
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Hülter N, Sørum V, Borch-Pedersen K, Liljegren MM, Utnes ALG, Primicerio R, Harms K, Johnsen PJ. Costs and benefits of natural transformation in Acinetobacter baylyi. BMC Microbiol 2017; 17:34. [PMID: 28202049 PMCID: PMC5312590 DOI: 10.1186/s12866-017-0953-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 02/10/2017] [Indexed: 11/10/2022] Open
Abstract
Background Natural transformation enables acquisition of adaptive traits and drives genome evolution in prokaryotes. Yet, the selective forces responsible for the evolution and maintenance of natural transformation remain elusive since taken-up DNA has also been hypothesized to provide benefits such as nutrients or templates for DNA repair to individual cells. Results We investigated the immediate effects of DNA uptake and recombination on the naturally competent bacterium Acinetobacter baylyi in both benign and genotoxic conditions. In head-to-head competition experiments between DNA uptake-proficient and -deficient strains, we observed a fitness benefit of DNA uptake independent of UV stress. This benefit was found with both homologous and heterologous DNA and was independent of recombination. Recombination with taken-up DNA reduced survival of transformed cells with increasing levels of UV-stress through interference with nucleotide excision repair, suggesting that DNA strand breaks occur during recombination attempts with taken-up DNA. Consistent with this, we show that absence of RecBCD and RecFOR recombinational DNA repair pathways strongly decrease natural transformation. Conclusions Our data show a physiological benefit of DNA uptake unrelated to recombination. In contrast, recombination during transformation is a strand break inducing process that represents a previously unrecognized cost of natural transformation. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0953-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nils Hülter
- Genomic Microbiology, Institute of Microbiology, Christian-Albrechts-University Kiel, Am Botanischen Garten 11, 24118, Kiel, Germany.,Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway
| | - Vidar Sørum
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway
| | - Kristina Borch-Pedersen
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, P.O. Box 8146 Dep, 0033, Oslo, Norway
| | - Mikkel M Liljegren
- Centre for Ecolgical and Evolutionary Synthesis, Faculty of Mathematics and Natural Sciences, University of Oslo, P.O. Box 1066 Blindern, 0316, Oslo, Norway
| | - Ane L G Utnes
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway
| | - Raul Primicerio
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway
| | - Klaus Harms
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway. .,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
| | - Pål J Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway.
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34
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ComB proteins expression levels determine Helicobacter pylori competence capacity. Sci Rep 2017; 7:41495. [PMID: 28128333 PMCID: PMC5269756 DOI: 10.1038/srep41495] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 12/21/2016] [Indexed: 12/17/2022] Open
Abstract
Helicobacter pylori chronically colonises half of the world’s human population and is the main cause of ulcers and gastric cancers. Its prevalence and the increase in antibiotic resistance observed recently reflect the high genetic adaptability of this pathogen. Together with high mutation rates and an efficient DNA recombination system, horizontal gene transfer through natural competence makes of H. pylori one of the most genetically diverse bacteria. We show here that transformation capacity is enhanced in strains defective for recN, extending previous work with other homologous recombination genes. However, inactivation of either mutY or polA has no effect on DNA transformation, suggesting that natural competence can be boosted in H. pylori by the persistence of DNA breaks but not by enhanced mutagenesis. The transformation efficiency of the different DNA repair impaired strains correlates with the number of transforming DNA foci formed on the cell surface and with the expression of comB8 and comB10 competence genes. Overexpression of the comB6-B10 operon is sufficient to increase the transformation capacity of a wild type strain, indicating that the ComB complex, present in the bacterial wall and essential for DNA uptake, can be a limiting factor for transformation efficiency.
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35
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Kandel PP, Lopez SM, Almeida RPP, De La Fuente L. Natural Competence of Xylella fastidiosa Occurs at a High Frequency Inside Microfluidic Chambers Mimicking the Bacterium's Natural Habitats. Appl Environ Microbiol 2016; 82:5269-77. [PMID: 27316962 PMCID: PMC4988197 DOI: 10.1128/aem.01412-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/13/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Xylella fastidiosa is a xylem-limited bacterium that is the causal agent of emerging diseases in a number of economically important crops. Genetic diversity studies have demonstrated homologous recombination occurring among X. fastidiosa strains, which has been proposed to contribute to host plant shifts. Moreover, experimental evidence confirmed that X. fastidiosa is naturally competent for recombination in vitro Here, as an approximation of natural habitats (plant xylem vessels and insect mouthparts), recombination was studied in microfluidic chambers (MCs) filled with media amended with grapevine xylem sap. First, different media were screened for recombination in solid agar plates using a pair of X. fastidiosa strains that were previously reported to recombine in coculture. The highest frequency of recombination was obtained with PD3 medium, compared to those with the other two media (X. fastidiosa medium [XFM] and periwinkle wilt [PW] medium) used in previous studies. Dissection of the media components led to the identification of bovine serum albumin as an inhibitor of recombination that was correlated to its previously known effect on inhibition of twitching motility. When recombination was performed in liquid culture, the frequencies were significantly higher under flow conditions (MCs) than under batch conditions (test tubes). The recombination frequencies in MCs and agar plates were not significantly different from each other. Grapevine xylem sap from both susceptible and tolerant varieties allowed high recombination frequency in MCs when mixed with PD3. These results suggest that X. fastidiosa has the ability to be naturally competent in the natural growth environment of liquid flow, and this phenomenon could have implications in X. fastidiosa environmental adaptation. IMPORTANCE Xylella fastidiosa is a plant pathogen that lives inside xylem vessels (where water and nutrients are transported inside the plant) and the mouthparts of insect vectors. This bacterium causes emerging diseases in various crops worldwide, including recent outbreaks in Europe. The mechanisms by which this bacterium adapts to new hosts is not understood, but it was previously shown that it is naturally competent, meaning that it can take up DNA from the environment and incorporate it into its genome (recombination). In this study, we show that the frequency of recombination is highest when the bacterium is grown under flow conditions in microfluidic chambers modeled after its natural habitats, and recombination was still high when the medium was amended with grapevine sap. Our results suggest that this bacterium is able to recombine when growing inside plants or insects, and this can be a mechanism of adaptation of this pathogen that causes incurable diseases.
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Affiliation(s)
- Prem P Kandel
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Samantha M Lopez
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | - Leonardo De La Fuente
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
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36
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Serum Albumin and Ca2+ Are Natural Competence Inducers in the Human Pathogen Acinetobacter baumannii. Antimicrob Agents Chemother 2016; 60:4920-9. [PMID: 27270286 DOI: 10.1128/aac.00529-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/28/2016] [Indexed: 01/07/2023] Open
Abstract
The increasing frequency of bacteria showing antimicrobial resistance (AMR) raises the menace of entering into a postantibiotic era. Horizontal gene transfer (HGT) is one of the prime reasons for AMR acquisition. Acinetobacter baumannii is a nosocomial pathogen with outstanding abilities to survive in the hospital environment and to acquire resistance determinants. Its capacity to incorporate exogenous DNA is a major source of AMR genes; however, few studies have addressed this subject. The transformation machinery as well as the factors that induce natural competence in A. baumannii are unknown. In this study, we demonstrate that naturally competent strain A118 increases its natural transformation frequency upon the addition of Ca(2+)or albumin. We show that comEA and pilQ are involved in this process since their expression levels are increased upon the addition of these compounds. An unspecific protein, like casein, does not reproduce this effect, showing that albumin's effect is specific. Our work describes the first specific inducers of natural competence in A. baumannii Overall, our results suggest that the main protein in blood enhances HGT in A. baumannii, contributing to the increase of AMR in this threatening human pathogen.
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37
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Krüger NJ, Knüver MT, Zawilak-Pawlik A, Appel B, Stingl K. Genetic Diversity as Consequence of a Microaerobic and Neutrophilic Lifestyle. PLoS Pathog 2016; 12:e1005626. [PMID: 27166672 PMCID: PMC4864210 DOI: 10.1371/journal.ppat.1005626] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 04/21/2016] [Indexed: 01/10/2023] Open
Abstract
As a neutrophilic bacterium, Helicobacter pylori is growth deficient under extreme acidic conditions. The gastric pathogen is equipped with an acid survival kit, regulating urease activity by a pH-gated urea channel, opening below pH 6.5. After overcoming acid stress, the bacterium’s multiplication site is situated at the gastric mucosa with near neutral pH. The pathogen exhibits exceptional genetic variability, mainly due to its capability of natural transformation, termed competence. Using single cell analysis, we show here that competence is highly regulated in H. pylori. DNA uptake complex activity was reversibly shut down below pH 6.5. pH values above 6.5 opened a competence window, in which competence development was triggered by the combination of pH increase and oxidative stress. In contrast, addition of sublethal concentrations of the DNA-damaging agents ciprofloxacin or mitomycin C did not trigger competence development under our conditions. An oxygen-sensitive mutant lacking superoxide dismutase (sodB) displayed a higher competent fraction of cells than the wild type under comparable conditions. In addition, the sodB mutant was dependent on adenine for growth in broth and turned into non-cultivable coccoid forms in its absence, indicating that adenine had radical quenching capacity. Quantification of periplasmically located DNA in competent wild type cells revealed outstanding median imported DNA amounts of around 350 kb per cell within 10 min of import, with maximally a chromosomal equivalent (1.6 Mb) in individual cells, far exceeding previous amounts detected in other Gram-negative bacteria. We conclude that the pathogen’s high genetic diversity is a consequence of its enormous DNA uptake capacity, triggered by intrinsic and extrinsic oxidative stress once a neutral pH at the site of chronic host colonization allows competence development. Natural transformation, i.e. the capacity to take up DNA from the environment, is one of the crucial means for horizontal gene transfer and genetic diversity in bacteria. The human gastric pathogen Helicobacter pylori is confronted with acid stress before entering its multiplication site, the gastric mucosa. The bacterium causes lifelong chronic gastritis and is perfectly adapted to the human host, crucially by displaying unusual genetic diversity. Using a single cell approach and well-controlled conditions, we show here that the amount of imported DNA in competent H. pylori is outstanding, far exceeding previous measurement with other Gram-negative bacteria. Furthermore, DNA uptake activity was tightly regulated and limited to pH above 6.5, conditions thought to be met in close contact with the gastric mucosa. In addition, we show that within this pH competence window, competence development was triggered by an increase in pH in combination with the level of oxidative stress. Our data provide explanations for the extraordinary high genetic diversity, often referred to as genome plasticity of this unusual microaerobic pathogen.
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Affiliation(s)
- Nora-Johanna Krüger
- Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Marie-Theres Knüver
- Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Anna Zawilak-Pawlik
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Department of Microbiology, Wroclaw, Poland
| | - Bernd Appel
- Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Kerstin Stingl
- Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
- * E-mail:
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38
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Croucher NJ, Mostowy R, Wymant C, Turner P, Bentley SD, Fraser C. Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict. PLoS Biol 2016; 14:e1002394. [PMID: 26934590 PMCID: PMC4774983 DOI: 10.1371/journal.pbio.1002394] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/29/2016] [Indexed: 01/21/2023] Open
Abstract
Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated.
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Affiliation(s)
- Nicholas J. Croucher
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Rafal Mostowy
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Christopher Wymant
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Stephen D. Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
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Abstract
ABSTRACT
Many Gram-positive and Gram-negative bacteria can become naturally competent to take up extracellular DNA from the environment via a dedicated uptake apparatus. The genetic material that is acquired can (i) be used for nutrients, (ii) aid in genome repair, and (iii) promote horizontal gene transfer when incorporated onto the genome by homologous recombination, the process of “transformation.” Recent studies have identified multiple environmental cues sufficient to induce natural transformation in
Vibrio cholerae
and several other
Vibrio
species. In
V. cholerae
, nutrient limitation activates the cAMP receptor protein regulator, quorum-sensing signals promote synthesis of HapR-controlled QstR, chitin stimulates production of TfoX, and low extracellular nucleosides allow CytR to serve as an additional positive regulator. The network of signaling systems that trigger expression of each of these required regulators is well described, but the mechanisms by which each in turn controls competence apparatus genes is poorly understood. Recent work has defined a minimal set of genes that encode apparatus components and begun to characterize the architecture of the machinery by fluorescence microscopy. While studies with a small set of
V. cholerae
reference isolates have identified regulatory and competence genes required for DNA uptake, future studies may identify additional genes and regulatory connections, as well as revealing how common natural competence is among diverse
V. cholerae
isolates and other
Vibrio
species.
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40
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Liang J, De Bruyne E, Ducatelle R, Smet A, Haesebrouck F, Flahou B. Purification of Helicobacter suis Strains From Biphasic Cultures by Single Colony Isolation: Influence on Strain Characteristics. Helicobacter 2015; 20:206-16. [PMID: 25582323 DOI: 10.1111/hel.12192] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Helicobacter (H.) suis causes gastritis and decreased weight gain in pigs. It is also the most prevalent non-Helicobacter pylori Helicobacter species in humans with gastric disease. H. suis is extremely fastidious, and so far, biphasic culture conditions were essential for isolation and culture, making it impossible to obtain single colonies. Hence, cultures obtained from an individual animal may contain multiple H. suis strains, which is undesirable for experiments aiming for instance at investigating H. suis strain differences. MATERIALS AND METHODS Pure cultures of H. suis were established by growing bacteria as colonies on 1% brucella agar plates, followed by purification and enrichment by biphasic subculture. Characteristics of these single colony-derived strains were compared with those of their parent strains using multilocus sequence typing (MLST) and by studying bacterium-host interactions using a gastric epithelial cell line and Mongolian gerbil model. RESULTS The purification/enrichment procedure required a nonstop culture of several weeks. For 4 of 17 H. suis strains, MLST revealed differences between parental and single colony-derived strains. For three of four single colony-derived strains tested, the cell death-inducing capacity was higher than for the parental strain. One single colony-derived strain lost its capacity to colonize Mongolian gerbils. For the four other strains tested, colonization capacity and histopathologic changes were similar to what has been described when using strains with only a history of limited biphasic culture. CONCLUSIONS A method was developed to obtain single colony-derived H. suis strains, but this procedure may affect the bacterial genotype and phenotype.
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Affiliation(s)
- Jungang Liang
- Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Merelbeke, Belgium
| | - Ellen De Bruyne
- Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Merelbeke, Belgium
| | - Richard Ducatelle
- Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Merelbeke, Belgium
| | - Annemieke Smet
- Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Merelbeke, Belgium
| | - Bram Flahou
- Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Merelbeke, Belgium
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Damke PP, Dhanaraju R, Marsin S, Radicella JP, Rao DN. The nuclease activities of both the Smr domain and an additional LDLK motif are required for an efficient anti-recombination function of Helicobacter pylori MutS2. Mol Microbiol 2015; 96:1240-56. [PMID: 25800579 DOI: 10.1111/mmi.13003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2015] [Indexed: 12/23/2022]
Abstract
Helicobacter pylori, a human pathogen, is a naturally and constitutively competent bacteria, displaying a high rate of intergenomic recombination. While recombination events are essential for evolution and adaptation of H. pylori to dynamic gastric niches and new hosts, such events should be regulated tightly to maintain genomic integrity. Here, we analyze the role of the nuclease activity of MutS2, a protein that limits recombination during transformation in H. pylori. In previously studied MutS2 proteins, the C-terminal Smr domain was mapped as the region responsible for its nuclease activity. We report here that deletion of Smr domain does not completely abolish the nuclease activity of HpMutS2. Using bioinformatics analysis and mutagenesis, we identified an additional and novel nuclease motif (LDLK) at the N-terminus of HpMutS2 unique to Helicobacter and related ε-proteobacterial species. A single point mutation (D30A) in the LDLK motif and the deletion of Smr domain resulted in ∼ 5-10-fold loss of DNA cleavage ability of HpMutS2. Interestingly, the mutant forms of HpMutS2 wherein the LDLK motif was mutated or the Smr domain was deleted were unable to complement the hyper-recombination phenotype of a mutS2(-) strain, suggesting that both nuclease sites are indispensable for an efficient anti-recombinase activity of HpMutS2.
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Affiliation(s)
- Prashant P Damke
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Rajkumar Dhanaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Stéphanie Marsin
- Institute of Cellular and Molecular Radiobiology, CEA, Fontenay-aux-Roses, France.,INSERM UMR967, Fontenay-aux-Roses, France.,Universités Paris Diderot et Paris Sud, Fontenay-aux-Roses, France
| | - Juan Pablo Radicella
- Institute of Cellular and Molecular Radiobiology, CEA, Fontenay-aux-Roses, France.,INSERM UMR967, Fontenay-aux-Roses, France.,Universités Paris Diderot et Paris Sud, Fontenay-aux-Roses, France
| | - Desirazu N Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
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Abstract
Bloodstream infections in the neonatal intensive care unit (NICU) are associated with many adverse outcomes in infants, including increased length of stay and cost, poor neurodevelopmental outcomes, and death. Attention to the insertion and maintenance of central lines, along with careful review of when the catheters can be safely discontinued, can minimize central-line-associated bloodstream infections rates. Good antibiotic stewardship can further decrease the incidence of bloodstream infections, minimize the emergence of drug-resistant organisms or Candida as pathogens in the NICU, and safeguard the use of currently available antibiotics for future infants.
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Affiliation(s)
- Joseph B Cantey
- Division of Neonatal/Perinatal Medicine, Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Division of Infectious Diseases, Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
| | - Aaron M Milstone
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, 200 North Wolfe Street, Room 3141, Baltimore, MD 21287, USA
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43
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Kumar N, Mariappan V, Baddam R, Lankapalli AK, Shaik S, Goh KL, Loke MF, Perkins T, Benghezal M, Hasnain SE, Vadivelu J, Marshall BJ, Ahmed N. Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution. Nucleic Acids Res 2014; 43:324-35. [PMID: 25452339 PMCID: PMC4288169 DOI: 10.1093/nar/gku1271] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The discordant prevalence of Helicobacter pylori and its related diseases, for a long time, fostered certain enigmatic situations observed in the countries of the southern world. Variation in H. pylori infection rates and disease outcomes among different populations in multi-ethnic Malaysia provides a unique opportunity to understand dynamics of host–pathogen interaction and genome evolution. In this study, we extensively analyzed and compared genomes of 27 Malaysian H. pylori isolates and identified three major phylogeographic lineages: hspEastAsia, hpEurope and hpSouthIndia. The analysis of the virulence genes within the core genome, however, revealed a comparable pathogenic potential of the strains. In addition, we identified four genes limited to strains of East-Asian lineage. Our analyses identified a few strain-specific genes encoding restriction modification systems and outlined 311 core genes possibly under differential evolutionary constraints, among the strains representing different ethnic groups. The cagA and vacA genes also showed variations in accordance with the host genetic background of the strains. Moreover, restriction modification genes were found to be significantly enriched in East-Asian strains. An understanding of these variations in the genome content would provide significant insights into various adaptive and host modulation strategies harnessed by H. pylori to effectively persist in a host-specific manner.
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Affiliation(s)
- Narender Kumar
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Vanitha Mariappan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ramani Baddam
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Aditya K Lankapalli
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Sabiha Shaik
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Khean-Lee Goh
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Mun Fai Loke
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Tim Perkins
- School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands 6009, Western Australia, Australia
| | - Mohammed Benghezal
- School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands 6009, Western Australia, Australia
| | - Seyed E Hasnain
- Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Jamuna Vadivelu
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Barry J Marshall
- School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands 6009, Western Australia, Australia
| | - Niyaz Ahmed
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Gachibowli, Hyderabad, 500046, India Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia
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Lin D, Koskella B. Friend and foe: factors influencing the movement of the bacterium Helicobacter pylori along the parasitism-mutualism continuum. Evol Appl 2014; 8:9-22. [PMID: 25667600 PMCID: PMC4310578 DOI: 10.1111/eva.12231] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/14/2014] [Indexed: 12/11/2022] Open
Abstract
Understanding the transition of bacterial species from commensal to pathogen, or vice versa, is a key application of evolutionary theory to preventative medicine. This requires working knowledge of the molecular interaction between hosts and bacteria, ecological interactions among microbes, spatial variation in bacterial prevalence or host life history, and evolution in response to these factors. However, there are very few systems for which such broad datasets are available. One exception is the gram-negative bacterium, Helicobacter pylori, which infects upwards of 50% of the global human population. This bacterium is associated with a wide breadth of human gastrointestinal disease, including numerous cancers, inflammatory disorders, and pathogenic infections, but is also known to confer fitness benefits to its host both indirectly, through interactions with other pathogens, and directly. Outstanding questions are therefore why, when, and how this bacterium transitions along the parasitism–mutualism continuum. We examine known virulence factors, genetic predispositions of the host, and environmental contributors that impact progression of clinical disease and help define geographical trends in disease incidence. We also highlight the complexity of the interaction and discuss future therapeutic strategies for disease management and public health in light of the longstanding evolutionary history between the bacterium and its human host.
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Antibiotic-induced replication stress triggers bacterial competence by increasing gene dosage near the origin. Cell 2014; 157:395-406. [PMID: 24725406 DOI: 10.1016/j.cell.2014.01.068] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 12/01/2013] [Accepted: 01/29/2014] [Indexed: 12/12/2022]
Abstract
Streptococcus pneumoniae (pneumococcus) kills nearly 1 million children annually, and the emergence of antibiotic-resistant strains poses a serious threat to human health. Because pneumococci can take up DNA from their environment by a process called competence, genes associated with antibiotic resistance can rapidly spread. Remarkably, competence is activated in response to several antibiotics. Here, we demonstrate that antibiotics targeting DNA replication cause an increase in the copy number of genes proximal to the origin of replication (oriC). As the genes required for competence initiation are located near oriC, competence is thereby activated. Transcriptome analyses show that antibiotics targeting DNA replication also upregulate origin-proximal gene expression in other bacteria. This mechanism is a direct, intrinsic consequence of replication fork stalling. Our data suggest that evolution has conserved the oriC-proximal location of important genes in bacteria to allow for a robust response to replication stress without the need for complex gene-regulatory pathways. PAPERCLIP:
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The Dynamic Interactions between Salmonella and the Microbiota, within the Challenging Niche of the Gastrointestinal Tract. INTERNATIONAL SCHOLARLY RESEARCH NOTICES 2014; 2014:846049. [PMID: 27437481 PMCID: PMC4897363 DOI: 10.1155/2014/846049] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/14/2014] [Indexed: 12/25/2022]
Abstract
Understanding how Salmonella species establish successful infections remains a foremost research priority. This gastrointestinal pathogen not only faces the hostile defenses of the host's immune system, but also faces fierce competition from the large and diverse community of microbiota for space and nutrients. Salmonella have solved these challenges ingeniously. To jump-start growth, Salmonella steal hydrogen produced by the gastrointestinal microbiota. Type 3 effector proteins are subsequently secreted by Salmonella to trigger potent inflammatory responses, which generate the alternative terminal electron acceptors tetrathionate and nitrate. Salmonella exclusively utilize these electron acceptors for anaerobic respiration, permitting metabolic access to abundant substrates such as ethanolamine to power growth blooms. Chemotaxis and flagella-mediated motility enable the identification of nutritionally beneficial niches. The resulting growth blooms also promote horizontal gene transfer amongst the resident microbes. Within the gastrointestinal tract there are opportunities for chemical signaling between host cells, the microbiota, and Salmonella. Host produced catecholamines and bacterial autoinducers form components of this chemical dialogue leading to dynamic interactions. Thus, Salmonella have developed remarkable strategies to initially shield against host defenses and to transiently compete against the intestinal microbiota leading to successful infections. However, the immunocompetent host is subsequently able to reestablish control and clear the infection.
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Fischer W, Breithaupt U, Kern B, Smith SI, Spicher C, Haas R. A comprehensive analysis of Helicobacter pylori plasticity zones reveals that they are integrating conjugative elements with intermediate integration specificity. BMC Genomics 2014; 15:310. [PMID: 24767410 PMCID: PMC4234485 DOI: 10.1186/1471-2164-15-310] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 04/16/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The human gastric pathogen Helicobacter pylori is a paradigm for chronic bacterial infections. Its persistence in the stomach mucosa is facilitated by several mechanisms of immune evasion and immune modulation, but also by an unusual genetic variability which might account for the capability to adapt to changing environmental conditions during long-term colonization. This variability is reflected by the fact that almost each infected individual is colonized by a genetically unique strain. Strain-specific genes are dispersed throughout the genome, but clusters of genes organized as genomic islands may also collectively be present or absent. RESULTS We have comparatively analysed such clusters, which are commonly termed plasticity zones, in a high number of H. pylori strains of varying geographical origin. We show that these regions contain fixed gene sets, rather than being true regions of genome plasticity, but two different types and several subtypes with partly diverging gene content can be distinguished. Their genetic diversity is incongruent with variations in the rest of the genome, suggesting that they are subject to horizontal gene transfer within H. pylori populations. We identified 40 distinct integration sites in 45 genome sequences, with a conserved heptanucleotide motif that seems to be the minimal requirement for integration. CONCLUSIONS The significant number of possible integration sites, together with the requirement for a short conserved integration motif and the high level of gene conservation, indicates that these elements are best described as integrating conjugative elements (ICEs) with an intermediate integration site specificity.
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Affiliation(s)
- Wolfgang Fischer
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universität, D-80336 Munich, Germany.
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Johnston C, Martin B, Fichant G, Polard P, Claverys JP. Bacterial transformation: distribution, shared mechanisms and divergent control. Nat Rev Microbiol 2014; 12:181-96. [DOI: 10.1038/nrmicro3199] [Citation(s) in RCA: 402] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Wang W, Ding J, Zhang Y, Hu Y, Wang DC. Structural insights into the unique single-stranded DNA-binding mode of Helicobacter pylori DprA. Nucleic Acids Res 2013; 42:3478-91. [PMID: 24369431 PMCID: PMC3950713 DOI: 10.1093/nar/gkt1334] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Natural transformation (NT) in bacteria is a complex process, including binding, uptake, transport and recombination of exogenous DNA into the chromosome, consequently generating genetic diversity and driving evolution. DNA processing protein A (DprA), which is distributed among virtually all bacterial species, is involved in binding to the internalized single-stranded DNA (ssDNA) and promoting the loading of RecA on ssDNA during NTs. Here we present the structures of DNA_processg_A (DprA) domain of the Helicobacter pylori DprA (HpDprA) and its complex with an ssDNA at 2.20 and 1.80 Å resolutions, respectively. The complex structure revealed for the first time how the conserved DprA domain binds to ssDNA. Based on structural comparisons and binding assays, a unique ssDNA-binding mode is proposed: the dimer of HpDprA binds to ssDNA through two small, positively charged binding pockets of the DprA domains with classical Rossmann folds and the key residue Arg52 is re-oriented to ‘open’ the pocket in order to accommodate one of the bases of ssDNA, thus enabling HpDprA to grasp substrate with high affinity. This mode is consistent with the oligomeric composition of the complex as shown by electrophoretic mobility-shift assays and static light scattering measurements, but differs from the direct polymeric complex of Streptococcus pneumoniae DprA–ssDNA.
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Affiliation(s)
- Wei Wang
- The National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
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Hyytiäinen H, Juntunen P, Scott T, Kytömäki L, Venho R, Laiho A, Junttila S, Gyenesei A, Revez J, Hänninen ML. Effect of ciprofloxacin exposure on DNA repair mechanisms in Campylobacter jejuni. Microbiology (Reading) 2013; 159:2513-2523. [DOI: 10.1099/mic.0.069203-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Heidi Hyytiäinen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P.O. Box 66, University of Helsinki 00014, Finland
| | - Pekka Juntunen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P.O. Box 66, University of Helsinki 00014, Finland
| | - Thomas Scott
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P.O. Box 66, University of Helsinki 00014, Finland
| | - Leena Kytömäki
- Finnish Microarray and Sequencing Centre (FMSC), Turku Centre for Biotechnology (BTK), University of Turku and Åbo Akademi University, Tykistökatu 6 A, Turku 20521, Finland
| | - Reija Venho
- Finnish Microarray and Sequencing Centre (FMSC), Turku Centre for Biotechnology (BTK), University of Turku and Åbo Akademi University, Tykistökatu 6 A, Turku 20521, Finland
| | - Asta Laiho
- Finnish Microarray and Sequencing Centre (FMSC), Turku Centre for Biotechnology (BTK), University of Turku and Åbo Akademi University, Tykistökatu 6 A, Turku 20521, Finland
| | - Sini Junttila
- Finnish Microarray and Sequencing Centre (FMSC), Turku Centre for Biotechnology (BTK), University of Turku and Åbo Akademi University, Tykistökatu 6 A, Turku 20521, Finland
| | - Attila Gyenesei
- Finnish Microarray and Sequencing Centre (FMSC), Turku Centre for Biotechnology (BTK), University of Turku and Åbo Akademi University, Tykistökatu 6 A, Turku 20521, Finland
| | - Joana Revez
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P.O. Box 66, University of Helsinki 00014, Finland
| | - Marja-Liisa Hänninen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P.O. Box 66, University of Helsinki 00014, Finland
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