1
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Meier D, Rauch C, Wagner M, Klemm P, Blumenkamp P, Müller R, Ellenberger E, Karia KM, Vecchione S, Serrania J, Lechner M, Fritz G, Goesmann A, Becker A. A MoClo-Compatible Toolbox of ECF Sigma Factor-Based Regulatory Switches for Proteobacterial Chassis. BIODESIGN RESEARCH 2024; 6:0025. [PMID: 38384496 PMCID: PMC10880074 DOI: 10.34133/bdr.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/04/2023] [Indexed: 02/23/2024] Open
Abstract
The construction of complex synthetic gene circuits with predetermined and reliable output depends on orthogonal regulatory parts that do not inadvertently interfere with the host machinery or with other circuit components. Previously, extracytoplasmic function sigma factors (ECFs), a diverse group of alternative sigma factors with distinct promoter specificities, were shown to have great potential as context-independent regulators, but so far, they have only been used in a few model species. Here, we show that the alphaproteobacterium Sinorhizobium meliloti, which has been proposed as a plant-associated bacterial chassis for synthetic biology, has a similar phylogenetic ECF acceptance range as the gammaproteobacterium Escherichia coli. A common set of orthogonal ECF-based regulators that can be used in both bacterial hosts was identified and used to create 2-step delay circuits. The genetic circuits were implemented in single copy in E. coli by chromosomal integration using an established method that utilizes bacteriophage integrases. In S. meliloti, we demonstrated the usability of single-copy pABC plasmids as equivalent carriers of the synthetic circuits. The circuits were either implemented on a single pABC or modularly distributed on 3 such plasmids. In addition, we provide a toolbox containing pABC plasmids compatible with the Golden Gate (MoClo) cloning standard and a library of basic parts that enable the construction of ECF-based circuits in S. meliloti and in E. coli. This work contributes to building a context-independent and species-overarching ECF-based toolbox for synthetic biology applications.
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Affiliation(s)
- Doreen Meier
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Christian Rauch
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Marcel Wagner
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Paul Klemm
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Patrick Blumenkamp
- Bioinformatics and Systems Biology,
Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Raphael Müller
- Bioinformatics and Systems Biology,
Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Eric Ellenberger
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Kinnari M. Karia
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Stefano Vecchione
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Javier Serrania
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Georg Fritz
- The University of Western Australia, School of Molecular Sciences, Perth, Australia
| | - Alexander Goesmann
- Bioinformatics and Systems Biology,
Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
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2
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Lysitsas M, Triantafillou E, Spyrou V, Billinis C, Valiakos G. Phenotypic Investigation of Florfenicol Resistance and Molecular Detection of floR Gene in Canine and Feline MDR Enterobacterales. Vet Sci 2024; 11:71. [PMID: 38393089 PMCID: PMC10892669 DOI: 10.3390/vetsci11020071] [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: 11/27/2023] [Revised: 01/23/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Florfenicol is a promising antibiotic for use in companion animals, especially as an alternative agent for infections caused by MDR bacteria. However, the emergence of resistant strains could hinder this potential. In this study, florfenicol resistance was investigated in a total of 246 MDR Enterobacterales obtained from canine and feline clinical samples in Greece over a two-year period (October 2020 to December 2022); a total of 44 (17,9%) florfenicol-resistant strains were recognized and further investigated. Most of these isolates originated from urine (41.9%) and soft tissue (37.2%) samples; E. coli (n = 14) and Enterobacter cloacae (n = 12) were the predominant species. The strains were examined for the presence of specific florfenicol-related resistance genes floR and cfr. In the majority of the isolates (31/44, 70.5%), the floR gene was detected, whereas none carried cfr. This finding creates concerns of co-acquisition of plasmid-mediated florfenicol-specific ARGs through horizontal transfer, along with several other resistance genes. The florfenicol resistance rates in MDR isolates seem relatively low but considerable for a second-line antibiotic; thus, in order to evaluate the potential of florfenicol to constitute an alternative antibiotic in companion animals, continuous monitoring of antibiotic resistance profiles is needed in order to investigate the distribution of florfenicol resistance under pressure of administration of commonly used agents.
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Affiliation(s)
- Marios Lysitsas
- Faculty of Veterinary Science, University of Thessaly, 431 00 Karditsa, Greece; (M.L.); (C.B.)
| | | | - Vassiliki Spyrou
- Department of Animal Science, University of Thessaly, 413 34 Larissa, Greece;
| | - Charalambos Billinis
- Faculty of Veterinary Science, University of Thessaly, 431 00 Karditsa, Greece; (M.L.); (C.B.)
| | - George Valiakos
- Faculty of Veterinary Science, University of Thessaly, 431 00 Karditsa, Greece; (M.L.); (C.B.)
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3
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Arcari G, Hennart M, Badell E, Brisse S. Multidrug-resistant toxigenic Corynebacterium diphtheriae sublineage 453 with two novel resistance genomic islands. Microb Genom 2023; 9:mgen000923. [PMID: 36748453 PMCID: PMC9973851 DOI: 10.1099/mgen.0.000923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Antimicrobial therapy is important for case management of diphtheria, but knowledge on the emergence of multidrug-resistance in Corynebacterium diphtheriae is scarce. We report on the genomic features of two multidrug-resistant toxigenic isolates sampled from wounds in France 3 years apart. Both isolates were resistant to spiramycin, clindamycin, tetracycline, kanamycin and trimethoprim-sulfamethoxazole. Genes ermX, cmx, aph(3')-Ib, aph(6)-Id, aph(3')-Ic, aadA1, dfrA15, sul1, cmlA, cmlR and tet(33) were clustered in two genomic islands, one consisting of two transposons and one integron, the other being flanked by two IS6100 insertion sequences. One isolate additionally presented mutations in gyrA and rpoB and was resistant to ciprofloxacin and rifampicin. Both isolates belonged to sublineage 453 (SL453), together with 25 isolates from 11 other countries (https://bigsdb.pasteur.fr/diphtheria/). SL453 is a cosmopolitan toxigenic sublineage of C. diphtheriae, a subset of which acquired multidrug resistance. Even though penicillin, amoxicillin and erythromycin, recommended as the first line in the treatment of diphtheria, remain active, surveillance of diphtheria should consider the risk of dissemination of multidrug-resistant strains and their genetic elements.
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Affiliation(s)
- Gabriele Arcari
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.,Department of Molecular Medicine, Sapienza Università di Roma, Rome, Italy
| | - Mélanie Hennart
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.,Collège doctoral, Sorbonne Université, F-75005 Paris, France
| | - Edgar Badell
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.,Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.,Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France
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4
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Jesus HNR, Ramos JN, Rocha DJPG, Alves DA, Silva CS, Cruz JVO, Vieira VV, Souza C, Santos LS, Navas J, Ramos RTJ, Azevedo V, Aguiar ERGR, Mattos-Guaraldi AL, Pacheco LGC. The pan-genome of the emerging multidrug-resistant pathogen Corynebacterium striatum. Funct Integr Genomics 2022; 23:5. [PMID: 36534203 DOI: 10.1007/s10142-022-00932-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 10/06/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022]
Abstract
Corynebacterium striatum, a common constituent of the human skin microbiome, is now considered an emerging multidrug-resistant pathogen of immunocompromised and chronically ill patients. However, little is known about the molecular mechanisms in the transition from colonization to the multidrug-resistant (MDR) invasive phenotype in clinical isolates. This study performed a comprehensive pan-genomic analysis of C. striatum, including isolates from "normal skin microbiome" and from MDR infections, to gain insights into genetic factors contributing to pathogenicity and multidrug resistance in this species. For this, three novel genome sequences were obtained from clinical isolates of C. striatum of patients from Brazil, and other 24 complete or draft C. striatum genomes were retrieved from GenBank, including the ATCC6940 isolate from the Human Microbiome Project. Analysis of C. striatum strains demonstrated the presence of an open pan-genome (α = 0.852803) containing 3816 gene families, including 15 antimicrobial resistance (AMR) genes and 32 putative virulence factors. The core and accessory genomes included 1297 and 1307 genes, respectively. The identified AMR genes are primarily associated with resistance to aminoglycosides and tetracyclines. Of these, 66.6% are present in genomic islands, and four AMR genes, including aac(6')-ib7, are located in a class 1-integron. In conclusion, our data indicated that C. striatum possesses genomic characteristics favorable to the invasive phenotype, with high genomic plasticity, a robust genetic arsenal for iron acquisition, and important virulence determinants and AMR genes present in mobile genetic elements.
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Affiliation(s)
- Hendor N R Jesus
- Multicenter Post-Graduate Program in Biochemistry and Molecular Biology (PMBqBM), Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Juliana N Ramos
- Laboratory of Diphtheria and Corinebacteria of Clinical Relevance, School of Medical Sciences, Rio de Janeiro State University - LDCIC/FCM/UERJ, Rio de Janeiro, RJ, Brazil
| | - Danilo J P G Rocha
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Daniele A Alves
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil.,Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Carolina S Silva
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - João V O Cruz
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Verônica V Vieira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório Interdisciplinar de Pesquisas Médicas, Rio de Janeiro, RJ, Brazil
| | - Cassius Souza
- Laboratory of Diphtheria and Corinebacteria of Clinical Relevance, School of Medical Sciences, Rio de Janeiro State University - LDCIC/FCM/UERJ, Rio de Janeiro, RJ, Brazil
| | - Louisy S Santos
- Laboratory of Diphtheria and Corinebacteria of Clinical Relevance, School of Medical Sciences, Rio de Janeiro State University - LDCIC/FCM/UERJ, Rio de Janeiro, RJ, Brazil
| | - Jesus Navas
- Cantabria University, Instituto de Investigación Valdecilla (IDIVAL), Santander, Spain
| | - Rommel T J Ramos
- Institute of Biological Sciences, Federal University of Para, Belem, PA, Brazil.,Biological Engineering Laboratory, Science and Technology Park Guama, Belem, PA, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Eric R G R Aguiar
- Department of Biological Sciences, State University of Santa Cruz, Ilhéus, BA, Brazil
| | - Ana L Mattos-Guaraldi
- Laboratory of Diphtheria and Corinebacteria of Clinical Relevance, School of Medical Sciences, Rio de Janeiro State University - LDCIC/FCM/UERJ, Rio de Janeiro, RJ, Brazil
| | - Luis G C Pacheco
- Multicenter Post-Graduate Program in Biochemistry and Molecular Biology (PMBqBM), Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil. .,Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil.
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5
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Wang J, Pei J, Liu M, Huang R, Li J, Liao S, Liang J. Identification and Evolutionary Relationship of Corynebacterium striatum Clinical Isolates. Pathogens 2022; 11:pathogens11091012. [PMID: 36145444 PMCID: PMC9501166 DOI: 10.3390/pathogens11091012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 08/27/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Corynebacterium striatum has developed into a new community-acquired and hospital-acquired multi-drug resistance (MDR) bacterium, and is a potential target pathogen for infection control and antibacterial management projects. In this study, non-duplicate samples of inpatients were collected from a local central hospital. Mass spectrometry showed that 54 C. striatum isolates mainly appeared in secretion and sputum from 14 departments. Protein fingerprint cluster analysis showed that the isolates were divided into four groups, most of which appeared in summer. The drug resistance test showed that all strains had multi-drug resistance, with high resistance rates to lincosamides, quinolones and tetracycline detected. Further analysis of the phylogenetic tree of C. striatum was conducted by cloning the 16S rRNA gene. It was found that isolates in the same department had high homology and tended to be located in the same branch or to be crossed in the same main branch. The strains in the same evolutionary branch group had the same drug resistance. Screening of site-specific recombinant elements revealed that 18 strains had integrase genes with the same sequence. This study shows that there may be mobile genetic elements in clinical isolates that drive gene exchange among strains, thus causing the cross-infection, spread and evolution of pathogenic bacteria in the hospital.
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Affiliation(s)
- Jiao Wang
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang 441053, China
- Correspondence: (J.W.); (J.P.)
| | - Jiao Pei
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang 441021, China
- Correspondence: (J.W.); (J.P.)
| | - Mingming Liu
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang 441053, China
| | - Rui Huang
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang 441053, China
| | - Jiqiang Li
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang 441053, China
| | - Shiying Liao
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang 441053, China
| | - Jian Liang
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang 441021, China
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6
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Unravelling complex transposable elements surrounding bla GES-16 in a Pseudomonas aeruginosa ExoU strain. J Glob Antimicrob Resist 2022; 30:143-147. [PMID: 35447384 DOI: 10.1016/j.jgar.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 03/16/2022] [Accepted: 04/11/2022] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES We characterised the complex surrounding regions of blaGES-16 in a Pseudomonas aeruginosa exoU+ strain (P-10.226) in Brazil. METHODS Species identification was performed by MALDI-TOF MS, and the antimicrobial susceptibility profile was determined by broth microdilution based on European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. The whole genome sequencing (WGS) of P-10.226 strain was performed using both short-read paired-end sequencing on the Illumina MiSeq platform as well as the long-read Oxford Nanopore MinION. RESULTS WGS analysis showed that P-10.226 carried blaGES-16, which was found as a gene cassette inserted into a novel class I integron, In1992 (aadB-blaOXA-56-blaGES-16-aadB-aadA6c), whose 3'-CS was truncated by a nested transposable element, IS5564::ISPa157. The structure was even more complex since IS6100-ΔIS6100 structure and a TnAs2-like harbouring the operon merRTPADE was found downstream In1992. Fragments of TnAs3 harbouring 25-bp imperfect inverted repeats were identified bordering the intl1 of In1992 and also flanking IS6100-ΔIS6100, which might be genetic marks of its previous presence in the genome. Interestingly, In1992 also shows a distinct cassette array from In581 (blaGES-16-dfrA22-aacA27-aadA1), which was previously reported in Serratia marcescens strains recovered in Brazil. Finally, exoU gene, which encodes a potent cytotoxin of type III secretion systems (T3SS) effector proteins from P. aeruginosa and is associated to severe infections, was also detected. CONCLUSION We described the novel In1992 carrying blaGES-16 surrounded by complex transposition events in a XDR P. aeruginosa strain. The identification of many sets of direct repeats adjacent to TnAs3 fragments indicates a major past of transposition events that shaped the current genetic environment of In1992.
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7
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Genetic characterization, mechanisms and dissemination risk of antibiotic resistance of multidrug-resistant Rothia nasimurium. INFECTION GENETICS AND EVOLUTION 2021; 90:104770. [PMID: 33588066 DOI: 10.1016/j.meegid.2021.104770] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/14/2021] [Accepted: 02/09/2021] [Indexed: 12/11/2022]
Abstract
Rothia nasimurium is part of the commensal flora of humans and other animals and has recently received increasing attention for its multidrug-resistance (MDR) and pathogenicity. Currently, no systematic reports characterize the genetics, mechanisms, and dissemination risks of antibiotic resistance in MDR R. nasimurium. Here, we present the first report outlining a MDR strain of R. nasimurium, E1706032a, isolated from ducks exhibiting clinical sickness. Phylogenetic analysis indicates that E1706032a mostly likely originated in the commensal bacteria of Amazona aestiva in Florida. E1706032a is resistant to beta-lactams, aminoglycosides, macrolides, sulfonamides, fluoroquinolones, rifamycins, tetracyclines, lincosamides and chloramphenicol. Genetic sequences related to drug resistance were detected, including resistance genes (aac(6')-Ib, ant(3″)-Ia, sul1, dfrA7, erm(X)), efflux pumps (tetZ, qacEΔ1, cmx, phosphate ABC transporter ATP-binding protein), and resistance-related proteins (hydrolase of the metallo-beta-lactamase (MBLs), mycinamicin resistance protein (myrA), DNA-directed RNA polymerase subunit beta (rpoB) variants, etc). E1706032a carries an IS481-like element, IS5564 and IS6-like elements, and IS6100 along with several novel transposases of the IS3 family. E1706032a also carries the class 1 integron gene IntI1, which is downstream adjacent to the gene cassettes aac(6')-Ib, tetZ, dfrA27, ant(3″)-Ia, qacEΔ1, sul1, cmx and upstream adjacent to gene tnpA of IS6100. Genetic analysis suggests that E1706032a carries wide antibiotic resistance and dissemination potential through movable elements and thus has the potential to cause difficult-to-treat infections in animals and humans. The dissemination of E1706032a from parrots in Florida to ducks in eastern China indicates a cross-regional public health infection risk that should be evaluated for risk of global spreading.
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8
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Antibiotic resistance genes in the Actinobacteria phylum. Eur J Clin Microbiol Infect Dis 2019; 38:1599-1624. [PMID: 31250336 DOI: 10.1007/s10096-019-03580-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/01/2019] [Indexed: 02/07/2023]
Abstract
The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum.
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9
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Hwang W, Yoon SS. Virulence Characteristics and an Action Mode of Antibiotic Resistance in Multidrug-Resistant Pseudomonas aeruginosa. Sci Rep 2019; 9:487. [PMID: 30679735 PMCID: PMC6345838 DOI: 10.1038/s41598-018-37422-9] [Citation(s) in RCA: 40] [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: 07/18/2018] [Accepted: 11/28/2018] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas aeruginosa displays intrinsic resistance to many antibiotics and known to acquire actively genetic mutations for further resistance. In this study, we attempted to understand genomic and transcriptomic landscapes of P. aeruginosa clinical isolates that are highly resistant to multiple antibiotics. We also aimed to reveal a mode of antibiotic resistance by elucidating transcriptional response of genes conferring antibiotic resistance. To this end, we sequenced the whole genomes and profiled genome-wide RNA transcripts of three different multi-drug resistant (MDR) clinical isolates that are phylogenetically distant from one another. Multi-layered genome comparisons with genomes of antibiotic-susceptible P. aeruginosa strains and 70 other antibiotic-resistance strains revealed both well-characterized conserved gene mutations and distinct distribution of antibiotic-resistant genes (ARGs) among strains. Transcriptions of genes involved in quorum sensing and type VI secretion systems were invariably downregulated in the MDR strains. Virulence-associated phenotypes were further examined and results indicate that our MDR strains are clearly avirulent. Transcriptions of 64 genes, logically selected to be related with antibiotic resistance in MDR strains, were active under normal growth conditions and remained unchanged during antibiotic treatment. These results propose that antibiotic resistance is achieved by a "constitutive" response scheme, where ARGs are actively expressed even in the absence of antibiotic stress, rather than a "reactive" response. Bacterial responses explored at the transcriptomic level in conjunction with their genome repertoires provided novel insights into (i) the virulence-associated phenotypes and (ii) a mode of antibiotic resistance in MDR P. aeruginosa strains.
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Affiliation(s)
- Wontae Hwang
- Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Sciences, Seoul, Korea
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Sang Sun Yoon
- Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Sciences, Seoul, Korea.
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Korea.
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10
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Learman DR, Ahmad Z, Brookshier A, Henson MW, Hewitt V, Lis A, Morrison C, Robinson A, Todaro E, Wologo E, Wynne S, Alm EW, Kourtev PS. Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics. PeerJ 2019; 6:e6258. [PMID: 30671291 PMCID: PMC6336093 DOI: 10.7717/peerj.6258] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/06/2018] [Indexed: 11/20/2022] Open
Abstract
A total of 16 different strains of Microbacterium spp. were isolated from contaminated soil and enriched on the carcinogen, hexavalent chromium [Cr(VI)]. The majority of the isolates (11 of the 16) were able to tolerate concentrations (0.1 mM) of cobalt, cadmium, and nickel, in addition to Cr(VI) (0.5–20 mM). Interestingly, these bacteria were also able to tolerate three different antibiotics (ranges: ampicillin 0–16 μg ml−1, chloramphenicol 0–24 μg ml−1, and vancomycin 0–24 μg ml−1). To gain genetic insight into these tolerance pathways, the genomes of these isolates were assembled and annotated. The genomes of these isolates not only have some shared genes (core genome) but also have a large amount of variability. The genomes also contained an annotated Cr(VI) reductase (chrR) that could be related to Cr(VI) reduction. Further, various heavy metal tolerance (e.g., Co/Zn/Cd efflux system) and antibiotic resistance genes were identified, which provide insight into the isolates’ ability to tolerate metals and antibiotics. Overall, these isolates showed a wide range of tolerances to heavy metals and antibiotics and genetic diversity, which was likely required of this population to thrive in a contaminated environment.
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Affiliation(s)
- Deric R Learman
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Zahra Ahmad
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Allison Brookshier
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Michael W Henson
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Victoria Hewitt
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Amanda Lis
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Cody Morrison
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Autumn Robinson
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Emily Todaro
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Ethan Wologo
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Sydney Wynne
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Elizabeth W Alm
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Peter S Kourtev
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
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11
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Thapa SP, Pattathil S, Hahn MG, Jacques MA, Gilbertson RL, Coaker G. Genomic Analysis of Clavibacter michiganensis Reveals Insight Into Virulence Strategies and Genetic Diversity of a Gram-Positive Bacterial Pathogen. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:786-802. [PMID: 28677494 DOI: 10.1094/mpmi-06-17-0146-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Clavibacter michiganensis subsp. michiganensis is a gram-positive bacterial pathogen that proliferates in the xylem vessels of tomato, causing bacterial canker disease. In this study, we sequenced and assembled genomes of 11 C. michiganensis subsp. michiganensis strains isolated from infected tomato fields in California as well as five Clavibacter strains that colonize tomato endophytically but are not pathogenic in this host. The analysis of the C. michiganensis subsp. michiganensis genomes supported the monophyletic nature of this pathogen but revealed genetic diversity among strains, consistent with multiple introduction events. Two tomato endophytes that clustered phylogenetically with C. michiganensis strains capable of infecting wheat and pepper and were also able to cause disease in these plants. Plasmid profiles of the California strains were variable and supported the essential role of the pCM1-like plasmid and the CelA cellulase in virulence, whereas the absence of the pCM2-like plasmid in some pathogenic C. michiganensis subsp. michiganensis strains revealed it is not essential. A large number of secreted C. michiganensis subsp. michiganensis proteins were carbohydrate-active enzymes (CAZymes). Glycome profiling revealed that C. michiganensis subsp. michiganensis but not endophytic Clavibacter strains is able to extensively alter tomato cell-wall composition. Two secreted CAZymes found in all C. michiganensis subsp. michiganensis strains, CelA and PelA1, enhanced pathogenicity on tomato. Collectively, these results provide a deeper understanding of C. michiganensis subsp. michiganensis diversity and virulence strategies.
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Affiliation(s)
- Shree P Thapa
- 1 Department of Plant Pathology, University of California, Davis, California, U.S.A
| | - Sivakumar Pattathil
- 2 Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia, U.S.A.; and
| | - Michael G Hahn
- 2 Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia, U.S.A.; and
| | | | - Robert L Gilbertson
- 1 Department of Plant Pathology, University of California, Davis, California, U.S.A
| | - Gitta Coaker
- 1 Department of Plant Pathology, University of California, Davis, California, U.S.A
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12
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Jiang X, Ellabaan MMH, Charusanti P, Munck C, Blin K, Tong Y, Weber T, Sommer MOA, Lee SY. Dissemination of antibiotic resistance genes from antibiotic producers to pathogens. Nat Commun 2017; 8:15784. [PMID: 28589945 PMCID: PMC5467266 DOI: 10.1038/ncomms15784] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 04/27/2017] [Indexed: 12/25/2022] Open
Abstract
It has been hypothesized that some antibiotic resistance genes (ARGs) found in pathogenic bacteria derive from antibiotic-producing actinobacteria. Here we provide bioinformatic and experimental evidence supporting this hypothesis. We identify genes in proteobacteria, including some pathogens, that appear to be closely related to actinobacterial ARGs known to confer resistance against clinically important antibiotics. Furthermore, we identify two potential examples of recent horizontal transfer of actinobacterial ARGs to proteobacterial pathogens. Based on this bioinformatic evidence, we propose and experimentally test a 'carry-back' mechanism for the transfer, involving conjugative transfer of a carrier sequence from proteobacteria to actinobacteria, recombination of the carrier sequence with the actinobacterial ARG, followed by natural transformation of proteobacteria with the carrier-sandwiched ARG. Our results support the existence of ancient and, possibly, recent transfers of ARGs from antibiotic-producing actinobacteria to proteobacteria, and provide evidence for a defined mechanism.
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Affiliation(s)
- Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Mostafa M. Hashim Ellabaan
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Pep Charusanti
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Christian Munck
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Yaojun Tong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Morten O. A. Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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13
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Rossi FA, Medeot DB, Liaudat JP, Pistorio M, Jofré E. In Azospirillum brasilense, mutations in flmA or flmB genes affect polar flagellum assembly, surface polysaccharides, and attachment to maize roots. Microbiol Res 2016; 190:55-62. [PMID: 27393999 DOI: 10.1016/j.micres.2016.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 04/02/2016] [Accepted: 05/13/2016] [Indexed: 11/28/2022]
Abstract
Azospirillum brasilense is a soil bacterium capable of promoting plant growth. Several surface components were previously reported to be involved in the attachment of A. brasilense to root plants. Among these components are the exopolysaccharide (EPS), lipopolysaccharide (LPS) and the polar flagellum. Flagellin from polar flagellum is glycosylated and it was suggested that genes involved in such a posttranslational modification are the same ones involved in the biosynthesis of sugars present in the O-antigen of the LPS. In this work, we report on the characterization of two homologs present in A. brasilense Cd, to the well characterized flagellin modification genes, flmA and flmB, from Aeromonas caviae. We show that mutations in either flmA or flmB genes of A. brasilense resulted in non-motile cells due to alterations in the polar flagellum assembly. Moreover, these mutations also affected the capability of A. brasilense cells to adsorb to maize roots and to produce LPS and EPS. By generating a mutant containing the polar flagellum affected in their rotation, we show the importance of the bacterial motility for the early colonization of maize roots.
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Affiliation(s)
- Fernando Ariel Rossi
- Departmento de Ciencias Naturales, Facultad de Ciencias Exactas Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional 36 Km 601, 5800 Río Cuarto, Argentina
| | - Daniela Beatriz Medeot
- Departmento de Biología Molecular, Facultad de Ciencias Exactas Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional 36 Km 601, 5800 Río Cuarto, Argentina
| | - Juan Pablo Liaudat
- Departmento de Ciencias Naturales, Facultad de Ciencias Exactas Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional 36 Km 601, 5800 Río Cuarto, Argentina
| | - Mariano Pistorio
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-La Plata CONICET-, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115, 1900 La Plata, Argentina
| | - Edgardo Jofré
- Departmento de Ciencias Naturales, Facultad de Ciencias Exactas Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional 36 Km 601, 5800 Río Cuarto, Argentina.
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Vandecraen J, Monsieurs P, Mergeay M, Leys N, Aertsen A, Van Houdt R. Zinc-Induced Transposition of Insertion Sequence Elements Contributes to Increased Adaptability of Cupriavidus metallidurans. Front Microbiol 2016; 7:359. [PMID: 27047473 PMCID: PMC4803752 DOI: 10.3389/fmicb.2016.00359] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/07/2016] [Indexed: 12/15/2022] Open
Abstract
Bacteria can respond to adverse environments by increasing their genomic variability and subsequently facilitating adaptive evolution. To demonstrate this, the contribution of Insertion Sequence (IS) elements to the genetic adaptation of Cupriavidus metallidurans AE126 to toxic zinc concentrations was determined. This derivative of type strain CH34, devoid of its main zinc resistance determinant, is still able to increase its zinc resistance level. Specifically, upon plating on medium supplemented with a toxic zinc concentration, resistant variants arose in which a compromised cnrYX regulatory locus caused derepression of CnrH sigma factor activity and concomitant induction of the corresponding RND-driven cnrCBA efflux system. Late-occurring zinc resistant variants likely arose in response to the selective conditions, as they were enriched in cnrYX disruptions caused by specific IS elements whose transposase expression was found to be zinc-responsive. Interestingly, deletion of cnrH, and consequently the CnrH-dependent adaptation potential, still enabled adaptation by transposition of IS elements (ISRme5 and IS1086) that provided outward-directed promoters driving cnrCBAT transcription. Finally, adaptation to zinc by IS reshuffling can also enhance the adaptation to subsequent environmental challenges. Thus, transposition of IS elements can be induced by stress conditions and play a multifaceted, pivotal role in the adaptation to these and subsequent stress conditions.
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Affiliation(s)
- Joachim Vandecraen
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN)Mol, Belgium; Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Katholieke Universiteit LeuvenLeuven, Belgium
| | - Pieter Monsieurs
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
| | - Max Mergeay
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
| | - Natalie Leys
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven Leuven, Belgium
| | - Rob Van Houdt
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
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15
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Medeot DB, Romina Rivero M, Cendoya E, Contreras-Moreira B, Rossi FA, Fischer SE, Becker A, Jofré E. Sinorhizobium meliloti low molecular mass phosphotyrosine phosphatase SMc02309 modifies activity of the UDP-glucose pyrophosphorylase ExoN involved in succinoglycan biosynthesis. MICROBIOLOGY-SGM 2016; 162:552-563. [PMID: 26813656 DOI: 10.1099/mic.0.000239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In Gram-negative bacteria, tyrosine phosphorylation has been shown to play a role in the control of exopolysaccharide (EPS) production. This study demonstrated that the chromosomal ORF SMc02309 from Sinorhizobium meliloti 2011 encodes a protein with significant sequence similarity to low molecular mass protein-tyrosine phosphatases (LMW-PTPs), such as the Escherichia coli Wzb. Unlike other well-characterized EPS biosynthesis gene clusters, which contain neighbouring LMW-PTPs and kinase, the S. meliloti succinoglycan (EPS I) gene cluster located on megaplasmid pSymB does not encode a phosphatase. Biochemical assays revealed that the SMc02309 protein hydrolyses p-nitrophenyl phosphate (p-NPP) with kinetic parameters similar to other bacterial LMW-PTPs. Furthermore, we show evidence that SMc02309 is not the LMW-PTP of the bacterial tyrosine-kinase (BY-kinase) ExoP. Nevertheless, ExoN, a UDP-glucose pyrophosphorylase involved in the first stages of EPS I biosynthesis, is phosphorylated at tyrosine residues and constitutes an endogenous substrate of the SMc02309 protein. Additionally, we show that the UDP-glucose pyrophosphorylase activity is modulated by SMc02309-mediated tyrosine dephosphorylation. Moreover, a mutation in the SMc02309 gene decreases EPS I production and delays nodulation on Medicago sativa roots.
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Affiliation(s)
- Daniela B Medeot
- Department of Natural Sciences, FCEFQyN, National University of Río Cuarto, Ruta Nacional 36 Km 601, Córdoba, Argentina
- Department of Molecular Biology, FCEFQyN, National University of Río Cuarto, Ruta Nacional 36 Km 601, Córdoba, Argentina
| | - María Romina Rivero
- Department of Natural Sciences, FCEFQyN, National University of Río Cuarto, Ruta Nacional 36 Km 601, Córdoba, Argentina
| | - Eugenia Cendoya
- Department of Natural Sciences, FCEFQyN, National University of Río Cuarto, Ruta Nacional 36 Km 601, Córdoba, Argentina
| | - Bruno Contreras-Moreira
- Laboratory of Computational Biology, Department of Genetics and Plant Production, Estación Experimental de Aula Dei/CSIC, Av. Montañana 1005, Zaragoza, Spain
| | - Fernando A Rossi
- Department of Natural Sciences, FCEFQyN, National University of Río Cuarto, Ruta Nacional 36 Km 601, Córdoba, Argentina
| | - Sonia E Fischer
- Department of Natural Sciences, FCEFQyN, National University of Río Cuarto, Ruta Nacional 36 Km 601, Córdoba, Argentina
| | - Anke Becker
- LOEWE-Center for Synthetic Microbiology, Philipps-Universität Marburg, D-35032, Marburg, Germany
| | - Edgardo Jofré
- Department of Natural Sciences, FCEFQyN, National University of Río Cuarto, Ruta Nacional 36 Km 601, Córdoba, Argentina
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16
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Complete Genome Sequence and Annotation of Corynebacterium singulare DSM 44357, Isolated from a Human Semen Specimen. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00183-15. [PMID: 25814602 PMCID: PMC4384142 DOI: 10.1128/genomea.00183-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Corynebacterium singulare DSM 44357 is a urease-positive microorganism isolated from human semen. The complete genome sequence of C. singulare DSM 44357 comprises 2,830,519 bp with a mean G+C content of 60.12% and 2,581 protein-coding genes. The deduced antibiotic resistance pattern of this strain includes macrolides, lincosamides, aminoglycosides, chloramphenicol, and tetracyline.
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17
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Schlüter JP, Czuppon P, Schauer O, Pfaffelhuber P, McIntosh M, Becker A. Classification of phenotypic subpopulations in isogenic bacterial cultures by triple promoter probing at single cell level. J Biotechnol 2015; 198:3-14. [PMID: 25661839 DOI: 10.1016/j.jbiotec.2015.01.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/17/2015] [Accepted: 01/26/2015] [Indexed: 10/24/2022]
Abstract
Phenotypic heterogeneity, defined as the unequal behavior of individuals in an isogenic population, is prevalent in microorganisms. It has a significant impact both on industrial bioprocesses and microbial ecology. We introduce a new versatile reporter system designed for simultaneous monitoring of the activities of three different promoters, where each promoter is fused to a dedicated fluorescent reporter gene (cerulean, mCherry, and mVenus). The compact 3.1 kb triple reporter cassette can either be carried on a replicating plasmid or integrated into the genome avoiding artifacts associated with variation in copy number of plasmid-borne reporter constructs. This construct was applied to monitor promoter activities related to quorum sensing (sinI promoter) and biosynthesis of the exopolysaccharide galactoglucan (wgeA promoter) at single cell level in colonies of the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti growing in a microfluidics system. The T5-promoter served as a constitutive and homogeneously active control promoter indicating cell viability. wgeA promoter activity was heterogeneous over the whole period of colony development, whereas sinI promoter activity passed through a phase of heterogeneity before becoming homogeneous at late stages. Although quorum sensing-dependent regulation is a major factor activating galactoglucan production, activities of both promoters did not correlate at single cell level. We developed a novel mathematical strategy for classification of the gene expression status in cell populations based on the increase in fluorescence over time in each individual. With respect to galactoglucan biosynthesis, cells in the population were classified into non-contributors, weak contributors, and strong contributors.
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Affiliation(s)
- Jan-Philip Schlüter
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, Marburg, Germany
| | - Peter Czuppon
- Department of Mathematical Stochastics, Faculty of Mathematics and Physics, Albert-Ludwigs University Freiburg, Freiburg im Breisgau, Germany
| | - Oliver Schauer
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, Marburg, Germany
| | - Peter Pfaffelhuber
- Department of Mathematical Stochastics, Faculty of Mathematics and Physics, Albert-Ludwigs University Freiburg, Freiburg im Breisgau, Germany
| | - Matthew McIntosh
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, Marburg, Germany.
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, Marburg, Germany.
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18
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Savidor A, Chalupowicz L, Teper D, Gartemann KH, Eichenlaub R, Manulis-Sasson S, Barash I, Sessa G. Clavibacter michiganensis subsp. michiganensis Vatr1 and Vatr2 Transcriptional Regulators Are Required for Virulence in Tomato. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 2015:1-12. [PMID: 27839071 DOI: 10.1094/mpmi-02-14-0018-r.testissue] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The plant pathogen Clavibacter michiganensis subsp. michiganensis (Cmm) is a Gram-positive bacterium responsible for wilt and canker disease of tomato. While disease development is well characterized and diagnosed, molecular mechanisms of Cmm virulence are poorly understood. Here, we identified and characterized two Cmm transcriptional regulators, Vatr1 and Vatr2, that are involved in pathogenicity of Cmm. Vatr1 and Vatr2 belong to TetR and MocR families of transcriptional regulators, respectively. Mutations in their corresponding genes caused attenuated virulence, with the Δvatr2 mutant showing a more dramatic effect than Δvatr1. While both mutants grew well in vitro and reached a high titer in planta, they caused reduced wilting and canker development in infected plants compared with the wild-type bacterium. They also led to a reduced expression of the ethylene-synthesizing tomato enzyme ACC-oxidase compared with wild-type Cmm and to reduced ethylene production in the plant. Transcriptomic analysis of wild-type Cmm and the two mutants under infection-mimicking conditions revealed that Vatr1 and Vatr2 regulate expression of virulence factors, membrane and secreted proteins, and signal transducing proteins. A 70% overlap between the sets of genes positively regulated by Vatr1 and Vatr2 suggests that these transcriptional regulators are on the same molecular pathway responsible for Cmm virulence.
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Affiliation(s)
- Alon Savidor
- 1 Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Laura Chalupowicz
- 2 Department of Plant Pathology and Weed Research, ARO, the Volcani Center, Bet Dagan 50250, Israel
| | - Doron Teper
- 1 Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Karl-Heinz Gartemann
- 1 Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
- 3 Department of Genetechnology/Microbiology, Faculty of Biology, University of Bielefeld, 33501 Bielefeld, Germany
| | - Rudolf Eichenlaub
- 3 Department of Genetechnology/Microbiology, Faculty of Biology, University of Bielefeld, 33501 Bielefeld, Germany
| | - Shulamit Manulis-Sasson
- 2 Department of Plant Pathology and Weed Research, ARO, the Volcani Center, Bet Dagan 50250, Israel
| | - Isaac Barash
- 1 Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guido Sessa
- 1 Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
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19
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Savidor A, Chalupowicz L, Teper D, Gartemann KH, Eichenlaub R, Manulis-Sasson S, Barash I, Sessa G. Clavibacter michiganensis subsp. michiganensis Vatr1 and Vatr2 transcriptional regulators are required for virulence in tomato. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:1035-1047. [PMID: 24940988 DOI: 10.1094/mpmi-02-14-0061-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The plant pathogen Clavibacter michiganensis subsp. michiganensis is a gram-positive bacterium responsible for wilt and canker disease of tomato. Although disease development is well characterized and diagnosed, molecular mechanisms of C. michiganensis subsp. michiganensis virulence are poorly understood. Here, we identified and characterized two C. michiganensis subsp. michiganensis transcriptional regulators, Vatr1 and Vatr2, that are involved in pathogenicity of C. michiganensis subsp. michiganensis. Vatr1 and Vatr2 belong to TetR and MocR families of transcriptional regulators, respectively. Mutations in their corresponding genes caused attenuated virulence, with the Δvatr2 mutant showing a more dramatic effect than Δvatr1. Although both mutants grew well in vitro and reached a high titer in planta, they caused reduced wilting and canker development in infected plants compared with the wild-type bacterium. They also led to a reduced expression of the ethylene-synthesizing tomato enzyme ACC-oxidase compared with wild-type C. michiganensis subsp. michiganensis and to reduced ethylene production in the plant. Transcriptomic analysis of wild-type C. michiganensis subsp. michiganensis and the two mutants under infection-mimicking conditions revealed that Vatr1 and Vatr2 regulate expression of virulence factors, membrane and secreted proteins, and signal-transducing proteins. A 70% overlap between the sets of genes positively regulated by Vatr1 and Vatr2 suggests that these transcriptional regulators are on the same molecular pathway responsible for C. michiganensis subsp. michiganensis virulence.
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20
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RNase E affects the expression of the acyl-homoserine lactone synthase gene sinI in Sinorhizobium meliloti. J Bacteriol 2014; 196:1435-47. [PMID: 24488310 DOI: 10.1128/jb.01471-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Quorum sensing of Sinorhizobium meliloti relies on N-acyl-homoserine lactones (AHLs) as autoinducers. AHL production increases at high population density, and this depends on the AHL synthase SinI and two transcriptional regulators, SinR and ExpR. Our study demonstrates that ectopic expression of the gene rne, coding for RNase E, an endoribonuclease that is probably essential for growth, prevents the accumulation of AHLs at detectable levels. The ectopic rne expression led to a higher level of rne mRNA and a lower level of sinI mRNA independently of the presence of ExpR, the AHL receptor, and AHLs. In line with this, IPTG (isopropyl-β-D-thiogalactopyranoside)-induced overexpression of rne resulted in a shorter half-life of sinI mRNA and a strong reduction of AHL accumulation. Moreover, using translational sinI-egfp fusions, we found that sinI expression is specifically decreased upon induced overexpression of rne, independently of the presence of the global posttranscriptional regulator Hfq. The 28-nucleotide 5' untranslated region (UTR) of sinI mRNA was sufficient for this effect. Random amplification of 5' cDNA ends (5'-RACE) analyses revealed a potential RNase E cleavage site at position +24 between the Shine-Dalgarno site and the translation start site. We postulate therefore that RNase E-dependent degradation of sinI mRNA from the 5' end is one of the steps mediating a high turnover of sinI mRNA, which allows the Sin quorum-sensing system to respond rapidly to changes in transcriptional control of AHL production.
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Suzuki N, Inui M. Genome Engineering of Corynebacterium glutamicum. CORYNEBACTERIUM GLUTAMICUM 2013. [DOI: 10.1007/978-3-642-29857-8_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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22
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Shkoporov AN, Khokhlova EV, Kulagina EV, Smeianov VV, Kuchmiy AA, Kafarskaya LI, Efimov BA. Analysis of a novel 8.9kb cryptic plasmid from Bacteroides uniformis, its long-term stability and spread within human microbiota. Plasmid 2012. [PMID: 23201047 DOI: 10.1016/j.plasmid.2012.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The analysis of plasmid content in dominant Bacteroidales order intestinal strains isolated from the same child at a 5 year interval identified a 8.9 kb plasmid in Bacteroides uniformis BUN24 strain isolated at age 6 and indistinguishably sized plasmids in the isolates of B. uniformis, B. vulgatus, B. intesinalis, and Parabacteroides distasonis at age 11. We sequenced a B. uniformis BUN24 plasmid, designated pBUN24, and using molecular surveys of diverse species we established that this 8944bp molecule (G+C content 43.5%) represents a novel family of small cryptic Bacteroidales plasmids. The replication region of pBUN24 was experimentally localized to a 1707-bp fragment that includes a putative repA gene, coding for a protein of Rep_3 superfamily of replication proteins of theta-type plasmids preceded by a putative iteron-containing origin of replication. The other open reading frames (ORFs) identified in pBUN24 sequence include a putative tad-ata-type toxin-antitoxin and mobA-mobB mobilization modules, as well as seven additional cryptic ORFs. The interaction of Tad and Ada components demonstrated by a pull-down assay and the toxicity of Tad in Escherichia coli host suggests the functionality of the plasmid addiction module. Re-sequencing of plasmids in two Bacteroides strains isolated at the age of 11 showed 100% nucleotide identity to pBUN24. This data supports the notion that this plasmid is transmissible to other Bacteroidales strains in the natural ecosystem. The possible roles of toxin-antitoxin system and other proteins encoded by pBUN24 in providing an apparent ecological advantage to the plasmid-harbouring strains of a bacterial symbiont in the human gut deserve further investigation.
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Affiliation(s)
- Andrei N Shkoporov
- Department of Microbiology and Virology, The Russian National Research Medical University, 1, Ostrovitjanova St., Moscow 117997, Russia.
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Krol E, Becker A. ppGpp in Sinorhizobium meliloti: biosynthesis in response to sudden nutritional downshifts and modulation of the transcriptome. Mol Microbiol 2011; 81:1233-54. [PMID: 21696469 DOI: 10.1111/j.1365-2958.2011.07752.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sinorhizobium meliloti Rm2011 responds to sudden shifts to nitrogen or carbon starvation conditions by an accumulation of the stringent response alarmone ppGpp and remodelling of the transcriptome. The gene product of relA, Rel(Sm) , responsible for synthesis of ppGpp, shows functional similarities to E. coli SpoT. Using promoter-egfp gene fusions, we showed that in Rm2011 relA is expressed at a low rate, as a readthrough from the rpoZ promoter and from its own weak promoter. The low level of relA expression is physiologically relevant, since overexpression of Rel(Sm) inhibits ppGpp accumulation. The N-terminal portion of Rel(Sm) is required for ppGpp degradation in nutrient-sufficient cells and might be involved in regulation of the ppGpp synthase and hydrolase activities of the protein. Expression profiling of S. meliloti subjected to sudden nitrogen or carbon downshifts revealed that repression of 'house-keeping' genes is largely dependent on relA whereas activation of gene targets of the stress sigma factor RpoE2 occurred independently of relA. The regulatory genes nifA, ntrB, aniA and sinR, as well as genes related to modulation of protein biosynthesis and nucleotide catabolism, were induced in a relA-dependent manner. dksA was required for the majority of the relA-dependent regulations.
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Affiliation(s)
- Elizaveta Krol
- Faculty of Biology and Center for Systems Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
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Sobrero P, Valverde C. Evidences of autoregulation of hfq expression in Sinorhizobium meliloti strain 2011. Arch Microbiol 2011; 193:629-39. [PMID: 21484295 DOI: 10.1007/s00203-011-0701-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 03/16/2011] [Accepted: 03/18/2011] [Indexed: 12/16/2022]
Abstract
Riboregulation comprises gene expression regulatory mechanisms that rely upon the activity of small non-coding RNAs (sRNAs) and in most cases RNA binding proteins. In γ-proteobacteria, the Sm-like protein Hfq is a key player in riboregulatory processes, because it promotes sRNA-mRNA interactions and influences mRNA polyadenylation or translation. In the α-proteobacterium Sinorhizobium meliloti, the large number of detected small RNA transcripts and the pleiotropic effects of hfq mutations lead to the hypothesis that riboregulatory mechanisms are important in this soil microorganism to adjust gene expression both in free-living conditions and as a nitrogen-fixing endosymbiont within legume root nodules. In this study, homology modeling of S. meliloti Hfq protein and cross-complementation experiments of S. meliloti and Escherichia coli mutants indicates that hfq ( Sm ) encodes an RNA chaperone that can be functionally exchanged by its homolog from E. coli. A transcriptional and translational analysis of S. meliloti hfq expression by means of lacZ reporter fusions strongly suggests that the S. meliloti Hfq protein autocontrols its expression at the translational level, a phenomenon that was evident in the natural host S. meliloti as well as in the heterologous host E. coli.
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Affiliation(s)
- Patricio Sobrero
- Programa Interacciones Biológicas, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
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Jofré E, Becker A. Production of succinoglycan polymer in Sinorhizobium meliloti is affected by SMb21506 and requires the N-terminal domain of ExoP. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2009; 22:1656-1668. [PMID: 19888830 DOI: 10.1094/mpmi-22-12-1656] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The protein tyrosine kinase ExoP, consisting of an N-terminal periplasmic and a C-terminal cytoplasmic domain, is important for polymerization of the exopolysaccharide succinoglycan (EPS I) in Sinorhizobium meliloti. We analyzed the contribution of the ExoP paralogs ExoP2 and SMb21506 to the production of the high molecular weight (HMW) form of EPS I. ExoP2, though not contributing to EPS I or lipopolysaccharide biosynthesis, showed increased expression at high osmolarity and was expressed in Medicago sativa nodules, suggesting an involvement in the synthesis of an as-yet-unidentified polysaccharide. Furthermore, a mutation in SMb21506 affected the production of HMW EPS I, particularly in the absence of the C-terminal ExoP domain. High salinity induced the production of HMW EPS I by the wild type and mutants whereas high osmolarity had the opposite effect. It was shown that ExoP localizes at the inner membrane of S. meliloti cells. Tyrosine phosphorylation of the C-terminal domain was strongly increased by amino acid substitutions in the polysaccharide co-polymerase motif (formerly proline-rich motif) located in the N-terminal domain, suggesting that this phosphorylation could be modulated by conformational changes of the N-terminal domain. Moreover, deletion of a coiled-coil motif present in the N-terminal domain abolished phosphorylation and EPS I production and, consequently, the ability to nodulate M. sativa.
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Affiliation(s)
- Edgardo Jofré
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Fisico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina.
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Stork I, Gartemann KH, Burger A, Eichenlaub R. A family of serine proteases of Clavibacter michiganensis subsp. michiganensis: chpC plays a role in colonization of the host plant tomato. MOLECULAR PLANT PATHOLOGY 2008; 9:599-608. [PMID: 19018991 PMCID: PMC6640399 DOI: 10.1111/j.1364-3703.2008.00484.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Genes for seven putative serine proteases (ChpA-ChpG) belonging to the trypsin subfamily and homologous to the virulence factor pat-1 were identified on the chromosome of Clavibacter michiganensis subsp. michiganensis (Cmm) NCPPB382. All proteases have signal peptides indicating export of these proteins. Their putative function is suggested by two motifs and an aspartate residue typical for serine proteases. Furthermore, six cysteine residues are located at conserved positions. The genes are clustered in a chromosomal region of about 50 kb with a significantly lower G + C content than common for Cmm. The genes chpA, chpB and chpD are pseudogenes as they contain frame shifts and/or in-frame stop codons. The genes chpC and chpG were inactivated by the insertion of an antibiotic resistance cassette. The chpG mutant was not impaired in virulence. However, in planta the titre of the chpC mutant was drastically reduced and only weak disease symptoms were observed. Complementation of the chpC mutant by the wild-type allele restored full virulence. ChpC is the first chromosomal gene of Cmm identified so far that affects the interaction of the pathogen with the host plant.
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Affiliation(s)
- Ines Stork
- Fakultät für Biologie, Lehrstuhl für Mikrobiologie/Gentechnologie, Universitaetsstr. 25, D-33615 Bielefeld, Germany
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Shkoporov AN, Efimov BA, Khokhlova EV, Steele JL, Kafarskaia LI, Smeianov VV. Characterization of plasmids from human infant Bifidobacterium strains: sequence analysis and construction of E. coli-Bifidobacterium shuttle vectors. Plasmid 2008; 60:136-48. [PMID: 18652842 DOI: 10.1016/j.plasmid.2008.06.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Revised: 06/26/2008] [Accepted: 06/27/2008] [Indexed: 11/29/2022]
Abstract
A survey of infant fecal Bifidobacterium isolates for plasmid DNA revealed that a significant portion of the strains, 17.6%, carry small plasmids. The majority of plasmid-harboring strains belonged to the Bifidobacterium longum/infantis group. Most of the plasmids could be assigned into two groups based on their sizes and the restriction profiles. Three plasmids, pB44 (3.6 kb) from B. longum, pB80 (4.9 kb) from Bifidobacterium bifidum, and pB21a (5.2kb) from Bifidobacterium breve were sequenced. While the former two plasmids were found to be highly similar to previously characterized rolling-circle replicating pKJ36 and pKJ56, respectively, the third plasmid, pB21a, does not share significant nucleotide homology with known plasmids. However, it might be placed into the pCIBb1-like group of bifidobacterial rolling-plasmids based on the homology of its Rep protein and the overall molecular organization. Two sets of Escherichia coli-Bifidobacterium shuttle vectors constructed based on pB44 and pB80 replicons were capable of transforming B. bifidum and B. breve strains with efficiency up to 3x10(4)cfu/microg DNA. Additionally, an attempt was made to employ a broad host range conjugation element, RP4, in developing of E. coli-Bifidobacterium gene transfer system.
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Affiliation(s)
- Andrei N Shkoporov
- Department of Microbiology, Russia State Medical University, Moscow, Russia
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Zerillo MM, Van Sluys MA, Camargo LEA, Monteiro-Vitorello CB. Characterization of new IS elements and studies of their dispersion in two subspecies of Leifsonia xyli. BMC Microbiol 2008; 8:127. [PMID: 18655699 PMCID: PMC2516522 DOI: 10.1186/1471-2180-8-127] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2007] [Accepted: 07/25/2008] [Indexed: 12/05/2022] Open
Abstract
Background Leifsonia xyli is a xylem-inhabiting bacterial species comprised of two subspecies: L. xyli subsp. xyli (Lxx) and L. xyli subsp. cynodontis (Lxc). Lxx is the causal agent of ratoon stunting disease in sugarcane commercial fields and Lxc colonizes the xylem of several grasses causing either mild or no symptoms of disease. The completely sequenced genome of Lxx provided insights into its biology and pathogenicity. Since IS elements are largely reported as an important source of bacterial genome diversification and nothing is known about their role in chromosome architecture of L. xyli, a comparative analysis of Lxc and Lxx elements was performed. Results Sample sequencing of Lxc genome and comparative analysis with Lxx complete DNA sequence revealed a variable number of IS transposable elements acting upon genomic diversity. A detailed characterization of Lxc IS elements and a comparative review with IS elements of Lxx are presented. Each genome showed a unique set of elements although related to same IS families when considering features such as similarity among transposases, inverted and direct repeats, and element size. Most of the Lxc and Lxx IS families assigned were reported to maintain transposition at low levels using translation regulatory mechanisms, consistent with our in silico analysis. Some of the IS elements were found associated with rearrangements and specific regions of each genome. Differences were also found in the effect of IS elements upon insertion, although none of the elements were preferentially associated with gene disruption. A survey of transposases among genomes of Actinobacteria showed no correlation between phylogenetic relatedness and distribution of IS families. By using Southern hybridization, we suggested that diversification of Lxc isolates is also mediated by insertion sequences in probably recent events. Conclusion Collectively our data indicate that transposable elements are involved in genome diversification of Lxc and Lxx. The IS elements were probably acquired after the divergence of the two subspecies and are associated with genome organization and gene contents. In addition to enhancing understanding of IS element dynamics in general, these data will contribute to our ongoing comparative analyses aimed at understanding the biological differences of the Lxc and Lxx.
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Affiliation(s)
- Marcelo M Zerillo
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-900, São Paulo, SP, Brazil.
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Abstract
The genetic environment of the 16S rRNA methylase gene rmtD was investigated. rmtD was flanked by a novel ISCR motif located downstream of class I integron In163 in the original Pseudomonas aeruginosa strain. rmtD found in Klebsiella pneumoniae appeared to have been mobilized from P. aeruginosa by an IS26-mediated event.
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Tauch A, Trost E, Tilker A, Ludewig U, Schneiker S, Goesmann A, Arnold W, Bekel T, Brinkrolf K, Brune I, Götker S, Kalinowski J, Kamp PB, Lobo FP, Viehoever P, Weisshaar B, Soriano F, Dröge M, Pühler A. The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing. J Biotechnol 2008; 136:11-21. [PMID: 18367281 DOI: 10.1016/j.jbiotec.2008.02.009] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Revised: 12/11/2007] [Accepted: 02/07/2008] [Indexed: 01/11/2023]
Abstract
Corynebacterium urealyticum is a lipid-requiring, urealytic bacterium of the human skin flora that has been recognized as causative agent of urinary tract infections. We report the analysis of the complete genome sequence of C. urealyticum DSM7109, which was initially recovered from a patient with alkaline-encrusted cystitis. The genome sequence was determined by a combination of pyrosequencing and Sanger technology. The chromosome of C. urealyticum DSM7109 has a size of 2,369,219bp and contains 2024 predicted coding sequences, of which 78% were considered as orthologous with genes in the Corynebacterium jeikeium K411 genome. Metabolic analysis of the lipid-requiring phenotype revealed the absence of a fatty acid synthase gene and the presence of a beta-oxidation pathway along with a large repertoire of auxillary genes for the degradation of exogenous fatty acids. A urease locus with the gene order ureABCEFGD may play a pivotal role in virulence of C. urealyticum by the alkalinization of human urine and the formation of struvite stones. Multidrug resistance of C. urealyticum DSM7109 is mediated by transposable elements, conferring resistances to macrolides, lincosamides, ketolides, aminoglycosides, chloramphenicol, and tetracycline. The complete genome sequence of C. urealyticum revealed a detailed picture of the lifestyle of this opportunistic human pathogen.
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Affiliation(s)
- Andreas Tauch
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany.
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Lin H, Li TY, Xie MH, Zhang Y. Characterization of the variants, flanking genes, and promoter activity of the Leifsonia xyli subsp. cynodontis insertion sequence IS1237. J Bacteriol 2007; 189:3217-27. [PMID: 17293427 PMCID: PMC1855863 DOI: 10.1128/jb.01403-06] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We performed a comprehensive study of the distribution and function of an insertion sequence (IS) element, IS1237, in the genome of Leifsonia xyli subsp. cynodontis, a useful genetic carrier for expressing beneficial foreign genes in plants. Two shorter IS1237 isoforms, IS1237d1 and IS1237d2 resulting from precise deletion between two nonperfect repeats, were found in the bacterial genome at a level that was one-fifth the level of wild-type IS1237. Both the genome and native plasmid pCXC100 harbor a truncated toxin-antitoxin cassette that is precisely fused with a 5'-truncated IS1237 sequence at one nonperfect repeat, indicating that it is a hot site for DNA rearrangement. Nevertheless, no transposition activity was detected when the putative transposase of IS1237 was overexpressed in Escherichia coli. Using thermal asymmetric interlaced PCR, we identified 13 upstream and 10 downstream unique flanking sequences, and two pairs of these sequences were from the same loci, suggesting that IS1237 has up to 65 unique loci in the L. xyli subsp. cynodontis chromosome. The presence of TAA or TTA direct repeat sequences at most insertion sites indicated that IS1237 inserts into the loci by active transposition. IS1237 showed a high propensity for insertion into other IS elements, such as ISLxc1 and ISLxc2, which could offer IS1237 a nonautonomous transposition pathway through the host IS elements. Interestingly, we showed that IS1237 has a strong promoter at the 3' end and a weak promoter at the 5' end, and both promoters promote the transcription of adjacent genes in different gram-positive bacteria. The high-copy-number nature of IS1237 and its promoter activity may contribute to bacterial fitness.
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Affiliation(s)
- Hui Lin
- State Key Laboratory of Virology, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Hubei 430072, China
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Mormann S, Lömker A, Rückert C, Gaigalat L, Tauch A, Pühler A, Kalinowski J. Random mutagenesis in Corynebacterium glutamicum ATCC 13032 using an IS6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway. BMC Genomics 2006; 7:205. [PMID: 16901339 PMCID: PMC1590026 DOI: 10.1186/1471-2164-7-205] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Accepted: 08/10/2006] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Corynebacterium glutamicum, a Gram-positive bacterium of the class Actinobacteria, is an industrially relevant producer of amino acids. Several methods for the targeted genetic manipulation of this organism and rational strain improvement have been developed. An efficient transposon mutagenesis system for the completely sequenced type strain ATCC 13032 would significantly advance functional genome analysis in this bacterium. RESULTS A comprehensive transposon mutant library comprising 10,080 independent clones was constructed by electrotransformation of the restriction-deficient derivative of strain ATCC 13032, C. glutamicum RES167, with an IS6100-containing non-replicative plasmid. Transposon mutants had stable cointegrates between the transposon vector and the chromosome. Altogether 172 transposon integration sites have been determined by sequencing of the chromosomal inserts, revealing that each integration occurred at a different locus. Statistical target site analyses revealed an apparent absence of a target site preference. From the library, auxotrophic mutants were obtained with a frequency of 2.9%. By auxanography analyses nearly two thirds of the auxotrophs were further characterized, including mutants with single, double and alternative nutritional requirements. In most cases the nutritional requirement observed could be correlated to the annotation of the mutated gene involved in the biosynthesis of an amino acid, a nucleotide or a vitamin. One notable exception was a clone mutagenized by transposition into the gene cg0910, which exhibited an auxotrophy for histidine. The protein sequence deduced from cg0910 showed high sequence similarities to inositol-1(or 4)-monophosphatases (EC 3.1.3.25). Subsequent genetic deletion of cg0910 delivered the same histidine-auxotrophic phenotype. Genetic complementation of the mutants as well as supplementation by histidinol suggests that cg0910 encodes the hitherto unknown essential L-histidinol-phosphate phosphatase (EC 3.1.3.15) in C. glutamicum. The cg0910 gene, renamed hisN, and its encoded enzyme have putative orthologs in almost all Actinobacteria, including mycobacteria and streptomycetes. CONCLUSION The absence of regional and sequence preferences of IS6100-transposition demonstrate that the established system is suitable for efficient genome-scale random mutagenesis in the sequenced type strain C.glutamicum ATCC 13032. The identification of the hisN gene encoding histidinol-phosphate phosphatase in C. glutamicum closed the last gap in histidine synthesis in the Actinobacteria. The system might be a valuable genetic tool also in other bacteria due to the broad host-spectrum of IS6100.
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Affiliation(s)
- Sascha Mormann
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
- Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Alexander Lömker
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
- Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Christian Rückert
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
- Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Lars Gaigalat
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
- Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Andreas Tauch
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Alfred Pühler
- Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Jörn Kalinowski
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
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Vertès AA, Inui M, Yukawa H. Manipulating corynebacteria, from individual genes to chromosomes. Appl Environ Microbiol 2006; 71:7633-42. [PMID: 16332735 PMCID: PMC1317429 DOI: 10.1128/aem.71.12.7633-7642.2005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Alain A Vertès
- Research Institute of Innovative Technology for the Earth, 9-2 Kizugawadai, Kizu, Soraku, Kyoto 619-0292, Japan
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Kaup O, Gräfen I, Zellermann EM, Eichenlaub R, Gartemann KH. Identification of a tomatinase in the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2005; 18:1090-8. [PMID: 16255248 DOI: 10.1094/mpmi-18-1090] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The insertion site of a transposon mutant of Clavibacter michiganensis subsp. michiganensis NCPPB382 was cloned and found to be located in the gene tomA encoding a member of the glycosyl hydrolase family 10. The intact gene was obtained from a cosmid library of C. michiganensis subsp. michiganensis. The deduced protein TomA (543 amino acids, 58 kDa) contains a predicted signal peptide and two domains, the N-terminal catalytic domain and a C-terminal fibronectin III-like domain. The closest well-characterized relatives of TomA were tomatinases from fungi involved in the detoxification of the tomato saponin alpha-tomatine which acts as a growth inhibitor. Growth inhibition of C. michiganensis subsp. michiganensis by alpha-tomatine was stronger in the tomA mutants than in the wild type. Tomatinase activity assayed by deglycosylation of alpha-tomatine to tomatidine was demonstrated in concentrated culture supernatants of C. michiganensis subsp. michiganensis. No activity was found with the tomA mutants. However, neither the transposon mutant nor a second mutant constructed by gene disruption was affected in virulence on the tomato cv. Moneymaker.
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Affiliation(s)
- Olaf Kaup
- Department of Genetechnology/Microbiology, University of Bielefeld, Universitaetsstr, Bielefeld, Germany
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Luo L, Yao SY, Becker A, Rüberg S, Yu GQ, Zhu JB, Cheng HP. Two new Sinorhizobium meliloti LysR-type transcriptional regulators required for nodulation. J Bacteriol 2005; 187:4562-72. [PMID: 15968067 PMCID: PMC1151776 DOI: 10.1128/jb.187.13.4562-4572.2005] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The establishment of an effective nitrogen-fixing symbiosis between Sinorhizobium meliloti and its legume host alfalfa (Medicago sativa) depends on the timely expression of nodulation genes that are controlled by LysR-type regulators. Ninety putative genes coding for LysR-type transcriptional regulators were identified in the recently sequenced S. meliloti genome. All 90 putative lysR genes were mutagenized using plasmid insertions as a first step toward determining their roles in symbiosis. Two new LysR-type symbiosis regulator genes, lsrA and lsrB, were identified in the screening. Both the lsrA and lsrB genes are expressed in free-living S. meliloti cells, but they are not required for cell growth. An lsrA1 mutant was defective in symbiosis and elicited only white nodules that exhibited no nitrogenase activity. Cells of the lsrA1 mutant were recovered from the white nodules, suggesting that the lsrA1 mutant was blocked early in nodulation. An lsrB1 mutant was deficient in symbiosis and elicited a mixture of pink and white nodules on alfalfa plants. These plants exhibited lower overall nitrogenase activity than plants inoculated with the wild-type strain, which is consistent with the fact that most of the alfalfa plants inoculated with the lsrB1 mutant were short and yellow. Cells of the lsrB1 mutant were recovered from both pink and white nodules, suggesting that lsrB1 mutants could be blocked at multiple points during nodulation. The identification of two new LysR-type symbiosis transcriptional regulators provides two new avenues for understanding the complex S. meliloti-alfalfa interactions which occur during symbiosis.
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Affiliation(s)
- Li Luo
- Biological Sciences Department, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, NY 10468, USA
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Chiribau CB, Sandu C, Igloi GL, Brandsch R. Characterization of PmfR, the transcriptional activator of the pAO1-borne purU-mabO-folD operon of Arthrobacter nicotinovorans. J Bacteriol 2005; 187:3062-70. [PMID: 15838033 PMCID: PMC1082840 DOI: 10.1128/jb.187.9.3062-3070.2005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nicotine catabolism by Arthrobacter nicotinovorans is linked to the presence of the megaplasmid pAO1. Genes involved in this catabolic pathway are arranged on the plasmid into gene modules according to function. During nicotine degradation gamma-N-methylaminobutyrate is formed from the pyrrolidine ring of nicotine. Analysis of the pAO1 open reading frames (ORF) resulted in identification of the gene encoding a demethylating gamma-N-methylaminobutyrate oxidase (mabO). This gene was shown to form an operon with purU- and folD-like genes. Only in bacteria grown in the presence of nicotine could transcripts of the purU-mabO-folD operon be detected, demonstrating that this operon constitutes part of the pAO1 nicotine regulon. Its transcriptional start site was determined by primer extension analysis. Transcription of the operon was shown to be controlled by a new transcriptional regulator, PmfR, the product of a gene that is transcribed divergently from the purU, mabO, and folD genes. PmfR was purified, and electromobility shift assays and DNase I-nuclease digestion experiments were used to determine that its DNA binding site is located between -48 and -88 nucleotides upstream of the transcriptional start site of the operon. Disruption of pmfR by homologous recombination with a chloramphenicol resistance cassette demonstrated that PmfR acts in vivo as a transcriptional activator. Mutagenesis of the PmfR target DNA suggested that the sequence GTTT-14 bp-AAAC is the core binding site of the regulator upstream of the -35 promoter region of the purU-mabO-folD operon.
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Affiliation(s)
- Calin B Chiribau
- Institute of Biochemistry and Molecular Biology, University of Freiburg, 76104 Freiburg, Germany
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Inui M, Tsuge Y, Suzuki N, Vertès AA, Yukawa H. Isolation and characterization of a native composite transposon, Tn14751, carrying 17.4 kilobases of Corynebacterium glutamicum chromosomal DNA. Appl Environ Microbiol 2005; 71:407-16. [PMID: 15640215 PMCID: PMC544269 DOI: 10.1128/aem.71.1.407-416.2005] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A native composite transposon was isolated from Corynebacterium glutamicum ATCC 14751. This transposon comprises two functional copies of a corynebacterial IS31831-like insertion sequence organized as converging terminal inverted repeats. This novel 20.3-kb element, Tn14751, carries 17.4 kb of C. glutamicum chromosomal DNA containing various genes, including genes involved in purine biosynthesis but not genes related to bacterial warfare, such as genes encoding mediators of antibiotic resistance or extracellular toxins. A derivative of this element carrying a kanamycin resistance cassette, minicomposite Tn14751, transposed into the genome of C. glutamicum at an efficiency of 1.8 x 10(2) transformants per mug of DNA. Random insertion of the Tn14751 derivative carrying the kanamycin resistance cassette into the chromosome was verified by Southern hybridization. This work paves the way for realization of the concept of minimum genome factories in the search for metabolic engineering via genome-scale directed evolution through a combination of random and directed approaches.
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Affiliation(s)
- Masayuki Inui
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth, Soraku-Gun, Kyoto 619-0292, Japan
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Schwarz S, Kehrenberg C, Doublet B, Cloeckaert A. Molecular basis of bacterial resistance to chloramphenicol and florfenicol. FEMS Microbiol Rev 2005; 28:519-42. [PMID: 15539072 DOI: 10.1016/j.femsre.2004.04.001] [Citation(s) in RCA: 420] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2004] [Revised: 04/05/2004] [Accepted: 04/17/2004] [Indexed: 11/21/2022] Open
Abstract
Chloramphenicol (Cm) and its fluorinated derivative florfenicol (Ff) represent highly potent inhibitors of bacterial protein biosynthesis. As a consequence of the use of Cm in human and veterinary medicine, bacterial pathogens of various species and genera have developed and/or acquired Cm resistance. Ff is solely used in veterinary medicine and has been introduced into clinical use in the mid-1990s. Of the Cm resistance genes known to date, only a small number also mediates resistance to Ff. In this review, we present an overview of the different mechanisms responsible for resistance to Cm and Ff with particular focus on the two different types of chloramphenicol acetyltransferases (CATs), specific exporters and multidrug transporters. Phylogenetic trees of the different CAT proteins and exporter proteins were constructed on the basis of a multisequence alignment. Moreover, information is provided on the mobile genetic elements carrying Cm or Cm/Ff resistance genes to provide a basis for the understanding of the distribution and the spread of Cm resistance--even in the absence of a selective pressure imposed by the use of Cm or Ff.
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Affiliation(s)
- Stefan Schwarz
- Institut für Tierzucht, Bundesforschungsanstalt für Landwirtschaft (FAL), Höltystrasse 10, 31535 Neustadt-Mariensee, Germany.
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39
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Tauch A, Bischoff N, Pühler A, Kalinowski J. Comparative genomics identified two conserved DNA modules in a corynebacterial plasmid family present in clinical isolates of the opportunistic human pathogen Corynebacterium jeikeium. Plasmid 2004; 52:102-18. [PMID: 15336488 DOI: 10.1016/j.plasmid.2004.05.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2004] [Revised: 05/25/2004] [Indexed: 11/30/2022]
Abstract
Investigation of 62 clinical isolates of the opportunistic human pathogen Corynebacterium jeikeium revealed that 17 possessed plasmids ranging in size from 7.6 to 14.9 kb. The plasmids formed four groups on DNA restriction analysis. The complete nucleotide sequence of a representative from each group (pK43, pK64, pCJ84, and pB85766) was subsequently determined. Additionally, two plasmids (pCo455 and pCo420) were shown to be derivatives of pK43 and pK64 carrying insertion sequences of the IS3 family. Comparative genomics identified a conserved plasmid backbone consisting of two distinct DNA modules. Conserved motifs in the parAB-repA module indicated that the sequenced plasmids from C. jeikeium are new members of the pNG2 family. Recombinant derivatives of pK43 were shown to replicate in the soil bacterium Corynebacterium glutamicum and in the human pathogen Corynebacterium diphtheriae. The second plasmid module most likely encodes a novel type of DNA invertase. The respective gene is flanked by highly conserved 112-bp inverted repeats. All plasmids are 'loaded' with a characteristic set of genes encoding products of unknown function. Plasmids indistinguishable from pK43 by DNA restriction analysis were identified in different C. jeikeium strains, which revealed 16S-23S rDNA spacer length polymorphisms and specific antibiotic susceptibility profiles, implying a wide dissemination of the plasmid in clinical isolates of C. jeikeium.
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MESH Headings
- Amino Acid Sequence
- Anti-Bacterial Agents/pharmacology
- Base Sequence
- Conserved Sequence
- Corynebacterium/genetics
- Corynebacterium Infections/microbiology
- DNA Replication/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Genomics
- Humans
- Microbial Sensitivity Tests
- Molecular Sequence Data
- Plasmids/genetics
- Polymerase Chain Reaction
- Polymorphism, Genetic
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- Sequence Alignment
- Sequence Analysis, DNA
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Affiliation(s)
- Andreas Tauch
- Institut für Genomforschung, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany.
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Gartemann KH, Kirchner O, Engemann J, Gräfen I, Eichenlaub R, Burger A. Clavibacter michiganensis subsp. michiganensis: first steps in the understanding of virulence of a Gram-positive phytopathogenic bacterium. J Biotechnol 2004; 106:179-91. [PMID: 14651860 DOI: 10.1016/j.jbiotec.2003.07.011] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Clavibacter michiganensis subsp. michiganensis is a plant-pathogenic actinomycete. It infects tomato, spreads through the xylem and causes bacterial wilt and canker. The wild-type strain NCPPB382 carries two plasmids, pCM1 and pCM2. The cured plasmid-free derivative CMM100 is still able to colonize tomato, but no disease symptoms develop indicating that all genes required for successful infection, establishment and growth in the plant reside on the chromosome. Both plasmids carry one virulence factor, a gene encoding a cellulase, CelA in case of pCM1 and a putative serine protease Pat-1 on pCM2. These genes can independently convert the non-virulent strain CMM100 into a pathogen causing wilt on tomatoes. Currently, genome projects for Cmm and the closely related potato-pathogen C. michiganensis subsp. sepedonicus have been initiated. The data from the genome project shall give clues on further genes involved in plant-microbe interaction that can be tested experimentally. Especially, identification of genes related to host-specificity through genome comparison of the two subspecies might be possible.
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Affiliation(s)
- Karl-Heinz Gartemann
- Lehrstuhl Gentechnologie/Mikrobiologie, Fakultät für Biologie, Universität Bielefeld, Universitätsstrasse 25, D-33501 Bielefeld, Germany
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41
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Borodina E, McDonald IR, Murrell JC. Chloromethane-dependent expression of the cmu gene cluster of Hyphomicrobium chloromethanicum. Appl Environ Microbiol 2004; 70:4177-86. [PMID: 15240299 PMCID: PMC444766 DOI: 10.1128/aem.70.7.4177-4186.2004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2004] [Accepted: 03/24/2004] [Indexed: 11/20/2022] Open
Abstract
The methylotrophic bacterium Hyphomicrobium chloromethanicum CM2 can utilize chloromethane (CH(3)Cl) as the sole carbon and energy source. Previously genes cmuB, cmuC, cmuA, and folD were shown to be essential for the growth of Methylobacterium chloromethanicum on CH(3)Cl. These CH(3)Cl-specific genes were subsequently detected in H. chloromethanicum. Transposon and marker exchange mutagenesis studies were carried out to identify the genes essential for CH(3)Cl metabolism in H. chloromethanicum. New developments in genetic manipulation of Hyphomicrobium are presented in this study. An electroporation protocol has been optimized and successfully applied for transformation of mutagenesis plasmids into H. chloromethanicum to generate stable CH(3)Cl-negative mutants. Both transposon and marker exchange mutageneses were highly applicable for genetic analysis of Hyphomicrobium. A reliable and reproducible selection procedure for screening of CH(3)Cl utilization-negative mutants has also been developed. Mutational inactivation of cmuB, cmuC, or hutI resulted in strains that were unable to utilize CH(3)Cl or to express the CH(3)Cl-dependent polypeptide CmuA. Reverse transcription-PCR analysis indicated that cmuB, cmuC, cmuA, fmdB, paaE, hutI, and metF formed a single cmuBCA-metF operon and were coregulated and coexpressed in H. chloromethanicum. This finding led to the conclusion that, in cmuB and cmuC mutants, impaired expression of cmuA was likely to be due to a polar effect of the defective gene (cmuB or cmuC) located upstream (5') of cmuA. The detrimental effect of mutation in hutI on the upstream (5')-located cmuA is not clear but indicated that all the genes located within the cmuBCA-metF operon are coordinately expressed. Expression of the cmuBCA-metF transcript was also shown to be strictly CH(3)Cl inducible and was not repressed by the alternative C(1) substrate methanol. Sequence analysis of a transposon mutant (D20) led to the discovery of the previously undetected hutI and metF genes located 3' of the paaE gene in H. chloromethanicum. MetF, a putative methylene-tetrahydrofolate reductase, had 27% identity to MetF from M. chloromethanicum. Mutational and transcriptional analysis data indicated that, in H. chloromethanicum, CH(3)Cl is metabolized via a corrinoid-specific (cmuA) and tetrahydrofolate-dependent (metF, purU, folD) methyltransfer system.
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Affiliation(s)
- Elena Borodina
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.
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Kirchner O, Tauch A. Tools for genetic engineering in the amino acid-producing bacterium Corynebacterium glutamicum. J Biotechnol 2003; 104:287-99. [PMID: 12948646 DOI: 10.1016/s0168-1656(03)00148-2] [Citation(s) in RCA: 234] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
During the last decades, the gram-positive soil bacterium Corynebacterium glutamicum has been shown to be a very versatile microorganism for the large-scale fermentative production of L-amino acids. Up to now, a vast amount of techniques and tools for genetic engineering and amplification of relevant structural genes have been developed. The objectives of this study are to summarize the published literature on tools for genetic engineering in C. glutamicum and to focus on new sophisticated and highly efficient methods in the fields of DNA transfer techniques, cloning vectors, integrative genetic tools, and antibiotic-free self-cloning. This repertoire of C. glutamicum methodology provides an experimental basis for efficient genetic analyses of the recently completed genome sequence.
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Affiliation(s)
- Oliver Kirchner
- Lehrstuhl für Gentechnologie/Mikrobiologie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany
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Sharypova LA, Niehaus K, Scheidle H, Holst O, Becker A. Sinorhizobium meliloti acpXL mutant lacks the C28 hydroxylated fatty acid moiety of lipid A and does not express a slow migrating form of lipopolysaccharide. J Biol Chem 2003; 278:12946-54. [PMID: 12566460 DOI: 10.1074/jbc.m209389200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lipid A is the hydrophobic anchor of lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria. Lipid A of all Rhizobiaceae is acylated with a long fatty acid chain, 27-hydroxyoctacosanoic acid. Biosynthesis of this long acyl substitution requires a special acyl carrier protein, AcpXL, which serves as a donor of C28 (omega-1)-hydroxylated fatty acid for acylation of rhizobial lipid A (Brozek, K.A., Carlson, R.W., and Raetz, C. R. (1996) J. Biol. Chem. 271, 32126-32136). To determine the biological function of the C28 acylation of lipid A, we constructed an acpXL mutant of Sinorhizobium meliloti strain 1021. Gas-liquid chromatography and mass spectrometry analysis of the fatty acid composition showed that the acpXL mutation indeed blocked C28 acylation of lipid A. SDS-PAGE analysis of acpXL mutant LPS revealed only a fast migrating band, rough LPS, whereas the parental strain 1021 manifested both rough and smooth LPS. Regardless of this, the LPS of parental and mutant strains had a similar sugar composition and exposed the same antigenic epitopes, implying that different electrophoretic profiles might account for different aggregation properties of LPS molecules with and without a long acyl chain. The acpXL mutant of strain 1021 displayed sensitivity to deoxycholate, delayed nodulation of Medicago sativa, and a reduced competitive ability. However, nodules elicited by this mutant on roots of M. sativa and Medicago truncatula had a normal morphology and fixed nitrogen. Thus, the C28 fatty acid moiety of lipid A is not crucial, but it is beneficial for establishing an effective symbiosis with host plants. acpXL lies upstream from a cluster of five genes, including msbB (lpxXL), which might be also involved in biosynthesis and transfer of the C28 fatty acid to the lipid A precursor.
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Affiliation(s)
- Larissa A Sharypova
- Institute of Genetics, Biology VI, University of Bielefeld, Postfach 100131, Bielefeld D-33501, Germany.
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Tauch A, Götker S, Pühler A, Kalinowski J, Thierbach G. The 27.8-kb R-plasmid pTET3 from Corynebacterium glutamicum encodes the aminoglycoside adenyltransferase gene cassette aadA9 and the regulated tetracycline efflux system Tet 33 flanked by active copies of the widespread insertion sequence IS6100. Plasmid 2002; 48:117-29. [PMID: 12383729 DOI: 10.1016/s0147-619x(02)00120-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We determined the complete nucleotide sequence of the 27.8-kb R-plasmid pTET3 from Corynebacterium glutamicum LP-6 which encodes streptomycin, spectinomycin, and tetracycline resistance. The antibiotic resistance determinant of pTET3 comprises an intI1-like gene, which was truncated by the insertion sequence IS6100, and the novel aminoglycoside adenyltransferase gene cassette aadA9. The deduced AADA9 protein showed 61% identity and 71% similarity to AADA6 of integron In51 from Pseudomonas aeruginosa. In addition, pTET3 carries the novel repressor-regulated tetracycline resistance determinant Tet 33 which revealed amino acid sequence homology to group 1 tetracycline efflux systems. The highest level of similarity was observed to the tetracycline efflux protein TetA(Z) from the C. glutamicum plasmid pAG1 with 65% identical and 77% similar amino acids. Each antibiotic resistance region of pTET3 is flanked by identical copies of the widespread insertion sequence IS6100 initially identified in Mycobacterium fortuitum. Transposition assays with a cloned copy of IS6100 revealed that this element is transpositionally active in C. glutamicum. These data suggest a central role of IS6100 in the evolutionary history of pTET3 by mediating the cointegrative assembly of resistance gene-carrying DNA segments.
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Affiliation(s)
- Andreas Tauch
- Degussa AG, Kantstrasse 2, D-33790 Halle-Künsebeck, Germany.
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45
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Kirchner O, Gartemann KH, Zellermann EM, Eichenlaub R, Burger A. A highly efficient transposon mutagenesis system for the tomato pathogen Clavibacter michiganensis subsp. michiganensis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2001; 14:1312-1318. [PMID: 11763129 DOI: 10.1094/mpmi.2001.14.11.1312] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A transposon mutagenesis system for Clavibacter michiganensis subsp. michiganensis was developed based on antibiotic resistance transposons that were derived from the insertion element IS1409 from Arthrobacter sp. strain TM1 NCIB12013. As a prerequisite, the electroporation efficiency was optimized by using unmethylated DNA and treatment of the cells with glycine such that about 5 x 10(6) transformants per microg of DNA were generally obtained. Electroporation of C. michiganensis subsp. michiganensis with a suicide vector carrying transposon Tn1409C resulted in approximately 1 x 10(3) transposon mutants per pg of DNA and thus is suitable for saturation mutagenesis. Analysis of Tn1409C insertion sites suggests a random mode of transposition. Transposition of Tn1409C was also demonstrated for other subspecies of C. michiganensis.
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Affiliation(s)
- O Kirchner
- Fakultät für Biologie, Lehrstuhl für Mikrobiologie/Gentechnologie, Universität Bielefeld, Germany
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46
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Gartemann KH, Eichenlaub R. Isolation and characterization of IS1409, an insertion element of 4-chlorobenzoate-degrading Arthrobacter sp. strain TM1, and development of a system for transposon mutagenesis. J Bacteriol 2001; 183:3729-36. [PMID: 11371537 PMCID: PMC95250 DOI: 10.1128/jb.183.12.3729-3736.2001] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new insertion element of 1,449 bp with 25-bp perfect terminal repeats, designated IS1409, was identified in the chromosome of 4-chlorobenzoate-degrading Arthrobacter sp. strain TM1 NCIB12013. Upon insertion, IS1409 causes a target duplication of 8 bp. IS1409 carries only a single open reading frame of 435 codons encoding the transposase TnpA. Both TnpA and the overall organization of IS1409 are highly similar to those of some related insertion elements of the ISL3 group (J. Mahillon and M. Chandler, Microbiol. Mol. Biol. Rev. 62:725--774, 1998). IS1409 was also found in other 4-chlorobenzoate-degrading Arthrobacter strains and Micrococcus luteus. Based on IS1409, a series of transposons carrying resistance genes for chloramphenicol and gentamicin were constructed. These transposons were used to demonstrate transposition events in vivo and to mutagenize Arthrobacter sp. strains.
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Affiliation(s)
- K H Gartemann
- Fakultät für Biologie, Lehrstuhl für Mikrobiologie/Gentechnologie, Universität Bielefeld, Bielefeld, Germany
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47
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Jore JP, van Luijk N, Luiten RG, van der Werf MJ, Pouwels PH. Efficient transformation system for Propionibacterium freudenreichii based on a novel vector. Appl Environ Microbiol 2001; 67:499-503. [PMID: 11157209 PMCID: PMC92613 DOI: 10.1128/aem.67.2.499-503.2001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A 3.6-kb endogenous plasmid was isolated from a Propionibacterium freudenreichii strain and sequenced completely. Based on homologies with plasmids from other bacteria, notably a plasmid from Mycobacterium, a region harboring putative replicative functions was defined. Outside this region two restriction enzyme recognition sites were used for insertion of an Escherichia coli-specific replicon and an erythromycin resistance gene for selection in Propionibacterium. Hybrid vectors obtained in this way replicated in both E. coli and P. freudenreichii. Whereas electroporation of P. freudenreichii with vector DNA isolated from an E. coli transformant yielded 10 to 30 colonies per microg of DNA, use of vector DNA reisolated from a Propionibacterium transformant dramatically increased the efficiency of transformation (> or =10(8) colonies per microg of DNA). It could be shown that restriction-modification was responsible for this effect. The high efficiency of the system described here permitted successful transformation of Propionibacterium with DNA ligation mixtures.
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Affiliation(s)
- J P Jore
- TNO Nutrition and Food Research, 3700 AJ Zeist, The Netherlands.
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48
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Tauch A, Krieft S, Pühler A, Kalinowski J. The tetAB genes of the Corynebacterium striatum R-plasmid pTP10 encode an ABC transporter and confer tetracycline, oxytetracycline and oxacillin resistance in Corynebacterium glutamicum. FEMS Microbiol Lett 1999; 173:203-9. [PMID: 10220896 DOI: 10.1111/j.1574-6968.1999.tb13503.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The tetracycline resistance region of the 50-kb R-plasmid pTP10 from the clinical isolate Corynebacterium striatum M82B was analyzed in Corynebacterium glutamicum ATCC 13032 and confined to a 4.4-kb SphI-Sa/I DNA fragment. Nucleotide sequence analysis revealed two open reading frames, termed tetA and tetB, specifying proteins of 513 and 528 amino acids, respectively. The deduced amino acid sequences of tetAB displayed similarity to ATP-binding cassette transporters including StrV and StrW of Streptomyces glaucescens which are proposed to play a role in the export of streptomycin-like aminoglycosides. An antibiotic susceptibility screening in C. glutamicum showed that the tetAB genes confer resistance to tetracycline, oxytetracycline and to the structurally and functionally unrelated beta-lactam antibiotic oxacillin.
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Affiliation(s)
- A Tauch
- Department of Genetics, University of Bielefeld, Germany
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Jahr H, Bahro R, Burger A, Ahlemeyer J, Eichenlaub R. Interactions between Clavibacter michiganensis and its host plants. Environ Microbiol 1999; 1:113-8. [PMID: 11207726 DOI: 10.1046/j.1462-2920.1999.00011.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- H Jahr
- Universität Bielefeld, Fakultät für Biologie, Gentechnologie/Mikrobiologie, Germany
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