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Song Y, Xu X, Huang Z, Xiao Y, Yu K, Jiang M, Yin S, Zheng M, Meng H, Han Y, Wang Y, Wang D, Wei Q. Genomic Characteristics Revealed Plasmid-Mediated Pathogenicity and Ubiquitous Rifamycin Resistance of Rhodococcus equi. Front Cell Infect Microbiol 2022; 12:807610. [PMID: 35252029 PMCID: PMC8891757 DOI: 10.3389/fcimb.2022.807610] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/27/2022] [Indexed: 11/22/2022] Open
Abstract
Rhodococcus equi is a zoonotic pathogen that can cause fatal disease in patients who are immunocompromised. At present, the epidemiology and pathogenic mechanisms of R. equi infection are not clear. This study characterized the genomes of 53 R. equi strains from different sources. Pan-genome analysis showed that all R. equi strains contained 11481 pan genes, including 3690 core genes and 602 ~ 1079 accessory genes. Functional annotation of pan genome focused on the genes related to basic lifestyle, such as the storage and expression of metabolic and genetic information. Phylogenetic analysis based on pan-genome showed that the R. equi strains were clustered into six clades, which was not directly related to the isolation location and host source. Also, a total of 84 virulence genes were predicted in 53 R. equi strains. These virulence factors can be divided into 20 categories related to substance metabolism, secreted protein and immune escape. Meanwhile, six antibiotic resistance genes (RbpA, tetA (33), erm (46), sul1, qacEdelta 1 and aadA9) were detected, and all strains carried RbpA related to rifamycin resistance. In addition, 28 plasmids were found in the 53 R. equi strains, belonging to Type-A (n = 14), Type-B (n = 8) and Type-N (n = 6), respectively. The genetic structures of the same type of plasmid were highly similar. In conclusion, R. equi strains show different genomic characteristics, virulence-related genes, potential drug resistance and virulence plasmid structures, which may be conducive to the evolution of its pathogenesis.
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Affiliation(s)
- Yang Song
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Xinmin Xu
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Zhenzhou Huang
- Center for human Pathogenic Culture Collection, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Yue Xiao
- Center for human Pathogenic Culture Collection, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Keyi Yu
- Center for human Pathogenic Culture Collection, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Mengnan Jiang
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Shangqi Yin
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Mei Zheng
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Huan Meng
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Ying Han
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Yajie Wang
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Qiang Wei, ; Duochun Wang, ; Yajie Wang,
| | - Duochun Wang
- Center for human Pathogenic Culture Collection, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
- *Correspondence: Qiang Wei, ; Duochun Wang, ; Yajie Wang,
| | - Qiang Wei
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
- *Correspondence: Qiang Wei, ; Duochun Wang, ; Yajie Wang,
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Natukunda MI, Hohenstein JD, McCabe CE, Graham MA, Qi Y, Singh AK, MacIntosh GC. Interaction between Rag genes results in a unique synergistic transcriptional response that enhances soybean resistance to soybean aphids. BMC Genomics 2021; 22:887. [PMID: 34895143 PMCID: PMC8665634 DOI: 10.1186/s12864-021-08147-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 11/03/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pyramiding different resistance genes into one plant genotype confers enhanced resistance at the phenotypic level, but the molecular mechanisms underlying this effect are not well-understood. In soybean, aphid resistance is conferred by Rag genes. We compared the transcriptional response of four soybean genotypes to aphid feeding to assess how the combination of Rag genes enhanced the soybean resistance to aphid infestation. RESULTS A strong synergistic interaction between Rag1 and Rag2, defined as genes differentially expressed only in the pyramid genotype, was identified. This synergistic effect in the Rag1/2 phenotype was very evident early (6 h after infestation) and involved unique biological processes. However, the response of susceptible and resistant genotypes had a large overlap 12 h after aphid infestation. Transcription factor (TF) analyses identified a network of interacting TF that potentially integrates signaling from Rag1 and Rag2 to produce the unique Rag1/2 response. Pyramiding resulted in rapid induction of phytochemicals production and deposition of lignin to strengthen the secondary cell wall, while repressing photosynthesis. We also identified Glyma.07G063700 as a novel, strong candidate for the Rag1 gene. CONCLUSIONS The synergistic interaction between Rag1 and Rag2 in the Rag1/2 genotype can explain its enhanced resistance phenotype. Understanding molecular mechanisms that support enhanced resistance in pyramid genotypes could facilitate more directed approaches for crop improvement.
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Affiliation(s)
- Martha I. Natukunda
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011 USA
| | - Jessica D. Hohenstein
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011 USA
| | - Chantal E. McCabe
- Corn Insects and Crop Genetics Research, USDA-ARS, Ames, IA 50011 USA
| | - Michelle A. Graham
- Corn Insects and Crop Genetics Research, USDA-ARS, Ames, IA 50011 USA
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Yunhui Qi
- Department of Statistics, Iowa State University, Ames, IA 50011 USA
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Gustavo C. MacIntosh
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011 USA
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Amadio A, Bono JL, Irazoqui M, Larzábal M, Marques da Silva W, Eberhardt MF, Riviere NA, Gally D, Manning SD, Cataldi A. Genomic analysis of shiga toxin-containing Escherichia coli O157:H7 isolated from Argentinean cattle. PLoS One 2021; 16:e0258753. [PMID: 34710106 PMCID: PMC8553066 DOI: 10.1371/journal.pone.0258753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/04/2021] [Indexed: 11/19/2022] Open
Abstract
Cattle are the main reservoir of Enterohemorrhagic Escherichia coli (EHEC), with O157:H7 the distinctive serotype. EHEC is the main causative agent of a severe systemic disease, Hemolytic Uremic Syndrome (HUS). Argentina has the highest pediatric HUS incidence worldwide with 12–14 cases per 100,000 children. Herein, we assessed the genomes of EHEC O157:H7 isolates recovered from cattle in the humid Pampas of Argentina. According to phylogenetic studies, EHEC O157 can be divided into clades. Clade 8 strains that were classified as hypervirulent. Most of the strains of this clade have a Shiga toxin stx2a-stx2c genotype. To better understand the molecular bases related to virulence, pathogenicity and evolution of EHEC O157:H7, we performed a comparative genomic analysis of these isolates through whole genome sequencing. The isolates classified as clade 8 (four strains) and clade 6 (four strains) contained 13 to 16 lambdoid prophages per genome, and the observed variability of prophages was analysed. An inter strain comparison show that while some prophages are highly related and can be grouped into families, other are unique. Prophages encoding for stx2a were highly diverse, while those encoding for stx2c were conserved. A cluster of genes exclusively found in clade 8 contained 13 genes that mostly encoded for DNA binding proteins. In the studied strains, polymorphisms in Q antiterminator, the Q-stx2A intergenic region and the O and P γ alleles of prophage replication proteins are associated with different levels of Stx2a production. As expected, all strains had the pO157 plasmid that was highly conserved, although one strain displayed a transposon interruption in the protease EspP gene. This genomic analysis may contribute to the understanding of the genetic basis of the hypervirulence of EHEC O157:H7 strains circulating in Argentine cattle. This work aligns with other studies of O157 strain variation in other populations that shows key differences in Stx2a-encoding prophages.
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Affiliation(s)
- Ariel Amadio
- Instituto de Investigación de la Cadena Láctea IDICaL (INTA-CONICET), Rafaela, Argentina
| | - James L. Bono
- U.S Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska, United States of America
| | - Matías Irazoqui
- Instituto de Investigación de la Cadena Láctea IDICaL (INTA-CONICET), Rafaela, Argentina
| | - Mariano Larzábal
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO)-CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
| | - Wanderson Marques da Silva
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO)-CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
| | | | - Nahuel A. Riviere
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO)-CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
| | - David Gally
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Shannon D. Manning
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Angel Cataldi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO)-CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
- * E-mail:
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Campa AR, Smith LM, Hampton HG, Sharma S, Jackson SA, Bischler T, Sharma CM, Fineran PC. The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR-Cas immune systems. Nucleic Acids Res 2021; 49:9508-9525. [PMID: 34403463 PMCID: PMC8450108 DOI: 10.1093/nar/gkab704] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/29/2021] [Accepted: 08/03/2021] [Indexed: 12/15/2022] Open
Abstract
CRISPR-Cas systems provide bacteria with adaptive immunity against phages and plasmids; however, pathways regulating their activity are not well defined. We recently developed a high-throughput genome-wide method (SorTn-seq) and used this to uncover CRISPR-Cas regulators. Here, we demonstrate that the widespread Rsm/Csr pathway regulates the expression of multiple CRISPR-Cas systems in Serratia (type I-E, I-F and III-A). The main pathway component, RsmA (CsrA), is an RNA-binding post-transcriptional regulator of carbon utilisation, virulence and motility. RsmA binds cas mRNAs and suppresses type I and III CRISPR-Cas interference in addition to adaptation by type I systems. Coregulation of CRISPR-Cas and flagella by the Rsm pathway allows modulation of adaptive immunity when changes in receptor availability would alter susceptibility to flagella-tropic phages. Furthermore, we show that Rsm controls CRISPR-Cas in other genera, suggesting conservation of this regulatory strategy. Finally, we identify genes encoding RsmA homologues in phages, which have the potential to manipulate the physiology of host bacteria and might provide an anti-CRISPR activity.
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Affiliation(s)
- Aroa Rey Campa
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Leah M Smith
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Hannah G Hampton
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Sahil Sharma
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Cynthia M Sharma
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Genetics Otago, University of Otago, Dunedin, New Zealand
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5
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Whole Genome Sequencing and Tn 5-Insertion Mutagenesis of Pseudomonas taiwanensis CMS to Probe Its Antagonistic Activity Against Rice Bacterial Blight Disease. Int J Mol Sci 2020; 21:ijms21228639. [PMID: 33207795 PMCID: PMC7696974 DOI: 10.3390/ijms21228639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 01/07/2023] Open
Abstract
The Gram-negative bacterium Pseudomonas taiwanensis is a novel bacterium that uses shrimp shell waste as its sole sources of carbon and nitrogen. It is a versatile bacterium with potential for use in biological control, with activities including toxicity toward insects, fungi, and the rice pathogen Xanthomonas oryzae pv.oryzae (Xoo). In this study, the complete 5.08-Mb genome sequence of P. taiwanensis CMS was determined by a combination of NGS/Sanger sequencing and optical mapping. Comparison of optical maps of seven Pseudomonas species showed that P. taiwanensis is most closely related to P. putida KT 2400. We screened a total of 11,646 individual Tn5-transponson tagged strains to identify genes that are involved in the production and regulation of the iron-chelator pyoverdine in P. taiwanensis, which is a key anti-Xoo factor. Our results indicated that the two-component system (TCS) EnvZ/OmpR plays a positive regulatory role in the production of pyoverdine, whereas the sigma factor RpoS functions as a repressor. The knowledge of the molecular basis of the regulation of pyoverdine by P. taiwanensis provided herein will be useful for its development for use in biological control, including as an anti-Xoo agent.
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6
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Siddiqui N, Yousaf F, Murtaza F, Ehatisham-ul-Haq M, Ashraf MU, Alghamdi AM, Alfakeeh AS. A highly nonlinear substitution-box (S-box) design using action of modular group on a projective line over a finite field. PLoS One 2020; 15:e0241890. [PMID: 33180847 PMCID: PMC7660566 DOI: 10.1371/journal.pone.0241890] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 10/21/2020] [Indexed: 11/19/2022] Open
Abstract
Cryptography is commonly used to secure communication and data transmission over insecure networks through the use of cryptosystems. A cryptosystem is a set of cryptographic algorithms offering security facilities for maintaining more cover-ups. A substitution-box (S-box) is the lone component in a cryptosystem that gives rise to a nonlinear mapping between inputs and outputs, thus providing confusion in data. An S-box that possesses high nonlinearity and low linear and differential probability is considered cryptographically secure. In this study, a new technique is presented to construct cryptographically strong 8×8 S-boxes by applying an adjacency matrix on the Galois field GF(28). The adjacency matrix is obtained corresponding to the coset diagram for the action of modular group [Formula: see text] on a projective line PL(F7) over a finite field F7. The strength of the proposed S-boxes is examined by common S-box tests, which validate their cryptographic strength. Moreover, we use the majority logic criterion to establish an image encryption application for the proposed S-boxes. The encryption results reveal the robustness and effectiveness of the proposed S-box design in image encryption applications.
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Affiliation(s)
- Nasir Siddiqui
- Department of Basic Sciences, University of Engineering and Technology (UET), Taxila, Punjab, Pakistan
| | - Fahim Yousaf
- Department of Basic Sciences, University of Engineering and Technology (UET), Taxila, Punjab, Pakistan
| | - Fiza Murtaza
- Sino-Pak Center for Artificial Intelligence, Pak-Austria Fachhochschule: Institute of Applied Sciences and Technology, Haripur, Khyber Pakthunkhwa (KPK), Pakistan
| | - Muhammad Ehatisham-ul-Haq
- Department of Computer Engineering, University of Engineering and Technology (UET), Taxila, Punjab, Pakistan
| | - M. Usman Ashraf
- Department of Computer Science, University of Management and Technology (UMT), Lahore (Sialkot), Punjab, Pakistan
| | - Ahmed M. Alghamdi
- Department of Software Engineering, College of Computer Science and Engineering, University of Jeddah, Jeddah, Saudi Arabia
| | - Ahmed S. Alfakeeh
- Department of Information Systems, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
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7
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Zhou X, Chlebowicz MA, Bathoorn E, Rosema S, Couto N, Lokate M, Arends JP, Friedrich AW, Rossen JWA. Elucidating vancomycin-resistant Enterococcus faecium outbreaks: the role of clonal spread and movement of mobile genetic elements. J Antimicrob Chemother 2019; 73:3259-3267. [PMID: 30219855 DOI: 10.1093/jac/dky349] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/06/2018] [Indexed: 12/27/2022] Open
Abstract
Background Vancomycin-resistant Enterococcus faecium (VREfm) has emerged as a nosocomial pathogen worldwide. The dissemination of VREfm is due to both clonal spread and spread of mobile genetic elements (MGEs) such as transposons. Objectives We aimed to combine vanB-carrying transposon data with core-genome MLST (cgMLST) typing and epidemiological data to understand the pathways of transmission in nosocomial outbreaks. Methods Retrospectively, 36 VREfm isolates obtained from 34 patients from seven VREfm outbreak investigations in 2014 were analysed. Isolates were sequenced on a MiSeq and a MinION instrument. De novo assembly was performed in CLC Genomics Workbench and the hybrid assemblies were obtained through Unicycler v0.4.1. Ridom SeqSphere+ was used to extract MLST and cgMLST data. Detailed analysis of each transposon and their integration points was performed using the Artemis Comparison Tool (ACT) and multiple blast analyses. Results Four different vanB transposons were found among the isolates. cgMLST divided ST80 isolates into three cluster types (CTs); CT16, CT104 and CT106. ST117 isolates were divided into CT24, CT103 and CT105. Within VREfm isolates belonging to CT103, two different vanB transposons were found. In contrast, VREfm isolates belonging to CT104 and CT106 harboured an identical vanB transposon. Conclusions cgMLST provides a high discriminatory power for the epidemiological analysis of VREfm. However, additional transposon analysis is needed to detect horizontal gene transfer. Combining these two methods allows investigation of both clonal spread as well as the spread of MGEs. This leads to new insights and thereby better understanding of the complex transmission routes in VREfm outbreaks.
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Affiliation(s)
- X Zhou
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - M A Chlebowicz
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - E Bathoorn
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - S Rosema
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - N Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - M Lokate
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - J P Arends
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - A W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - J W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
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Gosse JT, Ghosh S, Sproule A, Overy D, Cheeptham N, Boddy CN. Whole Genome Sequencing and Metabolomic Study of Cave Streptomyces Isolates ICC1 and ICC4. Front Microbiol 2019; 10:1020. [PMID: 31134037 PMCID: PMC6524458 DOI: 10.3389/fmicb.2019.01020] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 04/24/2019] [Indexed: 11/13/2022] Open
Abstract
The terrestrial subsurface microbiome has gained considerable amount of interests in the recent years because of its rich potential resource for biomining novel genes coding for metabolites possessing antimicrobial activities. In our previous study, we identified two Streptomyces isolates, designated as ICC1 and ICC4, from the Iron Curtain Cave, Chilliwack, Canada that exhibited antagonistic activities against the multidrug resistant strains of Escherichia coli. In this study, the genomes of these two isolates were sequenced by Illumina MiSeq, assembled and annotated. The genes associated with secondary metabolite production were identified and annotated using the bioinformatics platforms antiSMASH and BAGEL. ICC1 and ICC4 were then cultivated and ICC1 metabolome characterized by UHPLC-ESI-HRMS. The Global Natural Products Social Molecular Networking was used to identify metabolites based on the MS/MS spectral data. ICC1 and ICC4 showed a high level of sequence identity with the terrestrial bacteria Streptomyces lavendulae; however, they possess a greater secondary metabolite potential as estimated by the total number of identified biosynthetic gene clusters (BGCs). In particular, ICC1 and ICC4 had a greater number of polyketide and non-ribosomal peptide BGCs. The most frequently detected BGCs were those predicted to generate terpenes, small and low complexity dipeptides and lipids. Spectral analysis clearly identified a number of diketopiperazine products through matched reference spectra for cyclo (Leu-Pro), cyclo (Pro-Val) and cyclo [(4-hydroxyPro)-Leu]. One of the terpenes gene clusters predicted by antiSMASH possesses a seven-gene pathway consistent with diazepinomicin biosynthesis. This molecule contains a very rare core structure and its BGC, to date, has only been identified from a single bacterial genome. The tetrapeptide siderophore coelichelin BGC was unambiguously identified in the genome, however, the metabolite could not be identified from the culture extracts. Two type III polyketides, 2′, 5′ – dimethoxyflavone and nordentatin, were identified from the UHPLC-HRMS data of the aqueous and n-butanolic fractions of Streptomyces sp. ICC1, respectively. A BGC likely encoding these metabolites was predicted in both genomes. The predicted similarities in molecule production and genome shared by these two strains could be an indicative of a cooperative mode of living in extreme habitats instead of a competitive one. This secondary metabolite potential may contribute to the fitness of ICC1 and ICC4 in the Iron Curtain Cave.
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Affiliation(s)
- Jessica Thandara Gosse
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Soumya Ghosh
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, Canada
| | - Amanda Sproule
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - David Overy
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Naowarat Cheeptham
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
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9
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Impacts of horizontal gene transfer on the compact genome of the clavulanic acid-producing Streptomyces strain F613-1. 3 Biotech 2018; 8:472. [PMID: 30456006 DOI: 10.1007/s13205-018-1498-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/01/2018] [Indexed: 12/27/2022] Open
Abstract
Mobile genetic elements involved in mediating horizontal transfer events contribute to bacterial evolution, and bacterial genomic plasticity and instability result in variation in functional genetic information in Streptomyces secondary metabolism. In a previous study, we reported the complete genome sequence of the industrial Streptomyces strain F613-1, which produces high yields of clavulanic acid. In this study, we used comparative genomics and bioinformatics to investigate the unique genomic features of this strain. Taken together, comparative genomics were used to systematically investigate secondary metabolism capabilities and indicated that frequent exchange of genetic materials between Streptomyces replicons may shape the remarkable diversities in their secondary metabolite repertoires. Moreover, a 136.9-kb giant region of plasticity (RGP) was found in the F613-1 chromosome, and the chromosome and plasmid pSCL4 are densely packed with an exceptionally large variety of potential secondary metabolic gene clusters, involving several determinants putatively accounting for antibiotic production. In addition, the differences in the architecture and size of plasmid pSCL4 between F613-1 and ATCC 27064 suggest that the pSCL4 plasmid could evolve from pSCL4-like and pSCL2-like extrachromosomal replicons. Furthermore, the genomic analyses revealed that strain F613-1 has developed specific genomic architectures and genetic patterns that are well suited to meet the requirements of industrial innovation processes.
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10
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Pan F, Zhang L, Li M, Hu Y, Zeng B, Yuan H, Zhao L, Zhang C. Predominant gut Lactobacillus murinus strain mediates anti-inflammaging effects in calorie-restricted mice. MICROBIOME 2018; 6:54. [PMID: 29562943 PMCID: PMC5863386 DOI: 10.1186/s40168-018-0440-5] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/13/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND Calorie restriction (CR), which has a potent anti-inflammaging effect, has been demonstrated to induce dramatic changes in the gut microbiota. Whether the modulated gut microbiota contributes to the attenuation of inflammation during CR is unknown, as are the members of the microbial community that may be key mediators of this process. RESULTS Here, we report that a unique Lactobacillus-predominated microbial community was rapidly attained in mice within 2 weeks of CR, which decreased the levels of circulating microbial antigens and systemic inflammatory markers such as tumour necrosis factor alpha (TNF-α). Lactobacillus murinus CR147, an isolate in the most abundant operational taxonomic unit (OTU) enriched by CR, downregulated interleukin-8 production in TNF-α-stimulated Caco-2 cells and significantly increased the lifespan and the brood size of the nematode Caenorhabditis elegans. In gnotobiotic mice colonized with the gut microbiota from old mice, this strain decreased their intestinal permeability and serum endotoxin load, consequently attenuating the inflammation induced by the old microbiota. CONCLUSIONS Our study demonstrated that a strain of Lactobacillus murinus was promoted in CR mice and causatively contributed to the attenuation of ageing-associated inflammation.
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Affiliation(s)
- Fengwei Pan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Liying Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Min Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Yingxin Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Benhua Zeng
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing, 400038 China
| | - Huijuan Yuan
- Henan Provincial People’s Hospital, Zhengzhou, 450003 Henan Province China
| | - Liping Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Chenhong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
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11
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Aziz RK, Ackermann HW, Petty NK, Kropinski AM. Essential Steps in Characterizing Bacteriophages: Biology, Taxonomy, and Genome Analysis. Methods Mol Biol 2018; 1681:197-215. [PMID: 29134597 DOI: 10.1007/978-1-4939-7343-9_15] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Because of the rise in antimicrobial resistance there has been a significant increase in interest in phages for therapeutic use. Furthermore, the cost of sequencing phage genomes has decreased to the point where it is being used as a teaching tool for genomics. Unfortunately, the quality of the descriptions of the phage and its annotation frequently are substandard. The following chapter is designed to help people working on phages, particularly those new to the field, to accurately describe their newly isolated viruses.
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Affiliation(s)
- Ramy Karam Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Qasr El-Ainy, 11562, Cairo, Egypt.
| | - Hans-Wolfgang Ackermann
- Department of Microbiology, Immunology, and Infectiology, Faculty of Medicine, Université Laval, Quebec, QC, Canada, G1X 4C6
| | - Nicola K Petty
- The ithree Institute, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Andrew M Kropinski
- Departments of Food Science, Molecular and Cellular Biology, and Pathobiology, University of Guelph, Guelph, ON, Canada, N1G 2W1
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12
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Alterations in gp37 Expand the Host Range of a T4-Like Phage. Appl Environ Microbiol 2017; 83:AEM.01576-17. [PMID: 28939606 DOI: 10.1128/aem.01576-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/19/2017] [Indexed: 01/21/2023] Open
Abstract
The use of phages as antibacterial agents is limited by their generally narrow host ranges. The aim of this study was to make a T4-like phage, WG01, obtain the host range of another T4-like phage, QL01, by replacing its host-determinant gene region with that of QL01. This process triggered a direct expansion of the WG01 host range. The offspring of WG01 obtained the host ranges of both QL01 and WG01, as well as the ability to infect eight additional host bacteria in comparison to the wild-type strains. WQD had the widest host range; therefore, the corresponding fragments, named QD, could be used for constructing a homologous sequence library. Moreover, after a sequencing analysis of gene 37, we identified two different mechanisms responsible for the expanded host range: (i) the first generation of WG01 formed chimeras without mutations, and (ii) the second generation of WG01 mutants formed from the chimeras. The expansion of the host range indicated that regions other than the C-terminal region may indirectly change the receptor specificity by altering the supportive capacity of the binding site. Additionally, we also found the novel means by which subsequent generations expanded their host ranges, namely, by exchanging gene 37 to acquire a wider temperature range for lysis. The method developed in this work offers a quick way to change or expand the host range of a phage. Future clinical applications for screening phages against a given clinical isolate could be achieved after acquiring more suitable homologous sequences.IMPORTANCE T4-like phages have been established as safe in numerous phage therapy applications. The primary drawbacks to the use of phages as therapeutic agents include their highly specific host ranges. Thus, changing or expanding the host range of T4-like phages is beneficial for selecting phages for phage therapy. In this study, the host range of the T4-like phage WG01 was expanded using genetic manipulation. The WG01 derivatives acquired a novel means of expanding their host ranges by acquiring a wider temperature range for lysis. A region was located that had the potential to be used as a sequence region for homologous sequence recombination.
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13
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DiMarzio M, Rusconi B, Yennawar NH, Eppinger M, Patterson AD, Dudley EG. Identification of a mouse Lactobacillus johnsonii strain with deconjugase activity against the FXR antagonist T-β-MCA. PLoS One 2017; 12:e0183564. [PMID: 28910295 PMCID: PMC5598929 DOI: 10.1371/journal.pone.0183564] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 08/07/2017] [Indexed: 12/13/2022] Open
Abstract
Bile salt hydrolase (BSH) activity against the bile acid tauro-beta-muricholic acid (T-β-MCA) was recently reported to mediate host bile acid, glucose, and lipid homeostasis via the farnesoid X receptor (FXR) signaling pathway. An earlier study correlated decreased Lactobacillus abundance in the cecum with increased concentrations of intestinal T-β-MCA, an FXR antagonist. While several studies have characterized BSHs in lactobacilli, deconjugation of T-β-MCA remains poorly characterized among members of this genus, and therefore it was unclear what strain(s) were responsible for this activity. Here, a strain of L. johnsonii with robust BSH activity against T-β-MCA in vitro was isolated from the cecum of a C57BL/6J mouse. A screening assay performed on a collection of 14 Lactobacillus strains from nine different species identified BSH substrate specificity for T-β-MCA only in two of three L. johnsonii strains. Genomic analysis of the two strains with this BSH activity revealed the presence of three bsh genes that are homologous to bsh genes in the previously sequenced human-associated strain L. johnsonii NCC533. Heterologous expression of several bsh genes in E. coli followed by enzymatic assays revealed broad differences in substrate specificity even among closely related bsh homologs, and suggests that the phylogeny of these enzymes does not closely correlate with substrate specificity. Predictive modeling allowed us to propose a potential mechanism driving differences in BSH activity for T-β-MCA in these homologs. Our data suggests that L. johnsonii regulates T-β-MCA levels in the mouse intestinal environment, and that this species may play a central role in FXR signaling in the mouse.
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Affiliation(s)
- Michael DiMarzio
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States of America
| | - Brigida Rusconi
- Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Neela H. Yennawar
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States of America
| | - Mark Eppinger
- Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Andrew D. Patterson
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States of America
| | - Edward G. Dudley
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States of America
- * E-mail:
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14
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Identification of IncA/C Plasmid Replication and Maintenance Genes and Development of a Plasmid Multilocus Sequence Typing Scheme. Antimicrob Agents Chemother 2017; 61:AAC.01740-16. [PMID: 27872077 DOI: 10.1128/aac.01740-16] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 11/08/2016] [Indexed: 12/26/2022] Open
Abstract
Plasmids of incompatibility group A/C (IncA/C) are becoming increasingly prevalent within pathogenic Enterobacteriaceae They are associated with the dissemination of multiple clinically relevant resistance genes, including blaCMY and blaNDM Current typing methods for IncA/C plasmids offer limited resolution. In this study, we present the complete sequence of a blaNDM-1-positive IncA/C plasmid, pMS6198A, isolated from a multidrug-resistant uropathogenic Escherichia coli strain. Hypersaturated transposon mutagenesis, coupled with transposon-directed insertion site sequencing (TraDIS), was employed to identify conserved genetic elements required for replication and maintenance of pMS6198A. Our analysis of TraDIS data identified roles for the replicon, including repA, a toxin-antitoxin system; two putative partitioning genes, parAB; and a putative gene, 053 Construction of mini-IncA/C plasmids and examination of their stability within E. coli confirmed that the region encompassing 053 contributes to the stable maintenance of IncA/C plasmids. Subsequently, the four major maintenance genes (repA, parAB, and 053) were used to construct a new plasmid multilocus sequence typing (PMLST) scheme for IncA/C plasmids. Application of this scheme to a database of 82 IncA/C plasmids identified 11 unique sequence types (STs), with two dominant STs. The majority of blaNDM-positive plasmids examined (15/17; 88%) fall into ST1, suggesting acquisition and subsequent expansion of this blaNDM-containing plasmid lineage. The IncA/C PMLST scheme represents a standardized tool to identify, track, and analyze the dissemination of important IncA/C plasmid lineages, particularly in the context of epidemiological studies.
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Pasricha S, Schafferer L, Lindner H, Joanne Boyce K, Haas H, Andrianopoulos A. Differentially regulated high-affinity iron assimilation systems support growth of the various cell types in the dimorphic pathogenTalaromyces marneffei. Mol Microbiol 2016; 102:715-737. [DOI: 10.1111/mmi.13489] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Shivani Pasricha
- Department of Genetics; University of Melbourne; Victoria 3010 Australia
| | - Lukas Schafferer
- Division of Molecular Biology and Division of Clinical Biochemistry and the Protein Micro-Analysis Facility; Innsbruck Medical University; Innsbruck, Innrain 80-82 Innsbruck A-6020 Austria
| | - Herbert Lindner
- Division of Molecular Biology and Division of Clinical Biochemistry and the Protein Micro-Analysis Facility; Innsbruck Medical University; Innsbruck, Innrain 80-82 Innsbruck A-6020 Austria
| | - Kylie Joanne Boyce
- Department of Genetics; University of Melbourne; Victoria 3010 Australia
| | - Hubertus Haas
- Division of Molecular Biology and Division of Clinical Biochemistry and the Protein Micro-Analysis Facility; Innsbruck Medical University; Innsbruck, Innrain 80-82 Innsbruck A-6020 Austria
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16
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Luo P, He X, Wang Y, Liu Q, Hu C. Comparative genomic analysis of six new-found integrative conjugative elements (ICEs) in Vibrio alginolyticus. BMC Microbiol 2016; 16:79. [PMID: 27145747 PMCID: PMC4857294 DOI: 10.1186/s12866-016-0692-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 04/14/2016] [Indexed: 08/24/2023] Open
Abstract
Background Vibrio alginolyticus is ubiquitous in marine and estuarine environments. In 2012–2013, SXT/R391-like integrative conjugative elements (ICEs) in environmental V. alginolyticus strains were discovered and found to occur in 8.9 % of 192 V. alginolyticus strains, which suggests that V. alginolyticus may be a natural pool possessing resourceful ICEs. However, complete ICE sequences originating from this bacterium have not been reported, which represents a significant barrier to characterizing the ICEs of this bacterium and exploring their relationships with other ICEs. In the present study, we acquired six ICE sequences from five V. alginolyticus strains and performed a comparative analysis of these ICE genomes. Results A sequence analysis showed that there were only 14 variable bases dispersed between ICEValE0601 and ICEValHN492. ICEValE0601 and ICEValHN492 were treated as the same ICE. ICEValA056-1, ICEValE0601 and ICEValHN492 integrate into the 5′ end of the host’s prfC gene, and their Int and Xis share at least 97 % identity with their counterparts from SXT. ICEValE0601 or ICEValHN492 contain 50 of 52 conserved core genes in the SXT/R391 ICEs (not s025 or s026). ICEValA056-2, ICEValHN396 and ICEValHN437 have a different tRNA-ser integration site and a distinct int/xis module; however, the remaining backbone genes are highly similar to their counterparts in SXT/R391 ICEs. DNA sequences inserted into hotspot and variable regions of the ICEs are of various sizes. The variable genes of six ICEs encode a large array of functions to bestow various adaptive abilities upon their hosts, and only ICEValA056-1 contains drug-resistant genes. Many variable genes have orthologous and functionally related genes to those found in SXT/R391 ICEs, such as genes coding for a toxin-antitoxin system, a restriction-modification system, helicases and endonucleases. Six ICEs also contain a large number of unique genes or gene clusters that were not found in other ICEs. Six ICEs harbor more abundant transposase genes compared with other parts of their host genomes. A phylogenetic analysis indicated that transposase genes in these ICEs are highly diverse. Conclusions ICEValA056-1, ICEValE0601 and ICEValHN492 are typical members of the SXT/R391 family. ICEValA056-2, ICEValHN396 and ICEValHN437 form a new atypical group belonging to the SXT/R391 family. In addition to the many genes found to be present in other ICEs, six ICEs contain a large number of unique genes or gene clusters that were not found in other ICEs. ICEs may serve as a carrier for transposable genetic elements (TEs) and largely facilitate the dissemination of TEs. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0692-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peng Luo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.,Guangdong Key Laboratory of Applied Marine Biology, Chinese Academy of Sciences, Guangzhou, 510301, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510275, China
| | - Xiangyan He
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanhong Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.,Guangdong Key Laboratory of Applied Marine Biology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Qiuting Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaoqun Hu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China. .,Guangdong Key Laboratory of Applied Marine Biology, Chinese Academy of Sciences, Guangzhou, 510301, China. .,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510275, China.
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Raven KE, Reuter S, Gouliouris T, Reynolds R, Russell JE, Brown NM, Török ME, Parkhill J, Peacock SJ. Genome-based characterization of hospital-adapted Enterococcus faecalis lineages. Nat Microbiol 2016; 1:15033. [PMID: 27213049 PMCID: PMC4872833 DOI: 10.1038/nmicrobiol.2015.33] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 12/24/2015] [Indexed: 11/09/2022]
Abstract
Vancomycin-resistant Enterococcus faecalis (VREfs) is an important nosocomial pathogen1,2. We undertook whole genome sequencing of E. faecalis associated with bloodstream infection in the UK and Ireland over more than a decade to determine the population structure and genetic associations with hospital adaptation. Three lineages predominated in the population, two of which (L1 and L2) were nationally distributed, and one (L3) geographically restricted. Genome comparison with a global collection identified that L1 and L3 were also present in the USA, but were genetically distinct. Over 90% of VREfs belonged to L1-L3, with resistance acquired and lost multiple times in L1 and L2, but only once followed by clonal expansion in L3. Putative virulence and antibiotic resistance genes were over-represented in L1, L2 and L3 isolates combined, versus the remainder. Each of the three main lineages contained a mixture of vancomycin-resistant and -susceptible E. faecalis (VSEfs), which has important implications for infection control and antibiotic stewardship.
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Affiliation(s)
- Kathy E. Raven
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Sandra Reuter
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Theodore Gouliouris
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
- Clinical Microbiology and Public Health Laboratory, Public Health England, Box 236, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge CB2 0QQ, UK
| | - Rosy Reynolds
- British Society for Antimicrobial Chemotherapy, Griffin House, 53 Regent Place, Birmingham B1 3NJ, UK
- North Bristol NHS Trust, Southmead Hospital, Bristol, BS10 5NB, UK
| | - Julie E. Russell
- Culture Collections, Public Health England, Porton Down, Salisbury SP4 0JG, UK
| | - Nicholas M. Brown
- Clinical Microbiology and Public Health Laboratory, Public Health England, Box 236, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
- British Society for Antimicrobial Chemotherapy, Griffin House, 53 Regent Place, Birmingham B1 3NJ, UK
| | - M. Estée Török
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
- Clinical Microbiology and Public Health Laboratory, Public Health England, Box 236, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge CB2 0QQ, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge CB2 0QQ, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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18
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Losada L, DebRoy C, Radune D, Kim M, Sanka R, Brinkac L, Kariyawasam S, Shelton D, Fratamico PM, Kapur V, Feng PCH. Whole genome sequencing of diverse Shiga toxin-producing and non-producing Escherichia coli strains reveals a variety of virulence and novel antibiotic resistance plasmids. Plasmid 2015; 83:8-11. [PMID: 26746359 DOI: 10.1016/j.plasmid.2015.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 12/21/2015] [Accepted: 12/29/2015] [Indexed: 01/20/2023]
Abstract
The genomes of a diverse set of Escherichia coli, including many Shiga toxin-producing strains of various serotypes were determined. A total of 39 plasmids were identified among these strains, and many carried virulence or putative virulence genes of Shiga toxin-producing E. coli strains, virulence genes for other pathogenic E. coli groups, and some had combinations of these genes. Among the novel plasmids identified were eight that carried resistance genes to aminoglycosides, carbapenems, penicillins, cephalosporins, chloramphenicol, dihydrofolate reductase inhibitors, sulfonamides, tetracyclines and resistance to heavy metals. Two of the plasmids carried six of these resistance genes and two novel IncHI2 plasmids were also identified. The results of this study showed that plasmids carrying diverse resistance and virulence genes of various pathogenic E. coli groups can be found in E. coli strains and serotypes regardless of the isolate's source and therefore, is consistent with the premise that these mobile elements carrying these traits may be broadly disseminated among E. coli.
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Affiliation(s)
| | - Chitrita DebRoy
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | | | - Maria Kim
- J. Craig Venter Institute, Rockville, MD, USA
| | - Ravi Sanka
- J. Craig Venter Institute, Rockville, MD, USA
| | | | - Subhashinie Kariyawasam
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Daniel Shelton
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Pina M Fratamico
- Eastern Regional Research Center, Agricultural Research Service, USDA, Wyndmoor, PA, USA
| | - Vivek Kapur
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
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Wolters AMA, Caro M, Dong S, Finkers R, Gao J, Visser RGF, Wang X, Du Y, Bai Y. Detection of an inversion in the Ty-2 region between S. lycopersicum and S. habrochaites by a combination of de novo genome assembly and BAC cloning. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1987-97. [PMID: 26152571 PMCID: PMC4572051 DOI: 10.1007/s00122-015-2561-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 06/13/2015] [Indexed: 05/07/2023]
Abstract
A chromosomal inversion associated with the tomato Ty - 2 gene for TYLCV resistance is the cause of severe suppression of recombination in a tomato Ty - 2 introgression line. Among tomato and its wild relatives inversions are often observed, which result in suppression of recombination. Such inversions hamper the transfer of important traits from a related species to the crop by introgression breeding. Suppression of recombination was reported for the TYLCV resistance gene, Ty-2, which has been introgressed in cultivated tomato (Solanum lycopersicum) from the wild relative S. habrochaites accession B6013. Ty-2 was mapped to a 300-kb region on the long arm of chromosome 11. The suppression of recombination in the Ty-2 region could be caused by chromosomal rearrangements in S. habrochaites compared with S. lycopersicum. With the aim of visualizing the genome structure of the Ty-2 region, we compared the draft de novo assembly of S. habrochaites accession LYC4 with the sequence of cultivated tomato ('Heinz'). Furthermore, using populations derived from intraspecific crosses of S. habrochaites accessions, the order of markers in the Ty-2 region was studied. Results showed the presence of an inversion of approximately 200 kb in the Ty-2 region when comparing S. lycopersicum and S. habrochaites. By sequencing a BAC clone from the Ty-2 introgression line, one inversion breakpoint was identified. Finally, the obtained results are discussed with respect to introgression breeding and the importance of a priori de novo sequencing of the species involved.
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Affiliation(s)
- Anne-Marie A Wolters
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Myluska Caro
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Shufang Dong
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancunnandajie 12, Beijing, 100081, People's Republic of China
| | - Richard Finkers
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Jianchang Gao
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancunnandajie 12, Beijing, 100081, People's Republic of China
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Xiaoxuan Wang
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancunnandajie 12, Beijing, 100081, People's Republic of China
| | - Yongchen Du
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancunnandajie 12, Beijing, 100081, People's Republic of China
| | - Yuling Bai
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands.
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20
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Koziol U, Radio S, Smircich P, Zarowiecki M, Fernández C, Brehm K. A Novel Terminal-Repeat Retrotransposon in Miniature (TRIM) Is Massively Expressed in Echinococcus multilocularis Stem Cells. Genome Biol Evol 2015; 7:2136-53. [PMID: 26133390 PMCID: PMC4558846 DOI: 10.1093/gbe/evv126] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2015] [Indexed: 12/14/2022] Open
Abstract
Taeniid cestodes (including the human parasites Echinococcus spp. and Taenia solium) have very few mobile genetic elements (MGEs) in their genome, despite lacking a canonical PIWI pathway. The MGEs of these parasites are virtually unexplored, and nothing is known about their expression and silencing. In this work, we report the discovery of a novel family of small nonautonomous long terminal repeat retrotransposons (also known as terminal-repeat retrotransposons in miniature, TRIMs) which we have named ta-TRIM (taeniid TRIM). ta-TRIMs are only the second family of TRIM elements discovered in animals, and are likely the result of convergent reductive evolution in different taxonomic groups. These elements originated at the base of the taeniid tree and have expanded during taeniid diversification, including after the divergence of closely related species such as Echinococcus multilocularis and Echinococcus granulosus. They are massively expressed in larval stages, from a small proportion of full-length copies and from isolated terminal repeats that show transcriptional read-through into downstream regions, generating novel noncoding RNAs and transcriptional fusions to coding genes. In E. multilocularis, ta-TRIMs are specifically expressed in the germinative cells (the somatic stem cells) during asexual reproduction of metacestode larvae. This would provide a developmental mechanism for insertion of ta-TRIMs into cells that will eventually generate the adult germ line. Future studies of active and inactive ta-TRIM elements could give the first clues on MGE silencing mechanisms in cestodes.
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Affiliation(s)
- Uriel Koziol
- Institute of Hygiene and Microbiology, University of Würzburg, Germany Sección Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Santiago Radio
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Pablo Smircich
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Magdalena Zarowiecki
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Cecilia Fernández
- Cátedra de Inmunología, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Klaus Brehm
- Institute of Hygiene and Microbiology, University of Würzburg, Germany
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21
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Hadjirin NF, Lay EM, Paterson GK, Harrison EM, Peacock SJ, Parkhill J, Zadoks RN, Holmes MA. Detection of livestock-associated meticillin-resistant Staphylococcus aureus CC398 in retail pork, United Kingdom, February 2015. Euro Surveill 2015; 20:21156. [PMID: 26111237 PMCID: PMC4841384 DOI: 10.2807/1560-7917.es2015.20.24.21156] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Livestock-associated meticillin-resistant Staphylococcus aureus belonging to clonal complex 398 (LA-MRSA CC398) is an important cause of zoonotic infections in many countries. Here, we describe the isolation of LA-MRSA CC398 from retail meat samples of United Kingdom (UK) farm origin. Our findings indicate that this lineage is probably established in UK pig farms and demonstrate a potential pathway for the transmission of LA-MRSA CC398 from livestock to humans in the UK.
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Affiliation(s)
- N F Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - E M Lay
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - G K Paterson
- School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, United Kingdom
| | - E M Harrison
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - S J Peacock
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- The Wellcome Trust Sanger Institute, Wellcome Trust, Cambridge, United Kingdom
| | - J Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust, Cambridge, United Kingdom
| | - R N Zadoks
- Moredun Research Institute, Penicuik, United Kingdom
- University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Glasgow, United Kingdom
| | - M A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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Identification and characterization of regions of difference between the Salmonella Gallinarum biovar Gallinarum and the Salmonella Gallinarum biovar Pullorum genomes. INFECTION GENETICS AND EVOLUTION 2015; 30:74-81. [DOI: 10.1016/j.meegid.2014.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 12/01/2014] [Accepted: 12/04/2014] [Indexed: 11/18/2022]
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Genomic insights into the evolutionary origin of Xanthomonas axonopodis pv. citri and its ecological relatives. Appl Environ Microbiol 2014; 80:6266-79. [PMID: 25085494 DOI: 10.1128/aem.01654-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xanthomonas axonopodis pv. citri (Xac) is the causal agent of citrus bacterial canker (CBC) and is a serious problem worldwide. Like CBC, several important diseases in other fruits, such as mango, pomegranate, and grape, are also caused by Xanthomonas pathovars that display remarkable specificity toward their hosts. While citrus and mango diseases were documented more than 100 years ago, the pomegranate and grape diseases have been known only since the 1950s and 1970s, respectively. Interestingly, diseases caused by all these pathovars were noted first in India. Our genome-based phylogenetic studies suggest that these diverse pathogens belong to a single species and these pathovars may be just a group of rapidly evolving strains. Furthermore, the recently reported pathovars, such as those infecting grape and pomegranate, form independent clonal lineages, while the citrus and mango pathovars that have been known for a long time form one clonal lineage. Such an understanding of their phylogenomic relationship has further allowed us to understand major and unique variations in the lineages that give rise to these pathovars. Whole-genome sequencing studies including ecological relatives from their putative country of origin has allowed us to understand the evolutionary history of Xac and other pathovars that infect fruits.
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Everitt RG, Didelot X, Batty EM, Miller RR, Knox K, Young BC, Bowden R, Auton A, Votintseva A, Larner-Svensson H, Charlesworth J, Golubchik T, Ip CLC, Godwin H, Fung R, Peto TEA, Walker AS, Crook DW, Wilson DJ. Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus. Nat Commun 2014; 5:3956. [PMID: 24853639 PMCID: PMC4036114 DOI: 10.1038/ncomms4956] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 04/24/2014] [Indexed: 01/28/2023] Open
Abstract
Horizontal gene transfer is an important driver of bacterial evolution, but genetic exchange in the core genome of clonal species, including the major pathogen Staphylococcus aureus, is incompletely understood. Here we reveal widespread homologous recombination in S. aureus at the species level, in contrast to its near-complete absence between closely related strains. We discover a patchwork of hotspots and coldspots at fine scales falling against a backdrop of broad-scale trends in rate variation. Over megabases, homoplasy rates fluctuate 1.9-fold, peaking towards the origin-of-replication. Over kilobases, we find core recombination hotspots of up to 2.5-fold enrichment situated near fault lines in the genome associated with mobile elements. The strongest hotspots include regions flanking conjugative transposon ICE6013, the staphylococcal cassette chromosome (SCC) and genomic island νSaα. Mobile element-driven core genome transfer represents an opportunity for adaptation and challenges our understanding of the recombination landscape in predominantly clonal pathogens, with important implications for genotype–phenotype mapping. Horizontal gene transfer occurs in most bacteria, yet it is unclear whether it happens in clonal species. Here, Everitt et al. show widespread within-species recombination, driven by mobile elements, in the genome of the pathogen Staphylococcus aureus, but no recombination between closely related strains.
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Affiliation(s)
- Richard G Everitt
- 1] Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK [2]
| | - Xavier Didelot
- 1] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK [2]
| | - Elizabeth M Batty
- 1] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK [2] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Ruth R Miller
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Kyle Knox
- Department of Primary Care Health Sciences, University of Oxford, 23-38 Hythe Bridge Street, Oxford OX1 2ET, UK
| | - Bernadette C Young
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Rory Bowden
- 1] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK [2] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Adam Auton
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Antonina Votintseva
- 1] Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK [2] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Hanna Larner-Svensson
- 1] Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK [2] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jane Charlesworth
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Tanya Golubchik
- 1] Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK [2] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Camilla L C Ip
- 1] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK [2] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Heather Godwin
- Oxford University Hospitals National Health Service Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Rowena Fung
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Daniel J Wilson
- 1] Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK [2] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
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25
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Mihasan M, Brandsch R. pAO1 of Arthrobacter nicotinovorans and the spread of catabolic traits by horizontal gene transfer in gram-positive soil bacteria. J Mol Evol 2014; 77:22-30. [PMID: 23884627 DOI: 10.1007/s00239-013-9576-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 165-kb megaplasmid pAO1 of Arthrobacter nicotinovorans carries two large gene clusters, one involved in nicotine catabolism (nic-gene cluster) and one in carbohydrate utilization (ch-gene cluster). Here, we propose that both gene clusters were acquired by A. nicotinovorans by horizontal gene transfer mediated by pAO1. Protein-protein blast search showed that none of the published Arthrobacter genomes contains nic-genes, but Rhodococcus opacus carries on its chromosome a nic-gene cluster highly similar to that of pAO1. Analysis of the nic-genes in the two species suggested a recombination event between their nic-gene clusters. Apparently, there was a gene exchange between pAO1, or a precursor plasmid, and a nic-gene cluster of an as yet unidentified Arthrobacter specie or other soil bacterium, possibly related to Rhodococcus, leading to the transfer by pAO1 of this catabolic trait to A. nicotinovorans. Analysis of the pAO1 ch-gene cluster revealed a virtually identical counterpart on the chromosome of Arthrobacter phenanthrenivorans. Moreover, the sequence analysis of the genes flanking the ch-gene cluster suggested that it was acquired by pAO1 by Xer-related site directed recombination and transferred via the plasmid to A. nicotinovorans. The G+C content, the level of sequence identity, gene co-linearity of nic- and ch-gene clusters as well as the signs of recombination events clearly supports the notion of pAO1 and its precursor plasmids as vehicles in HGT among Gram + soil bacteria.
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Affiliation(s)
- Marius Mihasan
- Laboratory of Biochemistry, Faculty of Biology, University "A. I. Cuza" Iasi, Bulevardul Carol I, Nr. 20 A, 700506, Iasi, Romania,
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Carrión VJ, van der Voort M, Arrebola E, Gutiérrez-Barranquero JA, de Vicente A, Raaijmakers JM, Cazorla FM. Mangotoxin production of Pseudomonas syringae pv. syringae is regulated by MgoA. BMC Microbiol 2014; 14:46. [PMID: 24555804 PMCID: PMC3945005 DOI: 10.1186/1471-2180-14-46] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/12/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The antimetabolite mangotoxin is a key factor in virulence of Pseudomonas syringae pv. syringae strains which cause apical necrosis of mango trees. Previous studies showed that mangotoxin biosynthesis is governed by the mbo operon. Random mutagenesis led to the identification of two other gene clusters that affect mangotoxin biosynthesis. These are the gacS/gacA genes and mgo operon which harbors the four genes mgoBCAD. RESULTS The current study shows that disruption of the nonribosomal peptide synthetase (NRPS) gene mgoA resulted in loss of mangotoxin production and reduced virulence on tomato leaves. Transcriptional analyses by qPCR and promoter reporter fusions revealed that mbo expression is regulated by both gacS/gacA and mgo genes. Also, expression of the mgo operon was shown to be regulated by gacS/gacA. Heterologous expression under the native promoter of the mbo operon resulted in mangotoxin production in non-producing P. syringae strains, but not in other Pseudomonas species. Also introduction of the mbo and mgo operons in nonproducing P. protegens Pf-5 did not confer mangotoxin production but did enhance transcription of the mbo promoter. CONCLUSIONS From the data obtained in this study, we conclude that both mbo and mgo operons are under the control of the gacS/gacA two-component system and that the MgoA product acts as a positive regulator of mangotoxin biosynthesis.
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Affiliation(s)
- Víctor J Carrión
- Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
- Laboratory of Phytopathology, Wageningen University, Wageningen, 6708 PB The Netherlands
- Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Menno van der Voort
- Laboratory of Phytopathology, Wageningen University, Wageningen, 6708 PB The Netherlands
| | - Eva Arrebola
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental La Mayora, Algarrobo-Costa, 29750 Málaga, Spain
| | - José A Gutiérrez-Barranquero
- Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
- BIOMERIT Research Centre, School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - Antonio de Vicente
- Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
| | - Jos M Raaijmakers
- Laboratory of Phytopathology, Wageningen University, Wageningen, 6708 PB The Netherlands
- Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Francisco M Cazorla
- Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
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SMU.746-SMU.747, a putative membrane permease complex, is involved in aciduricity, acidogenesis, and biofilm formation in Streptococcus mutans. J Bacteriol 2013; 196:129-39. [PMID: 24142257 DOI: 10.1128/jb.00960-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dental caries induced by Streptococcus mutans is one of the most prevalent chronic infectious diseases worldwide. The pathogenicity of S. mutans relies on the bacterium's ability to colonize tooth surfaces and survive a strongly acidic environment. We performed an ISS1 transposon mutagenesis to screen for acid-sensitive mutants of S. mutans and identified an SMU.746-SMU.747 gene cluster that is needed for aciduricity. SMU.746 and SMU.747 appear to be organized in an operon and encode a putative membrane-associated permease. SMU.746- and SMU.747-deficient mutants showed a reduced ability to grow in acidified medium. However, the short-term or long-term acid survival capacity and F1F0 ATPase activity remained unaffected in the mutants. Furthermore, deletion of both genes did not change cell membrane permeability and the oxidative and heat stress responses. Growth was severely affected even with slight acidification of the defined medium (pH 6.5). The ability of the mutant strain to acidify the defined medium during growth in the presence of glucose and sucrose was significantly reduced, although the glycolysis rate was only slightly affected. Surprisingly, deletion of the SMU.746-SMU.747 genes triggered increased biofilm formation in low-pH medium. The observed effects were more striking in a chemically defined medium. We speculate that the SMU.746-SMU.747 complex is responsible for amino acid transport, and we discuss its possible role in colonization and survival in the oral environment.
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Jutkina J, Hansen LH, Li L, Heinaru E, Vedler E, Jõesaar M, Heinaru A. Complete nucleotide sequence of the self-transmissible TOL plasmid pD2RT provides new insight into arrangement of toluene catabolic plasmids. Plasmid 2013; 70:393-405. [PMID: 24095800 DOI: 10.1016/j.plasmid.2013.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 08/27/2013] [Accepted: 09/20/2013] [Indexed: 01/21/2023]
Abstract
In the present study we report the complete nucleotide sequence of the toluene catabolic plasmid pD2RT of Pseudomonas migulae strain D2RT isolated from Baltic Sea water. The pD2RT is 129,894 base pairs in size with an average G+C content of 53.75%. A total of 135 open reading frames (ORFs) were predicted to encode proteins, among them genes for catabolism of toluene, plasmid replication, maintenance and conjugative transfer. ORFs encoding proteins with putative functions in stress response, transposition and site-specific recombination were also predicted. Analysis of the organization and nucleotide sequence of pD2RT backbone region revealed high degree of similarity to the draft genome sequence data of the plant-pathogenic pseudomonad Pseudomonas syringae pv. glycinea strain B076, exhibiting relatedness to pPT23A plasmid family. The pD2RT backbone is also closely related to that of pGRT1 of Pseudomonas putida strain DOT-T1E and pBVIE04 of Burkholderia vietnamiensis strain G4, both plasmids are associated with resistance to toluene. The ability of pD2RT to self-transfer by conjugation to P. putida recipient strain PaW340 was experimentally determined. Genetic organization of toluene-degrading (xyl) genes and flanking DNA segments resembles the structure of Tn1721-related class II transposon Tn4656 of TOL plasmid pWW53 of P. putida strain MT53. The complete sequence of the plasmid pD2RT extends the known range of xyl genes carriers, being the first completely sequenced TOL plasmid, which is not related to well-studied IncP plasmid groups. We also verified the functionality of the catabolic route encoded by pD2RT by monitoring the expression of the xylE gene in pD2RT bearing hosts along with bacterial strains containing TOL plasmid of IncP-9 group. The growth kinetics of plasmid-bearing strains was found to be affected by particular TOL plasmid.
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Affiliation(s)
- Jekaterina Jutkina
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23a, 51010 Tartu, Estonia.
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Draft Genome Sequences of Helicobacter pylori Strains HPARG63 and HPARG8G, Cultured from Patients with Chronic Gastritis and Gastric Ulcer Disease. GENOME ANNOUNCEMENTS 2013; 1:1/5/e00700-13. [PMID: 24009126 PMCID: PMC3764421 DOI: 10.1128/genomea.00700-13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Helicobacter pylori colonizes the human gastric mucosa, leading to a spectrum of gastric diseases in susceptible populations. Here we announce the draft genome sequences of strains HPARG8G and HPARG63. The data for both genome sequences provide insights regarding the diversity in gene content and rearrangement of the genomic islands commonly harbored by H. pylori.
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Complete sequence of pSAM7, an IncX4 plasmid carrying a novel blaCTX-M-14b transposition unit isolated from Escherichia coli and Enterobacter cloacae from cattle. Antimicrob Agents Chemother 2013; 57:4590-4. [PMID: 23836183 DOI: 10.1128/aac.01157-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The same plasmid carrying blaCTX-M-14b was identified from an Escherichia coli isolate and an Enterobacter cloacae isolate collected from cattle in the United Kingdom by complete plasmid sequencing. This 35,341-bp plasmid, pSAM7, had an IncX4 backbone that is 99% identical to that of pJIE143 from a human isolate in Australia. PCR screening identified pSAM7-like plasmids in three other E. coli isolates of different multilocus sequence types isolated from cattle on different farms in the United Kingdom.
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Biswas A, Gagnon JN, Brouns SJ, Fineran PC, Brown CM. CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. RNA Biol 2013; 10:817-27. [PMID: 23492433 PMCID: PMC3737339 DOI: 10.4161/rna.24046] [Citation(s) in RCA: 217] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 12/19/2022] Open
Abstract
The bacterial and archaeal CRISPR/Cas adaptive immune system targets specific protospacer nucleotide sequences in invading organisms. This requires base pairing between processed CRISPR RNA and the target protospacer. For type I and II CRISPR/Cas systems, protospacer adjacent motifs (PAM) are essential for target recognition, and for type III, mismatches in the flanking sequences are important in the antiviral response. In this study, we examine the properties of each class of CRISPR. We use this information to provide a tool (CRISPRTarget) that predicts the most likely targets of CRISPR RNAs (http://bioanalysis.otago.ac.nz/CRISPRTarget). This can be used to discover targets in newly sequenced genomic or metagenomic data. To test its utility, we discover features and targets of well-characterized Streptococcus thermophilus and Sulfolobus solfataricus type II and III CRISPR/Cas systems. Finally, in Pectobacterium species, we identify new CRISPR targets and propose a model of temperate phage exposure and subsequent inhibition by the type I CRISPR/Cas systems.
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Affiliation(s)
- Ambarish Biswas
- Department of Biochemistry; University of Otago; Dunedin, New Zealand
| | - Joshua N. Gagnon
- Department of Biochemistry; University of Otago; Dunedin, New Zealand
| | - Stan J.J. Brouns
- Laboratory of Microbiology; Wageningen University; Wageningen, Netherlands
| | - Peter C. Fineran
- Laboratory of Microbiology; Wageningen University; Wageningen, Netherlands
- Department of Microbiology and Immunology; University of Otago; Dunedin, New Zealand
- Genetics Otago; University of Otago; New Zealand
| | - Chris M. Brown
- Department of Biochemistry; University of Otago; Dunedin, New Zealand
- Genetics Otago; University of Otago; New Zealand
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Reen FJ, Barret M, Fargier E, O’Muinneacháin M, O’Gara F. Molecular evolution of LysR-type transcriptional regulation in Pseudomonas aeruginosa. Mol Phylogenet Evol 2013; 66:1041-9. [DOI: 10.1016/j.ympev.2012.12.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 12/13/2012] [Accepted: 12/17/2012] [Indexed: 11/25/2022]
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Carrión VJ, Gutiérrez-Barranquero JA, Arrebola E, Bardaji L, Codina JC, de Vicente A, Cazorla FM, Murillo J. The mangotoxin biosynthetic operon (mbo) is specifically distributed within Pseudomonas syringae genomospecies 1 and was acquired only once during evolution. Appl Environ Microbiol 2013; 79:756-67. [PMID: 23144138 PMCID: PMC3568555 DOI: 10.1128/aem.03007-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 11/07/2012] [Indexed: 11/20/2022] Open
Abstract
Mangotoxin production was first described in Pseudomonas syringae pv. syringae strains. A phenotypic characterization of 94 P. syringae strains was carried out to determine the genetic evolution of the mangotoxin biosynthetic operon (mbo). We designed a PCR primer pair specific for the mbo operon to examine its distribution within the P. syringae complex. These primers amplified a 692-bp DNA fragment from 52 mangotoxin-producing strains and from 7 non-mangotoxin-producing strains that harbor the mbo operon, whereas 35 non-mangotoxin-producing strains did not yield any amplification. This, together with the analysis of draft genomes, allowed the identification of the mbo operon in five pathovars (pathovars aptata, avellanae, japonica, pisi, and syringae), all of which belong to genomospecies 1, suggesting a limited distribution of the mbo genes in the P. syringae complex. Phylogenetic analyses using partial sequences from housekeeping genes differentiated three groups within genomospecies 1. All of the strains containing the mbo operon clustered in groups I and II, whereas those lacking the operon clustered in group III; however, the relative branching order of these three groups is dependent on the genes used to construct the phylogeny. The mbo operon maintains synteny and is inserted in the same genomic location, with high sequence conservation around the insertion point, for all the strains in groups I and II. These data support the idea that the mbo operon was acquired horizontally and only once by the ancestor of groups I and II from genomospecies 1 within the P. syringae complex.
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Affiliation(s)
- Víctor J. Carrión
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - José A. Gutiérrez-Barranquero
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Eva Arrebola
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSMUMA-CSIC), Estación Experimental La Mayora, Algarrobo-Costa, Málaga, Spain
| | - Leire Bardaji
- Laboratorio de Patología Vegetal, ETS Ingenieros Agrónomos, Universidad Pública de Navarra, Pamplona, Spain
| | - Juan C. Codina
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Francisco M. Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Jesús Murillo
- Laboratorio de Patología Vegetal, ETS Ingenieros Agrónomos, Universidad Pública de Navarra, Pamplona, Spain
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Reen FJ, Haynes JM, Mooij MJ, O'Gara F. A non-classical LysR-type transcriptional regulator PA2206 is required for an effective oxidative stress response in Pseudomonas aeruginosa. PLoS One 2013; 8:e54479. [PMID: 23382903 PMCID: PMC3557286 DOI: 10.1371/journal.pone.0054479] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 12/12/2012] [Indexed: 01/13/2023] Open
Abstract
LysR-type transcriptional regulators (LTTRs) are emerging as key circuit components in regulating microbial stress responses and are implicated in modulating oxidative stress in the human opportunistic pathogen Pseudomonas aeruginosa. The oxidative stress response encapsulates several strategies to overcome the deleterious effects of reactive oxygen species. However, many of the regulatory components and associated molecular mechanisms underpinning this key adaptive response remain to be characterised. Comparative analysis of publically available transcriptomic datasets led to the identification of a novel LTTR, PA2206, whose expression was altered in response to a range of host signals in addition to oxidative stress. PA2206 was found to be required for tolerance to H2O2in vitro and lethality in vivo in the Zebrafish embryo model of infection. Transcriptomic analysis in the presence of H2O2 showed that PA2206 altered the expression of 58 genes, including a large repertoire of oxidative stress and iron responsive genes, independent of the master regulator of oxidative stress, OxyR. Contrary to the classic mechanism of LysR regulation, PA2206 did not autoregulate its own expression and did not influence expression of adjacent or divergently transcribed genes. The PA2214-15 operon was identified as a direct target of PA2206 with truncated promoter fragments revealing binding to the 5′-ATTGCCTGGGGTTAT-3′ LysR box adjacent to the predicted −35 region. PA2206 also interacted with the pvdS promoter suggesting a global dimension to the PA2206 regulon, and suggests PA2206 is an important regulatory component of P. aeruginosa adaptation during oxidative stress.
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Affiliation(s)
| | | | | | - Fergal O'Gara
- BIOMERIT Research Centre, Department of Microbiology, University College Cork, Cork, Ireland
- * E-mail:
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35
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Ibrahim M, Shi Y, Qiu H, Li B, Jabeen A, Li L, Liu H, Kube M, Xie G, Wang Y, Sun G. Differential expression of in vivo and in vitro protein profile of outer membrane of Acidovorax avenae subsp. avenae. PLoS One 2012; 7:e49657. [PMID: 23166741 PMCID: PMC3499465 DOI: 10.1371/journal.pone.0049657] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 10/11/2012] [Indexed: 12/24/2022] Open
Abstract
Outer membrane (OM) proteins play a significant role in bacterial pathogenesis. In this work, we examined and compared the expression of the OM proteins of the rice pathogen Acidovorax avenae subsp. avenae strain RS-1, a Gram-negative bacterium, both in an in vitro culture medium and in vivo rice plants. Global proteomic profiling of A. avenae subsp. avenae strain RS-1 comparing in vivo and in vitro conditions revealed the differential expression of proteins affecting the survival and pathogenicity of the rice pathogen in host plants. The shotgun proteomics analysis of OM proteins resulted in the identification of 97 proteins in vitro and 62 proteins in vivo by mass spectrometry. Among these OM proteins, there is a high number of porins, TonB-dependent receptors, lipoproteins of the NodT family, ABC transporters, flagellins, and proteins of unknown function expressed under both conditions. However, the major proteins such as phospholipase and OmpA domain containing proteins were expressed in vitro, while the proteins such as the surface anchored protein F, ATP-dependent Clp protease, OmpA and MotB domain containing proteins were expressed in vivo. This may indicate that these in vivo OM proteins have roles in the pathogenicity of A. avenae subsp. avenae strain RS-1. In addition, the LC-MS/MS identification of OmpA and MotB validated the in silico prediction of the existance of Type VI secretion system core components. To the best of our knowledge, this is the first study to reveal the in vitro and in vivo protein profiles, in combination with LC-MS/MS mass spectra, in silico OM proteome and in silico genome wide analysis, of pathogenicity or plant host required proteins of a plant pathogenic bacterium.
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Affiliation(s)
- Muhammad Ibrahim
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal, Pakistan
| | - Yu Shi
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Hui Qiu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Bin Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- * E-mail:
| | - Amara Jabeen
- Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal, Pakistan
| | - Liping Li
- Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - He Liu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Michael Kube
- Faculty of Agriculture and Horticulture, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Guanlin Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yanli Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guochang Sun
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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36
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Genome sequence of Sphingomonas wittichii DP58, the first reported phenazine-1-carboxylic acid-degrading strain. J Bacteriol 2012; 194:3535-6. [PMID: 22689229 DOI: 10.1128/jb.00330-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sphingomonas wittichii DP58 (CCTCC M 2012027), the first reported phenazine-1-carboxylic acid (PCA)-degrading strain, was isolated from pimiento rhizosphere soils. Here we present a 5.6-Mb assembly of its genome. This sequence would contribute to the elucidation of the molecular mechanism of PCA degradation to improve the antifungal's effectiveness or remove superfluous PCA.
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Juhas M, Stark M, von Mering C, Lumjiaktase P, Crook DW, Valvano MA, Eberl L. High confidence prediction of essential genes in Burkholderia cenocepacia. PLoS One 2012; 7:e40064. [PMID: 22768221 PMCID: PMC3386938 DOI: 10.1371/journal.pone.0040064] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 05/31/2012] [Indexed: 01/01/2023] Open
Abstract
Background Essential genes are absolutely required for the survival of an organism. The identification of essential genes, besides being one of the most fundamental questions in biology, is also of interest for the emerging science of synthetic biology and for the development of novel antimicrobials. New antimicrobial therapies are desperately needed to treat multidrug-resistant pathogens, such as members of the Burkholderia cepacia complex. Methodology/Principal Findings We hypothesize that essential genes may be highly conserved within a group of evolutionary closely related organisms. Using a bioinformatics approach we determined that the core genome of the order Burkholderiales consists of 649 genes. All but two of these identified genes were located on chromosome 1 of Burkholderia cenocepacia. Although many of the 649 core genes of Burkholderiales have been shown to be essential in other bacteria, we were also able to identify a number of novel essential genes present mainly, or exclusively, within this order. The essentiality of some of the core genes, including the known essential genes infB, gyrB, ubiB, and valS, as well as the so far uncharacterized genes BCAL1882, BCAL2769, BCAL3142 and BCAL3369 has been confirmed experimentally in B. cenocepacia. Conclusions/Significance We report on the identification of essential genes using a novel bioinformatics strategy and provide bioinformatics and experimental evidence that the large majority of the identified genes are indeed essential. The essential genes identified here may represent valuable targets for the development of novel antimicrobials and their detailed study may shed new light on the functions required to support life.
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Affiliation(s)
- Mario Juhas
- Department of Microbiology, Institute of Plant Biology, University of Zurich, Zurich, Switzerland
- * E-mail: (MJ); (LE)
| | - Manuel Stark
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | | | - Derrick W. Crook
- Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Miguel A. Valvano
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Leo Eberl
- Department of Microbiology, Institute of Plant Biology, University of Zurich, Zurich, Switzerland
- * E-mail: (MJ); (LE)
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Carrión VJ, Arrebola E, Cazorla FM, Murillo J, de Vicente A. The mbo operon is specific and essential for biosynthesis of mangotoxin in Pseudomonas syringae. PLoS One 2012; 7:e36709. [PMID: 22615797 PMCID: PMC3355146 DOI: 10.1371/journal.pone.0036709] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 04/05/2012] [Indexed: 12/31/2022] Open
Abstract
Mangotoxin is an antimetabolite toxin produced by certain Pseudomonas syringae pv. syringae strains. This toxin is an oligopeptide that inhibits ornithine N-acetyl transferase, a key enzyme in the biosynthesis of ornithine and arginine. Previous studies have reported the involvement of the putative nonribosomal peptide synthetase MgoA in virulence and mangotoxin production. In this study, we analyse a new chromosomal region of P. syringae pv. syringae UMAF0158, which contains six coding sequences arranged as an operon (mbo operon). The mbo operon was detected in only mangotoxin-producing strains, and it was shown to be essential for the biosynthesis of this toxin. Mutants in each of the six ORFs of the mbo operon were partially or completely impaired in the production of the toxin. In addition, Pseudomonas spp. mangotoxin non-producer strains transformed with the mbo operon gained the ability to produce mangotoxin, indicating that this operon contains all the genetic information necessary for mangotoxin biosynthesis. The generation of a single transcript for the mbo operon was confirmed and supported by the allocation of a unique promoter and Rho-independent terminator. The phylogenetic analysis of the P. syringae strains harbouring the mbo operon revealed that these strains clustered together.
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Affiliation(s)
- Víctor J. Carrión
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Eva Arrebola
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Estación Experimental La Mayora, Málaga, Spain
| | - Francisco M. Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Jesús Murillo
- Laboratorio de Patología Vegetal, ETS de Ingenieros Agrónomos, Universidad Pública de Navarra, Pamplona, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
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Genome sequence of Pseudomonas chlororaphis GP72, a root-colonizing biocontrol strain. J Bacteriol 2012; 194:1269-70. [PMID: 22328763 DOI: 10.1128/jb.06713-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas chlororaphis GP72 is a root-colonizing biocontrol strain isolated from a green pepper rhizosphere. It can produce several secondary metabolites to suppress phytopathogens. Here we present a 6.6-Mb assembly of its genome, which is the first genome sequence of the P. chlororaphis group and may provide insights into its antifungal activities.
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Nowell VJ, Kropinski AM, Songer JG, MacInnes JI, Parreira VR, Prescott JF. Genome sequencing and analysis of a type A Clostridium perfringens isolate from a case of bovine clostridial abomasitis. PLoS One 2012; 7:e32271. [PMID: 22412860 PMCID: PMC3297601 DOI: 10.1371/journal.pone.0032271] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2011] [Accepted: 01/24/2012] [Indexed: 01/25/2023] Open
Abstract
Clostridium perfringens is a common inhabitant of the avian and mammalian gastrointestinal tracts and can behave commensally or pathogenically. Some enteric diseases caused by type A C. perfringens, including bovine clostridial abomasitis, remain poorly understood. To investigate the potential basis of virulence in strains causing this disease, we sequenced the genome of a type A C. perfringens isolate (strain F262) from a case of bovine clostridial abomasitis. The ∼3.34 Mbp chromosome of C. perfringens F262 is predicted to contain 3163 protein-coding genes, 76 tRNA genes, and an integrated plasmid sequence, Cfrag (∼18 kb). In addition, sequences of two complete circular plasmids, pF262C (4.8 kb) and pF262D (9.1 kb), and two incomplete plasmid fragments, pF262A (48.5 kb) and pF262B (50.0 kb), were identified. Comparison of the chromosome sequence of C. perfringens F262 to complete C. perfringens chromosomes, plasmids and phages revealed 261 unique genes. No novel toxin genes related to previously described clostridial toxins were identified: 60% of the 261 unique genes were hypothetical proteins. There was a two base pair deletion in virS, a gene reported to encode the main sensor kinase involved in virulence gene activation. Despite this frameshift mutation, C. perfringens F262 expressed perfringolysin O, alpha-toxin and the beta2-toxin, suggesting that another regulation system might contribute to the pathogenicity of this strain. Two complete plasmids, pF262C (4.8 kb) and pF262D (9.1 kb), unique to this strain of C. perfringens were identified.
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Affiliation(s)
- Victoria J Nowell
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
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Hébert L, Moumen B, Pons N, Duquesne F, Breuil MF, Goux D, Batto JM, Laugier C, Renault P, Petry S. Genomic characterization of the Taylorella genus. PLoS One 2012; 7:e29953. [PMID: 22235352 PMCID: PMC3250509 DOI: 10.1371/journal.pone.0029953] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 12/07/2011] [Indexed: 01/21/2023] Open
Abstract
The Taylorella genus comprises two species: Taylorella equigenitalis, which causes contagious equine metritis, and Taylorella asinigenitalis, a closely-related species mainly found in donkeys. We herein report on the first genome sequence of T. asinigenitalis, analyzing and comparing it with the recently-sequenced T. equigenitalis genome. The T. asinigenitalis genome contains a single circular chromosome of 1,638,559 bp with a 38.3% GC content and 1,534 coding sequences (CDS). While 212 CDSs were T. asinigenitalis-specific, 1,322 had orthologs in T. equigenitalis. Two hundred and thirty-four T. equigenitalis CDSs had no orthologs in T. asinigenitalis. Analysis of the basic nutrition metabolism of both Taylorella species showed that malate, glutamate and alpha-ketoglutarate may be their main carbon and energy sources. For both species, we identified four different secretion systems and several proteins potentially involved in binding and colonization of host cells, suggesting a strong potential for interaction with their host. T. equigenitalis seems better-equipped than T. asinigenitalis in terms of virulence since we identified numerous proteins potentially involved in pathogenicity, including hemagluttinin-related proteins, a type IV secretion system, TonB-dependent lactoferrin and transferrin receptors, and YadA and Hep_Hag domains containing proteins. This is the first molecular characterization of Taylorella genus members, and the first molecular identification of factors potentially involved in T. asinigenitalis and T. equigenitalis pathogenicity and host colonization. This study facilitates a genetic understanding of growth phenotypes, animal host preference and pathogenic capacity, paving the way for future functional investigations into this largely unknown genus.
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Affiliation(s)
- Laurent Hébert
- ANSES, Dozulé Laboratory for Equine Diseases, Dozulé, France
- * E-mail: (LH); (SP)
| | - Bouziane Moumen
- Institut National de la Recherche Agronomique, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
| | - Nicolas Pons
- Institut National de la Recherche Agronomique, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
| | - Fabien Duquesne
- ANSES, Dozulé Laboratory for Equine Diseases, Dozulé, France
| | | | - Didier Goux
- Centre de Microscopie Appliquée à la Biologie, Université de Caen Basse-Normandie et IFR146 ICORE, Caen, France
| | - Jean-Michel Batto
- Institut National de la Recherche Agronomique, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
| | - Claire Laugier
- ANSES, Dozulé Laboratory for Equine Diseases, Dozulé, France
| | - Pierre Renault
- Institut National de la Recherche Agronomique, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
| | - Sandrine Petry
- ANSES, Dozulé Laboratory for Equine Diseases, Dozulé, France
- * E-mail: (LH); (SP)
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Abstract
Annotation of prokaryotic sequences can be separated into structural and functional annotation. Structural annotation is dependent on algorithmic interrogation of experimental evidence to discover the physical characteristics of a gene. This is done in an effort to construct accurate gene models, so understanding function or evolution of genes among organisms is not impeded. Functional annotation is dependent on sequence similarity to other known genes or proteins in an effort to assess the function of the gene. Combining structural and functional annotation across genomes in a comparative manner promotes higher levels of accurate annotation as well as an advanced understanding of genome evolution. As the availability of bacterial sequences increases and annotation methods improve, the value of comparative annotation will increase.
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Affiliation(s)
- Nicholas Beckloff
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
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Bi D, Xu Z, Harrison EM, Tai C, Wei Y, He X, Jia S, Deng Z, Rajakumar K, Ou HY. ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. Nucleic Acids Res 2011; 40:D621-6. [PMID: 22009673 PMCID: PMC3244999 DOI: 10.1093/nar/gkr846] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
ICEberg (http://db-mml.sjtu.edu.cn/ICEberg/) is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. We propose that ICEberg will facilitate efficient, multi-disciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community.
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Affiliation(s)
- Dexi Bi
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
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Bardaji L, Pérez-Martínez I, Rodríguez-Moreno L, Rodríguez-Palenzuela P, Sundin GW, Ramos C, Murillo J. Sequence and role in virulence of the three plasmid complement of the model tumor-inducing bacterium Pseudomonas savastanoi pv. savastanoi NCPPB 3335. PLoS One 2011; 6:e25705. [PMID: 22022435 PMCID: PMC3191145 DOI: 10.1371/journal.pone.0025705] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 09/08/2011] [Indexed: 12/18/2022] Open
Abstract
Pseudomonas savastanoi pv. savastanoi NCPPB 3335 is a model for the study of the molecular basis of disease production and tumor formation in woody hosts, and its draft genome sequence has been recently obtained. Here we closed the sequence of the plasmid complement of this strain, composed of three circular molecules of 78,357 nt (pPsv48A), 45,220 nt (pPsv48B), and 42,103 nt (pPsv48C), all belonging to the pPT23A-like family of plasmids widely distributed in the P. syringae complex. A total of 152 coding sequences were predicted in the plasmid complement, of which 38 are hypothetical proteins and seven correspond to putative virulence genes. Plasmid pPsv48A contains an incomplete Type IVB secretion system, the type III secretion system (T3SS) effector gene hopAF1, gene ptz, involved in cytokinin biosynthesis, and three copies of a gene highly conserved in plant-associated proteobacteria, which is preceded by a hrp box motif. A complete Type IVA secretion system, a well conserved origin of transfer (oriT), and a homolog of the T3SS effector gene hopAO1 are present in pPsv48B, while pPsv48C contains a gene with significant homology to isopentenyl-diphosphate delta-isomerase, type 1. Several potential mobile elements were found on the three plasmids, including three types of MITE, a derivative of IS801, and a new transposon effector, ISPsy30. Although the replication regions of these three plasmids are phylogenetically closely related, their structure is diverse, suggesting that the plasmid architecture results from an active exchange of sequences. Artificial inoculations of olive plants with mutants cured of plasmids pPsv48A and pPsv48B showed that pPsv48A is necessary for full virulence and for the development of mature xylem vessels within the knots; we were unable to obtain mutants cured of pPsv48C, which contains five putative toxin-antitoxin genes.
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Affiliation(s)
- Leire Bardaji
- Departamento de Producción Agraria, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Pública de Navarra, Pamplona, Spain
| | - Isabel Pérez-Martínez
- Área de Genética, Facultad de Ciencias, Universidad de Málaga, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Málaga, Spain
| | - Luis Rodríguez-Moreno
- Área de Genética, Facultad de Ciencias, Universidad de Málaga, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Málaga, Spain
| | - Pablo Rodríguez-Palenzuela
- Centro de Biotecnología y Genómica de Plantas, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
| | - George W. Sundin
- Department of Plant Pathology and Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
| | - Cayo Ramos
- Área de Genética, Facultad de Ciencias, Universidad de Málaga, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Málaga, Spain
| | - Jesús Murillo
- Departamento de Producción Agraria, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Pública de Navarra, Pamplona, Spain
- * E-mail:
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Miniature transposable sequences are frequently mobilized in the bacterial plant pathogen Pseudomonas syringae pv. phaseolicola. PLoS One 2011; 6:e25773. [PMID: 22016774 PMCID: PMC3189936 DOI: 10.1371/journal.pone.0025773] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 09/09/2011] [Indexed: 01/01/2023] Open
Abstract
Mobile genetic elements are widespread in Pseudomonas syringae, and often associate with virulence genes. Genome reannotation of the model bean pathogen P. syringae pv. phaseolicola 1448A identified seventeen types of insertion sequences and two miniature inverted-repeat transposable elements (MITEs) with a biased distribution, representing 2.8% of the chromosome, 25.8% of the 132-kb virulence plasmid and 2.7% of the 52-kb plasmid. Employing an entrapment vector containing sacB, we estimated that transposition frequency oscillated between 2.6×10−5 and 1.1×10−6, depending on the clone, although it was stable for each clone after consecutive transfers in culture media. Transposition frequency was similar for bacteria grown in rich or minimal media, and from cells recovered from compatible and incompatible plant hosts, indicating that growth conditions do not influence transposition in strain 1448A. Most of the entrapped insertions contained a full-length IS801 element, with the remaining insertions corresponding to sequences smaller than any transposable element identified in strain 1448A, and collectively identified as miniature sequences. From these, fragments of 229, 360 and 679-nt of the right end of IS801 ended in a consensus tetranucleotide and likely resulted from one-ended transposition of IS801. An average 0.7% of the insertions analyzed consisted of IS801 carrying a fragment of variable size from gene PSPPH_0008/PSPPH_0017, showing that IS801 can mobilize DNA in vivo. Retrospective analysis of complete plasmids and genomes of P. syringae suggests, however, that most fragments of IS801 are likely the result of reorganizations rather than one-ended transpositions, and that this element might preferentially contribute to genome flexibility by generating homologous regions of recombination. A further miniature sequence previously found to affect host range specificity and virulence, designated MITEPsy1 (100-nt), represented an average 2.4% of the total number of insertions entrapped in sacB, demonstrating for the first time the mobilization of a MITE in bacteria.
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Laing R, Hunt M, Protasio AV, Saunders G, Mungall K, Laing S, Jackson F, Quail M, Beech R, Berriman M, Gilleard JS. Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans. PLoS One 2011; 6:e23216. [PMID: 21858033 PMCID: PMC3156134 DOI: 10.1371/journal.pone.0023216] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 07/12/2011] [Indexed: 11/30/2022] Open
Abstract
The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes.
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Affiliation(s)
- Roz Laing
- Welcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Faculty of Veterinary Medicine, University of Glasgow, Glasgow, Strathclyde, United Kingdom
| | - Martin Hunt
- Welcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Anna V. Protasio
- Welcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gary Saunders
- Faculty of Veterinary Medicine, University of Glasgow, Glasgow, Strathclyde, United Kingdom
| | - Karen Mungall
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Steven Laing
- Faculty of Veterinary Medicine, University of Glasgow, Glasgow, Strathclyde, United Kingdom
| | - Frank Jackson
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, United Kingdom
| | - Michael Quail
- Welcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Robin Beech
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, Quebec, Canada
| | - Matthew Berriman
- Welcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - John S. Gilleard
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
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Variation in conservation of the cluster for biosynthesis of the phytotoxin phaseolotoxin in Pseudomonas syringae suggests at least two events of horizontal acquisition. Res Microbiol 2010; 162:253-61. [PMID: 21187143 DOI: 10.1016/j.resmic.2010.10.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2010] [Accepted: 10/14/2010] [Indexed: 11/21/2022]
Abstract
Certain strains of Pseudomonas syringae pathovars phaseolicola and actinidiae and P. syringae pv. syringae strain CFBP3388 produce the chlorosis-inducing phytotoxin phaseolotoxin, which inhibits biosynthesis of arginine and polyamines. The 25 kb Pht cluster, responsible for phaseolotoxin biosynthesis, is included in a putative pathogenicity island that is nearly identical in selected strains of the pathovars phaseolicola and actinidiae, suggesting that it has been recently acquired by horizontal transfer. The history of pathogenicity islands is pivotal for our understanding of the evolution of virulence in plant pathogenic bacteria; nevertheless, our knowledge of the origins, biology and genetics of this island is currently rather limited. The aim of this work was to explore the conservation of phaseolotoxin biosynthesis genes in a broader collection of isolates and in strain CFBP3388, in order to better understand its evolution and gene dynamics. PCR, hybridization and sequence analysis showed that the island is highly conserved among a diversity of strains of pathovars phaseolicola and actinidiae, suggesting that it was acquired only once by each pathovar. Strain CFBP3388 contained DNA homologous to the Pht cluster, and an insertional mutant in the regulatory gene phtL did not synthesize the toxin. A 6.5 kb fragment from strain CFBP3388 was syntenic to the Pht cluster, but showed nucleotide identity of only 85.3%. This contrasts with an identity higher than 99.8% among clusters of pathovars phaseolicola and actinidiae, in spite of the fact that pv. syringae is phylogenetically closer to pv. phaseolicola. In addition, strain CFBP3388 lacked the four integrases that are putatively responsible for the mobility of the pathogenicity island. These results indicate that genes for the biosynthesis of phaseolotoxin have a complex evolutionary history and were acquired by pathovars of P. syringae at least twice during evolution.
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48
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Duquesne F, Hébert L, Sévin C, Breuil MF, Tapprest J, Laugier C, Petry S. Analysis of plasmid diversity in 96 Rhodococcus equi strains isolated in Normandy (France) and sequencing of the 87-kb type I virulence plasmid. FEMS Microbiol Lett 2010; 311:76-81. [DOI: 10.1111/j.1574-6968.2010.02070.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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49
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Shao Y, He X, Harrison EM, Tai C, Ou HY, Rajakumar K, Deng Z. mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes. Nucleic Acids Res 2010; 38:W194-200. [PMID: 20435682 PMCID: PMC2896100 DOI: 10.1093/nar/gkq326] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
mGenomeSubtractor performs an mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes for investigation of strain variable accessory regions. With parallel computing architecture, mGenomeSubtractor is able to run rapid BLAST searches of the segmented reference genome against multiple subject genomes at the DNA or amino acid level within a minute. In addition to comparison of protein coding sequences, the highly flexible sliding window-based genome fragmentation approach offered can be used to identify short unique sequences within or between genes. mGenomeSubtractor provides powerful schematic outputs for exploration of identified core and accessory regions, including searches against databases of mobile genetic elements, virulence factors or bacterial essential genes, examination of G+C content and binucleotide distribution bias, and integrated primer design tools. mGenomeSubtractor also allows for the ready definition of species-specific gene pools based on available genomes. Pan-genomic arrays can be easily developed using the efficient oligonucleotide design tool. This simple high-throughput in silico ‘subtractive hybridization’ analytical tool will support the rapidly escalating number of comparative bacterial genomics studies aimed at defining genomic biomarkers of evolutionary lineage, phenotype, pathotype, environmental adaptation and/or disease-association of diverse bacterial species. mGenomeSubtractor is freely available to all users without any login requirement at: http://bioinfo-mml.sjtu.edu.cn/mGS/.
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Affiliation(s)
- Yucheng Shao
- Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, P. R. China
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50
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Losada L, Ronning CM, DeShazer D, Woods D, Fedorova N, Kim HS, Shabalina SA, Pearson TR, Brinkac L, Tan P, Nandi T, Crabtree J, Badger J, Beckstrom-Sternberg S, Saqib M, Schutzer SE, Keim P, Nierman WC. Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements. Genome Biol Evol 2010; 2:102-16. [PMID: 20333227 PMCID: PMC2839346 DOI: 10.1093/gbe/evq003] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2010] [Indexed: 11/25/2022] Open
Abstract
Burkholderia mallei (Bm), the causative agent of the
predominately equine disease glanders, is a genetically uniform species that is
very closely related to the much more diverse species Burkholderia
pseudomallei (Bp), an opportunistic human pathogen and the primary
cause of melioidosis. To gain insight into the relative lack of genetic
diversity within Bm, we performed whole-genome comparative analysis of seven Bm
strains and contrasted these with eight Bp strains. The Bm core genome (shared
by all seven strains) is smaller in size than that of Bp, but the inverse is
true for the variable gene sets that are distributed across strains.
Interestingly, the biological roles of the Bm variable gene sets are much more
homogeneous than those of Bp. The Bm variable genes are found mostly in
contiguous regions flanked by insertion sequence (IS) elements, which appear to
mediate excision and subsequent elimination of groups of genes that are under
reduced selection in the mammalian host. The analysis suggests that the Bm
genome continues to evolve through random IS-mediated recombination events, and
differences in gene content may contribute to differences in virulence observed
among Bm strains. The results are consistent with the view that Bm recently
evolved from a single strain of Bp upon introduction into an animal host
followed by expansion of IS elements, prophage elimination, and genome
rearrangements and reduction mediated by homologous recombination across IS
elements.
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