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An SQ, Potnis N, Dow M, Vorhölter FJ, He YQ, Becker A, Teper D, Li Y, Wang N, Bleris L, Tang JL. Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas. FEMS Microbiol Rev 2020; 44:1-32. [PMID: 31578554 PMCID: PMC8042644 DOI: 10.1093/femsre/fuz024] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/29/2019] [Indexed: 01/15/2023] Open
Abstract
Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause a variety of diseases in economically important crops worldwide. Genomic and functional studies of these phytopathogens have provided significant understanding of microbial-host interactions, bacterial virulence and host adaptation mechanisms including microbial ecology and epidemiology. In addition, several strains of Xanthomonas are important as producers of the extracellular polysaccharide, xanthan, used in the food and pharmaceutical industries. This polymer has also been implicated in several phases of the bacterial disease cycle. In this review, we summarise the current knowledge on the infection strategies and regulatory networks controlling virulence and adaptation mechanisms from Xanthomonas species and discuss the novel opportunities that this body of work has provided for disease control and plant health.
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Affiliation(s)
- Shi-Qi An
- National Biofilms Innovation Centre (NBIC), Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Rouse Life Science Building, Auburn University, Auburn AL36849, USA
| | - Max Dow
- School of Microbiology, Food Science & Technology Building, University College Cork, Cork T12 K8AF, Ireland
| | | | - Yong-Qiang He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
| | - Anke Becker
- Loewe Center for Synthetic Microbiology and Department of Biology, Philipps-Universität Marburg, Hans-Meerwein-Straße 6, Marburg 35032, Germany
| | - Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Yi Li
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Leonidas Bleris
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA.,Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX75080, USA
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
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Schulte F, Leßmeier L, Voss J, Ortseifen V, Vorhölter FJ, Niehaus K. Regulatory associations between the metabolism of sulfur-containing amino acids and xanthan biosynthesis in Xanthomonas campestris pv. campestris B100. FEMS Microbiol Lett 2019; 366:5289864. [PMID: 30649298 DOI: 10.1093/femsle/fnz005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/14/2019] [Indexed: 02/06/2023] Open
Abstract
The γ-proteobacterium Xanthomonas campestris pv. campestris (Xcc) B100 synthesizes the exopolysaccharide xanthan, a commercially relevant thickening agent produced commonly by industrial scale fermentation. This work was inspired by the observation that methionine is an inhibitor of xanthan formation in growth experiments. Therefore, the global effects of methionine supplementation were characterized through cultivation experiments, genome-wide microarray hybridizations and qRT-PCR. Specific pull down of DNA-binding proteins by using the intergenic regions upstream of xanA, gumB and gumD led to the identification of six transcriptional regulators, among them the LysR-family transcriptional regulator CysB. An insertion mutant of this gene was analyzed by growth experiments, microarray experiments and qRT-PCR. Based on our experimental data, we developed a model that describes the methionine-dependent co-regulation of xanthan and sulfur-containing compounds in Xanthomonas. These data substantially contribute to better understand the impact of methionine as a compound in xanthan production media used in industrial fermentations.
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Affiliation(s)
- Fabian Schulte
- Department of Proteome and Metabolome Research - Bio27, Faculty of Biology, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Lennart Leßmeier
- Chair of Genetics of Prokaryotes, Faculty of Biology, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Julia Voss
- Department of Proteome and Metabolome Research - Bio27, Faculty of Biology, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Vera Ortseifen
- Department of Proteome and Metabolome Research - Bio27, Faculty of Biology, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Frank-Jörg Vorhölter
- Department of Proteome and Metabolome Research - Bio27, Faculty of Biology, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Karsten Niehaus
- Department of Proteome and Metabolome Research - Bio27, Faculty of Biology, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
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Alkhateeb RS, Vorhölter FJ, Steffens T, Rückert C, Ortseifen V, Hublik G, Niehaus K, Pühler A. Comparative transcription profiling of two fermentation cultures of Xanthomonas campestris pv. campestris B100 sampled in the growth and in the stationary phase. Appl Microbiol Biotechnol 2018; 102:6613-6625. [DOI: 10.1007/s00253-018-9106-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 10/14/2022]
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Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ. Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. Microbiology (Reading) 2017; 163:1117-1144. [DOI: 10.1099/mic.0.000473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sarah Schatschneider
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jessica Schneider
- Bioinformatics Resource Facility, Centrum für Biotechnologie, Universität Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Karsten Niehaus
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Frank-Jörg Vorhölter
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: MVZ Dr. Eberhard & Partner Dortmund, Dortmund, Germany
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Steffens T, Duda K, Lindner B, Vorhölter FJ, Bednarz H, Niehaus K, Holst O. The lipopolysaccharide of the crop pathogen Xanthomonas translucens pv. translucens: chemical characterization and determination of signaling events in plant cells. Glycobiology 2017; 27:264-274. [PMID: 28177490 DOI: 10.1093/glycob/cww093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 08/29/2016] [Accepted: 08/29/2016] [Indexed: 12/23/2022] Open
Abstract
Xanthomonas translucens pv. translucens (Xtt) is a Gram-negative pathogen of crops from the plant family Poaceae. The lipopolysaccharide (LPS) of Xtt was isolated and chemically characterized. The analyses revealed the presence of rhamnose, xylose, mannose, glucose, galacturonic acid, phosphates, 3-deoxy-D-manno-oct-2-ulopyranosonic acid (Kdo) and fatty acids (10:0, 11:0, 11:0(3-OH) i/a, 11:0(3-OH), 12:0(3-OH) i/a, 12:0(3-OH), 12:0, 13:0(3-OH) i, 13:0(3-OH) a, 13:0(3-OH), 14:0(3-OH) i/a, 14:0(3-OH) and 16:0). The rough type of LPS (lipooligosaccharides; LOS) was isolated and its composition determined utilizing mass spectrometry. The structure of core-lipid A backbone was revealed by nuclear magnetic resonance (NMR) spectroscopy performed on O-deacylated LOS sample, and was shown to be: α-D-Manp-(1→3)-α-D-Manp-(1→3)-β-D-Glcp-(1→4)-α-D-Manp-(1→5)-α-Kdo-(2→6)-β-D-GlcpN-(1→6)-α-D-GlcpN. 4-α-Man and Kdo were further substituted via phosphodiester groups by two galactopyranuronic acids. Xtt LPS elicited a stress response in Nicotiana tabacum suspension cell cultures, namely a transient calcium signal and the generation of H2O2 was observed. Pharmacological studies indicated the involvement of plasma membrane calcium channels, kinases and phospholipase C as key factors in Xtt LPS induced pathogen signaling.
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Affiliation(s)
- Tim Steffens
- Abteilung 27, Proteom- und Metabolomforschung, Fakultät für Biologie & Centre for Biotechnology (CeBiTec) Universität Bielefeld, 33615 Bielefeld, Germany
| | - Katarzyna Duda
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Airway Research Center North (ARCN), German Center for Lung Research, 23845 Borstel, Germany
| | - Buko Lindner
- Division of Immunochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, 23845 Borstel, Germany
| | - Frank-Jörg Vorhölter
- Abteilung 27, Proteom- und Metabolomforschung, Fakultät für Biologie & Centre for Biotechnology (CeBiTec) Universität Bielefeld, 33615 Bielefeld, Germany
| | - Hanna Bednarz
- Abteilung 27, Proteom- und Metabolomforschung, Fakultät für Biologie & Centre for Biotechnology (CeBiTec) Universität Bielefeld, 33615 Bielefeld, Germany
| | - Karsten Niehaus
- Abteilung 27, Proteom- und Metabolomforschung, Fakultät für Biologie & Centre for Biotechnology (CeBiTec) Universität Bielefeld, 33615 Bielefeld, Germany
| | - Otto Holst
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Airway Research Center North (ARCN), German Center for Lung Research, 23845 Borstel, Germany
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Hersemann L, Wibberg D, Blom J, Goesmann A, Widmer F, Vorhölter FJ, Kölliker R. Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis. BMC Genomics 2017; 18:35. [PMID: 28056815 PMCID: PMC5217246 DOI: 10.1186/s12864-016-3422-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 12/14/2016] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Xanthomonas translucens pathovars differ in their individual host ranges among Poaceae. As the causal agent of bacterial wilt in Italian ryegrass (Lolium multiflorum Lam.), X. translucens pv. graminis (Xtg) is one of the most important bacterial pathogens in temperate grassland regions. The genomes of six Xtg strains from Switzerland, Norway, and New Zealand were sequenced in order to gain insight into conserved genomic traits from organisms covering a wide geographical range. Subsequent comparative analysis with previously published genome data of seven non-graminis X. translucens strains including the pathovars arrhenatheri, poae, phlei, cerealis, undulosa, and translucens was conducted to identify candidate genes linked to the host adaptation of Xtg to Italian ryegrass. RESULTS Phylogenetic analysis revealed a tight clustering of Xtg strains, which were found to share a large core genome. Conserved genomic traits included a non-canonical type III secretion system (T3SS) and a type IV pilus (T4P), which both revealed distinct primary structures of the pilins when compared to the non-graminis X. translucens strains. Xtg-specific traits that had no homologues in the other X. translucens strains were further found to comprise several hypothetical proteins, a TonB-dependent receptor, transporters, and effector proteins as well as toxin-antitoxin systems and DNA methyltransferases. While a nearly complete flagellar gene cluster was identified in one of the sequenced Xtg strains, phenotypic analysis pointed to swimming-deficiency as a common trait of the pathovar graminis. CONCLUSION Our study suggests that host adaptation of X. translucens pv. graminis may be conferred by a combination of pathovar-specific effector proteins, regulatory mechanisms, and adapted nutrient acquisition. Sequence deviations of pathogen-associated molecular patterns (PAMPs), as observed for the pilins of the T4P and T3SS, are moreover likely to impede perception by the plant defense machinery and thus facilitate successful host colonization of Italian ryegrass.
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Affiliation(s)
| | - Daniel Wibberg
- Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Franco Widmer
- Molecular Ecology, Agroscope, 8046, Zurich, Switzerland
| | - Frank-Jörg Vorhölter
- Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany
- MVZ Dr. Eberhard & Partner Dortmund, 44137, Dortmund, Germany
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Leßmeier L, Alkhateeb RS, Schulte F, Steffens T, Loka TP, Pühler A, Niehaus K, Vorhölter FJ. Applying DNA affinity chromatography to specifically screen for sucrose-related DNA-binding transcriptional regulators of Xanthomonas campestris. J Biotechnol 2016; 232:89-98. [DOI: 10.1016/j.jbiotec.2016.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/22/2016] [Accepted: 04/05/2016] [Indexed: 11/28/2022]
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Steffens T, Vorhölter FJ, Giampà M, Hublik G, Pühler A, Niehaus K. The influence of a modified lipopolysaccharide O-antigen on the biosynthesis of xanthan in Xanthomonas campestris pv. campestris B100. BMC Microbiol 2016; 16:93. [PMID: 27215401 PMCID: PMC4878081 DOI: 10.1186/s12866-016-0710-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/13/2016] [Indexed: 12/03/2022] Open
Abstract
Background The exopolysaccharide xanthan is a natural product which is extensively used in industry. It is a thickening agent in many fields, from oil recovery to the food sector. Xanthan is produced by the Gram negative bacterium Xanthomonas campestris pv. campestris (Xcc). We analyzed the lipopolysaccharide (LPS) of three mutant strains of the Xcc wild type B100 to distinguish if the xanthan production can be increased when LPS biosynthesis is affected. Results The Xcc B100 O-antigen (OA) is composed of a linear main chain of rhamnose residues with N-acetylfucosamine (FucNAc) side branches at every second rhamnose. It is the major LPS constituent. The O-antigen was missing completely in the mutant strain H21012 (deficient in wxcB), since neither rhamnose nor FucNAc could be detected as part of the LPS by MALDI-TOF-MS, and only a slight amount of rhamnose and no FucNAc was found by GC analysis. The LPS of two other mutants was analyzed, Xcc H28110 (deficient in wxcK) and H20110 (wxcN). In both of them no FucNAc could be detected in the LPS fraction, while the rhamnose moieties were more abundant than in wild type LPS. The measurements were carried out by GC and confirmed by MALDI-TOF-MS analyses that indicated an altered OA in which the branches are missing, while the rhamnan main chain seemed longer than in the wild type. Quantification of xanthan confirmed our hypothesis that a missing OA can lead to an increased production of the extracellular polysaccharide. About 6.3 g xanthan per g biomass were produced by the Xcc mutant H21012 (wxcB), as compared to the wild type production of approximately 5 g xanthan per g biomass. In the two mutant strains with modified OA however, Xcc H28110 (wxcK) and Xcc H20110 (wxcN), the xanthan production of 5.5 g and 5.3 g, respectively, was not significantly increased. Conclusions Mutations affecting LPS biosynthesis can be beneficial for the production of the extracellular polysaccharide xanthan. However, only complete inhibition of the OA resulted in increased xanthan production. The inhibition of the FucNAc side branches did not lead to increased production, but provoked a novel LPS phenotype. The data suggests an elongation of the linear rhamnan main chain of the LPS OA in both the Xcc H28110 (wxcK) and Xcc H20110 (wxcN) mutant strains. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0710-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tim Steffens
- Proteom- und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615, Bielefeld, Germany.,Genomforschung industrieller Mikroorganismen, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Frank-Jörg Vorhölter
- Proteom- und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615, Bielefeld, Germany.,Genomforschung industrieller Mikroorganismen, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615, Bielefeld, Germany.,Present address: MVZ Dr. Eberhard & Partner, Brauhausstr. 4, 44137, Dortmund, Germany
| | - Marco Giampà
- Proteom- und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Gerd Hublik
- Jungbunzlauer Austria AG, Pernhofen 1, 2064, Wulzeshofen, Austria
| | - Alfred Pühler
- Genomforschung industrieller Mikroorganismen, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Karsten Niehaus
- Proteom- und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615, Bielefeld, Germany.
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Alkhateeb RS, Vorhölter FJ, Rückert C, Mentz A, Wibberg D, Hublik G, Niehaus K, Pühler A. Genome wide transcription start sites analysis of Xanthomonas campestris pv. campestris B100 with insights into the gum gene cluster directing the biosynthesis of the exopolysaccharide xanthan. J Biotechnol 2016; 225:18-28. [PMID: 26975844 DOI: 10.1016/j.jbiotec.2016.03.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 01/18/2023]
Abstract
Xanthomonas campestris pv. campestris (Xcc) is the major producer of the exopolysaccharide xanthan, the commercially most important natural polysaccharide of microbial origin. The current work provides deeper insights into the yet uncharacterized transcriptomic features of the xanthan producing strain Xcc-B100. Towards this goal, RNA sequencing of a library based on the selective enrichment of the 5' ends of native transcripts was performed. This approach resulted in the genome wide identification of 3067 transcription start sites (TSSs) that were further classified based on their genomic positions. Among them, 1545 mapped upstream of an actively transcribed CDS and 1363 were classified as novel TSSs representing antisense, internal, and TSSs belonging to previously unidentified genomic features. Analyzing the transcriptional strength of primary and antisense TSSs revealed that in some instances antisense transcription seemed to be initiated at a higher level than its sense counterpart. Mapping the exact positions of TSSs aided in the identification of promoter consensus motifs, ribosomal binding sites, and enhanced the genome annotation of 159 in silico predicted translational start (TLS) sites. The global view on length distribution of the 5' untranslated regions (5'-UTRs) deduced from the data pointed to the occurrence of leaderless transcripts and transcripts with unusually long 5'-UTRs, in addition to identifying seven putative riboswitch elements for Xcc-B100. Concerning the biosynthesis of xanthan, we focused on the transcriptional organization of the gum gene cluster. Under the conditions tested, we present evidence for a complex transcription pattern of the gum genes with multiple TSSs and an obvious considerable role of antisense transcription. The gene gumB, encoding an outer membrane xanthan exporter, is presented here as an example for genes that possessed a strong antisense TSS.
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Affiliation(s)
- Rabeaa S Alkhateeb
- Abteilung für Proteom und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Frank-Jörg Vorhölter
- Abteilung für Proteom und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany; Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Christian Rückert
- Technologie Platform Genomics, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Almut Mentz
- Technologie Platform Genomics, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Daniel Wibberg
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Gerd Hublik
- Jungbunzlauer Austria AG, Pernhofen 1, 2064 Wulzeshofen, Austria
| | - Karsten Niehaus
- Abteilung für Proteom und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Alfred Pühler
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
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Wibberg D, Alkhateeb RS, Winkler A, Albersmeier A, Schatschneider S, Albaum S, Niehaus K, Hublik G, Pühler A, Vorhölter FJ. Draft genome of the xanthan producer Xanthomonas campestris NRRL B-1459 (ATCC 13951). J Biotechnol 2015; 204:45-6. [DOI: 10.1016/j.jbiotec.2015.03.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 03/25/2015] [Indexed: 10/23/2022]
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Schatschneider S, Huber C, Neuweger H, Watt TF, Pühler A, Eisenreich W, Wittmann C, Niehaus K, Vorhölter FJ. Metabolic flux pattern of glucose utilization by Xanthomonas campestris pv. campestris: prevalent role of the Entner–Doudoroff pathway and minor fluxes through the pentose phosphate pathway and glycolysis. ACTA ACUST UNITED AC 2014; 10:2663-76. [DOI: 10.1039/c4mb00198b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Complex metabolic flux pattern ofX. campestris.
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Affiliation(s)
- Sarah Schatschneider
- Abteilung für Proteom- und Metabolomforschung
- Fakultät für Biologie
- Universität Bielefeld
- Bielefeld, Germany
| | - Claudia Huber
- Lehrstuhl für Biochemie
- Center of Isotopologue Profiling
- Technische Universität München
- Garching, Germany
| | - Heiko Neuweger
- Computational Genomics
- Centrum für Biotechnology (CeBiTec)
- Universität Bielefeld
- Germany
| | - Tony Francis Watt
- Abteilung für Proteom- und Metabolomforschung
- Fakultät für Biologie
- Universität Bielefeld
- Bielefeld, Germany
| | - Alfred Pühler
- Institut für Genomforschung und Systembiologie
- Centrum für Biotechnology (CeBiTec)
- Universität Bielefeld
- Bielefeld, Germany
| | - Wolfgang Eisenreich
- Lehrstuhl für Biochemie
- Center of Isotopologue Profiling
- Technische Universität München
- Garching, Germany
| | - Christoph Wittmann
- Institut für Systembiotechnologie
- Universität des Saarlandes
- Saarbrücken, Germany
| | - Karsten Niehaus
- Abteilung für Proteom- und Metabolomforschung
- Fakultät für Biologie
- Universität Bielefeld
- Bielefeld, Germany
| | - Frank-Jörg Vorhölter
- Abteilung für Proteom- und Metabolomforschung
- Fakultät für Biologie
- Universität Bielefeld
- Bielefeld, Germany
- Institut für Genomforschung und Systembiologie
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Wichmann F, Vorhölter FJ, Hersemann L, Widmer F, Blom J, Niehaus K, Reinhard S, Conradin C, Kölliker R. The noncanonical type III secretion system of Xanthomonas translucens pv. graminis is essential for forage grass infection. Mol Plant Pathol 2013; 14:576-88. [PMID: 23578314 PMCID: PMC6638798 DOI: 10.1111/mpp.12030] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Xanthomonas translucens pv. graminis (Xtg) is a gammaproteobacterium that causes bacterial wilt on a wide range of forage grasses. To gain insight into the host-pathogen interaction and to identify the virulence factors of Xtg, we compared a draft genome sequence of one isolate (Xtg29) with other Xanthomonas spp. with sequenced genomes. The type III secretion system (T3SS) encoding a protein transport system for type III effector (T3E) proteins represents one of the most important virulence factors of Xanthomonas spp. In contrast with other Xanthomonas spp. assigned to clade 1 on the basis of phylogenetic analyses, we identified an hrp (hypersensitive response and pathogenicity) gene cluster encoding T3SS components and a representative set of 35 genes encoding putative T3Es in the genome of Xtg29. The T3SS was shown to be divergent from the hrp gene clusters of other sequenced Xanthomonas spp. Xtg mutants deficient in T3SS regulating and structural genes were constructed to clarify the role of the T3SS in forage grass colonization. Italian ryegrass infection with these mutants led to significantly reduced symptoms (P < 0.05) relative to plants infected with the wild-type strain. This showed that the T3SS is required for symptom evocation. In planta multiplication of the T3SS mutants was not impaired significantly relative to the wild-type, indicating that the T3SS is not required for survival until 14 days post-infection. This study represents the first major step to understanding the bacterial colonization strategies deployed by Xtg and may assist in the identification of resistance (R) genes in forage grasses.
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Affiliation(s)
- Fabienne Wichmann
- Agroscope Reckenholz-Tänikon Research Station ART, Reckenholzstrasse 191, 8046 Zurich, Switzerland
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Vorhölter FJ. RNA-Seq facilitates a new perspective on signal transduction and gene regulation in important plant pathogens. Mol Microbiol 2013; 88:1041-6. [PMID: 23659691 DOI: 10.1111/mmi.12259] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2013] [Indexed: 02/04/2023]
Abstract
RNA-Seq is opening new doors for the functional understanding of microorganisms. Advances in RNA-Seq technology are allowing investigators to focus their studies on specific functional questions. An interesting example is presented by An et al. (2013) in this issue of Molecular Microbiology. New genes were identified for proteins and ncRNAs when the authors concentrated on the role of the rpf genes, which code for key components of a signal transduction hub in the plant pathogen Xanthomonas campestris pv. campestris. Although rpf gene products were already known to be involved in controlling transcription of many genes, including those encoding several important virulence factors, novel and unexpected properties of this signal transduction system emerged from the RNA-Seq analysis. In addition to identifying new target genes influenced by the rpf genes, the study found that the regulons of RpfC and RpfG, the sensor and response regulator of the master two-component regulatory system, only partially overlapped, indicating that the Rpf signalling system is even more complex than previously appreciated.
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Vorhölter FJ, Wiggerich HG, Scheidle H, Sidhu VK, Mrozek K, Küster H, Pühler A, Niehaus K. Involvement of bacterial TonB-dependent signaling in the generation of an oligogalacturonide damage-associated molecular pattern from plant cell walls exposed to Xanthomonas campestris pv. campestris pectate lyases. BMC Microbiol 2012; 12:239. [PMID: 23082751 PMCID: PMC3551730 DOI: 10.1186/1471-2180-12-239] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 09/25/2012] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Efficient perception of attacking pathogens is essential for plants. Plant defense is evoked by molecules termed elicitors. Endogenous elicitors or damage-associated molecular patterns (DAMPs) originate from plant materials upon injury or pathogen activity. While there are comparably well-characterized examples for DAMPs, often oligogalacturonides (OGAs), generated by the activity of fungal pathogens, endogenous elicitors evoked by bacterial pathogens have been rarely described. In particular, the signal perception and transduction processes involved in DAMP generation are poorly characterized. RESULTS A mutant strain of the phytopathogenic bacterium Xanthomonas campestris pv. campestris deficient in exbD2, which encodes a component of its unusual elaborate TonB system, had impaired pectate lyase activity and caused no visible symptoms for defense on the non-host plant pepper (Capsicum annuum). A co-incubation of X. campestris pv. campestris with isolated cell wall material from C. annuum led to the release of compounds which induced an oxidative burst in cell suspension cultures of the non-host plant. Lipopolysaccharides and proteins were ruled out as elicitors by polymyxin B and heat treatment, respectively. After hydrolysis with trifluoroacetic acid and subsequent HPAE chromatography, the elicitor preparation contained galacturonic acid, the monosaccharide constituent of pectate. OGAs were isolated from this crude elicitor preparation by HPAEC and tested for their biological activity. While small OGAs were unable to induce an oxidative burst, the elicitor activity in cell suspension cultures of the non-host plants tobacco and pepper increased with the degree of polymerization (DP). Maximal elicitor activity was observed for DPs exceeding 8. In contrast to the X. campestris pv. campestris wild type B100, the exbD2 mutant was unable to generate elicitor activity from plant cell wall material or from pectin. CONCLUSIONS To our knowledge, this is the second report on a DAMP generated by bacterial features. The generation of the OGA elicitor is embedded in a complex exchange of signals within the framework of the plant-microbe interaction of C. annuum and X. campestris pv. campestris. The bacterial TonB-system is essential for the substrate-induced generation of extracellular pectate lyase activity. This is the first demonstration that a TonB-system is involved in bacterial trans-envelope signaling in the context of a pathogenic interaction with a plant.
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Affiliation(s)
- Frank-Jörg Vorhölter
- Department of Proteome and Metabolome Research, Faculty of Biology, Universität Bielefeld, Universitätsstr 25, Bielefeld 33615, Germany.
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15
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Schneiker-Bekel S, Wibberg D, Bekel T, Blom J, Linke B, Neuweger H, Stiens M, Vorhölter FJ, Weidner S, Goesmann A, Pühler A, Schlüter A. The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome. J Biotechnol 2011; 155:20-33. [DOI: 10.1016/j.jbiotec.2010.12.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 11/25/2010] [Accepted: 12/08/2010] [Indexed: 10/18/2022]
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Pothier JF, Vorhölter FJ, Blom J, Goesmann A, Pühler A, Smits THM, Duffy B. The ubiquitous plasmid pXap41 in the invasive phytopathogen Xanthomonas arboricola pv. pruni: complete sequence and comparative genomic analysis. FEMS Microbiol Lett 2011; 323:52-60. [PMID: 21732961 DOI: 10.1111/j.1574-6968.2011.02352.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The complete DNA sequence of the 41 102-bp plasmid pXap41 from the invasive plant pathogen Xanthomonas arboricola pv. pruni CFBP 5530 was determined and its 44 coding regions were annotated. Comparative analysis with 15 Xanthomonas plasmids and 19 complete genomes revealed that nearly one-fourth of this plasmid has high sequence identity to plasmid pXAC64 and an 8.8-kb chromosomal region of Xanthomonas axonopodis pv. citri strain 306 carrying genes that encode type III effectors and helper proteins. The presence of pXap41 in all X. arboricola pv. pruni genotypes was confirmed for eight strains by plasmid profiling and for 35 X. arboricola pv. pruni isolates with a new plasmid multiplex PCR assay. This plasmid was not detected in any other X. arboricola pathovars (n=12), indicating the potential for the application of the pXap41 PCR method as a pathovar-level detection and identification tool.
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Affiliation(s)
- Joël F Pothier
- Agroscope Changins-Wädenswil ACW, Plant Protection Division, Wädenswil, SwitzerlandCeBiTec, Bielefeld University, Bielefeld, Germany
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Zhou L, Vorhölter FJ, He YQ, Jiang BL, Tang JL, Xu Y, Pühler A, He YW. Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris. BMC Genomics 2011; 12:359. [PMID: 21745409 PMCID: PMC3142249 DOI: 10.1186/1471-2164-12-359] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 07/12/2011] [Indexed: 11/24/2022] Open
Abstract
Background One of the major tasks of the post-genomic era is "reading" genomic sequences in order to extract all the biological information contained in them. Although a wide variety of techniques is used to solve the gene finding problem and a number of prokaryotic gene-finding software are available, gene recognition in bacteria is far from being always straightforward. Results This study reported a thorough search for new CDS in the two published Xcc genomes. In the first, putative CDSs encoded in the two genomes were re-predicted using three gene finders, resulting in the identification of 2850 putative new CDSs. In the second, similarity searching was conducted and 278 CDSs were found to have homologs in other bacterial species. In the third, oligonucleotide microarray and RT-PCR analysis identified 147 CDSs with detectable mRNA transcripts. Finally, in-frame deletion and subsequent phenotype analysis of confirmed that Xcc_CDS002 encoding a novel SIR2-like domain protein is involved in virulence and Xcc_CDS1553 encoding a ArsR family transcription factor is involved in arsenate resistance. Conclusions Despite sophisticated approaches available for genome annotation, many cellular transcripts have remained unidentified so far in Xcc genomes. Through a combined strategy involving bioinformatic, postgenomic and genetic approaches, a reliable list of 306 new CDSs was identified and a more thorough understanding of some cellular processes was gained.
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Affiliation(s)
- Lian Zhou
- National Center for Molecular Characterization of GMOs and State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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18
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Keck M, Gisch N, Moll H, Vorhölter FJ, Gerth K, Kahmann U, Lissel M, Lindner B, Niehaus K, Holst O. Unusual outer membrane lipid composition of the gram-negative, lipopolysaccharide-lacking myxobacterium Sorangium cellulosum So ce56. J Biol Chem 2011; 286:12850-9. [PMID: 21321121 PMCID: PMC3075632 DOI: 10.1074/jbc.m110.194209] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 02/11/2011] [Indexed: 11/06/2022] Open
Abstract
The gram-negative myxobacterium Sorangium cellulosum So ce56 bears the largest bacterial genome published so far, coding for nearly 10,000 genes. Careful analysis of this genome data revealed that part of the genes coding for the very well conserved biosynthesis of lipopolysaccharides (LPS) are missing in this microbe. Biochemical analysis gave no evidence for the presence of LPS in the membranes of So ce56. By analyzing the lipid composition of its outer membrane sphingolipids were identified as the major lipid class, together with ornithine-containing lipids (OL) and ether lipids. A detailed analysis of these lipids resulted in the identification of more than 50 structural variants within these three classes, which possessed several interesting properties regarding to LPS replacement, mediators in myxobacterial differentiation, as well as potential bioactive properties. The sphingolipids with the basic structure C9-methyl-C(20)-sphingosine possessed as an unusual trait C9-methylation, which is common to fungi but highly uncommon to bacteria. Such sphingolipids have not been found in bacteria before, and they may have a function in myxobacterial development. The OL, also identified in myxobacteria for the first time, contained acyloxyacyl groups, which are also characteristic for LPS and might replace those in certain functions. Finally, the ether lipids may serve as biomarkers in myxobacterial development.
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Affiliation(s)
- Matthias Keck
- From the Department of Proteome and Metabolome Research, Faculty of Biology and
| | | | | | | | - Klaus Gerth
- the Research Group Microbial Drugs, Helmholtz Center for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Uwe Kahmann
- ZUD in the IIT GmbH, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Manfred Lissel
- From the Department of Proteome and Metabolome Research, Faculty of Biology and
| | | | - Karsten Niehaus
- From the Department of Proteome and Metabolome Research, Faculty of Biology and
| | - Otto Holst
- Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 4a/c, 23845 Borstel, Germany, and
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Ryan RP, Vorhölter FJ, Potnis N, Jones JB, Van Sluys MA, Bogdanove AJ, Dow JM. Pathogenomics of Xanthomonas: understanding bacterium-plant interactions. Nat Rev Microbiol 2011; 9:344-55. [PMID: 21478901 DOI: 10.1038/nrmicro2558] [Citation(s) in RCA: 303] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant hosts, including many economically important crops. Pathogenic species and pathovars within species show a high degree of host plant specificity and many exhibit tissue specificity, invading either the vascular system or the mesophyll tissue of the host. In this Review, we discuss the insights that functional and comparative genomic studies are providing into the adaptation of this group of bacteria to exploit the extraordinary diversity of plant hosts and different host tissues.
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Affiliation(s)
- Robert P Ryan
- BIOMERIT Research Centre, Department of Microbiology, BioSciences Institute, University College Cork, Ireland
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20
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Blom J, Albaum SP, Doppmeier D, Pühler A, Vorhölter FJ, Zakrzewski M, Goesmann A. EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 2009; 10:154. [PMID: 19457249 PMCID: PMC2696450 DOI: 10.1186/1471-2105-10-154] [Citation(s) in RCA: 320] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 05/20/2009] [Indexed: 11/16/2022] Open
Abstract
Background The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. Results To support these studies EDGAR – "Efficient Database framework for comparative Genome Analyses using BLAST score Ratios" – was developed. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. To demonstrate a specific application case, we analyzed ten genomes of the bacterial genus Xanthomonas, for which phylogenetic studies were awkward due to divergent taxonomic systems. The resultant phylogeny EDGAR provided was consistent with outcomes from traditional approaches performed recently and moreover, it was possible to root each strain with unprecedented accuracy. Conclusion EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes. The software supports a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes. Visualization features, like synteny plots or Venn diagrams, are offered to the scientific community through a web-based and therefore platform independent user interface , where the precomputed data sets can be browsed.
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Affiliation(s)
- Jochen Blom
- Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
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21
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Gross R, Guzman CA, Sebaihia M, dos Santos VAPM, Pieper DH, Koebnik R, Lechner M, Bartels D, Buhrmester J, Choudhuri JV, Ebensen T, Gaigalat L, Herrmann S, Khachane AN, Larisch C, Link S, Linke B, Meyer F, Mormann S, Nakunst D, Rückert C, Schneiker-Bekel S, Schulze K, Vorhölter FJ, Yevsa T, Engle JT, Goldman WE, Pühler A, Göbel UB, Goesmann A, Blöcker H, Kaiser O, Martinez-Arias R. The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae. BMC Genomics 2008; 9:449. [PMID: 18826580 PMCID: PMC2572626 DOI: 10.1186/1471-2164-9-449] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2008] [Accepted: 09/30/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus Bordetella. Phylogenetically, it connects the pathogenic Bordetellae and environmental bacteria of the genera Achromobacter and Alcaligenes, which are opportunistic pathogens. B. petrii strains have been isolated from very different environmental niches, including river sediment, polluted soil, marine sponges and a grass root. Recently, clinical isolates associated with bone degenerative disease or cystic fibrosis have also been described. RESULTS In this manuscript we present the results of the analysis of the completely annotated genome sequence of the B. petrii strain DSMZ12804. B. petrii has a mosaic genome of 5,287,950 bp harboring numerous mobile genetic elements, including seven large genomic islands. Four of them are highly related to the clc element of Pseudomonas knackmussii B13, which encodes genes involved in the degradation of aromatics. Though being an environmental isolate, the sequenced B. petrii strain also encodes proteins related to virulence factors of the pathogenic Bordetellae, including the filamentous hemagglutinin, which is a major colonization factor of B. pertussis, and the master virulence regulator BvgAS. However, it lacks all known toxins of the pathogenic Bordetellae. CONCLUSION The genomic analysis suggests that B. petrii represents an evolutionary link between free-living environmental bacteria and the host-restricted obligate pathogenic Bordetellae. Its remarkable metabolic versatility may enable B. petrii to thrive in very different ecological niches.
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Affiliation(s)
- Roy Gross
- Chair of Microbiology, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.
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22
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Sidhu VK, Vorhölter FJ, Niehaus K, Watt SA. Analysis of outer membrane vesicle associated proteins isolated from the plant pathogenic bacterium Xanthomonas campestris pv. campestris. BMC Microbiol 2008; 8:87. [PMID: 18518965 PMCID: PMC2438364 DOI: 10.1186/1471-2180-8-87] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Accepted: 06/02/2008] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Outer membrane vesicles (OMVs) are released from the outer membrane of many Gram-negative bacteria. These extracellular compartments are known to transport compounds involved in cell-cell signalling as well as virulence associated proteins, e.g. the cytolysine from enterotoxic E. coli. RESULTS We have demonstrated that Xanthomonas campestris pv. campestris (Xcc) releases OMVs into the culture supernatant during growth. A proteome study identified 31 different proteins that associate with the OMV fraction of which half are virulence-associated. A comparison with the most abundant outer membrane (OM) proteins revealed that some proteins are enriched in the OMV fraction. This may be connected to differences in the LPS composition between the OMVs and the OM. Furthermore, a comparison of the OMV proteomes from two different culture media indicated that the culture conditions have an impact on the protein composition. Interestingly, the proteins that are common to both culture conditions are mainly involved in virulence. CONCLUSION Outer membrane vesicles released from the OM of Xcc contain membrane- and virulence-associated proteins. Future experiments will prove whether these structures can serve as "vehicles" for the transport of virulence factors into the host membrane.
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Affiliation(s)
- Vishaldeep K Sidhu
- Dep.7 Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, POB 10 01 31, D-33501 Bielefeld, Germany.
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Serrania J, Vorhölter FJ, Niehaus K, Pühler A, Becker A. Identification of Xanthomonas campestris pv. campestris galactose utilization genes from transcriptome data. J Biotechnol 2008; 135:309-17. [PMID: 18538881 DOI: 10.1016/j.jbiotec.2008.04.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Revised: 04/10/2008] [Accepted: 04/16/2008] [Indexed: 11/15/2022]
Abstract
A 70 mer oligonucleotide microarray was constructed to analyze genome-wide expression profiles of Xanthomonas campestris pv. campestris B100, a plant-pathogenic bacterium that is industrially employed to produce the exopolysaccharide xanthan gum which has many applications as a stabilizing, thickening, gelling, and emulsifying agent in food, pharmaceutical, and cosmetic industries. As an application example, global changes of gene expression were monitored during growth of X. campestris pv. campestris B100 on two different carbon sources. Exponential growing bacterial cultures were incubated either for 1h or permanently in minimal medium supplemented with 1% galactose in comparison to growth in minimal medium supplemented with 1% glucose. Six genes were identified that were significantly increased in gene expression under both growth conditions. These genes were located in three distinguished chromosomal regions in operon-like gene clusters. Genes from these clusters encode secreted glycosidases, which were predicted to be specific for galactose-containing carbohydrates, as well as transport proteins probably located in the outer and inner cell membrane. Finally genes from one cluster code for cytoplasmic enzymes of a metabolic pathway specific for the breakdown of galactose to intermediates of glycolysis.
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Affiliation(s)
- Javier Serrania
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
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24
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Vorhölter FJ, Schneiker S, Goesmann A, Krause L, Bekel T, Kaiser O, Linke B, Patschkowski T, Rückert C, Schmid J, Sidhu VK, Sieber V, Tauch A, Watt SA, Weisshaar B, Becker A, Niehaus K, Pühler A. The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis. J Biotechnol 2008; 134:33-45. [PMID: 18304669 DOI: 10.1016/j.jbiotec.2007.12.013] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Revised: 12/04/2007] [Accepted: 12/24/2007] [Indexed: 10/22/2022]
Abstract
The complete genome sequence of the Xanthomonas campestris pv. campestris strain B100 was established. It consisted of a chromosome of 5,079,003bp, with 4471 protein-coding genes and 62 RNA genes. Comparative genomics showed that the genes required for the synthesis of xanthan and xanthan precursors were highly conserved among three sequenced X. campestris pv. campestris genomes, but differed noticeably when compared to the remaining four Xanthomonas genomes available. For the xanthan biosynthesis genes gumB and gumK earlier translational starts were proposed, while gumI and gumL turned out to be unique with no homologues beyond the Xanthomonas genomes sequenced. From the genomic data the biosynthesis pathways for the production of the exopolysaccharide xanthan could be elucidated. The first step of this process is the uptake of sugars serving as carbon and energy sources wherefore genes for 15 carbohydrate import systems could be identified. Metabolic pathways playing a role for xanthan biosynthesis could be deduced from the annotated genome. These reconstructed pathways concerned the storage and metabolization of the imported sugars. The recognized sugar utilization pathways included the Entner-Doudoroff and the pentose phosphate pathway as well as the Embden-Meyerhof pathway (glycolysis). The reconstruction indicated that the nucleotide sugar precursors for xanthan can be converted from intermediates of the pentose phosphate pathway, some of which are also intermediates of glycolysis or the Entner-Doudoroff pathway. Xanthan biosynthesis requires in particular the nucleotide sugars UDP-glucose, UDP-glucuronate, and GDP-mannose, from which xanthan repeat units are built under the control of the gum genes. The updated genome annotation data allowed reconsidering and refining the mechanistic model for xanthan biosynthesis.
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Affiliation(s)
- Frank-Jörg Vorhölter
- Universität Bielefeld, Biologie VI (Genetik), Universitätsstr. 25, D-33615 Bielefeld, Germany
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25
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Schneiker S, Perlova O, Kaiser O, Gerth K, Alici A, Altmeyer MO, Bartels D, Bekel T, Beyer S, Bode E, Bode HB, Bolten CJ, Choudhuri JV, Doss S, Elnakady YA, Frank B, Gaigalat L, Goesmann A, Groeger C, Gross F, Jelsbak L, Jelsbak L, Kalinowski J, Kegler C, Knauber T, Konietzny S, Kopp M, Krause L, Krug D, Linke B, Mahmud T, Martinez-Arias R, McHardy AC, Merai M, Meyer F, Mormann S, Muñoz-Dorado J, Perez J, Pradella S, Rachid S, Raddatz G, Rosenau F, Rückert C, Sasse F, Scharfe M, Schuster SC, Suen G, Treuner-Lange A, Velicer GJ, Vorhölter FJ, Weissman KJ, Welch RD, Wenzel SC, Whitworth DE, Wilhelm S, Wittmann C, Blöcker H, Pühler A, Müller R. Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat Biotechnol 2007; 25:1281-9. [PMID: 17965706 DOI: 10.1038/nbt1354] [Citation(s) in RCA: 267] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 10/04/2007] [Indexed: 12/11/2022]
Abstract
The genus Sorangium synthesizes approximately half of the secondary metabolites isolated from myxobacteria, including the anti-cancer metabolite epothilone. We report the complete genome sequence of the model Sorangium strain S. cellulosum So ce56, which produces several natural products and has morphological and physiological properties typical of the genus. The circular genome, comprising 13,033,779 base pairs, is the largest bacterial genome sequenced to date. No global synteny with the genome of Myxococcus xanthus is apparent, revealing an unanticipated level of divergence between these myxobacteria. A large percentage of the genome is devoted to regulation, particularly post-translational phosphorylation, which probably supports the strain's complex, social lifestyle. This regulatory network includes the highest number of eukaryotic protein kinase-like kinases discovered in any organism. Seventeen secondary metabolite loci are encoded in the genome, as well as many enzymes with potential utility in industry.
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Affiliation(s)
- Susanne Schneiker
- Department of Genetics, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
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26
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Krause A, Ramakumar A, Bartels D, Battistoni F, Bekel T, Boch J, Böhm M, Friedrich F, Hurek T, Krause L, Linke B, McHardy AC, Sarkar A, Schneiker S, Syed AA, Thauer R, Vorhölter FJ, Weidner S, Pühler A, Reinhold-Hurek B, Kaiser O, Goesmann A. Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72. Nat Biotechnol 2006; 24:1385-91. [PMID: 17057704 DOI: 10.1038/nbt1243] [Citation(s) in RCA: 148] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2006] [Accepted: 08/04/2006] [Indexed: 11/09/2022]
Abstract
Azoarcus sp. strain BH72, a mutualistic endophyte of rice and other grasses, is of agrobiotechnological interest because it supplies biologically fixed nitrogen to its host and colonizes plants in remarkably high numbers without eliciting disease symptoms. The complete genome sequence is 4,376,040-bp long and contains 3,992 predicted protein-coding sequences. Genome comparison with the Azoarcus-related soil bacterium strain EbN1 revealed a surprisingly low degree of synteny. Coding sequences involved in the synthesis of surface components potentially important for plant-microbe interactions were more closely related to those of plant-associated bacteria. Strain BH72 appears to be 'disarmed' compared to plant pathogens, having only a few enzymes that degrade plant cell walls; it lacks type III and IV secretion systems, related toxins and an N-acyl homoserine lactones-based communication system. The genome contains remarkably few mobile elements, indicating a low rate of recent gene transfer that is presumably due to adaptation to a stable, low-stress microenvironment.
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Affiliation(s)
- Andrea Krause
- Laboratory of General Microbiology, University of Bremen, PO Box 330440, D-28334 Bremen, Germany
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27
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Schneiker S, dos Santos VAPM, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Pühler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorhölter FJ, Weidner S, Kaiser O, Golyshin PN. Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol 2006; 24:997-1004. [PMID: 16878126 PMCID: PMC7416663 DOI: 10.1038/nbt1232] [Citation(s) in RCA: 272] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Accepted: 06/19/2006] [Indexed: 11/25/2022]
Abstract
Alcanivorax borkumensis is a cosmopolitan marine bacterium that uses oil hydrocarbons as its exclusive source of carbon and energy. Although barely detectable in unpolluted environments, A. borkumensis becomes the dominant microbe in oil-polluted waters. A. borkumensis SK2 has a streamlined genome with a paucity of mobile genetic elements and energy generation–related genes, but with a plethora of genes accounting for its wide hydrocarbon substrate range and efficient oil-degradation capabilities. The genome further specifies systems for scavenging of nutrients, particularly organic and inorganic nitrogen and oligo-elements, biofilm formation at the oil-water interface, biosurfactant production and niche-specific stress responses. The unique combination of these features provides A. borkumensis SK2 with a competitive edge in oil-polluted environments. This genome sequence provides the basis for the future design of strategies to mitigate the ecological damage caused by oil spills.
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Affiliation(s)
- Susanne Schneiker
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, D-33594 Germany
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | | | - Daniela Bartels
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Thomas Bekel
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Martina Brecht
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, D-33594 Germany
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Jens Buhrmester
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Tatyana N Chernikova
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, D-38106 Germany
| | - Renata Denaro
- Istituto per l'Ambiente Marino Costiero (CNR), Messina, I-98122 Italy
| | - Manuel Ferrer
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Institute of Catalysis, Campus UAM, E-28049 Madrid, Spain (M.F.), Bioinformatics & Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, New York, 10598 USA
- Division Biogeochemistry, Research Centre Rossendorf, Dresden, D-01314 Germany
| | - Christoph Gertler
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, D-38106 Germany
| | - Alexander Goesmann
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Olga V Golyshina
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, D-38106 Germany
| | - Filip Kaminski
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
| | - Amit N Khachane
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
| | - Siegmund Lang
- Institute of Biochemistry and Biotechnology, Technical University of Braunschweig, Braunschweig, D-38106 Germany
| | - Burkhard Linke
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Alice C McHardy
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
- Institute of Catalysis, Campus UAM, E-28049 Madrid, Spain (M.F.), Bioinformatics & Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, New York, 10598 USA
- Division Biogeochemistry, Research Centre Rossendorf, Dresden, D-01314 Germany
| | - Folker Meyer
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Taras Nechitaylo
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, D-38106 Germany
| | - Alfred Pühler
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, D-33594 Germany
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Daniela Regenhardt
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Institute of Catalysis, Campus UAM, E-28049 Madrid, Spain (M.F.), Bioinformatics & Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, New York, 10598 USA
- Division Biogeochemistry, Research Centre Rossendorf, Dresden, D-01314 Germany
| | - Oliver Rupp
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Julia S Sabirova
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, D-38106 Germany
| | - Werner Selbitschka
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, D-33594 Germany
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Michail M Yakimov
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Istituto per l'Ambiente Marino Costiero (CNR), Messina, I-98122 Italy
| | - Kenneth N Timmis
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, D-38106 Germany
| | - Frank-Jörg Vorhölter
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, D-33594 Germany
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Stefan Weidner
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, D-33594 Germany
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Olaf Kaiser
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, D-33594 Germany
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Peter N Golyshin
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
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28
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Thieme F, Koebnik R, Bekel T, Berger C, Boch J, Büttner D, Caldana C, Gaigalat L, Goesmann A, Kay S, Kirchner O, Lanz C, Linke B, McHardy AC, Meyer F, Mittenhuber G, Nies DH, Niesbach-Klösgen U, Patschkowski T, Rückert C, Rupp O, Schneiker S, Schuster SC, Vorhölter FJ, Weber E, Pühler A, Bonas U, Bartels D, Kaiser O. Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J Bacteriol 2005; 187:7254-66. [PMID: 16237009 PMCID: PMC1272972 DOI: 10.1128/jb.187.21.7254-7266.2005] [Citation(s) in RCA: 292] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria is the causative agent of bacterial spot disease in pepper and tomato plants, which leads to economically important yield losses. This pathosystem has become a well-established model for studying bacterial infection strategies. Here, we present the whole-genome sequence of the pepper-pathogenic Xanthomonas campestris pv. vesicatoria strain 85-10, which comprises a 5.17-Mb circular chromosome and four plasmids. The genome has a high G+C content (64.75%) and signatures of extensive genome plasticity. Whole-genome comparisons revealed a gene order similar to both Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris and a structure completely different from Xanthomonas oryzae pv. oryzae. A total of 548 coding sequences (12.2%) are unique to X. campestris pv. vesicatoria. In addition to a type III secretion system, which is essential for pathogenicity, the genome of strain 85-10 encodes all other types of protein secretion systems described so far in gram-negative bacteria. Remarkably, one of the putative type IV secretion systems encoded on the largest plasmid is similar to the Icm/Dot systems of the human pathogens Legionella pneumophila and Coxiella burnetii. Comparisons with other completely sequenced plant pathogens predicted six novel type III effector proteins and several other virulence factors, including adhesins, cell wall-degrading enzymes, and extracellular polysaccharides.
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Affiliation(s)
- Frank Thieme
- Martin-Luther-Universität, Institut für Genetik, Weinbergweg 10, D-06120 Halle (Saale), Germany
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29
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Vorhölter FJ, Niehaus K, Pühler A. Lipopolysaccharide biosynthesis in Xanthomonas campestris pv. campestris: a cluster of 15 genes is involved in the biosynthesis of the LPS O-antigen and the LPS core. Mol Genet Genomics 2001; 266:79-95. [PMID: 11589581 DOI: 10.1007/s004380100521] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
As a result of mutational and DNA sequence analysis, a wxc gene cluster involved in the synthesis of the surface lipopolysaccharide (LPS) was identified in Xanthomonas campestris pv. campestris. This gene cluster comprises 15 genes. It was located on a cloned 35-kb fragment of chromosomal DNA, close, but not directly adjacent, to previously characterized genes for LPS biosynthesis. The G + C content of all but one of the wxc genes was atypically low for X. campestris pv. campestris, while the G + C distribution was uniform throughout the cluster. An SDS-PAGE analysis of mutant strains defective in various wxc genes confirmed that genes from this cluster were involved in LPS biosynthesis. The mutant phenotypes allowed the differentiation of three regions within the wxc cluster. Genes from wxc region 1 are necessary for the biosynthesis of the water-soluble LPS O-antigen. Analysis of DNA and deduced amino acid sequences led to the identification of two glycosyltransferases, two components of an ABC transport system, and a possible kinase among the seven putative proteins encoded by genes constituting wxc region 1. The two genes in wxc region 2 were similar to gmd and rmd, which direct the synthesis of the sugar nucleotide GDP-D-rhamnose. Mutations affecting wxc region 2 demonstrated its involvement in the formation of the LPS core. Genes from wxc region 3 showed similarities to genes that code for enzymes that modify nucleotide sugars, and to components of sugar translocation systems that have so far been rarely described in bacteria.
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Affiliation(s)
- F J Vorhölter
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Germany
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30
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Finan TM, Weidner S, Wong K, Buhrmester J, Chain P, Vorhölter FJ, Hernandez-Lucas I, Becker A, Cowie A, Gouzy J, Golding B, Pühler A. The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti. Proc Natl Acad Sci U S A 2001; 98:9889-94. [PMID: 11481431 PMCID: PMC55548 DOI: 10.1073/pnas.161294698] [Citation(s) in RCA: 249] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Analysis of the 1,683,333-nt sequence of the pSymB megaplasmid from the symbiotic N(2)-fixing bacterium Sinorhizobium meliloti revealed that the replicon has a high gene density with a total of 1,570 protein-coding regions, with few insertion elements and regions duplicated elsewhere in the genome. The only copies of an essential arg-tRNA gene and the minCDE genes are located on pSymB. Almost 20% of the pSymB sequence carries genes encoding solute uptake systems, most of which were of the ATP-binding cassette family. Many previously unsuspected genes involved in polysaccharide biosynthesis were identified and these, together with the two known distinct exopolysaccharide synthesis gene clusters, show that 14% of the pSymB sequence is dedicated to polysaccharide synthesis. Other recognizable gene clusters include many involved in catabolic activities such as protocatechuate utilization and phosphonate degradation. The functions of these genes are consistent with the notion that pSymB plays a major role in the saprophytic competence of the bacteria in the soil environment.
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Affiliation(s)
- T M Finan
- Department of Biology, McMaster University, Hamilton, ON, Canada.
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