Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid

Wibberg D, Blom J, Jaenicke S, Kollin F, Rupp O, Scharf B, Schneiker-Bekel S, Szczepanowski R, Goesmann A, Setubal JC, Schmitt R, et al. (2011)
Journal of Biotechnology 155(1): 50-62.

Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
Agrobacterium sp. H13-3, formerly known as Rhizobium lupini H13-3, is a soil bacterium that was isolated from the rhizosphere of Lupinus luteus. The isolate has been established as a model system for studying novel features of flagellum structure, motility and chemotaxis within the family Rhizobiaceae. The complete genome sequence of Agrobacterium sp. H13-3 has been established and the genome structure and phylogenetic assignment of the organism was analysed. For de novo sequencing of the Agrobacterium sp. H13-3 genome, a combined strategy comprising 454-pyrosequencing on the Genome Sequencer FLX platform and PCR-based amplicon sequencing for gap closure was applied. The finished genome consists of three replicons and comprises 5,573,770 bases. Based on phylogenetic analyses, the isolate could be assigned to the genus Agrobacterium biovar I and represents a genomic species G1 strain within this biovariety. The highly conserved circular chromosome (2.82Mb) of Agrobacterium sp. H13-3 mainly encodes housekeeping functions characteristic for an aerobic, heterotrophic bacterium. Agrobacterium sp. H13-3 is a motile bacterium driven by the rotation of several complex flagella. Its behaviour towards external stimuli is regulated by a large chemotaxis regulon and a total of 17 chemoreceptors. Comparable to the genome of Agrobacterium tumefaciens C58, Agrobacterium sp. H13-3 possesses a linear chromosome (2.15Mb) that is related to its reference replicon and features chromosomal and plasmid-like properties. The accessory plasmid pAspH13-3a (0.6Mb) is only distantly related to the plasmid pAtC58 of A. tumefaciens C58 and shows a mosaic structure. A tumor-inducing Ti-plasmid is missing in the sequenced strain H13-3 indicating that it is a non-virulent isolate. Copyright 2011 Elsevier B.V. All rights reserved.
Erscheinungsjahr
Zeitschriftentitel
Journal of Biotechnology
Band
155
Zeitschriftennummer
1
Seite
50-62
ISSN
PUB-ID

Zitieren

Wibberg D, Blom J, Jaenicke S, et al. Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. Journal of Biotechnology. 2011;155(1):50-62.
Wibberg, D., Blom, J., Jaenicke, S., Kollin, F., Rupp, O., Scharf, B., Schneiker-Bekel, S., et al. (2011). Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. Journal of Biotechnology, 155(1), 50-62. doi:10.1016/j.jbiotec.2011.01.010
Wibberg, D., Blom, J., Jaenicke, S., Kollin, F., Rupp, O., Scharf, B., Schneiker-Bekel, S., Szczepanowski, R., Goesmann, A., Setubal, J. C., et al. (2011). Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. Journal of Biotechnology 155, 50-62.
Wibberg, D., et al., 2011. Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. Journal of Biotechnology, 155(1), p 50-62.
D. Wibberg, et al., “Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid”, Journal of Biotechnology, vol. 155, 2011, pp. 50-62.
Wibberg, D., Blom, J., Jaenicke, S., Kollin, F., Rupp, O., Scharf, B., Schneiker-Bekel, S., Szczepanowski, R., Goesmann, A., Setubal, J.C., Schmitt, R., Pühler, A., Schlüter, A.: Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. Journal of Biotechnology. 155, 50-62 (2011).
Wibberg, Daniel, Blom, Jochen, Jaenicke, Sebastian, Kollin, Florian, Rupp, Oliver, Scharf, Birgit, Schneiker-Bekel, Susanne, Szczepanowski, Rafael, Goesmann, Alexander, Setubal, Joao Carlos, Schmitt, Rüdiger, Pühler, Alfred, and Schlüter, Andreas. “Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid”. Journal of Biotechnology 155.1 (2011): 50-62.

61 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae.
Stępkowski T, Banasiewicz J, Granada CE, Andrews M, Passaglia LMP., Genes (Basel) 9(3), 2018
PMID: 29538303
Complete Genome Sequencing of Acinetobacter baumannii Strain K50 Discloses the Large Conjugative Plasmid pK50a Encoding Carbapenemase OXA-23 and Extended-Spectrum β-Lactamase GES-11.
Wibberg D, Salto IP, Eikmeyer FG, Maus I, Winkler A, Nordmann P, Pühler A, Poirel L, Schlüter A., Antimicrob Agents Chemother 62(5), 2018
PMID: 29463529
More than rotating flagella: LPS as a secondary receptor for flagellotropic phage 7-7-1.
Gonzalez F, Helm RF, Broadway KM, Scharf BE., J Bacteriol (), 2018
PMID: 30012730
Presence of an Agrobacterium-Type Tumor-Inducing Plasmid in Neorhizobium sp. NCHU2750 and the Link to Phytopathogenicity.
Haryono M, Tsai YM, Lin CT, Huang FC, Ye YC, Deng WL, Hwang HH, Kuo CH., Genome Biol Evol 10(12), 2018
PMID: 30398651
Draft Genome Sequence of Donghicola sp. Strain KarMa, a Model Organism for Monomethylamine-Degrading Nonmethylotrophic Bacteria.
Zecher K, Suleiman M, Wibberg D, Winkler A, Philipp B, Kalinowski J., Genome Announc 5(7), 2017
PMID: 28209825
A Mitochondrial Autonomously Replicating Sequence from Pichia pastoris for Uniform High Level Recombinant Protein Production.
Schwarzhans JP, Luttermann T, Wibberg D, Winkler A, Hübner W, Huser T, Kalinowski J, Friehs K., Front Microbiol 8(), 2017
PMID: 28512458
Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes.
Maus I, Bremges A, Stolze Y, Hahnke S, Cibis KG, Koeck DE, Kim YS, Kreubel J, Hassa J, Wibberg D, Weimann A, Off S, Stantscheff R, Zverlov VV, Schwarz WH, König H, Liebl W, Scherer P, McHardy AC, Sczyrba A, Klocke M, Pühler A, Schlüter A., Biotechnol Biofuels 10(), 2017
PMID: 29158776
Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium.
Lassalle F, Planel R, Penel S, Chapulliot D, Barbe V, Dubost A, Calteau A, Vallenet D, Mornico D, Bigot T, Guéguen L, Vial L, Muller D, Daubin V, Nesme X., Genome Biol Evol 9(12), 2017
PMID: 29220487
Diffusion of Bacterial Cells in Porous Media.
Licata NA, Mohari B, Fuqua C, Setayeshgar S., Biophys J 110(1), 2016
PMID: 26745427
Complete genome sequence of Streptomyces reticuli, an efficient degrader of crystalline cellulose.
Wibberg D, Al-Dilaimi A, Busche T, Wedderhoff I, Schrempf H, Kalinowski J, Ortiz de Orué Lucana D., J Biotechnol 222(), 2016
PMID: 26851387
Complete mitochondrial genome of the scleractinian coral Porites rus.
Celis JS, Wibberg D, Winkler A, Wilke T, Kalinowski J., Mitochondrial DNA A DNA Mapp Seq Anal 27(5), 2016
PMID: 27158873
Intraspecies Transfer of the Chromosomal Acinetobacter baumannii blaNDM-1 Carbapenemase Gene.
Krahn T, Wibberg D, Maus I, Winkler A, Bontron S, Sczyrba A, Nordmann P, Pühler A, Poirel L, Schlüter A., Antimicrob Agents Chemother 60(5), 2016
PMID: 26953198
Integration event induced changes in recombinant protein productivity in Pichia pastoris discovered by whole genome sequencing and derived vector optimization.
Schwarzhans JP, Wibberg D, Winkler A, Luttermann T, Kalinowski J, Friehs K., Microb Cell Fact 15(), 2016
PMID: 27206580
Complete Chloroplast and Mitochondrial Genome Sequences of the Hydrocarbon Oil-Producing Green Microalga Botryococcus braunii Race B (Showa).
Blifernez-Klassen O, Wibberg D, Winkler A, Blom J, Goesmann A, Kalinowski J, Kruse O., Genome Announc 4(3), 2016
PMID: 27284138
Genomics of high molecular weight plasmids isolated from an on-farm biopurification system.
Martini MC, Wibberg D, Lozano M, Torres Tejerizo G, Albicoro FJ, Jaenicke S, van Elsas JD, Petroni A, Garcillán-Barcia MP, de la Cruz F, Schlüter A, Pühler A, Pistorio M, Lagares A, Del Papa MF., Sci Rep 6(), 2016
PMID: 27321040
Complete Genome Sequence of the Methanogen Methanoculleus bourgensis BA1 Isolated from a Biogas Reactor.
Maus I, Wibberg D, Winkler A, Pühler A, Schnürer A, Schlüter A., Genome Announc 4(3), 2016
PMID: 27340059
Draft Genome Sequence of Propionispora sp. Strain 2/2-37, a New Xylan-Degrading Bacterium Isolated from a Mesophilic Biogas Reactor.
Koeck DE, Maus I, Wibberg D, Winkler A, Zverlov VV, Zverlov VV, Liebl W, Pühler A, Schwarz WH, Schlüter A., Genome Announc 4(3), 2016
PMID: 27340074
Complete Genome Sequence of Herbinix luporum SD1D, a New Cellulose-Degrading Bacterium Isolated from a Thermophilic Biogas Reactor.
Koeck DE, Maus I, Wibberg D, Winkler A, Zverlov VV, Zverlov VV, Liebl W, Pühler A, Schwarz WH, Schlüter A., Genome Announc 4(4), 2016
PMID: 27445379
Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates.
Maus I, Koeck DE, Cibis KG, Hahnke S, Kim YS, Langer T, Kreubel J, Erhard M, Bremges A, Off S, Stolze Y, Jaenicke S, Goesmann A, Sczyrba A, Scherer P, König H, Schwarz WH, Zverlov VV, Zverlov VV, Liebl W, Pühler A, Schlüter A, Klocke M., Biotechnol Biofuels 9(), 2016
PMID: 27525040
An assemblage of Frankia Cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH.
Nguyen TV, Wibberg D, Battenberg K, Blom J, Vanden Heuvel B, Berry AM, Kalinowski J, Pawlowski K., BMC Genomics 17(1), 2016
PMID: 27729005
Genomic Comparison of Agrobacterium pusense Strains Isolated from Bean Nodules.
Aguilar A, Peralta H, Mora Y, Díaz R, Vargas-Lagunas C, Girard L, Mora J., Front Microbiol 7(), 2016
PMID: 27833604
Deep Sequencing Analysis Reveals the Mycoviral Diversity of the Virome of an Avirulent Isolate of Rhizoctonia solani AG-2-2 IV.
Bartholomäus A, Wibberg D, Winkler A, Pühler A, Schlüter A, Varrelmann M., PLoS One 11(11), 2016
PMID: 27814394
Non-canonical integration events in Pichia pastoris encountered during standard transformation analysed with genome sequencing.
Schwarzhans JP, Wibberg D, Winkler A, Luttermann T, Kalinowski J, Friehs K., Sci Rep 6(), 2016
PMID: 27958335
Successful heterologous expression of a novel chitinase identified by sequence analyses of the metagenome from a chitin-enriched soil sample.
Stöveken J, Singh R, Kolkenbrock S, Zakrzewski M, Wibberg D, Eikmeyer FG, Pühler A, Schlüter A, Moerschbacher BM., J Biotechnol 201(), 2015
PMID: 25240439
Complete genome sequence of the novel Porphyromonadaceae bacterium strain ING2-E5B isolated from a mesophilic lab-scale biogas reactor.
Hahnke S, Maus I, Wibberg D, Tomazetto G, Pühler A, Klocke M, Schlüter A., J Biotechnol 193(), 2015
PMID: 25444871
Insights into the annotated genome sequence of Methanoculleus bourgensis MS2(T), related to dominant methanogens in biogas-producing plants.
Maus I, Wibberg D, Stantscheff R, Stolze Y, Blom J, Eikmeyer FG, Fracowiak J, König H, Pühler A, Schlüter A., J Biotechnol 201(), 2015
PMID: 25455016
Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions.
Stolze Y, Zakrzewski M, Maus I, Eikmeyer F, Jaenicke S, Rottmann N, Siebner C, Pühler A, Schlüter A., Biotechnol Biofuels 8(), 2015
PMID: 25688290
Genome Sequence of the Urethral Catheter Isolate Pseudomonas aeruginosa MH19.
Vorhölter FJ, Tielen P, Wibberg D, Narten M, Schobert M, Tüpker R, Blom J, Schatschneider S, Winkler A, Albersmeier A, Goesmann A, Pühler A, Jahn D., Genome Announc 3(2), 2015
PMID: 25767242
Complete genome sequence of the strain Defluviitoga tunisiensis L3, isolated from a thermophilic, production-scale biogas plant.
Maus I, Cibis KG, Wibberg D, Winkler A, Stolze Y, König H, Pühler A, Schlüter A., J Biotechnol 203(), 2015
PMID: 25801333
Draft genome of the xanthan producer Xanthomonas campestris NRRL B-1459 (ATCC 13951).
Wibberg D, Alkhateeb RS, Winkler A, Albersmeier A, Schatschneider S, Albaum S, Niehaus K, Hublik G, Pühler A, Vorhölter FJ., J Biotechnol 204(), 2015
PMID: 25865276
Draft Genome Sequence of Pseudomonas aeruginosa Strain WS136, a Highly Cytotoxic ExoS-Positive Wound Isolate Recovered from Pyoderma Gangrenosum.
Arnold M, Wibberg D, Blom J, Schatschneider S, Winkler A, Kutter Y, Rückert C, Albersmeier A, Albaum S, Goesmann A, Zange S, Heesemann J, Pühler A, Hogardt M, Vorhölter FJ., Genome Announc 3(4), 2015
PMID: 26139712
Genome Sequence of the Urethral Isolate Pseudomonas aeruginosa RN21.
Wibberg D, Tielen P, Narten M, Schobert M, Blom J, Schatschneider S, Meyer AK, Neubauer R, Albersmeier A, Albaum S, Jahn M, Goesmann A, Vorhölter FJ, Pühler A, Jahn D., Genome Announc 3(4), 2015
PMID: 26184943
Complete Genome Sequence of Acinetobacter baumannii CIP 70.10, a Susceptible Reference Strain for Comparative Genome Analyses.
Krahn T, Wibberg D, Maus I, Winkler A, Pühler A, Poirel L, Schlüter A., Genome Announc 3(4), 2015
PMID: 26227605
Complete Genome Sequence of the Clinical Strain Acinetobacter baumannii R2090 Carrying the Chromosomally Encoded Metallo-β-Lactamase Gene blaNDM-1.
Krahn T, Wibberg D, Maus I, Winkler A, Nordmann P, Pühler A, Poirel L, Schlüter A., Genome Announc 3(5), 2015
PMID: 26358593
Genome sequence of the acid-tolerant strain Rhizobium sp. LPU83.
Wibberg D, Tejerizo GT, Del Papa MF, Martini C, Pühler A, Lagares A, Schlüter A, Pistorio M., J Biotechnol 176(), 2014
PMID: 24556327
Utilization of glyphosate as phosphate source: biochemistry and genetics of bacterial carbon-phosphorus lyase.
Hove-Jensen B, Zechel DL, Jochimsen B., Microbiol Mol Biol Rev 78(1), 2014
PMID: 24600043
Genome Sequence of the Octopine-Type Agrobacterium tumefaciens Strain Ach5.
Henkel CV, den Dulk-Ras A, Zhang X, Hooykaas PJ., Genome Announc 2(2), 2014
PMID: 24675863
IncH-type plasmid harboring bla CTX-M-15, bla DHA-1, and qnrB4 genes recovered from animal isolates.
Schlüter A, Nordmann P, Bonnin RA, Millemann Y, Eikmeyer FG, Wibberg D, Pühler A, Poirel L., Antimicrob Agents Chemother 58(7), 2014
PMID: 24752252
Complete genome sequence of the cellulolytic thermophile Ruminoclostridium cellulosi wild-type strain DG5 isolated from a thermophilic biogas plant.
Koeck DE, Wibberg D, Maus I, Winkler A, Albersmeier A, Zverlov VV, Zverlov VV, Liebl W, Pühler A, Schwarz WH, Schlüter A., J Biotechnol 188(), 2014
PMID: 25173616
Complete genome sequence of the methanogenic neotype strain Methanobacterium formicicum MF(T.).
Maus I, Stantscheff R, Wibberg D, Stolze Y, Winkler A, Pühler A, König H, Schlüter A., J Biotechnol 192 Pt A(), 2014
PMID: 25270020
Draft whole genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344.
Luque-Almagro VM, Acera F, Igeño MI, Wibberg D, Roldán MD, Sáez LP, Hennig M, Quesada A, Huertas MJ, Blom J, Merchán F, Escribano MP, Jaenicke S, Estepa J, Guijo MI, Martínez-Luque M, Macías D, Szczepanowski R, Becerra G, Ramirez S, Carmona MI, Gutiérrez O, Manso I, Pühler A, Castillo F, Moreno-Vivián C, Schlüter A, Blasco R., Environ Microbiol 15(1), 2013
PMID: 22998548
Reconciliation of sequence data and updated annotation of the genome of Agrobacterium tumefaciens C58, and distribution of a linear chromosome in the genus Agrobacterium.
Slater S, Setubal JC, Goodner B, Houmiel K, Sun J, Kaul R, Goldman BS, Farrand SK, Almeida N, Burr T, Nester E, Rhoads DM, Kadoi R, Ostheimer T, Pride N, Sabo A, Henry E, Telepak E, Cromes L, Harkleroad A, Oliphant L, Pratt-Szegila P, Welch R, Wood D., Appl Environ Microbiol 79(4), 2013
PMID: 23241979
The Sinorhizobium meliloti essential porin RopA1 is a target for numerous bacteriophages.
Crook MB, Draper AL, Guillory RJ, Griffitts JS., J Bacteriol 195(16), 2013
PMID: 23749981
Complete genome sequence of the hydrogenotrophic Archaeon Methanobacterium sp. Mb1 isolated from a production-scale biogas plant.
Maus I, Wibberg D, Stantscheff R, Cibis K, Eikmeyer FG, König H, Pühler A, Schlüter A., J Biotechnol 168(4), 2013
PMID: 24184088
Draft genome sequence of Sinorhizobium meliloti RU11/001, a model organism for flagellum structure, motility and chemotaxis.
Wibberg D, Blom J, Rückert C, Winkler A, Albersmeier A, Pühler A, Schlüter A, Scharf BE., J Biotechnol 168(4), 2013
PMID: 24184089
Linear chromosome-generating system of Agrobacterium tumefaciens C58: protelomerase generates and protects hairpin ends.
Huang WM, DaGloria J, Fox H, Ruan Q, Tillou J, Shi K, Aihara H, Aron J, Casjens S., J Biol Chem 287(30), 2012
PMID: 22582388
Genome and proteome analysis of 7-7-1, a flagellotropic phage infecting Agrobacterium sp H13-3.
Kropinski AM, Van den Bossche A, Lavigne R, Noben JP, Babinger P, Schmitt R., Virol J 9(), 2012
PMID: 22650361
Complete genome sequence of the hydrogenotrophic, methanogenic archaeon Methanoculleus bourgensis strain MS2(T), Isolated from a sewage sludge digester.
Maus I, Wibberg D, Stantscheff R, Eikmeyer FG, Seffner A, Boelter J, Szczepanowski R, Blom J, Jaenicke S, König H, Pühler A, Schlüter A., J Bacteriol 194(19), 2012
PMID: 22965103
Genomic basis of broad host range and environmental adaptability of Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 which are used in inoculants for common bean (Phaseolus vulgaris L.).
Ormeño-Orrillo E, Menna P, Almeida LG, Ollero FJ, Nicolás MF, Pains Rodrigues E, Shigueyoshi Nakatani A, Silva Batista JS, Oliveira Chueire LM, Souza RC, Ribeiro Vasconcelos AT, Megías M, Hungria M, Martínez-Romero E., BMC Genomics 13(), 2012
PMID: 23270491

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 21329740
PubMed | Europe PMC

Suchen in

Google Scholar