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Science 14 December 2001:
Vol. 294. no. 5550, pp. 2317 - 2323
DOI: 10.1126/science.1066804
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Research Articles

The Genome of the Natural Genetic Engineer Agrobacterium tumefaciens C58

Derek W. Wood,1 Joao C. Setubal,24 Rajinder Kaul,5 Dave E. Monks,1 Joao P. Kitajima,23 Vagner K. Okura,2 Yang Zhou,5 Lishan Chen,1* Gwendolyn E. Wood,1 Nalvo F. Almeida Jr.,6 Lisa Woo,1 Yuching Chen,1dagger Ian T. Paulsen,7 Jonathan A. Eisen,7 Peter D. Karp,8 Donald Bovee Sr.,5 Peter Chapman,5 James Clendenning,5 Glenda Deatherage,5 Will Gillet,5 Charles Grant,5 Tatyana Kutyavin,5 Ruth Levy,5 Meng-Jin Li,5 Erin McClelland,5 Anthony Palmieri,5 Christopher Raymond,5 Gregory Rouse,5 Channakhone Saenphimmachak,5 Zaining Wu,5 Pedro Romero,8 David Gordon,9 Shiping Zhang,10 Heayun Yoo,10 Yumin Tao,11 Phyllis Biddle,10 Mark Jung,10 William Krespan,10 Michael Perry,10 Bill Gordon-Kamm,11 Li Liao,10 Sun Kim,10 Carol Hendrick,11 Zuo-Yu Zhao,11 Maureen Dolan,10 Forrest Chumley,10ddagger Scott V. Tingey,10 Jean-Francois Tomb,10 Milton P. Gordon,12 Maynard V. Olson,5 Eugene W. Nester113§

The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids. Extensive orthology and nucleotide colinearity between the genomes of A. tumefaciens and the plant symbiont Sinorhizobium meliloti suggest a recent evolutionary divergence. Their similarities include metabolic, transport, and regulatory systems that promote survival in the highly competitive rhizosphere; differences are apparent in their genome structure and virulence gene complement. Availability of the A. tumefaciens sequence will facilitate investigations into the molecular basis of pathogenesis and the evolutionary divergence of pathogenic and symbiotic lifestyles.

1 Department of Microbiology, University of Washington, 1959 NE Pacific Street, Box 357242, Seattle, WA 98195, USA.
2 Bioinformatics Laboratory, Institute of Computing,
3 Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, CP 6176, Campinas SP 13083-970, Brazil.
4 Department of Genome Sciences, University of Washington, Box 357730, Seattle, WA 98195, USA.
5 Genome Center, University of Washington, Fluke Hall on Mason Road, Box 352145, Seattle, WA 98195, USA.
6 Department of Computing and Statistics, Federal University of Mato Grosso do Sul, CP 549, Campo Grande MS 79070-900, Brazil.
7 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
8 Bioinformatics Research Group, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA.
9 Howard Hughes Medical Institute, University of Washington, Box 357730, Seattle, WA 98195, USA.
10 E. I. du Pont de Nemours Company, 1 Innovation Way, Newark, DE 19714, USA.
11 Pioneer Hi-Bred International Inc., 7300 NW 62nd Avenue, Post Office Box 1004, Johnston, IA 50131, USA.
12 Department of Biochemistry, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA.
13 Department of Botany, University of Washington, 1959 NE Pacific Street, Box 355325, Seattle, WA 98195, USA.
*   Present address: Department of Pathology, University of Washington, Box 357470, Seattle, WA 98195, USA.

dagger    Present address: Gene Function & Target Validation, Celltech R&D Inc., Bothell, WA 98021, USA.

ddagger    Present address: Department of Plant Pathology, Kansas State University, 113 Waters Hall, Manhattan, KS 66506, USA.

§   To whom correspondence should be addressed. E-mail: gnester{at}u.washington.edu

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   Abstract »    Full Text »    PDF »
Transfer of the Symbiotic Plasmid of Rhizobium etli CFN42 Requires Cointegration with p42a, Which May Be Mediated by Site-Specific Recombination.
S. Brom, L. Girard, C. Tun-Garrido, A. Garcia-de los Santos, P. Bustos, V. Gonzalez, and D. Romero (2004)
J. Bacteriol. 186, 7538-7548
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Identification and analysis of a siderophore biosynthetic gene cluster from Agrobacterium tumefaciens C58.
M. R. Rondon, K. S. Ballering, and M. G. Thomas (2004)
Microbiology 150, 3857-3866
   Abstract »    Full Text »    PDF »
Replicon-Specific Regulation of Small Heat Shock Genes in Agrobacterium tumefaciens.
S. Balsiger, C. Ragaz, C. Baron, and F. Narberhaus (2004)
J. Bacteriol. 186, 6824-6829
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New Protein-Protein Interactions Identified for the Regulatory and Structural Components and Substrates of the Type III Secretion System of the Phytopathogen Xanthomonas axonopodis Pathovar citri.
M. C. Alegria, C. Docena, L. Khater, C. H. I. Ramos, A. C. R. da Silva, and C. S. Farah (2004)
J. Bacteriol. 186, 6186-6197
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Molecular Cloning, Expression, and Properties of an Unusual Aldo-Keto Reductase Family Enzyme, Pyridoxal 4-Dehydrogenase, That Catalyzes Irreversible Oxidation of Pyridoxal.
N. Yokochi, Y. Yoshikane, Y. Trongpanich, K. Ohnishi, and T. Yagi (2004)
J. Biol. Chem. 279, 37377-37384
   Abstract »    Full Text »    PDF »
Comparative Whole-Genome Hybridization Reveals Genomic Islands in Brucella Species.
G. Rajashekara, J. D. Glasner, D. A. Glover, and G. A. Splitter (2004)
J. Bacteriol. 186, 5040-5051
   Abstract »    Full Text »    PDF »
The novel extracellular Streptomyces reticuli haem-binding protein HbpS influences the production of the catalase-peroxidase CpeB.
D. O. d. O. Lucana, T. Schaa, and H. Schrempf (2004)
Microbiology 150, 2575-2585
   Abstract »    Full Text »    PDF »
Fungal Metabolic Model for Type I 3-Methylglutaconic Aciduria.
J. M. Rodriguez, P. Ruiz-Sala, M. Ugarte, and M. A. Penalva (2004)
J. Biol. Chem. 279, 32385-32392
   Abstract »    Full Text »    PDF »
Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors.
K. S. Bell, M. Sebaihia, L. Pritchard, M. T. G. Holden, L. J. Hyman, M. C. Holeva, N. R. Thomson, S. D. Bentley, L. J. C. Churcher, K. Mungall, et al. (2004)
PNAS 101, 11105-11110
   Abstract »    Full Text »    PDF »
Phosphorus Limitation Enhances Biofilm Formation of the Plant Pathogen Agrobacterium tumefaciens through the PhoR-PhoB Regulatory System.
T. Danhorn, M. Hentzer, M. Givskov, M. R. Parsek, and C. Fuqua (2004)
J. Bacteriol. 186, 4492-4501
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Computational inference of scenarios for {alpha}-proteobacterial genome evolution.
B. Boussau, E. O. Karlberg, A. C. Frank, B.-A. Legault, and S. G. E. Andersson (2004)
PNAS 101, 9722-9727
   Abstract »    Full Text »    PDF »
Highly Stable L-Lysine 6-Dehydrogenase from the Thermophile Geobacillus stearothermophilus Isolated from a Japanese Hot Spring: Characterization, Gene Cloning and Sequencing, and Expression.
M. Heydari, T. Ohshima, N. Nunoura-Kominato, and H. Sakuraba (2004)
Appl. Envir. Microbiol. 70, 937-942
   Abstract »    Full Text »    PDF »
Characterization of a gene cluster encoding the maleylacetate reductase from Ralstonia eutropha 335T, an enzyme recruited for growth with 4-fluorobenzoate.
V. Seibert, M. Thiel, I.-S. Hinner, and M. Schlomann (2004)
Microbiology 150, 463-472
   Abstract »    Full Text »    PDF »
An Evolutionary Hot Spot: the pNGR234b Replicon of Rhizobium sp. Strain NGR234.
W. R. Streit, R. A. Schmitz, X. Perret, C. Staehelin, W. J. Deakin, C. Raasch, H. Liesegang, and W. J. Broughton (2004)
J. Bacteriol. 186, 535-542
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Reexamining the Role of the Accessory Plasmid pAtC58 in the Virulence of Agrobacterium tumefaciens Strain C58.
G. R. Nair, Z. Liu, and A. N. Binns (2003)
Plant Physiology 133, 989-999
   Abstract »    Full Text »    PDF »
Expression Cloning and Biochemical Characterization of a Rhizobium leguminosarum Lipid A 1-Phosphatase.
M. J. Karbarz, S. R. Kalb, R. J. Cotter, and C. R. H. Raetz (2003)
J. Biol. Chem. 278, 39269-39279
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Physical and gene maps of Agrobacterium biovar 2 strains and their relationship to biovar 1 chromosomes.
H. Urbanczyk, K. Suzuki, K. Yoshida, and K. Kondo (2003)
Microbiology 149, 3035-3042
   Abstract »    Full Text »    PDF »
Topological characterization of an inner membrane (1->3)-{beta}-D-glucan (curdlan) synthase from Agrobacterium sp. strain ATCC31749.
T. Karnezis, V. C. Epa, B. A. Stone, and V. A. Stanisich (2003)
Glycobiology 13, 693-706
   Abstract »    Full Text »    PDF »
De novo synthesis of bacterial glycogen: Agrobacterium tumefaciens glycogen synthase is involved in glucan initiation and elongation.
J. E. Ugalde, A. J. Parodi, and R. A. Ugalde (2003)
PNAS 100, 10659-10663
   Abstract »    Full Text »    PDF »
The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000.
C. R. Buell, V. Joardar, M. Lindeberg, J. Selengut, I. T. Paulsen, M. L. Gwinn, R. J. Dodson, R. T. Deboy, A. S. Durkin, J. F. Kolonay, et al. (2003)
PNAS 100, 10181-10186
   Abstract »    Full Text »    PDF »
Agrobacterium is a definable genus of the family Rhizobiaceae.
S. K. Farrand, P. B. van Berkum, and P. Oger (2003)
Int J Syst Evol Microbiol 53, 1681-1687
   Abstract »    Full Text »    PDF »
Classification and nomenclature of Agrobacterium and Rhizobium - a reply to Farrand et al. (2003).
J. M. Young, L. D. Kuykendall, E. Martinez-Romero, A. Kerr, and H. Sawada (2003)
Int J Syst Evol Microbiol 53, 1689-1695
   Abstract »    Full Text »    PDF »
Analysis of genes of tetrahydrofolate-dependent metabolism from cultivated spirochaetes and the gut community of the termite Zootermopsis angusticollis.
T. M. Salmassi and J. R. Leadbetter (2003)
Microbiology 149, 2529-2537
   Abstract »    Full Text »    PDF »
Use of a Green Fluorescent Protein-Based Reporter Fusion for Detection of Nitric Oxide Produced by Denitrifiers.
S. Yin, M. Fuangthong, W. P. Laratta, and J. P. Shapleigh (2003)
Appl. Envir. Microbiol. 69, 3938-3944
   Abstract »    Full Text »    PDF »


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