title: 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.
abstract: 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 (2.82 Mb) 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 (2.15 Mb) that is related to its reference replicon and features chromosomal and plasmid-like properties. The accessory plasmid pAspH13-3a (0.6 Mb) 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.
authors.affiliation: Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Wibberg
authors.forename: Jochen
authors.initials: J
authors.lastname: Blom
authors.forename: Sebastian
authors.initials: S
authors.lastname: Jaenicke
authors.forename: Florian
authors.initials: F
authors.lastname: Kollin
authors.forename: Oliver
authors.initials: O
authors.lastname: Rupp
authors.forename: Birgit
authors.initials: B
authors.lastname: Scharf
authors.forename: Susanne
authors.initials: S
authors.lastname: Schneiker-Bekel
authors.forename: Rafael
authors.initials: R
authors.lastname: Sczcepanowski
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.forename: Joao Carlos
authors.initials: JC
authors.lastname: Setubal
authors.forename: Rüdiger
authors.initials: R
authors.lastname: Schmitt
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
authors.forename: Andreas
authors.initials: A
authors.lastname: Schlüter
mesh_terms: D060054:Agrobacterium / Q000145:classification / Q000235:genetics* / Q000502:physiology; D002876:Chromosomes, Bacterial; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D031297:Lupinus / Q000382:microbiology; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics*; D016133:Polymerase Chain Reaction; D058441:Rhizosphere; D017422:Sequence Analysis, DNA