Sequence-based analysis of pQBR103; A representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet

Tett, Adrian, Spiers, Andrew J., Crossman, Lisa C., Ager, Duane, Ciric, Lena, Dow, J. Maxwell, Fry, John C., Harris, David, Lilley, Andrew, Oliver, Anna, Parkhill, Julian, Quail, Michael A., Rainey, Paul B., Saunders, Nigel J., Seeger, Kathy, Snyder, Lori A. S., Squares, Rob, Thomas, Christopher M., Turner, Sarah L., Zhang, Xue Xian, Field, Dawn and Bailey, Mark J. (2007) Sequence-based analysis of pQBR103; A representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet. ISME Journal, 1 (4). pp. 331-340. ISSN 1751-7362

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The plasmid pQBR103 was found within Pseudomonas populations colonizing the leaf and root surfaces of sugar beet plants growing at Wytham, Oxfordshire, UK. At 425kb it is the largest self-transmissible plasmid yet sequenced from the phytosphere. It is known to enhance the competitive fitness of its host, and parts of the plasmid are known to be actively transcribed in the plant environment. Analysis of the complete sequence of this plasmid predicts a coding sequence (CDS)-rich genome containing 478 CDSs and an exceptional degree of genetic novelty; 80 of predicted coding sequences cannot be ascribed a function and 60 are orphans. Of those to which function could be assigned, 40 bore greatest similarity to sequences from Pseudomonas spp, and the majority of the remainder showed similarity to other -proteobacterial genera and plasmids. pQBR103 has identifiable regions presumed responsible for replication and partitioning, but despite being tra+ lacks the full complement of any previously described conjugal transfer functions. The DNA sequence provided few insights into the functional significance of plant-induced transcriptional regions, but suggests that 14 of CDSs may be expressed (11 CDSs with functional annotation and 54 without), further highlighting the ecological importance of these novel CDSs. Comparative analysis indicates that pQBR103 shares significant regions of sequence with other plasmids isolated from sugar beet plants grown at the same geographic location. These plasmid sequences indicate there is more novelty in the mobile DNA pool accessible to phytosphere pseudomonas than is currently appreciated or understood.

Item Type: Article
Additional Information: Funding Information: We thank G Wilson and C Ekeke for their help in the analysis of the pQBR103 sequence and Bela Tiwari for consultation on the microarray analysis. AT was funded by a UK NERC studentship. The sequencing of pQBR103 was funded via a UK BBSRC grant (P16729) to PR and CT. The unpublished P. fluorescens Pf0-1 and SBW25 genomes were accessed from the USA DOE Joint Genome Institute and the UK Wellcome Trust Sanger Institute, respectively.
Uncontrolled Keywords: environmental,phytosphere,plasmid,pseudomonas,sequence,microbiology,ecology, evolution, behavior and systematics ,/dk/atira/pure/subjectarea/asjc/2400/2404
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 14 May 2024 10:31
Last Modified: 14 May 2024 10:31
DOI: 10.1038/ismej.2007.47

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