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

Adrian Tett, Andrew J. Spiers, Lisa C. Crossman, Duane Ager, Lena Ciric, J. Maxwell Dow, John C. Fry, David Harris, Andrew Lilley, Anna Oliver, Julian Parkhill, Michael A. Quail, Paul B. Rainey, Nigel J. Saunders, Kathy Seeger, Lori A. S. Snyder, Rob Squares, Christopher M. Thomas, Sarah L. Turner, Xue-Xian ZhangDawn Field, Mark J. Bailey

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Abstract

The plasmid pQBR103 was found within Pseudomonas populations colonizing the leaf and root surfaces of sugar beet plants growing at Wytham, Oxfordshire, UK. At 425 kb it is the largest selftransmissible 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 c-proteobacterial genera and plasmids. pQBR103 has identifiable regions presumed responsible for replication and partitioning, but despite being traþ 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.
Original languageEnglish
Pages (from-to)331-340
Number of pages8
JournalThe ISME Journal
Volume1
Issue number4
DOIs
Publication statusPublished - Aug 2007

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Tett, A., Spiers, A. J., Crossman, L. C., Ager, D., Ciric, L., Dow, J. M., Fry, J. C., Harris, D., Lilley, A., Oliver, A., Parkhill, J., Quail, M. A., Rainey, P. B., Saunders, N. J., Seeger, K., Snyder, L. A. S., Squares, R., Thomas, C. M., Turner, S. L., ... Bailey, M. J. (2007). Sequence-based analysis of pQBR103: a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet. The ISME Journal, 1(4), 331-340. https://doi.org/10.1038/ismej.2007.47