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 Zhang & 2 others Dawn 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
StatePublished - Aug 2007

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plasmids
sugar beet
Pseudomonas
microbial communities
complement
nucleotide sequences
genome
DNA
leaves

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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; Bailey, Mark J. / Sequence-based analysis of pQBR103 : a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet.

In: The ISME Journal, Vol. 1, No. 4, 08.2007, p. 331-340.

Research output: Contribution to journalArticle

@article{5f2b35dde7f54b2cbd1a7d8f8ca737e3,
title = "Sequence-based analysis of pQBR103: a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet",
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.",
author = "Adrian Tett and Spiers, {Andrew J.} and Crossman, {Lisa C.} and Duane Ager and Lena Ciric and Dow, {J. Maxwell} and Fry, {John C.} and David Harris and Andrew Lilley and Anna Oliver and Julian Parkhill and Quail, {Michael A.} and Rainey, {Paul B.} and Saunders, {Nigel J.} and Kathy Seeger and Snyder, {Lori A. S.} and Rob Squares and Thomas, {Christopher M.} and Turner, {Sarah L.} and Xue-Xian Zhang and Dawn Field and Bailey, {Mark J.}",
year = "2007",
month = "8",
doi = "10.1038/ismej.2007.47",
volume = "1",
pages = "331--340",
journal = "The ISME Journal",
issn = "1751-7362",
number = "4",

}

Tett, A, Spiers, AJ, Crossman, LC, Ager, D, Ciric, L, Dow, JM, Fry, JC, Harris, D, Lilley, A, Oliver, A, Parkhill, J, Quail, MA, Rainey, PB, Saunders, NJ, Seeger, K, Snyder, LAS, Squares, R, Thomas, CM, Turner, SL, Zhang, X-X, Field, D & Bailey, MJ 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, vol 1, no. 4, pp. 331-340. DOI: 10.1038/ismej.2007.47

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; Bailey, Mark J.

In: The ISME Journal, Vol. 1, No. 4, 08.2007, p. 331-340.

Research output: Contribution to journalArticle

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AU - Tett,Adrian

AU - Spiers,Andrew J.

AU - Crossman,Lisa C.

AU - Ager,Duane

AU - Ciric,Lena

AU - Dow,J. Maxwell

AU - Fry,John C.

AU - Harris,David

AU - Lilley,Andrew

AU - Oliver,Anna

AU - Parkhill,Julian

AU - Quail,Michael A.

AU - Rainey,Paul B.

AU - Saunders,Nigel J.

AU - Seeger,Kathy

AU - Snyder,Lori A. S.

AU - Squares,Rob

AU - Thomas,Christopher M.

AU - Turner,Sarah L.

AU - Zhang,Xue-Xian

AU - Field,Dawn

AU - Bailey,Mark J.

PY - 2007/8

Y1 - 2007/8

N2 - 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.

AB - 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.

U2 - 10.1038/ismej.2007.47

DO - 10.1038/ismej.2007.47

M3 - Article

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JO - The ISME Journal

JF - The ISME Journal

SN - 1751-7362

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