Comparative genomics of pAKD4, the prototype IncP-1δ plasmid with a complete backbone

Diya Sen, Hirokazu Yano, Haruo Suzuki, Jaroslaw E. Król, Linda Rogers, Celeste J. Brown, Eva M. Top

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Plasmids of the incompatibility group IncP-1 are important agents of horizontal gene transfer and contribute to the spread of antibiotic resistance and xenobiotic degradation within bacterial communities. Even though some prototype plasmids have been studied in much detail, the diversity of this plasmid group was still greatly underestimated until recently, as only two of the five currently known divergent sub-groups had been described. To further improve our insight into the diversity and evolutionary history of this family of broad-host-range plasmids, we compared the complete nucleotide sequence of a new IncP-1δ plasmid pAKD4 to the genomes of other IncP-1 plasmids. Plasmid pAKD4 was previously isolated by exogenous plasmid isolation from an agricultural soil in Norway. Its 56,803. bp nucleotide sequence shows high similarity in gene sequence and gene order to both plasmids pEST4011 and pIJB1, the only other IncP-1δ plasmids sequenced so far. While all three plasmids have a typical IncP-1 backbone comprising replication, transfer, and stable inheritance/control genes, the low sequence similarity in some regions and presence/absence of some backbone genes compared to other IncP-1 plasmids cluster them in a divergent sub-group. Therefore this study validates the presence of a real IncP-1δ clade with multiple plasmids. Moreover, since both pEST4011 and pIJB1 are missing a portion of their transfer genes, pAKD4 represents the first completely sequenced self-transferable plasmid with a complete IncP-1δ backbone. We therefore propose it to be the prototype IncP-1δ plasmid.

Original languageEnglish
Pages (from-to)98-107
Number of pages10
JournalPlasmid
Volume63
Issue number2
DOIs
Publication statusPublished - 2010 Mar
Externally publishedYes

Fingerprint

Genomics
Plasmids
Genes
Horizontal Gene Transfer
Gene Order
Host Specificity
Xenobiotics
Norway
Microbial Drug Resistance
Soil

Keywords

  • Broad host range
  • Horizontal gene transfer
  • IncP-1 plasmid
  • Mercury resistance
  • Plasmid
  • Transposon

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Comparative genomics of pAKD4, the prototype IncP-1δ plasmid with a complete backbone. / Sen, Diya; Yano, Hirokazu; Suzuki, Haruo; Król, Jaroslaw E.; Rogers, Linda; Brown, Celeste J.; Top, Eva M.

In: Plasmid, Vol. 63, No. 2, 03.2010, p. 98-107.

Research output: Contribution to journalArticle

Sen, Diya ; Yano, Hirokazu ; Suzuki, Haruo ; Król, Jaroslaw E. ; Rogers, Linda ; Brown, Celeste J. ; Top, Eva M. / Comparative genomics of pAKD4, the prototype IncP-1δ plasmid with a complete backbone. In: Plasmid. 2010 ; Vol. 63, No. 2. pp. 98-107.
@article{7267c35002a84861a2aea513e2170a6c,
title = "Comparative genomics of pAKD4, the prototype IncP-1δ plasmid with a complete backbone",
abstract = "Plasmids of the incompatibility group IncP-1 are important agents of horizontal gene transfer and contribute to the spread of antibiotic resistance and xenobiotic degradation within bacterial communities. Even though some prototype plasmids have been studied in much detail, the diversity of this plasmid group was still greatly underestimated until recently, as only two of the five currently known divergent sub-groups had been described. To further improve our insight into the diversity and evolutionary history of this family of broad-host-range plasmids, we compared the complete nucleotide sequence of a new IncP-1δ plasmid pAKD4 to the genomes of other IncP-1 plasmids. Plasmid pAKD4 was previously isolated by exogenous plasmid isolation from an agricultural soil in Norway. Its 56,803. bp nucleotide sequence shows high similarity in gene sequence and gene order to both plasmids pEST4011 and pIJB1, the only other IncP-1δ plasmids sequenced so far. While all three plasmids have a typical IncP-1 backbone comprising replication, transfer, and stable inheritance/control genes, the low sequence similarity in some regions and presence/absence of some backbone genes compared to other IncP-1 plasmids cluster them in a divergent sub-group. Therefore this study validates the presence of a real IncP-1δ clade with multiple plasmids. Moreover, since both pEST4011 and pIJB1 are missing a portion of their transfer genes, pAKD4 represents the first completely sequenced self-transferable plasmid with a complete IncP-1δ backbone. We therefore propose it to be the prototype IncP-1δ plasmid.",
keywords = "Broad host range, Horizontal gene transfer, IncP-1 plasmid, Mercury resistance, Plasmid, Transposon",
author = "Diya Sen and Hirokazu Yano and Haruo Suzuki and Kr{\'o}l, {Jaroslaw E.} and Linda Rogers and Brown, {Celeste J.} and Top, {Eva M.}",
year = "2010",
month = "3",
doi = "10.1016/j.plasmid.2009.11.005",
language = "English",
volume = "63",
pages = "98--107",
journal = "Plasmid",
issn = "0147-619X",
publisher = "Academic Press Inc.",
number = "2",

}

TY - JOUR

T1 - Comparative genomics of pAKD4, the prototype IncP-1δ plasmid with a complete backbone

AU - Sen, Diya

AU - Yano, Hirokazu

AU - Suzuki, Haruo

AU - Król, Jaroslaw E.

AU - Rogers, Linda

AU - Brown, Celeste J.

AU - Top, Eva M.

PY - 2010/3

Y1 - 2010/3

N2 - Plasmids of the incompatibility group IncP-1 are important agents of horizontal gene transfer and contribute to the spread of antibiotic resistance and xenobiotic degradation within bacterial communities. Even though some prototype plasmids have been studied in much detail, the diversity of this plasmid group was still greatly underestimated until recently, as only two of the five currently known divergent sub-groups had been described. To further improve our insight into the diversity and evolutionary history of this family of broad-host-range plasmids, we compared the complete nucleotide sequence of a new IncP-1δ plasmid pAKD4 to the genomes of other IncP-1 plasmids. Plasmid pAKD4 was previously isolated by exogenous plasmid isolation from an agricultural soil in Norway. Its 56,803. bp nucleotide sequence shows high similarity in gene sequence and gene order to both plasmids pEST4011 and pIJB1, the only other IncP-1δ plasmids sequenced so far. While all three plasmids have a typical IncP-1 backbone comprising replication, transfer, and stable inheritance/control genes, the low sequence similarity in some regions and presence/absence of some backbone genes compared to other IncP-1 plasmids cluster them in a divergent sub-group. Therefore this study validates the presence of a real IncP-1δ clade with multiple plasmids. Moreover, since both pEST4011 and pIJB1 are missing a portion of their transfer genes, pAKD4 represents the first completely sequenced self-transferable plasmid with a complete IncP-1δ backbone. We therefore propose it to be the prototype IncP-1δ plasmid.

AB - Plasmids of the incompatibility group IncP-1 are important agents of horizontal gene transfer and contribute to the spread of antibiotic resistance and xenobiotic degradation within bacterial communities. Even though some prototype plasmids have been studied in much detail, the diversity of this plasmid group was still greatly underestimated until recently, as only two of the five currently known divergent sub-groups had been described. To further improve our insight into the diversity and evolutionary history of this family of broad-host-range plasmids, we compared the complete nucleotide sequence of a new IncP-1δ plasmid pAKD4 to the genomes of other IncP-1 plasmids. Plasmid pAKD4 was previously isolated by exogenous plasmid isolation from an agricultural soil in Norway. Its 56,803. bp nucleotide sequence shows high similarity in gene sequence and gene order to both plasmids pEST4011 and pIJB1, the only other IncP-1δ plasmids sequenced so far. While all three plasmids have a typical IncP-1 backbone comprising replication, transfer, and stable inheritance/control genes, the low sequence similarity in some regions and presence/absence of some backbone genes compared to other IncP-1 plasmids cluster them in a divergent sub-group. Therefore this study validates the presence of a real IncP-1δ clade with multiple plasmids. Moreover, since both pEST4011 and pIJB1 are missing a portion of their transfer genes, pAKD4 represents the first completely sequenced self-transferable plasmid with a complete IncP-1δ backbone. We therefore propose it to be the prototype IncP-1δ plasmid.

KW - Broad host range

KW - Horizontal gene transfer

KW - IncP-1 plasmid

KW - Mercury resistance

KW - Plasmid

KW - Transposon

UR - http://www.scopus.com/inward/record.url?scp=75549087004&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=75549087004&partnerID=8YFLogxK

U2 - 10.1016/j.plasmid.2009.11.005

DO - 10.1016/j.plasmid.2009.11.005

M3 - Article

VL - 63

SP - 98

EP - 107

JO - Plasmid

JF - Plasmid

SN - 0147-619X

IS - 2

ER -