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Full sequence and comparative analysis of the plasmid pAPEC-1 of avian pathogenic E. coli chi7122 (O78:K80:H9).

Mellata M, Touchman JW, Curtiss R - PLoS ONE (2009)

Bottom Line: The full length of the transfer region in pAPEC-1 (11 kb) is shorter compared to the tra region of other sequenced F plasmids; the absence of some tra genes in pAPEC-1 affects its self-transferability, and the conjugative function of the plasmid was effective only in the presence of other plasmids.The presence of pAPEC-1-associated genes is assessed in human ExPEC by PCR.Many patterns of association between genes are found.

View Article: PubMed Central - PubMed

Affiliation: The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America.

ABSTRACT

Background: Extra-intestinal pathogenic E. coli (ExPEC), including Avian Pathogenic E. coli (APEC), are very diverse. They cause a complex of diseases in Human, animals, and birds. Even though large plasmids are often associated with the virulence of ExPEC, their characterization is still in its infancy.

Methodology/principal findings: We fully sequenced and analyzed the large plasmid pAPEC-1 (103,275-bp) associated with the APEC strain chi7122, from worldwide serogroup O78ratioK80ratioH9. A putative virulence region spanning an 80-kb region of pAPEC-1 possesses four iron acquisition systems (iutA iucABCD, sitABCD, iroBCDN, and temperature-sensitive hemagglutinin tsh), a colicin V operon, increasing serum sensitivity iss, ompT, hlyF, and etsABC. Thirty three ORFs in pAPEC-1 are identified as insertion sequences (ISs) that belong to nine families with diverse origins. The full length of the transfer region in pAPEC-1 (11 kb) is shorter compared to the tra region of other sequenced F plasmids; the absence of some tra genes in pAPEC-1 affects its self-transferability, and the conjugative function of the plasmid was effective only in the presence of other plasmids. Two-replicon systems, repFIIA-repFIC and repFIB, and two post-segregational systems, srnB and hok/sok, are also present in the sequence of pAPEC-1. The comparison of the pAPEC-1 sequence with the two available plasmid sequences reveals more gene loss and reorganization than previously appreciated. The presence of pAPEC-1-associated genes is assessed in human ExPEC by PCR. Many patterns of association between genes are found.

Conclusions/significance: The pathotype typical of pAPEC-1 was present in some human strains, which indicates a horizontal transfer between strains and the zoonotic risk of APEC strains. ColV plasmids could have common virulence genes that could be acquired by transposition, without sharing genes of plasmid function.

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Comparison of the genetic map of the replication region of pAPEC-1 to that of pAPEC-O2-ColV (NC_007675) and pAPEC-O1-ColBM (NC_009837).Black arrows represent known ORFs genes, grey arrows represent truncated genes, and white arrows represent hypothetical protein genes and hatched arrows are Insertion Sequences genes.
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pone-0004232-g004: Comparison of the genetic map of the replication region of pAPEC-1 to that of pAPEC-O2-ColV (NC_007675) and pAPEC-O1-ColBM (NC_009837).Black arrows represent known ORFs genes, grey arrows represent truncated genes, and white arrows represent hypothetical protein genes and hatched arrows are Insertion Sequences genes.

Mentions: Many plasmids of the IncF group have been shown to possess more than one replicon [15], [19], [34], [35]. Two-replicon systems are identified in the sequence of pAPEC-1. Of interest, the organization of the first replicon repFIIA-repFIC, located upstream of the transfer region, is more similar to the replicon identified on pAPEC-O1-ColBM [19] than to the homologue on pAPEC-O2-ColV [15] (Fig. 4), which suggests that ColV plasmids are not necessarily from the same backbone. The particularity of the pAPEC-1 transfer region is the presence of repA, a component of repFIC in the repFIIA region (Fig. 4) and an ORF that has similarity with sequence of pAPEC-O1-ColBM only. Genes of this region are identical (at the nucleotide and protein levels) to the genes of the repFIIA region in pAPEC-O1-ColBM. In pAPEC-1, with the exception of the repA4 that has the lowest homology (93%) and contains a punctuation mutation (G-T) that creates the stop codon TGA in position 88. Two ORFs upstream of repA4 do not have any homology with either pAPEC-O1-ColBM or pAPEC-O2-ColV plasmid sequences. The replication regions of the three sequenced avian plasmids pAPEC-O2-ColV, pAPEC-1, and pAPEC-O1-ColBM are flanked by different insertion sequences, IS1414, IS91, and IS629 respectively (Fig. 4), which demonstrates that these regions could have different origins.


Full sequence and comparative analysis of the plasmid pAPEC-1 of avian pathogenic E. coli chi7122 (O78:K80:H9).

Mellata M, Touchman JW, Curtiss R - PLoS ONE (2009)

Comparison of the genetic map of the replication region of pAPEC-1 to that of pAPEC-O2-ColV (NC_007675) and pAPEC-O1-ColBM (NC_009837).Black arrows represent known ORFs genes, grey arrows represent truncated genes, and white arrows represent hypothetical protein genes and hatched arrows are Insertion Sequences genes.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2626276&req=5

pone-0004232-g004: Comparison of the genetic map of the replication region of pAPEC-1 to that of pAPEC-O2-ColV (NC_007675) and pAPEC-O1-ColBM (NC_009837).Black arrows represent known ORFs genes, grey arrows represent truncated genes, and white arrows represent hypothetical protein genes and hatched arrows are Insertion Sequences genes.
Mentions: Many plasmids of the IncF group have been shown to possess more than one replicon [15], [19], [34], [35]. Two-replicon systems are identified in the sequence of pAPEC-1. Of interest, the organization of the first replicon repFIIA-repFIC, located upstream of the transfer region, is more similar to the replicon identified on pAPEC-O1-ColBM [19] than to the homologue on pAPEC-O2-ColV [15] (Fig. 4), which suggests that ColV plasmids are not necessarily from the same backbone. The particularity of the pAPEC-1 transfer region is the presence of repA, a component of repFIC in the repFIIA region (Fig. 4) and an ORF that has similarity with sequence of pAPEC-O1-ColBM only. Genes of this region are identical (at the nucleotide and protein levels) to the genes of the repFIIA region in pAPEC-O1-ColBM. In pAPEC-1, with the exception of the repA4 that has the lowest homology (93%) and contains a punctuation mutation (G-T) that creates the stop codon TGA in position 88. Two ORFs upstream of repA4 do not have any homology with either pAPEC-O1-ColBM or pAPEC-O2-ColV plasmid sequences. The replication regions of the three sequenced avian plasmids pAPEC-O2-ColV, pAPEC-1, and pAPEC-O1-ColBM are flanked by different insertion sequences, IS1414, IS91, and IS629 respectively (Fig. 4), which demonstrates that these regions could have different origins.

Bottom Line: The full length of the transfer region in pAPEC-1 (11 kb) is shorter compared to the tra region of other sequenced F plasmids; the absence of some tra genes in pAPEC-1 affects its self-transferability, and the conjugative function of the plasmid was effective only in the presence of other plasmids.The presence of pAPEC-1-associated genes is assessed in human ExPEC by PCR.Many patterns of association between genes are found.

View Article: PubMed Central - PubMed

Affiliation: The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America.

ABSTRACT

Background: Extra-intestinal pathogenic E. coli (ExPEC), including Avian Pathogenic E. coli (APEC), are very diverse. They cause a complex of diseases in Human, animals, and birds. Even though large plasmids are often associated with the virulence of ExPEC, their characterization is still in its infancy.

Methodology/principal findings: We fully sequenced and analyzed the large plasmid pAPEC-1 (103,275-bp) associated with the APEC strain chi7122, from worldwide serogroup O78ratioK80ratioH9. A putative virulence region spanning an 80-kb region of pAPEC-1 possesses four iron acquisition systems (iutA iucABCD, sitABCD, iroBCDN, and temperature-sensitive hemagglutinin tsh), a colicin V operon, increasing serum sensitivity iss, ompT, hlyF, and etsABC. Thirty three ORFs in pAPEC-1 are identified as insertion sequences (ISs) that belong to nine families with diverse origins. The full length of the transfer region in pAPEC-1 (11 kb) is shorter compared to the tra region of other sequenced F plasmids; the absence of some tra genes in pAPEC-1 affects its self-transferability, and the conjugative function of the plasmid was effective only in the presence of other plasmids. Two-replicon systems, repFIIA-repFIC and repFIB, and two post-segregational systems, srnB and hok/sok, are also present in the sequence of pAPEC-1. The comparison of the pAPEC-1 sequence with the two available plasmid sequences reveals more gene loss and reorganization than previously appreciated. The presence of pAPEC-1-associated genes is assessed in human ExPEC by PCR. Many patterns of association between genes are found.

Conclusions/significance: The pathotype typical of pAPEC-1 was present in some human strains, which indicates a horizontal transfer between strains and the zoonotic risk of APEC strains. ColV plasmids could have common virulence genes that could be acquired by transposition, without sharing genes of plasmid function.

Show MeSH
Related in: MedlinePlus