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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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Circular representation of the E. coli pAPEC-1 plasmid.The different rings represent (from outer to inner) all genes and insertion elements, which are color coded by functional group (rings 1 and 2), deviation from average G+C content (ring 3), and GC skew ((G−C)/(G+C); ring 4). Colors represent the following: red, virulence associated; green, mobile elements; blue, plasmid transfer; yellow, plasmid replication; orange, unknown; pink, plasmid maintenance; black, hypothetical proteins; and gray, other functions.
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pone-0004232-g002: Circular representation of the E. coli pAPEC-1 plasmid.The different rings represent (from outer to inner) all genes and insertion elements, which are color coded by functional group (rings 1 and 2), deviation from average G+C content (ring 3), and GC skew ((G−C)/(G+C); ring 4). Colors represent the following: red, virulence associated; green, mobile elements; blue, plasmid transfer; yellow, plasmid replication; orange, unknown; pink, plasmid maintenance; black, hypothetical proteins; and gray, other functions.

Mentions: The entire nucleotide sequence of the first large plasmid, pAPEC-1, of APEC strain χ7122 (O78∶K80∶H9) was determined. pAPEC-1, an IncF colicin V plasmid [[16], Fig. 1] consists of 103,275 base pairs forming a circular plasmid (Fig. 2) with an average GC content of 48.7%, slightly lower than the genome of E. coli (50.8%) [29], the G+C content fluctuates along the pAPEC-1 sequence (Fig. 2). Detailed analysis of the plasmid sequence predicted the presence of 163 open reading frames (ORFs) and 3 pseudogenes as determined by automated annotation (see Methods) (Table S2). The distribution of the pAPEC-1 ORF start codon usage is 67.5% ATG, 19.9% GTG and 12.7% TTG. Of the 163 ORFs, 31 genes (19%) encode proteins similar to known and putative virulence genes (Table S2), 26 (15.95%) encode proteins involved in plasmid functions (Table S3), 33 (20.24%) are similar to insertion sequence genes (Table S4), 27 (16.6%) are predicted proteins conserved in other species, and 46 genes (28.22%) are predicted proteins with no similarity to proteins in public databases.


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)

Circular representation of the E. coli pAPEC-1 plasmid.The different rings represent (from outer to inner) all genes and insertion elements, which are color coded by functional group (rings 1 and 2), deviation from average G+C content (ring 3), and GC skew ((G−C)/(G+C); ring 4). Colors represent the following: red, virulence associated; green, mobile elements; blue, plasmid transfer; yellow, plasmid replication; orange, unknown; pink, plasmid maintenance; black, hypothetical proteins; and gray, other functions.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0004232-g002: Circular representation of the E. coli pAPEC-1 plasmid.The different rings represent (from outer to inner) all genes and insertion elements, which are color coded by functional group (rings 1 and 2), deviation from average G+C content (ring 3), and GC skew ((G−C)/(G+C); ring 4). Colors represent the following: red, virulence associated; green, mobile elements; blue, plasmid transfer; yellow, plasmid replication; orange, unknown; pink, plasmid maintenance; black, hypothetical proteins; and gray, other functions.
Mentions: The entire nucleotide sequence of the first large plasmid, pAPEC-1, of APEC strain χ7122 (O78∶K80∶H9) was determined. pAPEC-1, an IncF colicin V plasmid [[16], Fig. 1] consists of 103,275 base pairs forming a circular plasmid (Fig. 2) with an average GC content of 48.7%, slightly lower than the genome of E. coli (50.8%) [29], the G+C content fluctuates along the pAPEC-1 sequence (Fig. 2). Detailed analysis of the plasmid sequence predicted the presence of 163 open reading frames (ORFs) and 3 pseudogenes as determined by automated annotation (see Methods) (Table S2). The distribution of the pAPEC-1 ORF start codon usage is 67.5% ATG, 19.9% GTG and 12.7% TTG. Of the 163 ORFs, 31 genes (19%) encode proteins similar to known and putative virulence genes (Table S2), 26 (15.95%) encode proteins involved in plasmid functions (Table S3), 33 (20.24%) are similar to insertion sequence genes (Table S4), 27 (16.6%) are predicted proteins conserved in other species, and 46 genes (28.22%) are predicted proteins with no similarity to proteins in public databases.

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