Full Sequence and Comparative Analysis of the Plasmid pAPEC-1 of Avian Pathogenic E. coli χ7122 (O78∶K80∶H9)
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{"title"=>"Full sequence and comparative analysis of the plasmid pAPEC-1 of avian pathogenic E. coli χ7122 (O78:k80:H9)", "type"=>"journal", "authors"=>[{"first_name"=>"Melha", "last_name"=>"Mellata", "scopus_author_id"=>"6507731651"}, {"first_name"=>"Jeffrey W.", "last_name"=>"Touchman", "scopus_author_id"=>"6603666665"}, {"first_name"=>"Roy", "last_name"=>"Curtis", "scopus_author_id"=>"36742477500"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-58849136299", "sgr"=>"58849136299", "pui"=>"354109735", "isbn"=>"0027-8424 (Print)\\n0027-8424 (Linking)", "pmid"=>"19156210", "doi"=>"10.1371/journal.pone.0004232"}, "id"=>"9e94d5ec-d6bc-3cbf-9f4d-e4c894740d29", "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.\\n\\nMETHODOLOGY/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.\\n\\nCONCLUSIONS/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.", "link"=>"http://www.mendeley.com/research/full-sequence-comparative-analysis-plasmid-papec1-avian-pathogenic-e-coli-%CF%877122-o78k80h9", "reader_count"=>33, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>5, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>2, "Student > Master"=>4, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>5, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>2, "Student > Master"=>4, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>19, "Medicine and Dentistry"=>3, "Social Sciences"=>3, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Social Sciences"=>{"Social Sciences"=>3}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>19}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>1, "Brazil"=>1, "United Kingdom"=>1, "Kenya"=>1}, "group_count"=>1}

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  • {"files"=>["https://ndownloader.figshare.com/files/450070", "https://ndownloader.figshare.com/files/450114", "https://ndownloader.figshare.com/files/450206", "https://ndownloader.figshare.com/files/450269", "https://ndownloader.figshare.com/files/450334", "https://ndownloader.figshare.com/files/450398"], "description"=>"<div><h3>Background</h3><p>Extra-intestinal pathogenic <em>E. coli</em> (ExPEC), including Avian Pathogenic <em>E. coli</em> (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.</p><h3>Methodology/Principal Findings</h3><p>We fully sequenced and analyzed the large plasmid pAPEC-1 (103,275-bp) associated with the APEC strain χ7122, from worldwide serogroup O78∶K80∶H9. A putative virulence region spanning an 80-kb region of pAPEC-1 possesses four iron acquisition systems (<em>iutA iucABCD</em>, <em>sitABCD</em>, <em>iroBCDN</em>, and temperature-sensitive hemagglutinin <em>tsh</em>), a colicin V operon, increasing serum sensitivity <em>iss</em>, <em>ompT</em>, <em>hlyF</em>, and <em>etsABC</em>. 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 <em>tra</em> region of other sequenced F plasmids; the absence of some <em>tra</em> 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, <em>repFIIA-repFIC</em> and <em>repFIB</em>, and two post-segregational systems, <em>srnB</em> and <em>hok/sok</em>, 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.</p><h3>Conclusions/Significance</h3><p>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.</p></div>", "links"=>[], "tags"=>["comparative", "plasmid", "papec-1", "avian", "pathogenic"], "article_id"=>148705, "categories"=>["Cancer", "Genetics"], "users"=>["Melha Mellata", "Jeffrey W. Touchman", "Roy Curtiss III"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0004232.s001", "https://dx.doi.org/10.1371/journal.pone.0004232.s002", "https://dx.doi.org/10.1371/journal.pone.0004232.s003", "https://dx.doi.org/10.1371/journal.pone.0004232.s004", "https://dx.doi.org/10.1371/journal.pone.0004232.s005", "https://dx.doi.org/10.1371/journal.pone.0004232.s006"], "stats"=>{"downloads"=>11, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Full_Sequence_and_Comparative_Analysis_of_the_Plasmid_pAPEC_1_of_Avian_Pathogenic_E_coli_7122_O78_K80_H9_/148705", "title"=>"Full Sequence and Comparative Analysis of the Plasmid pAPEC-1 of Avian Pathogenic <em>E. coli</em> χ7122 (O78∶K80∶H9)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-01-21 02:25:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/911410"], "description"=>"<p>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.</p>", "links"=>[], "tags"=>["replication", "papec-1", "papec-o2-colv", "papec-o1-colbm"], "article_id"=>581864, "categories"=>["Virology", "Genetics"], "users"=>["Melha Mellata", "Jeffrey W. Touchman", "Roy Curtiss III"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004232.g004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_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_/581864", "title"=>"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).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-01-21 00:31:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/911126"], "description"=>"<p>Four plasmids (147 kb, 63 kb, 35.85 kb, and 6.9 kb) of the strain 39R681 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004232#pone.0004232-Mainil1\" target=\"_blank\">[83]</a> were used as a ladder (L). Each lane contained plasmids from the following bacterial strains: (1) χ7122, (2) χ7273, (3) χ7277, (4) 7345, (5) 7346, (6) χ7396, (7) χ833, (8) χ2934, (9) χ6092, (10) MGN-617, and (11) TOP10; Colicin production of strains (B). (1) χ7122, (2) χ6092, (3) χ7346.</p>", "links"=>[], "tags"=>["profiles", "strains", "agarose", "gel"], "article_id"=>581582, "categories"=>["Virology", "Genetics"], "users"=>["Melha Mellata", "Jeffrey W. Touchman", "Roy Curtiss III"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004232.g001", "stats"=>{"downloads"=>4, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Plasmid_profiles_of_strains_on_0_5_agarose_gel_A_/581582", "title"=>"Plasmid profiles of strains on 0.5% agarose gel (A).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-01-21 00:26:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/911837"], "description"=>"*<p>UTI, Urinary Tract Infection.</p>", "links"=>[], "tags"=>["papec-1", "combinations"], "article_id"=>582296, "categories"=>["Virology", "Genetics"], "users"=>["Melha Mellata", "Jeffrey W. Touchman", "Roy Curtiss III"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004232.t003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Prevalence_of_different_pAPEC_1_gene_combinations_in_human_isolates_/582296", "title"=>"Prevalence of different pAPEC-1 gene combinations in human isolates.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-01-21 00:38:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/911515"], "description"=>"<p>Same-strand DNA similarity is shaded red, while reverse similarity is shaded blue. Aligned regions greater than 1000 base pairs with a percent-identity >96% are shown. Comparisons were generated with the Artemis comparison tool, ACT <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004232#pone.0004232-Carver1\" target=\"_blank\">[84]</a>.</p>", "links"=>[], "tags"=>["nucleotide", "papec-1", "dna", "papec-o1-colbm", "papec-o2-colv"], "article_id"=>581971, "categories"=>["Virology", "Genetics"], "users"=>["Melha Mellata", "Jeffrey W. Touchman", "Roy Curtiss III"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004232.g005", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_nucleotide_comparison_of_the_complete_pAPEC_1_DNA_sequence_to_that_of_pAPEC_O1_ColBM_NC_009837_and_pAPEC_O2_ColV_NC_007675_/581971", "title"=>"Pairwise nucleotide comparison of the complete pAPEC-1 DNA sequence to that of pAPEC-O1-ColBM (NC_009837) and pAPEC-O2-ColV (NC_007675).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-01-21 00:32:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/911193"], "description"=>"<p>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.</p>", "links"=>[], "tags"=>["papec-1"], "article_id"=>581656, "categories"=>["Virology", "Genetics"], "users"=>["Melha Mellata", "Jeffrey W. Touchman", "Roy Curtiss III"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004232.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Circular_representation_of_the_E_coli_pAPEC_1_plasmid_/581656", "title"=>"Circular representation of the <i>E. coli</i> pAPEC-1 plasmid.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-01-21 00:27:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/911867"], "description"=>"*<p>UTI, Urinary Tract Infection.</p>", "links"=>[], "tags"=>["papec-1", "virulence-associated", "genes"], "article_id"=>582330, "categories"=>["Virology", "Genetics"], "users"=>["Melha Mellata", "Jeffrey W. Touchman", "Roy Curtiss III"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004232.t002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Prevalence_of_pAPEC_1_virulence_associated_genes_in_human_isolates_/582330", "title"=>"Prevalence (%) of pAPEC-1 virulence-associated genes in human isolates.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-01-21 00:38:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/911654"], "description"=>"<p>The phylogenetic trees were constructed by neighbor-joining analysis. The phylogenetic groups are given on the right. Genes from pAPEC-1 (*); genes of APEC (normal arrow); and genes of other ExPEC (round arrow) are indicated.</p>", "links"=>[], "tags"=>["relationships", "sequences", "papec-1-associated", "virulence", "genes"], "article_id"=>582107, "categories"=>["Virology", "Genetics"], "users"=>["Melha Mellata", "Jeffrey W. Touchman", "Roy Curtiss III"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004232.g006", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_between_protein_sequences_of_nine_pAPEC_1_associated_virulence_genes_a_tsh_b_iss_c_cvaC_d_iroN_e_sitA_f_iucC_g_ompT_h_hlyF_and_i_etsA_and_related_genes_from_other_sources_/582107", "title"=>"Phylogenetic relationships between protein sequences of nine pAPEC-1-associated virulence genes (a) <i>tsh</i>, (b) <i>iss</i>, (c) <i>cvaC</i>, (d) <i>iroN</i>, (e) <i>sitA</i>, (f) <i>iucC</i>, (g) <i>ompT</i>, (h) <i>hlyF</i>, and (i) <i>etsA</i> and related genes from other sources.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-01-21 00:35:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/911900"], "description"=>"*<p>Km, kanamycin; Nal, nalidixic acid; Str, streptomycin; Tc, tetracyclin.</p>", "links"=>[], "tags"=>["strains", "plasmids"], "article_id"=>582365, "categories"=>["Virology", "Genetics"], "users"=>["Melha Mellata", "Jeffrey W. Touchman", "Roy Curtiss III"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004232.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bacterial_strains_and_plasmids_used_in_this_study_/582365", "title"=>"Bacterial strains and plasmids used in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-01-21 00:39:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/911302"], "description"=>"<p>Capital letters represent <i>tra</i> genes and lower case letters represent <i>trb</i> genes. Black arrows represent known ORFs genes, grey arrows represent truncated genes, and white arrows represent hypothetical protein genes. PCR of the <i>traI-traB</i> region on 0.8% agarose gel (C), (L) 10 kb ladder (Promega), (1) χ7122, (2) χ7346, (3) χ6092.</p>", "links"=>[], "tags"=>["papec-1", "orfs", "papec-o2-colv", "absent"], "article_id"=>581759, "categories"=>["Virology", "Genetics"], "users"=>["Melha Mellata", "Jeffrey W. Touchman", "Roy Curtiss III"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004232.g003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_map_of_the_transfer_region_of_pAPEC_1_A_ORFs_of_pAPEC_O2_ColV_absent_in_pAPEC_1_B_/581759", "title"=>"Genetic map of the transfer region of pAPEC-1 (A), ORFs of pAPEC-O2-ColV absent in pAPEC-1 (B).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-01-21 00:29:19"}

PMC Usage Stats | Further Information

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Relative Metric

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