Revised Phylogeny and Novel Horizontally Acquired Virulence Determinants of the Model Soft Rot Phytopathogen Pectobacterium wasabiae SCC3193
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{"title"=>"Revised Phylogeny and Novel Horizontally Acquired Virulence Determinants of the Model Soft Rot Phytopathogen Pectobacterium wasabiae SCC3193", "type"=>"journal", "authors"=>[{"first_name"=>"Johanna", "last_name"=>"Nykyri", "scopus_author_id"=>"24767976100"}, {"first_name"=>"Outi", "last_name"=>"Niemi", "scopus_author_id"=>"55457717500"}, {"first_name"=>"Patrik", "last_name"=>"Koskinen", "scopus_author_id"=>"36994470500"}, {"first_name"=>"Jussi", "last_name"=>"Nokso-Koivisto", "scopus_author_id"=>"35747037100"}, {"first_name"=>"Miia", "last_name"=>"Pasanen", "scopus_author_id"=>"35789136700"}, {"first_name"=>"Martin", "last_name"=>"Broberg", "scopus_author_id"=>"55516592700"}, {"first_name"=>"Ilja", "last_name"=>"Plyusnin", "scopus_author_id"=>"24401761200"}, {"first_name"=>"Petri", "last_name"=>"Törönen", "scopus_author_id"=>"6602343880"}, {"first_name"=>"Liisa", "last_name"=>"Holm", "scopus_author_id"=>"7103303388"}, {"first_name"=>"Minna", "last_name"=>"Pirhonen", "scopus_author_id"=>"6603583195"}, {"first_name"=>"E. Tapio", "last_name"=>"Palva", "scopus_author_id"=>"24535145300"}], "year"=>2012, "source"=>"PLoS Pathogens", "identifiers"=>{"pui"=>"366234385", "sgr"=>"84870811273", "issn"=>"15537366", "pmid"=>"23133391", "scopus"=>"2-s2.0-84870811273", "doi"=>"10.1371/journal.ppat.1003013", "isbn"=>"1553-7374 (Electronic) 1553-7366 (Linking)"}, "id"=>"d6dbc33c-2a87-37b9-b1b3-83ba10ede143", "abstract"=>"Soft rot disease is economically one of the most devastating bacterial diseases affecting plants worldwide. In this study, we present novel insights into the phylogeny and virulence of the soft rot model Pectobacterium sp. SCC3193, which was isolated from a diseased potato stem in Finland in the early 1980s. Genomic approaches, including proteome and genome comparisons of all sequenced soft rot bacteria, revealed that SCC3193, previously included in the species Pectobacterium carotovorum, can now be more accurately classified as Pectobacterium wasabiae. Together with the recently revised phylogeny of a few P. carotovorum strains and an increasing number of studies on P. wasabiae, our work indicates that P. wasabiae has been unnoticed but present in potato fields worldwide. A combination of genomic approaches and in planta experiments identified features that separate SCC3193 and other P. wasabiae strains from the rest of soft rot bacteria, such as the absence of a type III secretion system that contributes to virulence of other soft rot species. Experimentally established virulence determinants include the putative transcriptional regulator SirB, two partially redundant type VI secretion systems and two horizontally acquired clusters (Vic1 and Vic2), which contain predicted virulence genes. Genome comparison also revealed other interesting traits that may be related to life in planta or other specific environmental conditions. These traits include a predicted benzoic acid/salicylic acid carboxyl methyltransferase of eukaryotic origin. The novelties found in this work indicate that soft rot bacteria have a reservoir of unknown traits that may be utilized in the poorly understood latent stage in planta. The genomic approaches and the comparison of the model strain SCC3193 to other sequenced Pectobacterium strains, including the type strain of P. wasabiae, provides a solid basis for further investigation of the virulence, distribution and phylogeny of soft rot bacteria and, potentially, other bacteria as well.", "link"=>"http://www.mendeley.com/research/revised-phylogeny-novel-horizontally-acquired-virulence-determinants-model-soft-rot-phytopathogen-pe", "reader_count"=>47, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>13, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>2, "Student > Master"=>6, "Other"=>2, "Student > Bachelor"=>4, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>13, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>2, "Student > Master"=>6, "Other"=>2, "Student > Bachelor"=>4, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>10, "Agricultural and Biological Sciences"=>29, "Chemistry"=>1, "Social Sciences"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>29}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>10}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United Kingdom"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/550302"], "description"=>"<p>The virulence of mutants was experimentally determined on tobacco and potato. Experiments were repeated a minimum of three times. The data from one experiment is shown for tobacco, and the combined data from five experiments are shown for potato. The strains shown are <i>Pectobacterium wasabiae</i> SCC3193, <i>sirB<sup>−</sup></i>, <i>sirB<sup>−</sup></i>(pSirB), <i>sirB<sup>−</sup></i>(pSirB1), <i>sirB<sup>−</sup></i>(pSirB2), <i>sirB<sup>−</sup></i>(pMW119), Vic1, Vic2 and T6SS-double mutant. (A) Axenic tobacco seedlings (cv. Samsun) were inoculated locally with 5×10<sup>4</sup> cfu, and symptoms were documented after 48 h as follows: 0 = no maceration, 1 = maceration in less than half of the inoculated leaf, 2 = maceration in more than half of the inoculated leaf, 3 = inoculated leaf was completely macerated, 4 = maceration spread to other leaves, but less than half of the plant was macerated, 5 = maceration spread to other leaves, and more than half of the plant was macerated and 6 = the whole plant was macerated. (B) To determine the bacterial growth on tobacco, samples were taken at 24 and 44 h post-inoculation, and the amount of living bacteria was measured by plate counting. For one sample, two inoculated plants were combined, and the result shows the average of 8 samples. Bars represent standard deviations. (C) Potato tuber slices (cv. Van Gogh) were inoculated with 1×10<sup>4</sup> cfu, and after three days the macerated area (%) on the tuber slice was documented as follows: 0 = 0%, 1 = ∼5%, 2 = ∼25%, 3 = ∼50%, 4 = ∼75%, 5 = ∼90% and 6 = 100%.</p>", "links"=>[], "tags"=>["vic2", "t6ss-double", "mutants", "showed", "virulence"], "article_id"=>220776, "categories"=>["Genetics"], "users"=>["Johanna Nykyri", "Outi Niemi", "Patrik Koskinen", "Jussi Nokso-Koivisto", "Miia Pasanen", "Martin Broberg", "Ilja Plyusnin", "Petri Toronen", "Liisa Holm", "Minna Pirhonen", "E. Tapio Palva"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003013.g005", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_sirB_8722_Vic1_Vic2_and_T6SS_double_mutants_showed_decreased_virulence_in_planta_/220776", "title"=>"<i>sirB<sup>−</sup></i>, Vic1, Vic2 and T6SS-double mutants showed decreased virulence in planta.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-01 00:12:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/550398"], "description"=>"<p>Visualization and a comparison of the Vic2 locus was completed in <i>Pectobacterium wasabiae</i> SCC3193, which contains a putative lipoprotein transporting system and a HopL1-like protein. A comparison of the gene cluster was conducted using blastn and blastp against a nucleotide collection and against non-redundant protein sequences to obtain strains with similar loci. ORFs are indicated using colored and scaled arrows, except in case of <i>P. wasabiae</i> CFPB 3304T for which operons were not predicted.</p>", "links"=>[], "tags"=>["locus"], "article_id"=>220885, "categories"=>["Genetics"], "users"=>["Johanna Nykyri", "Outi Niemi", "Patrik Koskinen", "Jussi Nokso-Koivisto", "Miia Pasanen", "Martin Broberg", "Ilja Plyusnin", "Petri Toronen", "Liisa Holm", "Minna Pirhonen", "E. Tapio Palva"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003013.g006", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Virulence_cluster_2_locus_comparison_/220885", "title"=>"Virulence cluster 2 locus comparison.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-01 00:14:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/550000"], "description"=>"<p>The strain numbers correspond to the following species: <i>Yersinia pestis</i> CO92 (outgroup), <i>Dickeya dadantii</i> Ech703, <i>Dickeya dadantii</i> Ech586, <i>Dickeya dadantii</i> 3937, <i>Dickeya zeae</i> Ech1591, <i>Pectobacterium carotovorum</i> subsp. <i>brasiliensis</i> PBR1692, <i>Pectobacterium carotovorum</i> WPP14, <i>Pectobacterium carotovorum</i> subsp. <i>carotovorum</i> PC1, <i>Pectobacterium atrosepticum</i> SCRI1043, <i>Pectobacterium wasabiae</i> WPP163, <i>Pectobacterium wasabiae</i> SCC3193 and <i>Pectobacterium wasabiae</i> CFBP 3304<sup>T</sup>. (A) OrthoMCL clusters were converted into an orthologs vs. species matrix and visualized as a heat map. The core genome is visualized in the middle of the figure, and species and strain-specific protein clusters can be found above and below the core. (B) The correlations between proteomes were calculated and visualized to indicate their phylogenetic relationships.</p>", "links"=>[], "tags"=>["proteomes"], "article_id"=>220486, "categories"=>["Genetics"], "users"=>["Johanna Nykyri", "Outi Niemi", "Patrik Koskinen", "Jussi Nokso-Koivisto", "Miia Pasanen", "Martin Broberg", "Ilja Plyusnin", "Petri Toronen", "Liisa Holm", "Minna Pirhonen", "E. Tapio Palva"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003013.g002", "stats"=>{"downloads"=>4, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_proteomes_of_Pectobacterium_and_Dickeya_strains_/220486", "title"=>"Comparison of proteomes of <i>Pectobacterium</i> and <i>Dickeya</i> strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-01 00:08:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/294481", "https://ndownloader.figshare.com/files/294507", "https://ndownloader.figshare.com/files/294526", "https://ndownloader.figshare.com/files/294552", "https://ndownloader.figshare.com/files/294605", "https://ndownloader.figshare.com/files/294677", "https://ndownloader.figshare.com/files/294699", "https://ndownloader.figshare.com/files/294762", "https://ndownloader.figshare.com/files/294825"], "description"=>"<div><p>Soft rot disease is economically one of the most devastating bacterial diseases affecting plants worldwide. In this study, we present novel insights into the phylogeny and virulence of the soft rot model <em>Pectobacterium</em> sp. SCC3193, which was isolated from a diseased potato stem in Finland in the early 1980s. Genomic approaches, including proteome and genome comparisons of all sequenced soft rot bacteria, revealed that SCC3193, previously included in the species <em>Pectobacterium carotovorum</em>, can now be more accurately classified as <em>Pectobacterium wasabiae</em>. Together with the recently revised phylogeny of a few <em>P. carotovorum</em> strains and an increasing number of studies on <em>P. wasabiae</em>, our work indicates that <em>P. wasabiae</em> has been unnoticed but present in potato fields worldwide. A combination of genomic approaches and in planta experiments identified features that separate SCC3193 and other <em>P. wasabiae</em> strains from the rest of soft rot bacteria, such as the absence of a type III secretion system that contributes to virulence of other soft rot species. Experimentally established virulence determinants include the putative transcriptional regulator SirB, two partially redundant type VI secretion systems and two horizontally acquired clusters (Vic1 and Vic2), which contain predicted virulence genes. Genome comparison also revealed other interesting traits that may be related to life in planta or other specific environmental conditions. These traits include a predicted benzoic acid/salicylic acid carboxyl methyltransferase of eukaryotic origin. The novelties found in this work indicate that soft rot bacteria have a reservoir of unknown traits that may be utilized in the poorly understood latent stage in planta. The genomic approaches and the comparison of the model strain SCC3193 to other sequenced <em>Pectobacterium</em> strains, including the type strain of <em>P. wasabiae</em>, provides a solid basis for further investigation of the virulence, distribution and phylogeny of soft rot bacteria and, potentially, other bacteria as well.</p> </div>", "links"=>[], "tags"=>["revised", "phylogeny", "horizontally", "acquired", "virulence", "determinants", "rot", "phytopathogen", "scc3193"], "article_id"=>117987, "categories"=>["Genetics"], "users"=>["Johanna Nykyri", "Outi Niemi", "Patrik Koskinen", "Jussi Nokso-Koivisto", "Miia Pasanen", "Martin Broberg", "Ilja Plyusnin", "Petri Toronen", "Liisa Holm", "Minna Pirhonen", "E. Tapio Palva"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1003013.s001", "https://dx.doi.org/10.1371/journal.ppat.1003013.s002", "https://dx.doi.org/10.1371/journal.ppat.1003013.s003", "https://dx.doi.org/10.1371/journal.ppat.1003013.s004", "https://dx.doi.org/10.1371/journal.ppat.1003013.s005", "https://dx.doi.org/10.1371/journal.ppat.1003013.s006", "https://dx.doi.org/10.1371/journal.ppat.1003013.s007", "https://dx.doi.org/10.1371/journal.ppat.1003013.s008", "https://dx.doi.org/10.1371/journal.ppat.1003013.s009"], "stats"=>{"downloads"=>30, "page_views"=>45, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Revised_Phylogeny_and_Novel_Horizontally_Acquired_Virulence_Determinants_of_the_Model_Soft_Rot_Phytopathogen_Pectobacterium_wasabiae_SCC3193__/117987", "title"=>"Revised Phylogeny and Novel Horizontally Acquired Virulence Determinants of the Model Soft Rot Phytopathogen <em>Pectobacterium wasabiae</em> SCC3193", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-11-01 02:13:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/549828"], "description"=>"<p>For the selection of the orthologous groups, reciprocal best hits were determined based on similarities detected using the fast protein sequence database search tool SANS. The ortholog groups were aligned using Muscle and bootstrapped trees were created with RAxML. Consensus tree was built using Consense and visualized with iTOL. The values presented in the figure indicate bootstrap values calculated based on 51000 bootstrapped trees. The <i>Pectobacterium</i> and <i>Dickeya</i> groups are highlighted.</p>", "links"=>[], "tags"=>["constructed", "51", "orthologous", "groups", "53", "bacterial", "strains", "yeast"], "article_id"=>220304, "categories"=>["Genetics"], "users"=>["Johanna Nykyri", "Outi Niemi", "Patrik Koskinen", "Jussi Nokso-Koivisto", "Miia Pasanen", "Martin Broberg", "Ilja Plyusnin", "Petri Toronen", "Liisa Holm", "Minna Pirhonen", "E. Tapio Palva"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003013.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_constructed_of_51_orthologous_protein_groups_from_53_bacterial_strains_and_yeast_as_an_outgroup_/220304", "title"=>"Phylogenetic tree constructed of 51 orthologous protein groups from 53 bacterial strains and yeast as an outgroup.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-01 00:05:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/550187"], "description"=>"<p>The circles from outer to inner represent open reading frames on both strands, tRNAs (green) and rRNAs (orange), manually curated genomic islands (red), SIGI-HMM predicted islands (orange), IslandPath-DIMOB predicted islands (blue), IslandPick predicted islands (green) and GC percentage (gray).</p>", "links"=>[], "tags"=>["chromosome"], "article_id"=>220677, "categories"=>["Genetics"], "users"=>["Johanna Nykyri", "Outi Niemi", "Patrik Koskinen", "Jussi Nokso-Koivisto", "Miia Pasanen", "Martin Broberg", "Ilja Plyusnin", "Petri Toronen", "Liisa Holm", "Minna Pirhonen", "E. Tapio Palva"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003013.g004", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Circular_representation_of_the_chromosome_of_Pectobacterium_wasabiae_SCC3193_/220677", "title"=>"Circular representation of the chromosome of <i>Pectobacterium wasabiae</i> SCC3193.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-01 00:11:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/550090"], "description"=>"<p>Pairwise alignments of genomes were generated using Mauve. <i>P. wasabiae</i> CFBP 3304<sup>T</sup> contigs were aligned according to <i>P. wasabiae</i> SCC3193. The sequence similarity in the pairwise alignment of <i>P. wasabiae</i> SCC3193 and CFBP 3304<sup>T</sup> was 80.6%. The similarity between SCC3193 and WPP163 was 92.6% and between WPP163 and CFBP 3304<sup>T</sup> was 80.9%. The sequence similarity compared to <i>P. atrosepticum</i> was 71.3% in the case of SCC3193, 69.6% for CFBP 3304<sup>T</sup> and 72.2% for WPP163.</p>", "links"=>[], "tags"=>["genetics and genomics"], "article_id"=>220581, "categories"=>["Genetics"], "users"=>["Johanna Nykyri", "Outi Niemi", "Patrik Koskinen", "Jussi Nokso-Koivisto", "Miia Pasanen", "Martin Broberg", "Ilja Plyusnin", "Petri Toronen", "Liisa Holm", "Minna Pirhonen", "E. Tapio Palva"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003013.g003", "stats"=>{"downloads"=>5, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Synteny_of_Pectobacterium_wasabiae_and_Pectobacterium_atrosepticum_genomes_/220581", "title"=>"Synteny of <i>Pectobacterium wasabiae</i> and <i>Pectobacterium atrosepticum</i> genomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-01 00:09:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/550542"], "description"=>"<p><i>Pectobacterium wasabiae</i> SCC3193 genomic islands of 10 kb or larger and selected smaller islands.</p>", "links"=>[], "tags"=>["scc3193", "genomic", "islands", "10", "kb", "larger", "smaller"], "article_id"=>221014, "categories"=>["Genetics"], "users"=>["Johanna Nykyri", "Outi Niemi", "Patrik Koskinen", "Jussi Nokso-Koivisto", "Miia Pasanen", "Martin Broberg", "Ilja Plyusnin", "Petri Toronen", "Liisa Holm", "Minna Pirhonen", "E. Tapio Palva"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1003013.t001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pectobacterium_wasabiae_SCC3193_genomic_islands_of_10_kb_or_larger_and_selected_smaller_islands_/221014", "title"=>"<i>Pectobacterium wasabiae</i> SCC3193 genomic islands of 10 kb or larger and selected smaller islands.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-11-01 00:16:54"}

PMC Usage Stats | Further Information

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