Transcriptome Changes Associated with Anaerobic Growth in Yersinia intermedia (ATCC29909)
Publication Date
October 07, 2013
Journal
PLOS ONE
Authors
Lavanya Babujee, Venkatesh Balakrishnan, Patricia J. Kiley, Jeremy D. Glasner, et al
Volume
8
Issue
10
Pages
e76567
DOI
https://dx.plos.org/10.1371/journal.pone.0076567
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0076567
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24116118
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3792023
Europe PMC
http://europepmc.org/abstract/MED/24116118
Web of Science
000325501300065
Scopus
84885055372
Mendeley
http://www.mendeley.com/research/transcriptome-changes-associated-anaerobic-growth-yersinia-intermedia-atcc29909
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Mendeley | Further Information

{"title"=>"Transcriptome Changes Associated with Anaerobic Growth in Yersinia intermedia (ATCC29909)", "type"=>"journal", "authors"=>[{"first_name"=>"Lavanya", "last_name"=>"Babujee", "scopus_author_id"=>"14024166000"}, {"first_name"=>"Venkatesh", "last_name"=>"Balakrishnan", "scopus_author_id"=>"55121468200"}, {"first_name"=>"Patricia J.", "last_name"=>"Kiley", "scopus_author_id"=>"7003423944"}, {"first_name"=>"Jeremy D.", "last_name"=>"Glasner", "scopus_author_id"=>"6603386759"}, {"first_name"=>"Nicole T.", "last_name"=>"Perna", "scopus_author_id"=>"7004881904"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84885055372", "doi"=>"10.1371/journal.pone.0076567", "pui"=>"369965521", "pmid"=>"24116118", "scopus"=>"2-s2.0-84885055372", "issn"=>"19326203"}, "id"=>"3617d45c-c5b6-3deb-864b-cf3196ca644f", "abstract"=>"BACKGROUND: The yersiniae (Enterobacteriaceae) occupy a variety of niches, including some in human and flea hosts. Metabolic adaptations of the yersiniae, which contribute to their success in these specialized environments, remain largely unknown. We report results of an investigation of the transcriptome under aerobic and anaerobic conditions for Y. intermedia, a non-pathogenic member of the genus that has been used as a research surrogate for Y. pestis. Y. intermedia shares characteristics of pathogenic yersiniae, but is not known to cause disease in humans. Oxygen restriction is an important environmental stimulus experienced by many bacteria during their life-cycles and greatly influences their survival in specific environments. How oxygen availability affects physiology in the yersiniae is of importance in their life cycles but has not been extensively characterized.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: Tiled oligonucleotide arrays based on a draft genome sequence of Y. intermedia were used in transcript profiling experiments to identify genes that change expression in response to oxygen availability during growth in minimal media with glucose. The expression of more than 400 genes, constituting about 10% of the genome, was significantly altered due to oxygen-limitation in early log phase under these conditions. Broad functional categorization indicated that, in addition to genes involved in central metabolism, genes involved in adaptation to stress and genes likely involved with host interactions were affected by oxygen-availability. Notable among these, were genes encoding functions for motility, chemotaxis and biosynthesis of cobalamin, which were up-regulated and those for iron/heme utilization, methionine metabolism and urease, which were down-regulated.\\n\\nCONCLUSIONS/SIGNIFICANCE: This is the first transcriptome analysis of a non-pathogenic Yersinia spp. and one of few elucidating the global response to oxygen limitation for any of the yersiniae. Thus this study lays the foundation for further experimental characterization of oxygen-responsive genes and pathways in this ecologically diverse genus.", "link"=>"http://www.mendeley.com/research/transcriptome-changes-associated-anaerobic-growth-yersinia-intermedia-atcc29909", "reader_count"=>19, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Master"=>1, "Other"=>2, "Student > Bachelor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Master"=>1, "Other"=>2, "Student > Bachelor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>13, "Medicine and Dentistry"=>1, "Arts and Humanities"=>1, "Psychology"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1226618"], "description"=>"<p>Gene expression data for <i>Y</i>. <i>intermedia</i> grown under aerobic and anaerobic conditions was used to derive log<sub>2</sub> ratios (X-axis) which are plotted against posterior probability of differential expression for each of the genes derived using EBarrays (Y-axis) to generate a volcano plot to visualize differential expression. Significant and insignificant genes are represented by black and grey diamonds, respectively. Red diamonds represent orthologs of genes identified as constituting the core anaerobic transcriptome of three enterobacterial members grown in the presence of glucose. A set of 20 genes were identified as likely to constitute the minimal core anaerobic transcriptome of the Enterobacteriaceae in the presence of glucose as the carbon source [22]. These 20 genes shared a 1-1-1 orthologous relationship between three members of the Enterobacteriaceae, namely <i>E</i>. <i>coli</i> K-12-MG1655, <i>Dickeya </i><i>dadantii</i> 3937 and <i>Pectobacterium </i><i>atrosepticum</i> SCRI1043 and for all of the 20 genes the pattern of expression was similar, the magnitude of change was greater than 3-fold and the genetic architecture was highly conserved. While the exact functions of most of these genes are established in the model organism <i>E</i>. <i>coli</i> that of few others still remain elusive. Of these 20 genes, 18 were differentially expressed and showed similar pattern of expression in <i>Y</i>. <i>intermedia</i> in this study. These are <i>frdABCD</i> (fumarate reductase), <i>focA, yfiD</i>, (pyruvate formate lyase), <i>adhE</i> (aldehyde dehydrogenases), <i>ynfK</i> (dethiobiotin synthetase)<i>, hypC</i> (hydrogenase components), <i>nrdD</i> (anaerobic ribonucleotide reductase), <i>dcuB</i> (dicarboxylate transporter), <i>yhbUV</i> (collagenase-like proteins), <i>pepT</i> (peptidase), <i>ycbJ</i> (uncharacterized protein), <i>exbB</i> (the membrane-spanning protein of the TonB-exbBD complex), <i>yceJ</i> (cytochrome), <i>yceI</i> (uncharacterized protein). Except for five genes (yfiD, yhbV,ycbJ, yceJ, yceI), all of the remaining 13 genes showed fold changes greater than 3 (our stringent criteria established in a previous study) in <i>Y</i>. <i>intermedia</i>. The only gene which is present in the core but missing in the differentially expressed set in <i>Y</i>. <i>intermedia</i> is <i>nrdG</i> (anaerobically functioning ribonucleotide reductase).</p>", "links"=>[], "tags"=>[], "article_id"=>816112, "categories"=>["Biological Sciences"], "users"=>["Lavanya Babujee", "Venkatesh Balakrishnan", "Patricia J. Kiley", "Jeremy D. Glasner", "Nicole T. Perna"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076567.g001", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Volcano_Plot_of_fold_change_versus_significance_/816112", "title"=>"Volcano Plot of fold change versus significance.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-07 01:42:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1226621", "https://ndownloader.figshare.com/files/1226622", "https://ndownloader.figshare.com/files/1226623"], "description"=>"<div><p>Background</p><p>The yersiniae (Enterobacteriaceae) occupy a variety of niches, including some in human and flea hosts. Metabolic adaptations of the yersiniae, which contribute to their success in these specialized environments, remain largely unknown. We report results of an investigation of the transcriptome under aerobic and anaerobic conditions for <i>Y. intermedia</i>, a non-pathogenic member of the genus that has been used as a research surrogate for <i>Y. pestis</i>. <i>Y. intermedia</i> shares characteristics of pathogenic yersiniae, but is not known to cause disease in humans. Oxygen restriction is an important environmental stimulus experienced by many bacteria during their life-cycles and greatly influences their survival in specific environments. How oxygen availability affects physiology in the yersiniae is of importance in their life cycles but has not been extensively characterized.</p> <p>Methodology/Principal Findings</p><p>Tiled oligonucleotide arrays based on a draft genome sequence of <i>Y. intermedia</i> were used in transcript profiling experiments to identify genes that change expression in response to oxygen availability during growth in minimal media with glucose. The expression of more than 400 genes, constituting about 10% of the genome, was significantly altered due to oxygen-limitation in early log phase under these conditions. Broad functional categorization indicated that, in addition to genes involved in central metabolism, genes involved in adaptation to stress and genes likely involved with host interactions were affected by oxygen-availability. Notable among these, were genes encoding functions for motility, chemotaxis and biosynthesis of cobalamin, which were up-regulated and those for iron/heme utilization, methionine metabolism and urease, which were down-regulated.</p> <p>Conclusions/Significance</p><p>This is the first transcriptome analysis of a non-pathogenic <i>Yersinia</i><i>spp.</i> and one of few elucidating the global response to oxygen limitation for any of the yersiniae. Thus this study lays the foundation for further experimental characterization of oxygen-responsive genes and pathways in this ecologically diverse genus.</p> </div>", "links"=>[], "tags"=>["transcriptome", "anaerobic"], "article_id"=>816115, "categories"=>["Biological Sciences"], "users"=>["Lavanya Babujee", "Venkatesh Balakrishnan", "Patricia J. Kiley", "Jeremy D. Glasner", "Nicole T. Perna"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0076567.s001", "https://dx.doi.org/10.1371/journal.pone.0076567.s002", "https://dx.doi.org/10.1371/journal.pone.0076567.s003"], "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Transcriptome_Changes_Associated_with_Anaerobic_Growth_in_Yersinia_intermedia_ATCC29909_/816115", "title"=>"Transcriptome Changes Associated with Anaerobic Growth in <i>Yersinia intermedia</i> (ATCC29909)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-10-07 01:42:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1226619"], "description"=>"<p>Phylogenprofiler (Integrated Microbial Genomes) was used with analytical settings as described in methods to obtain homologs of <i>Y</i>. <i>intermedia</i> in other yersiniae. A Venn diagram was built to display the number of differentially expressed genes in <i>Y</i>. <i>intermedia</i> that have homologs in <i>Y</i>. <i>enterocolitica</i> (<i>Ye8081</i>, blue circle, 376 genes), <i>Y</i>. <i>pseudotuberculosis</i> (<i>Ytb31758</i>, purple circle, 319 genes) and <i>Y</i>. <i>pestis</i> (<i>YpCO92</i>, red circle, 299 genes).</p>", "links"=>[], "tags"=>["392", "differentially", "genes", "intermedia", "homologs", "pathogenic"], "article_id"=>816113, "categories"=>["Biological Sciences"], "users"=>["Lavanya Babujee", "Venkatesh Balakrishnan", "Patricia J. Kiley", "Jeremy D. Glasner", "Nicole T. Perna"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076567.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Graphical_representation_of_392_differentially_expressed_genes_in_Y_intermedia_which_have_homologs_in_at_least_one_of_the_pathogenic_yersiniae_/816113", "title"=>"Graphical representation of 392 differentially expressed genes in Y. intermedia which have homologs in at least one of the pathogenic yersiniae.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-07 01:42:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1226620"], "description"=>"<p>Genes from Table S1 were broadly categorized according to their biological function. Each bar represents the actual number of genes.</p>", "links"=>[], "tags"=>["categories", "anaerobically", "up-regulated", "down-regulated"], "article_id"=>816114, "categories"=>["Biological Sciences"], "users"=>["Lavanya Babujee", "Venkatesh Balakrishnan", "Patricia J. Kiley", "Jeremy D. Glasner", "Nicole T. Perna"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076567.g003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Functional_categories_of_anaerobically_up_regulated_yellow_and_anaerobically_down_regulated_blue_genes_/816114", "title"=>"Functional categories of anaerobically up-regulated (yellow) and anaerobically down-regulated (blue) genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-07 01:42:02"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"9", "full-text"=>"8", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"15", "full-text"=>"14", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2020", "month"=>"2"}
  • {"unique-ip"=>"13", "full-text"=>"14", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"3"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[269, 466, 588, 697, 800, 896, 988, 1076, 1165, 1254, 1340, 1417]}, {"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[302, 488, 607, 717, 832, 931, 1024, 1117, 1212, 1302, 1389, 1469, 1535]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[284, 491, 620, 738, 843, 945, 1043, 1137, 1225, 1315, 1400, 1479, 1555]}, {"subject_area"=>"/Biology and life sciences/Microbiology", "average_usage"=>[293, 503, 638, 755, 861, 960, 1056, 1146, 1239, 1323, 1403, 1491, 1568]}, {"subject_area"=>"/Physical sciences/Chemistry", "average_usage"=>[247, 429, 544, 647, 747, 842, 929, 1012, 1099, 1179, 1263, 1339, 1409]}]}
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