Complete Genome and Transcriptomes of Streptococcus parasanguinis FW213: Phylogenic Relations and Potential Virulence Mechanisms
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{"title"=>"Complete genome and transcriptomes of streptococcus parasanguinis FW213: Phylogenic relations and potential virulence mechanisms", "type"=>"journal", "authors"=>[{"first_name"=>"Jianing", "last_name"=>"Geng", "scopus_author_id"=>"12777948600"}, {"first_name"=>"Cheng Hsun", "last_name"=>"Chiu", "scopus_author_id"=>"57198732465"}, {"first_name"=>"Petrus", "last_name"=>"Tang", "scopus_author_id"=>"8938268600"}, {"first_name"=>"Yaping", "last_name"=>"Chen", "scopus_author_id"=>"18133622300"}, {"first_name"=>"Hui Ru", "last_name"=>"Shieh", "scopus_author_id"=>"57196561231"}, {"first_name"=>"Songnian", "last_name"=>"Hu", "scopus_author_id"=>"8938269000"}, {"first_name"=>"Yi Ywan M.", "last_name"=>"Chen", "scopus_author_id"=>"7601439803"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"22529932", "doi"=>"10.1371/journal.pone.0034769", "sgr"=>"84859967531", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84859967531", "issn"=>"19326203", "pui"=>"364660925"}, "id"=>"43e6e6ef-4644-3bbd-ba10-ee51d83276d6", "abstract"=>"Streptococcus parasanguinis, a primary colonizer of the tooth surface, is also an opportunistic pathogen for subacute endocarditis. The complete genome of strain FW213 was determined using the traditional shotgun sequencing approach and further refined by the transcriptomes of cells in early exponential and early stationary growth phases in this study. The transcriptomes also discovered 10 transcripts encoding known hypothetical proteins, one pseudogene, five transcripts matched to the Rfam and additional 87 putative small RNAs within the intergenic regions defined by the GLIMMER analysis. The genome contains five acquired genomic islands (GIs) encoding proteins which potentially contribute to the overall pathogenic capacity and fitness of this microbe. The differential expression of the GIs and various open reading frames outside the GIs at the two growth phases suggested that FW213 possess a range of mechanisms to avoid host immune clearance, to colonize host tissues, to survive within oral biofilms and to overcome various environmental insults. Furthermore, the comparative genome analysis of five S. parasanguinis strains indicates that albeit S. parasanguinis strains are highly conserved, variations in the genome content exist. These variations may reflect differences in pathogenic potential between the strains.", "link"=>"http://www.mendeley.com/research/complete-genome-transcriptomes-streptococcus-parasanguinis-fw213-phylogenic-relations-potential-viru", "reader_count"=>20, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>5, "Student > Master"=>2, "Other"=>2, "Student > Bachelor"=>5, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>5, "Student > Master"=>2, "Other"=>2, "Student > Bachelor"=>5, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Medicine and Dentistry"=>1, "Agricultural and Biological Sciences"=>13, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>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"=>2}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United States"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/652202"], "description"=>"a<p>, same as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034769#pone-0034769-t003\" target=\"_blank\">Table 3</a>.</p>b<p>, the ratio of the expression levels in cells grown at OD<sub>600</sub> = 0.8 divided by that from cells grown at OD<sub>600</sub> = 0.3.</p>", "links"=>[], "tags"=>["virulence", "factors", "up-regulated", "stationary"], "article_id"=>322689, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Jianing Geng", "Cheng-Hsun Chiu", "Petrus Tang", "Yaping Chen", "Hui-Ru Shieh", "Songnian Hu", "Yi-Ywan M. Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034769.t004", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Potential_virulence_factors_that_are_up_regulated_in_the_early_stationary_phase_in_S_parasanguinis_FW213_/322689", "title"=>"Potential virulence factors that are up-regulated in the early stationary phase in <i>S. parasanguinis</i> FW213.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-18 00:44:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/651211"], "description"=>"<p>(A) The expression levels of the sense and anti-sense strands are present at single-nt resolution in black and grey, respectively. The coverage is calculated as log(the number of reads+1)/log(1.1). (B) The numbers of genes differentially expressed under the two growth conditions according to COG classification.</p>", "links"=>[], "tags"=>["transcriptomes", "od"], "article_id"=>321699, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Jianing Geng", "Cheng-Hsun Chiu", "Petrus Tang", "Yaping Chen", "Hui-Ru Shieh", "Songnian Hu", "Yi-Ywan M. Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034769.g002", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_global_transcriptomes_of_S_parasanguinis_at_OD_600_8202_8202_0_3_and_OD_600_8202_8202_0_8_/321699", "title"=>"The global transcriptomes of <i>S. parasanguinis</i> at OD <sub>600</sub> = 0.3 and OD <sub>600</sub> = 0.8.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:28:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/335014", "https://ndownloader.figshare.com/files/335054", "https://ndownloader.figshare.com/files/335097", "https://ndownloader.figshare.com/files/335133", "https://ndownloader.figshare.com/files/335186", "https://ndownloader.figshare.com/files/335238", "https://ndownloader.figshare.com/files/335312", "https://ndownloader.figshare.com/files/335403", "https://ndownloader.figshare.com/files/335483", "https://ndownloader.figshare.com/files/335536"], "description"=>"<div><p><em>Streptococcus parasanguinis</em>, a primary colonizer of the tooth surface, is also an opportunistic pathogen for subacute endocarditis. The complete genome of strain FW213 was determined using the traditional shotgun sequencing approach and further refined by the transcriptomes of cells in early exponential and early stationary growth phases in this study. The transcriptomes also discovered 10 transcripts encoding known hypothetical proteins, one pseudogene, five transcripts matched to the Rfam and additional 87 putative small RNAs within the intergenic regions defined by the GLIMMER analysis. The genome contains five acquired genomic islands (GIs) encoding proteins which potentially contribute to the overall pathogenic capacity and fitness of this microbe. The differential expression of the GIs and various open reading frames outside the GIs at the two growth phases suggested that FW213 possess a range of mechanisms to avoid host immune clearance, to colonize host tissues, to survive within oral biofilms and to overcome various environmental insults. Furthermore, the comparative genome analysis of five <em>S. parasanguinis</em> strains indicates that albeit <em>S. parasanguinis</em> strains are highly conserved, variations in the genome content exist. These variations may reflect differences in pathogenic potential between the strains.</p> </div>", "links"=>[], "tags"=>["genome", "transcriptomes", "phylogenic", "relations", "virulence", "mechanisms"], "article_id"=>126183, "categories"=>["Cancer", "Genetics", "Microbiology"], "users"=>["Jianing Geng", "Cheng-Hsun Chiu", "Petrus Tang", "Yaping Chen", "Hui-Ru Shieh", "Songnian Hu", "Yi-Ywan M. Chen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034769.s001", "https://dx.doi.org/10.1371/journal.pone.0034769.s002", "https://dx.doi.org/10.1371/journal.pone.0034769.s003", "https://dx.doi.org/10.1371/journal.pone.0034769.s004", "https://dx.doi.org/10.1371/journal.pone.0034769.s005", "https://dx.doi.org/10.1371/journal.pone.0034769.s006", "https://dx.doi.org/10.1371/journal.pone.0034769.s007", "https://dx.doi.org/10.1371/journal.pone.0034769.s008", "https://dx.doi.org/10.1371/journal.pone.0034769.s009", "https://dx.doi.org/10.1371/journal.pone.0034769.s010"], "stats"=>{"downloads"=>10, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Complete_Genome_and_Transcriptomes_of_Streptococcus_parasanguinis_FW213_Phylogenic_Relations_and_Potential_Virulence_Mechanisms/126183", "title"=>"Complete Genome and Transcriptomes of <em>Streptococcus parasanguinis</em> FW213: Phylogenic Relations and Potential Virulence Mechanisms", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-04-18 01:43:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/652085"], "description"=>"a<p>, the PRKM was calculated as described in the materials and methods.</p>b<p>, the ratio of the expression levels in cells grown at OD<sub>600</sub> = 0.3 divided by that from cells grown at OD<sub>600</sub> = 0.8.</p>", "links"=>[], "tags"=>["virulence", "factors", "exponential"], "article_id"=>322568, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Jianing Geng", "Cheng-Hsun Chiu", "Petrus Tang", "Yaping Chen", "Hui-Ru Shieh", "Songnian Hu", "Yi-Ywan M. Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034769.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Potential_virulence_factors_for_the_early_exponential_growth_phase_in_S_parasanguinis_FW213_/322568", "title"=>"Potential virulence factors for the early exponential growth phase in <i>S. parasanguinis</i> FW213.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-18 00:42:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/652046"], "description"=>"a<p>, identified by RNA-seq results.</p>b<p>, predicted by sRNAPredict2 and confirmed by RNA-seq results.</p>c<p>, from reference 29.</p>", "links"=>[], "tags"=>["fw213"], "article_id"=>322536, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Jianing Geng", "Cheng-Hsun Chiu", "Petrus Tang", "Yaping Chen", "Hui-Ru Shieh", "Songnian Hu", "Yi-Ywan M. Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034769.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_General_features_of_S_parasanguinis_FW213_genome_/322536", "title"=>"General features of <i>S. parasanguinis</i> FW213 genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-18 00:42:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/651320"], "description"=>"<p>The primer extension analysis of Spaf_0344 is shown on the left side of the figure. The nucleotide sequence of the 5′ flanking region and the read counts at each nucleotide are shown on the right side of the figure. The primer extension analysis was performed with the total cellular RNA of <i>S. parasanguinis</i> FW213and a primer located 116-base 3′ to the ATG and containing the antisense sequence of Spaf_0344. The extended product was analyzed alongside a DNA-sequencing reaction by using the same primer. The location of the ATG start site of orf344 and the transcription initiation site (TSS) are indicated.</p>", "links"=>[], "tags"=>["transcription", "initiation"], "article_id"=>321810, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Jianing Geng", "Cheng-Hsun Chiu", "Petrus Tang", "Yaping Chen", "Hui-Ru Shieh", "Songnian Hu", "Yi-Ywan M. Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034769.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Determination_of_the_transcription_initiation_site_of_Spaf_0344_/321810", "title"=>"Determination of the transcription initiation site of Spaf_0344.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:30:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/651775"], "description"=>"<p>The red and blue bars represent the forward and reverse matches, respectively.</p>", "links"=>[], "tags"=>["visualization", "genome", "strains", "fw213"], "article_id"=>322259, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Jianing Geng", "Cheng-Hsun Chiu", "Petrus Tang", "Yaping Chen", "Hui-Ru Shieh", "Songnian Hu", "Yi-Ywan M. Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034769.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ACT_visualization_of_the_whole_genome_comparison_based_on_BLAST_between_strains_FW213_and_ATCC15912_/322259", "title"=>"ACT visualization of the whole genome comparison based on BLAST between strains FW213 and ATCC15912.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:37:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/651936"], "description"=>"<p>(A), FW213island_1; (B), FW213island_2; (C), FW213island_3; (D), FW213island_4; (E), FW213island_5. The expression levels in cultures at OD <sub>600</sub> = 0.3 and OD <sub>600</sub> = 0.8 are present at single-nt resolution in red and green, respectively. The relative sizes, locations, and orientations of the ORFs are indicated by color-coded horizontal arrows as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034769#pone-0034769-g001\" target=\"_blank\">Fig. 1</a> legend with the exception that genes of the cellular processes and signaling category are in sienna.</p>", "links"=>[], "tags"=>["putative", "gis"], "article_id"=>322422, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Jianing Geng", "Cheng-Hsun Chiu", "Petrus Tang", "Yaping Chen", "Hui-Ru Shieh", "Songnian Hu", "Yi-Ywan M. Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034769.g007", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_the_putative_GIs_and_their_expression_in_S_parasanguinis_FW213_/322422", "title"=>"Schematic representation of the putative GIs and their expression in <i>S. parasanguinis</i> FW213.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:40:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/652125"], "description"=>"<p>Properties of the genomic islands in <i>S. parasanguinis</i> FW213.</p>", "links"=>[], "tags"=>["genomic", "islands"], "article_id"=>322615, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Jianing Geng", "Cheng-Hsun Chiu", "Petrus Tang", "Yaping Chen", "Hui-Ru Shieh", "Songnian Hu", "Yi-Ywan M. Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034769.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Properties_of_the_genomic_islands_in_S_parasanguinis_FW213_/322615", "title"=>"Properties of the genomic islands in <i>S. parasanguinis</i> FW213.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-18 00:43:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/651454"], "description"=>"<p>The sequence coverage from 753,521 to 767,556 bp of the <i>S. parasanguinis</i> FW213 chromosome is shown. The operon is defined based on continuous expression and sequence coverage change, and the limits of the operon (Spaf_0735-Spaf_0738) are indicated by vertical arrows. The tag number of each gene is listed below the arrows. The ORFs are color-coded as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034769#pone-0034769-g001\" target=\"_blank\">Fig. 1</a> legend. The coverage is calculated as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034769#pone-0034769-g002\" target=\"_blank\">Fig. 2</a> legend.</p>", "links"=>[], "tags"=>["operons"], "article_id"=>321946, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Jianing Geng", "Cheng-Hsun Chiu", "Petrus Tang", "Yaping Chen", "Hui-Ru Shieh", "Songnian Hu", "Yi-Ywan M. Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034769.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_operons_based_on_the_expression_profiles_/321946", "title"=>"Identification of operons based on the expression profiles.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:32:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/651016"], "description"=>"<p>The genome position scaled in kb from base 1 is shown on the outer circle. The second and third circles show the coding sequences on the plus and minus strands, respectively. All genes are color-coded based on the COG functional category as follows: cyan, information storage and processing; yellow, cellular processes and signaling; magenta, metabolism; black, poorly characterized. The fourth circle shows rRNA in cobalt blue and tRNA in brown. The fifth circle shows GC content (in 1-kb windows). The values that are greater than and below the average (41.62%) are in green and red, respectively. The sixth circle shows GC skew curve (10-kb window and 1-kb incremental shift). The values for plus and minus strands are shown in cobalt blue and purple, respectively. The relative locations and sizes of the five putative pathogenic islands are shown outside the scale.</p>", "links"=>[], "tags"=>["fw213"], "article_id"=>321500, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Jianing Geng", "Cheng-Hsun Chiu", "Petrus Tang", "Yaping Chen", "Hui-Ru Shieh", "Songnian Hu", "Yi-Ywan M. Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034769.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Circular_presentation_of_the_S_parasanguinis_FW213_chromosome_/321500", "title"=>"Circular presentation of the <i>S. parasanguinis</i> FW213 chromosome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:25:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/652160"], "description"=>"a<p>, same as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034769#pone-0034769-t003\" target=\"_blank\">Table 3</a>.</p>b<p>, Spaf_449, encoding the structure protein (CadD) is part of a 2-gene operon.</p>", "links"=>[], "tags"=>["virulence"], "article_id"=>322653, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Jianing Geng", "Cheng-Hsun Chiu", "Petrus Tang", "Yaping Chen", "Hui-Ru Shieh", "Songnian Hu", "Yi-Ywan M. Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034769.t005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Additional_virulence_factors_/322653", "title"=>"Additional virulence factors.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-18 00:44:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/651583"], "description"=>"<p>Venn diagram representation of unique and shared gene numbers between and among strains FW213, ATCC15912, F0405 and SK236.</p>", "links"=>[], "tags"=>["genome"], "article_id"=>322078, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Jianing Geng", "Cheng-Hsun Chiu", "Petrus Tang", "Yaping Chen", "Hui-Ru Shieh", "Songnian Hu", "Yi-Ywan M. Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034769.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_whole_genome_comparison_between_S_parasanguinis_strains_/322078", "title"=>"The whole genome comparison between <i>S. parasanguinis</i> strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:34:38"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"21", "full-text"=>"23", "pdf"=>"7", "abstract"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2013", "month"=>"1"}
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  • {"unique-ip"=>"10", "full-text"=>"12", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"1"}
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  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2014", "month"=>"5"}
  • {"unique-ip"=>"8", "full-text"=>"7", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"6"}
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Relative Metric

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