Investigation of the Staphylococcus aureus GraSR Regulon Reveals Novel Links to Virulence, Stress Response and Cell Wall Signal Transduction Pathways
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{"title"=>"Investigation of the Staphylococcus aureus GraSR regulon reveals novel links to virulence, stress response and cell wall signal transduction pathways", "type"=>"journal", "authors"=>[{"first_name"=>"Mélanie", "last_name"=>"Falord", "scopus_author_id"=>"40261288900"}, {"first_name"=>"Ulrike", "last_name"=>"Mäder", "scopus_author_id"=>"7003437511"}, {"first_name"=>"Aurélia", "last_name"=>"Hiron", "scopus_author_id"=>"17134733900"}, {"first_name"=>"Michel", "last_name"=>"Dbarbouillé", "scopus_author_id"=>"54781223500"}, {"first_name"=>"Tarek", "last_name"=>"Msadek", "scopus_author_id"=>"6701630337"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"21765893", "sgr"=>"79959811246", "doi"=>"10.1371/journal.pone.0021323", "scopus"=>"2-s2.0-79959811246", "pui"=>"362049640", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203"}, "id"=>"71b0298b-8cf7-37a9-ae6b-45778c376cee", "abstract"=>"The GraS/GraR two-component system has been shown to control cationic antimicrobial peptide (CAMP) resistance in the major human pathogen Staphylococcus aureus. We demonstrated that graX, also involved in CAMP resistance and cotranscribed with graRS, encodes a regulatory cofactor of the GraSR signaling pathway, effectively constituting a three-component system. We identified a highly conserved ten base pair palindromic sequence (5' ACAAA TTTGT 3') located upstream from GraR-regulated genes (mprF and the dlt and vraFG operons), which we show to be essential for transcriptional regulation by GraR and induction in response to CAMPs, suggesting it is the likely GraR binding site. Genome-based predictions and transcriptome analysis revealed several novel GraR target genes. We also found that the GraSR TCS is required for growth of S. aureus at high temperatures and resistance to oxidative stress. The GraSR system has previously been shown to play a role in S. aureus pathogenesis and we have uncovered previously unsuspected links with the AgrCA peptide quorum-sensing system controlling virulence gene expression. We also show that the GraSR TCS controls stress reponse and cell wall metabolism signal transduction pathways, sharing an extensive overlap with the WalKR regulon. This is the first report showing a role for the GraSR TCS in high temperature and oxidative stress survival and linking this system to stress response, cell wall and pathogenesis control pathways.", "link"=>"http://www.mendeley.com/research/investigation-staphylococcus-aureus-grasr-regulon-reveals-novel-links-virulence-stress-response-cell", "reader_count"=>77, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Student > Doctoral Student"=>8, "Researcher"=>14, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>1, "Student > Master"=>12, "Other"=>3, "Student > Bachelor"=>8, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Student > Doctoral Student"=>8, "Researcher"=>14, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>1, "Student > Master"=>12, "Other"=>3, "Student > Bachelor"=>8, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>7, "Medicine and Dentistry"=>9, "Agricultural and Biological Sciences"=>49, "Veterinary Science and Veterinary Medicine"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Immunology and Microbiology"=>5}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>9}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>5}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>49}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>1, "Denmark"=>1, "Russia"=>1}, "group_count"=>5}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/381904", "https://ndownloader.figshare.com/files/381916", "https://ndownloader.figshare.com/files/381923", "https://ndownloader.figshare.com/files/381934"], "description"=>"<div><p>The GraS/GraR two-component system has been shown to control cationic antimicrobial peptide (CAMP) resistance in the major human pathogen <em>Staphylococcus aureus</em>. We demonstrated that <em>graX</em>, also involved in CAMP resistance and cotranscribed with <em>graRS</em>, encodes a regulatory cofactor of the GraSR signaling pathway, effectively constituting a three-component system. We identified a highly conserved ten base pair palindromic sequence (5′ ACAAA TTTGT 3′) located upstream from GraR-regulated genes (<em>mprF</em> and the <em>dlt</em> and <em>vraFG</em> operons), which we show to be essential for transcriptional regulation by GraR and induction in response to CAMPs, suggesting it is the likely GraR binding site. Genome-based predictions and transcriptome analysis revealed several novel GraR target genes. We also found that the GraSR TCS is required for growth of <em>S. aureus</em> at high temperatures and resistance to oxidative stress. The GraSR system has previously been shown to play a role in <em>S. aureus</em> pathogenesis and we have uncovered previously unsuspected links with the AgrCA peptide quorum-sensing system controlling virulence gene expression. We also show that the GraSR TCS controls stress reponse and cell wall metabolism signal transduction pathways, sharing an extensive overlap with the WalKR regulon. This is the first report showing a role for the GraSR TCS in high temperature and oxidative stress survival and linking this system to stress response, cell wall and pathogenesis control pathways.</p> </div>", "links"=>[], "tags"=>["grasr", "regulon", "reveals", "links", "transduction", "pathways"], "article_id"=>135436, "categories"=>["Genetics", "Microbiology"], "users"=>["Mélanie Falord", "Ulrike Mäder", "Aurélia Hiron", "Michel Debarbouille", "Tarek Msadek"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021323.s001", "https://dx.doi.org/10.1371/journal.pone.0021323.s002", "https://dx.doi.org/10.1371/journal.pone.0021323.s003", "https://dx.doi.org/10.1371/journal.pone.0021323.s004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Investigation_of_the_Staphylococcus_aureus_GraSR_Regulon_Reveals_Novel_Links_to_Virulence_Stress_Response_and_Cell_Wall_Signal_Transduction_Pathways/135436", "title"=>"Investigation of the <em>Staphylococcus aureus</em> GraSR Regulon Reveals Novel Links to Virulence, Stress Response and Cell Wall Signal Transduction Pathways", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-07-01 01:30:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/758949"], "description"=>"<p>(A) The <i>graXRS</i>/<i>vraFG</i> locus of <i>S</i>. <i>aureus</i> HG001. (B) Primer extension analysis of <i>graXRS</i> mRNA was carried out using total RNA extracted from <i>S. aureus</i> strain HG001 during mid-exponential growth in TSB at 37°C. Primer extension experiments were performed using the <i>graX</i>-specific oligonucleotide MF63 (lane 1). The corresponding Sanger dideoxy chain termination sequencing reactions (GATC) were carried out on a PCR-generated DNA fragment fragment corresponding to the <i>graX</i> upstream region (MF62/MF63). The transcriptional start site is boxed. (C) Nucleotide sequence of the <i>graXRS</i> operon upstream region. Potential σ<sup>A</sup>-type -35 and −10 sequences are boxed and the transcriptional start site is labelled +1.</p>", "links"=>[], "tags"=>["operon", "transcribed"], "article_id"=>429330, "categories"=>["Genetics", "Microbiology"], "users"=>["Mélanie Falord", "Ulrike Mäder", "Aurélia Hiron", "Michel Debarbouille", "Tarek Msadek"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021323.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_graXRS_operon_is_transcribed_from_a_A_promoter_/429330", "title"=>"The <i>graXRS</i> operon is transcribed from a σ<sup>A</sup> promoter.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-01 02:35:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/759078"], "description"=>"<p>Expression of the <i>graXRS</i> operon was followed using a <i>graX</i>'<i>-lacZ</i> transcriptional fusion in <i>S. aureus</i> strains HG001, ST1036 (Δ<i>graRS</i>) and ST1070 (Δ<i>graX</i>). β-Galactosidase assays were performed as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021323#s4\" target=\"_blank\">Materials and Methods</a> and measured during mid-exponential growth at 37°C in TSB (grey bars) or after treatment with 200 µg ml<sup>−1</sup> colistin for the HG001 strain (black bar). Means and standard deviations values are presented from at least three independent experiments.</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology"], "article_id"=>429449, "categories"=>["Genetics", "Microbiology"], "users"=>["Mélanie Falord", "Ulrike Mäder", "Aurélia Hiron", "Michel Debarbouille", "Tarek Msadek"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021323.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GraXSR_do_not_control_their_own_synthesis_/429449", "title"=>"GraXSR do not control their own synthesis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-01 02:37:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/759226"], "description"=>"<p>(A) Primer extension analysis of <i>mprF</i>, <i>dltXABCD</i> and <i>vraFG</i> transcripts was carried out using total RNA extracted from <i>S. aureus</i> strain HG001 treated with 200 µg ml<sup>−1</sup> colistin during mid-exponential growth at 37°C in TSB, using specific oligonucleotides for <i>mprF</i>, <i>dltX</i> and <i>vraF</i> (lanes 1 to 3 respectively). The corresponding Sanger dideoxy chain termination sequencing reactions (GATC) were carried out on PCR-generated DNA fragments corresponding to the respective upstream regions (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021323#pone-0021323-t005\" target=\"_blank\">Table 5</a>). The transcriptional start sites are boxed. (B) Alignment of the potential GraR DNA-binding sites in the <i>mprF</i>, <i>dltXABCD</i> and <i>vraFG</i> promoter regions. The potential GraR-binding site is shaded and conserved nucleotides are shown in white. Potential −35 and −10 sequences are underlined and the transcriptional start sites are indicated in bold.</p>", "links"=>[], "tags"=>["grar-binding", "sites", "promoters", "grar-regulated"], "article_id"=>429595, "categories"=>["Genetics", "Microbiology"], "users"=>["Mélanie Falord", "Ulrike Mäder", "Aurélia Hiron", "Michel Debarbouille", "Tarek Msadek"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021323.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_potential_GraR_binding_sites_in_the_promoters_of_known_GraR_regulated_genes_/429595", "title"=>"Identification of potential GraR-binding sites in the promoters of known GraR-regulated genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-01 02:39:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/759314"], "description"=>"<p><i>vraFG</i> (A) and <i>mprF</i> (B) expression was followed using transcriptional <i>lacZ</i> fusions, with or without the upstream GraR operator sequence (<i>vraF</i>'-<i>lacZ</i>, <i>mprF</i>'-<i>lacZ</i> and ΔA<i>vraF</i>'-<i>lacZ</i>, ΔA<i>mprF</i>'-<i>lacZ</i>, respectively). The fusions were introduced in <i>S. aureus</i> strains HG001, ST1036 (Δ<i>graRS</i>) and ST1070 (Δ<i>graX</i>). Expression was measured during mid-exponential growth in TSB at 37°C (grey bars) or after treatment with 50 µg ml<sup>−1</sup> colistin (black bars). β-Galactosidase assays were performed as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021323#s4\" target=\"_blank\">Materials and Methods</a>. Means and standard deviation values are presented from three independent experiments.</p>", "links"=>[], "tags"=>["requires", "colistin", "binding"], "article_id"=>429693, "categories"=>["Genetics", "Microbiology"], "users"=>["Mélanie Falord", "Ulrike Mäder", "Aurélia Hiron", "Michel Debarbouille", "Tarek Msadek"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021323.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GraSR_dependent_gene_expression_requires_GraX_colistin_and_the_consensus_binding_site_/429693", "title"=>"GraSR-dependent gene expression requires GraX, colistin and the consensus binding site.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-01 02:41:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/759425"], "description"=>"<p>(A) Alignment of the DNA sequences used to construct the <i>vraF</i>2'-<i>lacZ</i> and <i>vraF</i>2*-<i>lacZ</i> fusions. Potential −35 and −10 sequences are underlined, the identified transcriptional start site is indicated in bold and the GraR-binding site is shaded. Point mutations introduced in the <i>vraF</i>2*-<i>lacZ</i> fusion are shown in white. (B) <i>vraF</i>2'-<i>lacZ</i> and <i>vraF</i>2*-<i>lacZ</i> fusion expression was measured in <i>S. aureus</i> HG001 (strains ST1168 and ST1169, respectively) during mid-exponential growth at 37°C in TSB (grey bars) or after treatment with 200 µg ml<sup>−1</sup> colistin (black bars). β-Galactosidase assays were performed as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021323#s4\" target=\"_blank\">Materials and Methods</a>. Means and standard deviations values are presented from three independent experiments.</p>", "links"=>[], "tags"=>["mutations", "grar-binding", "colistin"], "article_id"=>429805, "categories"=>["Genetics", "Microbiology"], "users"=>["Mélanie Falord", "Ulrike Mäder", "Aurélia Hiron", "Michel Debarbouille", "Tarek Msadek"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021323.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Point_mutations_in_the_GraR_binding_site_prevent_vraFG_expression_and_colistin_induction_/429805", "title"=>"Point mutations in the GraR-binding site prevent <i>vraFG</i> expression and colistin induction.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-01 02:43:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/759536"], "description"=>"<p>The consensus sequence for the GraR-binding site was generated using the WebLogo tool (<a href=\"http://weblogo.berkeley.edu/\" target=\"_blank\">http://weblogo.berkeley.edu/</a>) by alignment of the upstream sequences of the 29 potential regulon genes identified by <i>in silico</i> analysis (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021323#pone-0021323-t002\" target=\"_blank\">Table 2</a>).</p>", "links"=>[], "tags"=>["grar", "inverted", "alignment", "regulon", "upstream"], "article_id"=>429908, "categories"=>["Genetics", "Microbiology"], "users"=>["Mélanie Falord", "Ulrike Mäder", "Aurélia Hiron", "Michel Debarbouille", "Tarek Msadek"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021323.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_GraR_operator_consensus_is_a_perfect_inverted_repeat_obtained_by_alignment_of_regulon_gene_upstream_sequences_/429908", "title"=>"The GraR operator consensus is a perfect inverted repeat obtained by alignment of regulon gene upstream sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-01 02:45:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/759638"], "description"=>"<p>The expression levels of <i>qoxA</i>, <i>ssaA</i>, SAOUHSC_00669 and <i>agrB</i> genes were analyzed by qRT-PCR in the HG001 and ST1036 (Δ<i>graRS</i>) strains. RNA samples were prepared from cultures during mid exponential growth after treatment with 50 µg ml<sup>−1</sup> colistin. Comparative analysis (fold-change) of transcriptome analysis (black bars) and qRT-PCR experiments (grey bars) are shown. Means and standard deviation values for the qRT-PCR data are presented from at least three independent experiments.</p>", "links"=>[], "tags"=>["microarray", "qrt-pcr", "experiments", "grasr-dependent"], "article_id"=>430006, "categories"=>["Genetics", "Microbiology"], "users"=>["Mélanie Falord", "Ulrike Mäder", "Aurélia Hiron", "Michel Debarbouille", "Tarek Msadek"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021323.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_between_microarray_and_qRT_PCR_experiments_for_expression_of_GraSR_dependent_genes_/430006", "title"=>"Correlation between microarray and qRT-PCR experiments for expression of GraSR-dependent genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-01 00:00:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/759753"], "description"=>"<p>The effect of 40 mM paraquat was analyzed on HG001 (•, ○), ST1036 (▪, □; Δ<i>graRS</i>), ST1070 (▴, ▵; Δ<i>graX</i>) strains grown in TSB at 37°C, and diluted to a final OD <sub>600 nm</sub> of 0.025. Growth was followed at 600 nm using a microtiter plate reader in the presence (closed symbols) or absence (open symbols) of 40 mM paraquat (methylviologen). A representative curve of three independent experiments is shown for each strain.</p>", "links"=>[], "tags"=>["oxidative"], "article_id"=>430130, "categories"=>["Genetics", "Microbiology"], "users"=>["Mélanie Falord", "Ulrike Mäder", "Aurélia Hiron", "Michel Debarbouille", "Tarek Msadek"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021323.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GraXSR_are_involved_in_oxidative_stress_resistance_/430130", "title"=>"GraXSR are involved in oxidative stress resistance.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-01 00:02:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/759905"], "description"=>"<p>The effect of high temperature was tested on growth of <i>S. aureus</i> strains ST1120 (HG001 pMK4-Pprot), ST1117 (Δ<i>graRS</i> pMK4-Pprot) and the complemented Δ<i>graRS</i> mutant, Δ<i>graRS</i>-c (strain ST1116; Δ<i>graRS</i> pMK4-Pprot<i>-graR</i>). Strains were grown at 37°C in TSB and diluted to an OD <sub>600 nm</sub> of 0.2. Serial dilutions were then carried out and 10 µl of each dilution was spotted on TSA plates, and incubated at 37°C or 44°C for 48 h.</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology"], "article_id"=>430284, "categories"=>["Genetics", "Microbiology"], "users"=>["Mélanie Falord", "Ulrike Mäder", "Aurélia Hiron", "Michel Debarbouille", "Tarek Msadek"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021323.g009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GraSR_are_required_for_growth_of_Staphylococcus_aureus_at_high_temperature_/430284", "title"=>"GraSR are required for growth of <i>Staphylococcus aureus</i> at high temperature.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-01 00:04:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/760013"], "description"=>"<p>*Added restriction site sequences are indicated in italics.</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology"], "article_id"=>430385, "categories"=>["Genetics", "Microbiology"], "users"=>["Mélanie Falord", "Ulrike Mäder", "Aurélia Hiron", "Michel Debarbouille", "Tarek Msadek"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021323.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Oligonucleotides_used_in_this_study_/430385", "title"=>"Oligonucleotides used in this study<sup>*</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-07-01 00:06:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/760040"], "description"=>"a<p>Arrows indicate plasmid introduction by electroporation.</p>", "links"=>[], "tags"=>["strains", "plasmids"], "article_id"=>430415, "categories"=>["Genetics", "Microbiology"], "users"=>["Mélanie Falord", "Ulrike Mäder", "Aurélia Hiron", "Michel Debarbouille", "Tarek Msadek"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021323.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bacterial_strains_and_plasmids_used_in_this_study_/430415", "title"=>"Bacterial strains and plasmids used in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-07-01 00:06:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/760073"], "description"=>"<p>Strains were grown at 37°C in TSB with decreasing colistin concentrations. Growth was followed by measuring absorbance at 600 nm using a microtiter plate reader and MICs were determined as the colistin concentration inhibiting strain growth after 12 h. Each experiment was repeated at least three times.</p>", "links"=>[], "tags"=>["gras", "grar", "colistin"], "article_id"=>430443, "categories"=>["Genetics", "Microbiology"], "users"=>["Mélanie Falord", "Ulrike Mäder", "Aurélia Hiron", "Michel Debarbouille", "Tarek Msadek"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021323.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GraX_GraS_and_GraR_are_required_for_colistin_resistance_/430443", "title"=>"GraX, GraS and GraR are required for colistin resistance.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-07-01 00:07:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/760105"], "description"=>"a<p>Gene names correspond to the annotation of the <i>S</i>. <i>aureus</i> NCTC 8325 genome sequence <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021323#pone.0021323-Gillaspy1\" target=\"_blank\">[69]</a>.</p>b<p>HP: hypothetical protein.</p>c<p>Fold-change of selected positively regulated genes determined as the ratio of the signal values between strain HG001 and the Δ<i>graRS</i> mutant. * Indicates genes known or predicted to be controlled by the WalKR TCS <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021323#pone.0021323-Dubrac1\" target=\"_blank\">[44]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021323#pone.0021323-Michel1\" target=\"_blank\">[46]</a>.</p>", "links"=>[], "tags"=>["profiling"], "article_id"=>430483, "categories"=>["Genetics", "Microbiology"], "users"=>["Mélanie Falord", "Ulrike Mäder", "Aurélia Hiron", "Michel Debarbouille", "Tarek Msadek"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021323.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_profiling_of_the_graRS_mutant_/430483", "title"=>"Expression profiling of the Δ<i>graRS</i> mutant.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-07-01 00:08:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/760146"], "description"=>"a<p>Gene names correspond to the annotation of the <i>S</i>. <i>aureus</i> NCTC 8325 genome sequence <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021323#pone.0021323-Gillaspy1\" target=\"_blank\">[69]</a>. Only the first gene is indicated for operons.</p>b<p>Positions of the inverted repeats of the potential GraR-binding sites are indicated for the given DNA strand with respect to the translation initiation codon.</p>c<p>Known and putative functions for each regulon member based on genome annotations are indicated. Based on these predictions, the potential regulon members were divided in six categories (antimicrobial resistance, transport, cell envelope modification, oxidoreduction processes, other functions and unknown function).</p><p>*Indicates genes known or predicted to be controlled by the WalKR TCS <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021323#pone.0021323-Dubrac1\" target=\"_blank\">[44]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021323#pone.0021323-Michel1\" target=\"_blank\">[46]</a>.</p>", "links"=>[], "tags"=>["grar", "regulon", "members", "genome"], "article_id"=>430515, "categories"=>["Genetics", "Microbiology"], "users"=>["Mélanie Falord", "Ulrike Mäder", "Aurélia Hiron", "Michel Debarbouille", "Tarek Msadek"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021323.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_potential_new_GraR_regulon_members_by_in_silico_genome_scanning_/430515", "title"=>"Identification of potential new GraR regulon members by <i>in silico</i> genome scanning.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-07-01 00:08:35"}

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Relative Metric

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