CytR Is a Global Positive Regulator of Competence, Type VI Secretion, and Chitinases in Vibrio cholerae
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{"title"=>"SOX2 and SOX2-MYC reprogramming process of fibroblasts to the neural stem cells compromised by senescence", "type"=>"journal", "authors"=>[{"first_name"=>"Marta", "last_name"=>"Winiecka-Klimek", "scopus_author_id"=>"55980097800"}, {"first_name"=>"Maciej", "last_name"=>"Smolarz", "scopus_author_id"=>"57015680100"}, {"first_name"=>"Maciej P.", "last_name"=>"Walczak", "scopus_author_id"=>"56389346900"}, {"first_name"=>"Jolanta", "last_name"=>"Zieba", "scopus_author_id"=>"56157716100"}, {"first_name"=>"Krystyna", "last_name"=>"Hulas-Bigoszewska", "scopus_author_id"=>"8607357400"}, {"first_name"=>"Blazej", "last_name"=>"Kmieciak", "scopus_author_id"=>"36080798800"}, {"first_name"=>"Sylwester", "last_name"=>"Piaskowski", "scopus_author_id"=>"13104115700"}, {"first_name"=>"Piotr", "last_name"=>"Rieske", "scopus_author_id"=>"6602807005"}, {"first_name"=>"Dawid P.", "last_name"=>"Grzela", "scopus_author_id"=>"24075747400"}, {"first_name"=>"Ewelina", "last_name"=>"Stoczynska-Fidelus", "scopus_author_id"=>"36186004200"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84956661974", "pui"=>"607325424", "doi"=>"10.1371/journal.pone.0138834", "sgr"=>"84956661974", "pmid"=>"26535892"}, "id"=>"5f51c862-6a46-3d48-a724-4a5180037050", "abstract"=>"Tumorigenic potential of induced pluripotent stem cells (iPSCs) infiltrating population of induced neural stem cells (iNSCs) generated from iPSCs may limit their medical applications. To overcome such a difficulty, direct reprogramming of adult somatic cells into iNSCs was proposed. The aim of this study was the systematic comparison of induced neural cells (iNc) obtained with different methods-direct reprogramming of human adult fibroblasts with either SOX2 (SiNSc-like) or SOX2 and c-MYC (SMiNSc-like) and induced pluripotent stem cells differentiation to ebiNSc-in terms of gene expression profile, differentiation potential as well as proliferation properties. Immunocytochemistry and real-time PCR analyses were used to evaluate gene expression profile and differentiation potential of various iNc types. Bromodeoxyuridine (BrdU) incorporation and senescence-associated beta-galactosidase (SA-beta-gal) assays were used to estimate proliferation potential. All three types of iNc were capable of neuronal differentiation; however, astrocytic differentiation was possible only in case of ebiNSc. Contrary to ebiNSc generation, the direct reprogramming was rarely a propitious process, despite 100% transduction efficiency. The potency of direct iNSCs-like cells generation was lower as compared to iNSCs obtained by iPSCs differentiation, and only slightly improved when c-MYC was added. Directly reprogrammed iNSCs-like cells were lacking the ability to differentiate into astrocytic cells and characterized by poor efficiency of neuronal cells formation. Such features indicated that these cells could not be fully reprogrammed, as confirmed mainly with senescence detection. Importantly, SiNSc-like and SMiNSc-like cells were unable to achieve the long-term survival and became senescent, which limits their possible therapeutic applicability. Our results suggest that iNSCs-like cells, generated in the direct reprogramming attempts, were either not fully reprogrammed or reprogrammed only into neuronal progenitors, mainly because of the inaccuracies of currently available protocols.", "link"=>"http://www.mendeley.com/research/sox2-sox2myc-reprogramming-process-fibroblasts-neural-stem-cells-compromised-senescence", "reader_count"=>21, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Student > Doctoral Student"=>1, "Researcher"=>4, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Student > Doctoral Student"=>1, "Researcher"=>4, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>14, "Medicine and Dentistry"=>1, "Neuroscience"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>14}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>2}}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2287440", "https://ndownloader.figshare.com/files/2287441", "https://ndownloader.figshare.com/files/2287442", "https://ndownloader.figshare.com/files/2287443", "https://ndownloader.figshare.com/files/2287444", "https://ndownloader.figshare.com/files/2287445", "https://ndownloader.figshare.com/files/2287446"], "description"=>"<div><p>The facultative pathogen <i>Vibrio cholerae</i> transitions between its human host and aquatic reservoirs where it colonizes chitinous surfaces. Growth on chitin induces expression of chitin utilization genes, genes involved in DNA uptake by natural transformation, and a type VI secretion system that allows contact-dependent killing of neighboring bacteria. We have previously shown that the transcription factor CytR, thought to primarily regulate the pyrimidine nucleoside scavenging response, is required for natural competence in <i>V</i>. <i>cholerae</i>. Through high-throughput RNA sequencing (RNA-seq), we show that CytR positively regulates the majority of competence genes, the three type VI secretion operons, and the four known or predicted chitinases. We used transcriptional reporters and phenotypic analysis to determine the individual contributions of quorum sensing, which is controlled by the transcription factors HapR and QstR; chitin utilization that is mediated by TfoX; and pyrimidine starvation that is orchestrated by CytR, toward each of these processes. We find that in <i>V</i>. <i>cholerae</i>, CytR is a global regulator of multiple behaviors affecting fitness and adaptability in the environment.</p></div>", "links"=>[], "tags"=>["type VI secretion operons", "pyrimidine nucleoside", "Vibrio cholerae", "chitin utilization", "type VI secretion system", "type VI secretion", "facultative pathogen Vibrio cholerae transitions", "pyrimidine starvation", "transcriptional reporters", "transcription factor CytR", "DNA uptake", "chitin utilization genes", "rna", "transcription factors HapR", "competence genes", "colonizes chitinous surfaces", "Phenotypic analysis"], "article_id"=>1555367, "categories"=>["Biological Sciences"], "users"=>["Samit S. Watve", "Jacob Thomas", "Brian K. Hammer"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0138834.s001", "https://dx.doi.org/10.1371/journal.pone.0138834.s002", "https://dx.doi.org/10.1371/journal.pone.0138834.s003", "https://dx.doi.org/10.1371/journal.pone.0138834.s004", "https://dx.doi.org/10.1371/journal.pone.0138834.s005", "https://dx.doi.org/10.1371/journal.pone.0138834.s006", "https://dx.doi.org/10.1371/journal.pone.0138834.s007"], "stats"=>{"downloads"=>23, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/CytR_Is_a_Global_Positive_Regulator_of_Competence_Type_VI_Secretion_and_Chitinases_in_Vibrio_cholerae_/1555367", "title"=>"CytR Is a Global Positive Regulator of Competence, Type VI Secretion, and Chitinases in <i>Vibrio cholerae</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-09-24 03:23:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/2287439"], "description"=>"<p>Natural transformation requires inputs from four regulators TfoX, CytR, HapR and QstR. Type VI secretion requires inputs from the four regulators above, but QstR overexpression bypasses the need for TfoX, CytR, and HapR. Chitinase expression requires inputs from TfoX, CytR but not from HapR and QstR under the conditions tested.</p>", "links"=>[], "tags"=>["type VI secretion operons", "pyrimidine nucleoside", "Vibrio cholerae", "chitin utilization", "type VI secretion system", "type VI secretion", "facultative pathogen Vibrio cholerae transitions", "pyrimidine starvation", "transcriptional reporters", "transcription factor CytR", "DNA uptake", "chitin utilization genes", "rna", "transcription factors HapR", "competence genes", "colonizes chitinous surfaces", "Phenotypic analysis"], "article_id"=>1555366, "categories"=>["Biological Sciences"], "users"=>["Samit S. Watve", "Jacob Thomas", "Brian K. Hammer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0138834.g005", "stats"=>{"downloads"=>1, "page_views"=>26, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_differential_roles_of_TfoX_CytR_HapR_and_QstR_in_natural_transformation_Type_VI_secretion_and_chitinase_expression_/1555366", "title"=>"The differential roles of TfoX, CytR, HapR and QstR in natural transformation, Type VI secretion and chitinase expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-24 03:23:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/2287425"], "description"=>"<p><i>V</i>. <i>cholerae</i> C6706 with indicated alleles of <i>tfoX</i>, <i>cytR</i>, <i>hapR</i>, and <i>qstR</i> (+, native;-, deletion; *, constitutively expressed) were analyzed for expression of bioluminescence from a plasmid-encoded <i>lux</i> transcriptional reporter fusion to the promoter of first gene of a T6SS auxiliary cluster, <i>vca0017</i> (Panel A). Bioluminescence is defined as relative light production per OD<sub>600</sub> (RLU). All strains are deleted for <i>luxO</i> and are therefore constitutive for HapR expression (*) when the <i>hapR</i> gene is present. Data shown are mean values ± standard deviation for triplicates from one representative experiment of three performed. ‡ indicates a p-value < 0.01, † indicates a p-value <0.05. N.S. denotes not significant, calculated using a two-tailed Student’s t-test. Bars 2–5 are compared to bar 1 and bars 7–9 are compared to bar 6. Panel B: Chloramphenicol resistant <i>E</i>. <i>coli</i> prey were incubated with the indicated <i>V</i>. <i>cholerae</i> predator strains at a ratio of 1:10 on membrane filters to monitor contact-dependent killing. Total surviving prey cfus are represented in each case.</p>", "links"=>[], "tags"=>["type VI secretion operons", "pyrimidine nucleoside", "Vibrio cholerae", "chitin utilization", "type VI secretion system", "type VI secretion", "facultative pathogen Vibrio cholerae transitions", "pyrimidine starvation", "transcriptional reporters", "transcription factor CytR", "DNA uptake", "chitin utilization genes", "rna", "transcription factors HapR", "competence genes", "colonizes chitinous surfaces", "Phenotypic analysis"], "article_id"=>1555363, "categories"=>["Biological Sciences"], "users"=>["Samit S. Watve", "Jacob Thomas", "Brian K. Hammer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0138834.g003", "stats"=>{"downloads"=>3, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_of_Type_VI_secretion_system_genes_and_T6SS_mediated_killing_are_positively_regulated_by_CytR_TfoX_HapR_and_QstR_/1555363", "title"=>"Expression of Type VI secretion system genes and T6SS-mediated killing are positively regulated by CytR, TfoX, HapR, and QstR.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-24 03:23:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/2287424"], "description"=>"<p><i>V</i>. <i>cholerae</i> C6706 derivatives with native alleles of <i>tfoX</i>, <i>cytR</i> and <i>qstR</i> (not constitutively expressed, denoted by +), alleles of <i>tfoX</i> or <i>qstR</i> made constitutive by replacing the chromosomal native promoter with a <i>ptac</i> promoter (indicated by *), or containing in-frame deletions of <i>tfoX</i>, <i>cytR</i>, <i>hapR</i> and <i>qstR</i> (-), were analyzed for expression of bioluminescence from plasmid-encoded <i>lux</i> transcriptional reporter fusions. Expression profiles are shown for the transcriptional regulator <i>qstR</i> (Panel A) and for a member of each regulatory class: class I, <i>comEA</i> (Panel B) class II, <i>pilM</i> (Panel C) class III, <i>pilF</i>, (Panel D), and class IV, <i>pilT</i> (Panel E). All strains are deleted for <i>luxO</i> and are therefore constitutive for HapR expression (*) when the <i>hapR</i> gene is present. Bioluminescence is represented as relative light production per OD<sub>600</sub> (RLU) and data shown are mean values ± standard deviation from three biological replicates of one representative experiment of three. Data are shown as mean values ± standard deviation. ‡ indicates a p-value < 0.01, † indicates a p-value <0.05. N.S. denotes not significant, calculated using a two-tailed Student’s t-test. In Panels A to E, bars 2–5 are compared to bar 1; in Panels A and B, bars 7–9 are compared to bar 6. Panel F: A TfoX* CytR<sup>+</sup> HapR* QstR* strain is transformable in LB in the absence of chitin induction, but an isogenic strain carrying a <i>qstR</i> deletion was poorly transformable. The <i>hapR</i> deletion strain was partially restored for transformation by constitutive expression of QstR (*), but strains deleted for <i>cytR</i> or <i>tfoX</i> were not restored for competence by the QstR* allele. The limit of detection is 1 x 10<sup>−8</sup> cfu. mL<sup>-1</sup> (d.l.).</p>", "links"=>[], "tags"=>["type VI secretion operons", "pyrimidine nucleoside", "Vibrio cholerae", "chitin utilization", "type VI secretion system", "type VI secretion", "facultative pathogen Vibrio cholerae transitions", "pyrimidine starvation", "transcriptional reporters", "transcription factor CytR", "DNA uptake", "chitin utilization genes", "rna", "transcription factors HapR", "competence genes", "colonizes chitinous surfaces", "Phenotypic analysis"], "article_id"=>1555362, "categories"=>["Biological Sciences"], "users"=>["Samit S. Watve", "Jacob Thomas", "Brian K. Hammer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0138834.g002", "stats"=>{"downloads"=>17, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Competence_genes_are_differentially_regulated_by_TfoX_CytR_HapR_and_QstR_/1555362", "title"=>"Competence genes are differentially regulated by TfoX, CytR, HapR and QstR.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-24 03:23:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/2287419"], "description"=>"<p>Panel A: <i>V</i>. <i>cholerae</i> C6706 is capable of natural transformation in LB medium lacking chitin if <i>tfoX</i> is constitutively expressed (TfoX*, bar 1) but not if <i>tfoX</i> is under control of its native promoter (TfoX<sup>+</sup>, bars 3 and 4). No transformants were detected in the absence of CytR (CytR<sup>-</sup>, bars 2 and 4). Transformation frequency is expressed as the number of kanamycin resistant cfu mL<sup>-1</sup> divided by total cfu mL<sup>-1</sup>. The limit of detection (d.l.) is 1 x 10<sup>−8</sup>. Data are shown as mean ± standard deviation from three independent biological replicates. Panel B: Heat map of genes differentially regulated by CytR in the absence (TfoX<sup>+</sup>, column 1) or presence (TfoX*, column 2) of TfoX induction, and genes differentially regulated by TfoX in the absence (CytR<sup>-</sup>, column 3) or presence (CytR<sup>+</sup>, column 4) of a functional <i>cytR</i> gene. The majority of known competence genes are positively regulated by both TfoX and CytR and can be classified into four distinct regulatory classes (see text for details). CytR and TfoX positively regulate the three known T6SS gene clusters as well as four chitinase genes. CytR negatively regulates nucleoside uptake and catabolism genes in a TfoX-independent manner.</p>", "links"=>[], "tags"=>["type VI secretion operons", "pyrimidine nucleoside", "Vibrio cholerae", "chitin utilization", "type VI secretion system", "type VI secretion", "facultative pathogen Vibrio cholerae transitions", "pyrimidine starvation", "transcriptional reporters", "transcription factor CytR", "DNA uptake", "chitin utilization genes", "rna", "transcription factors HapR", "competence genes", "colonizes chitinous surfaces", "Phenotypic analysis"], "article_id"=>1555357, "categories"=>["Biological Sciences"], "users"=>["Samit S. Watve", "Jacob Thomas", "Brian K. Hammer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0138834.g001", "stats"=>{"downloads"=>8, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CytR_and_TfoX_co_regulate_natural_competence_chitinase_expression_and_the_type_VI_secretion_system_/1555357", "title"=>"CytR and TfoX co-regulate natural competence, chitinase expression and the type VI secretion system.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-24 03:23:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/2287438"], "description"=>"<p>Panel A: <i>V</i>. <i>cholerae</i> strains with indicated alleles of <i>tfoX</i>, <i>cytR</i>, <i>hapR</i> and <i>qstR</i> (+, native;-, deletion; *, constitutively expressed), were analyzed for expression of bioluminescence from a plasmid-encoded <i>lux</i> transcriptional reporter fusion to the promoter of the chitinase <i>chiA1</i>. All strains are deleted for <i>luxO</i> and are therefore constitutive for HapR expression (*) when the <i>hapR</i> gene is present. Bioluminescence is defined as relative light production per OD<sub>600</sub> (RLU). ‡ indicates a p-value < 0.01, † indicates a p-value <0.05. N.S. denotes not significant, calculated using a two-tailed Student’s t-test. Bars 2–5 are compared to bar 1. Panel B and C: Chitin agar plate assays. <i>V</i>. <i>cholerae</i> strains with indicated alleles of <i>tfoX</i>, <i>cytR</i>, <i>hapR</i>, and <i>qstR</i> were assayed for chitinase activity which results in a zone of clearing on LB plates containing 2% colloidal chitin (panel B). Strains constitutive for TfoX (*) and isogenic strains deleted for <i>cytR</i>, <i>tfoX</i> and the CytR-dependent chitinases <i>chiA1</i>, <i>chiA2</i>, <i>vc0769</i>, <i>vca0700</i>, a <i>chiA1 chiA2</i> double mutant and a strain deleted for all four chitinases were assayed for the contribution of individual chitinase genes to chitinase activity (panel C).</p>", "links"=>[], "tags"=>["type VI secretion operons", "pyrimidine nucleoside", "Vibrio cholerae", "chitin utilization", "type VI secretion system", "type VI secretion", "facultative pathogen Vibrio cholerae transitions", "pyrimidine starvation", "transcriptional reporters", "transcription factor CytR", "DNA uptake", "chitin utilization genes", "rna", "transcription factors HapR", "competence genes", "colonizes chitinous surfaces", "Phenotypic analysis"], "article_id"=>1555365, "categories"=>["Biological Sciences"], "users"=>["Samit S. Watve", "Jacob Thomas", "Brian K. Hammer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0138834.g004", "stats"=>{"downloads"=>3, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_of_V_cholerae_chitinases_requires_TfoX_and_CytR_but_not_HapR_or_QstR_/1555365", "title"=>"Expression of <i>V</i>. <i>cholerae</i> chitinases requires TfoX and CytR, but not HapR or QstR.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-24 03:23:24"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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