Tracking the Elusive Function of Bacillus subtilis Hfq
Publication Date
April 27, 2015
Journal
PLOS ONE
Authors
Tatiana Rochat, Olivier Delumeau, Nara Figueroa Bossi, Philippe Noirot, et al
Volume
10
Issue
4
Pages
e0124977
DOI
https://dx.plos.org/10.1371/journal.pone.0124977
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0124977
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/25915524
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410918
Europe PMC
http://europepmc.org/abstract/MED/25915524
Web of Science
000353659100086
Scopus
84928615890
Mendeley
http://www.mendeley.com/research/tracking-elusive-function-bacillus-subtilis-hfq
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2040697"], "description"=>"<p>A) Co-cultures were performed with <i>hfq</i><sub><i>Bs</i></sub>-expressing strain and Δ<i>hfq</i><sub><i>Bs</i></sub> mutant in LB medium and incubated at 37°C during 5 days. An antibiotic resistance gene (<i>cat</i> or <i>spc</i>) was inserted in the intergenic region <i>hfq-ymzE</i> (control, black) or in replacement of the <i>hfq</i><sub><i>Bs</i></sub> coding sequence (mutant, white). Each population was numbered on LB plates supplemented with spectinomycin or chloramphenicol. To number spores, samples were incubated 15 min at 80°C before plating (dot lines). Two combinations of co-cultures were performed using two sets of isogenic strains (●) TR247 (<i>hfq</i><sub><i>Bs</i></sub><sup>+</sup><i>igr</i>::<i>cat</i>) and (◊) TR232 (Δ<i>hfq</i><sub><i>Bs</i></sub>::<i>spc igr</i>+) or strains (○) TR223 (Δ<i>hfq</i><sub><i>Bs</i></sub>::<i>cat igr</i>+) and (♦) TR241 (<i>hfq</i><sub><i>Bs</i></sub><sup>+</sup><i>igr</i>::<i>spc</i>). B) The same experiments were performed with sporulation-deficient derivative strains (<i>sigE</i>::<i>erm</i>). The two co-cultures were performed using strains (●) TR243 and (◊) TR237 or strains (○) TR235 and (♦) TR245. C) Competition experiments were performed with TR259 and TR255 strains which are deleted of the <i>bsrE</i>-asBsrE type 1 TA and express (●) or not (◊) Hfq<sub><i>Bs</i></sub>. D) Competition experiments were performed with the TF8A (<i>txpA</i>-RatA deleted) derivative strains using Δ<i>hfq</i><sub><i>Bs</i></sub> TR248 (◊) and control TR252 (●) strains.</p>", "links"=>[], "tags"=>["phase fitness defect", "Salmonella", "Hfq proteins", "rna", "subtilis hfq"], "article_id"=>1395125, "categories"=>["Biological Sciences"], "users"=>["Tatiana Rochat", "Olivier Delumeau", "Nara Figueroa-Bossi", "Philippe Noirot", "Lionello Bossi", "Etienne Dervyn", "Philippe Bouloc"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0124977.g003", "stats"=>{"downloads"=>1, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Survival_of_B_subtilis_hfq_Bs_in_competition_with_hfq_expressing_strain_/1395125", "title"=>"Survival of <i>B</i>. <i>subtilis</i> Δ<i>hfq</i><sub><i>Bs</i></sub> in competition with <i>hfq</i>-expressing strain.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-27 02:47:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/2040696"], "description"=>"<p>The apparition and the proportion of competent cells in cultures of wild-type (BSB1) and Δ<i>hfq</i> mutant (TR223) strains were monitoring by calculating the number of cells able to integrate an antibiotic resistance gene in their chromosomal DNA during the competence process development.</p>", "links"=>[], "tags"=>["phase fitness defect", "Salmonella", "Hfq proteins", "rna", "subtilis hfq"], "article_id"=>1395124, "categories"=>["Biological Sciences"], "users"=>["Tatiana Rochat", "Olivier Delumeau", "Nara Figueroa-Bossi", "Philippe Noirot", "Lionello Bossi", "Etienne Dervyn", "Philippe Bouloc"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0124977.g002", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Competence_efficiency_/1395124", "title"=>"Competence efficiency.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-27 02:47:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/2040693"], "description"=>"<p>Cultures of strain carrying <i>hfq</i><sub><i>Bs</i></sub><i>-spa</i> translational fusion (TR229) or wild-type strain (BSB1) were performed in LB medium at 37°C under vigorous agitation. Harvested cells from exponential, early and late transition and stationary phase cultures (OD<sub>600nm</sub> 1, 2.4, 3 and 4, respectively) were lysed by sonication and 2.75 μg of total protein extracts of each sample were separated by electrophoresis in 12.5% SDS-PAGE. Hfq<sub>Bs</sub><sup>SPA</sup> was detected by immunoblotting using anti-FLAG M2 antibodies (Sigma).</p>", "links"=>[], "tags"=>["phase fitness defect", "Salmonella", "Hfq proteins", "rna", "subtilis hfq"], "article_id"=>1395121, "categories"=>["Biological Sciences"], "users"=>["Tatiana Rochat", "Olivier Delumeau", "Nara Figueroa-Bossi", "Philippe Noirot", "Lionello Bossi", "Etienne Dervyn", "Philippe Bouloc"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0124977.g001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_of_Hfq_Bs_during_growth_/1395121", "title"=>"Expression of Hfq<sub>Bs</sub> during growth.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-27 02:47:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/2040733", "https://ndownloader.figshare.com/files/2040734", "https://ndownloader.figshare.com/files/2040735", "https://ndownloader.figshare.com/files/2040736", "https://ndownloader.figshare.com/files/2040737", "https://ndownloader.figshare.com/files/2040739", "https://ndownloader.figshare.com/files/2040740", "https://ndownloader.figshare.com/files/2040741", "https://ndownloader.figshare.com/files/2040742", "https://ndownloader.figshare.com/files/2040743", "https://ndownloader.figshare.com/files/2040744"], "description"=>"<div><p>RNA-binding protein Hfq is a key component of the adaptive responses of many proteobacterial species including <i>Escherichia coli</i>, <i>Salmonella enterica</i> and <i>Vibrio cholera</i>. In these organisms, the importance of Hfq largely stems from its participation to regulatory mechanisms involving small non-coding RNAs. In contrast, the function of Hfq in Gram-positive bacteria has remained elusive and somewhat controversial. In the present study, we have further addressed this point by comparing growth phenotypes and transcription profiles between wild-type and an <i>hfq</i> deletion mutant of the model Gram-positive bacterium, <i>Bacillus subtilis</i>. The absence of Hfq had no significant consequences on growth rates under nearly two thousand metabolic conditions and chemical treatments. The only phenotypic difference was a survival defect of <i>B</i>. <i>subtilis hfq</i> mutant in rich medium in stationary phase. Transcriptomic analysis correlated this phenotype with a change in the levels of nearly one hundred transcripts. Albeit a significant fraction of these RNAs (36%) encoded sporulation-related functions, analyses in a strain unable to sporulate ruled out sporulation <i>per se</i> as the basis of the <i>hfq</i> mutant’s stationary phase fitness defect. When expressed in <i>Salmonella</i>, <i>B</i>. <i>subtilis hfq</i> complemented the sharp loss of viability of a <i>degP hfq</i> double mutant, attenuating the chronic σ<sup>E</sup>-activated phenotype of this strain. However, <i>B</i>. <i>subtilis hfq</i> did not complement other regulatory deficiencies resulting from loss of Hfq-dependent small RNA activity in <i>Salmonella</i> indicating a limited functional overlap between <i>Salmonella</i> and <i>B</i>. <i>subtilis</i> Hfqs. Overall, this study confirmed that, despite structural similarities with other Hfq proteins, <i>B</i>. <i>subtilis</i> Hfq does not play a central role in post-transcriptional regulation but might have a more specialized function connected with stationary phase physiology. This would account for the high degree of conservation of Hfq proteins in all 17 <i>B</i>. <i>subtilis</i> strains whose genomes have been sequenced.</p></div>", "links"=>[], "tags"=>["phase fitness defect", "Salmonella", "Hfq proteins", "rna", "subtilis hfq"], "article_id"=>1395147, "categories"=>["Biological Sciences"], "users"=>["Tatiana Rochat", "Olivier Delumeau", "Nara Figueroa-Bossi", "Philippe Noirot", "Lionello Bossi", "Etienne Dervyn", "Philippe Bouloc"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0124977.s001", "https://dx.doi.org/10.1371/journal.pone.0124977.s002", "https://dx.doi.org/10.1371/journal.pone.0124977.s003", "https://dx.doi.org/10.1371/journal.pone.0124977.s004", "https://dx.doi.org/10.1371/journal.pone.0124977.s005", "https://dx.doi.org/10.1371/journal.pone.0124977.s006", "https://dx.doi.org/10.1371/journal.pone.0124977.s007", "https://dx.doi.org/10.1371/journal.pone.0124977.s008", "https://dx.doi.org/10.1371/journal.pone.0124977.s009", "https://dx.doi.org/10.1371/journal.pone.0124977.s010", "https://dx.doi.org/10.1371/journal.pone.0124977.s011"], "stats"=>{"downloads"=>45, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Tracking_the_Elusive_Function_of_Bacillus_subtilis_Hfq/1395147", "title"=>"Tracking the Elusive Function of <i>Bacillus subtilis</i> Hfq", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-04-27 02:47:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/2040699"], "description"=>"<p><sup>a</sup> All <i>B</i>. <i>subtilis</i> strains (name starting by BSB and TR) are derived from BSB1 which is a tryptophan-prototrophic (trp+) of <i>B</i>. <i>subtilis</i> 168 [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0124977#pone.0124977.ref034\" target=\"_blank\">34</a>] excepted TF8A derivative strains. All <i>Salmonella</i> strains (name starting with MA) are derived from <i>Salmonella enterica</i> serovar Typhimurium strain MA3409 which is a derivative of strain LT2 cured for the Gifsy-1 prophage [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0124977#pone.0124977.ref060\" target=\"_blank\">60</a>].</p><p><i>S</i>trains used in this work.</p>", "links"=>[], "tags"=>["phase fitness defect", "Salmonella", "Hfq proteins", "rna", "subtilis hfq"], "article_id"=>1395127, "categories"=>["Biological Sciences"], "users"=>["Tatiana Rochat", "Olivier Delumeau", "Nara Figueroa-Bossi", "Philippe Noirot", "Lionello Bossi", "Etienne Dervyn", "Philippe Bouloc"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0124977.t001", "stats"=>{"downloads"=>1, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_S_trains_used_in_this_work_/1395127", "title"=>"<i>S</i>trains used in this work.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-27 02:47:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/2040698"], "description"=>"<p>(A). <i>S</i>. <i>enterica</i> strains carrying <i>hfq</i><sub><i>ST</i></sub><i>-flag</i> (MA11054) or <i>hfq</i><sub><i>Bs</i></sub><i>-flag</i> (MA12275) translational fusion were grown in LB medium at 37°C under vigorous agitation. Harvested cells were lysed and crude extracts were used for western blot analysis using anti-FLAG M2 antibodies. ß-galactosidase activity was measured in exponentially growing LB cultures (OD<sub>600</sub> ≈ 0.3) (B and C) or in early stationary phase cultures (OD<sub>600</sub> ≈1.5) (D). Strains used were: B. MA9132, MA10744 and MA11214; C. MA8020, MA8021, and MA11215; D. MA9591, MA9603, and MA11216 (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0124977#pone.0124977.t001\" target=\"_blank\">Table 1</a> for full genotypes). (E) Cultures from strains in D were incubated 24 hours in stationary phase, serially diluted, and spotted on LB agar. <i>hfq</i><sub><i>STM</i></sub> (top row); Δ<i>hfq</i><sub><i>STM</i></sub> (middle row); Δ<i>hfq</i><sub><i>STM</i></sub>:: <i>hfq</i><sub><i>Bs</i></sub> (bottom row).</p>", "links"=>[], "tags"=>["phase fitness defect", "Salmonella", "Hfq proteins", "rna", "subtilis hfq"], "article_id"=>1395126, "categories"=>["Biological Sciences"], "users"=>["Tatiana Rochat", "Olivier Delumeau", "Nara Figueroa-Bossi", "Philippe Noirot", "Lionello Bossi", "Etienne Dervyn", "Philippe Bouloc"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0124977.g004", "stats"=>{"downloads"=>3, "page_views"=>66, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_of_translational_lacZ_fusions_to_chromosomal_genes_sensitive_to_Hfq_function_in_Salmonella_enterica_and_growth_phenotype_of_degP_lacZ_strains_carrying_different_hfq_alleles_/1395126", "title"=>"Expression of translational <i>lacZ</i> fusions to chromosomal genes sensitive to Hfq function in <i>Salmonella enterica</i> and growth phenotype of <i>degP</i>::<i>lacZ</i> strains carrying different <i>hfq</i> alleles.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-27 02:47:39"}

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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