Escherichia coli K-12 Survives Anaerobic Exposure at pH 2 without RpoS, Gad, or Hydrogenases, but Shows Sensitivity to Autoclaved Broth Products
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{"title"=>"Escherichia coli K-12 Survives Anaerobic Exposure at pH 2 without RpoS, Gad, or Hydrogenases, but Shows Sensitivity to Autoclaved Broth Products", "type"=>"journal", "authors"=>[{"first_name"=>"Daniel P.", "last_name"=>"Riggins", "scopus_author_id"=>"36638304400"}, {"first_name"=>"Maria J.", "last_name"=>"Narvaez", "scopus_author_id"=>"55618134700"}, {"first_name"=>"Keith A.", "last_name"=>"Martinez", "scopus_author_id"=>"55221369400"}, {"first_name"=>"Mark M.", "last_name"=>"Harden", "scopus_author_id"=>"55618132700"}, {"first_name"=>"Joan L.", "last_name"=>"Slonczewski", "scopus_author_id"=>"7005244208"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84874764415", "doi"=>"10.1371/journal.pone.0056796", "sgr"=>"84874764415", "pmid"=>"23520457", "issn"=>"19326203", "pui"=>"368490111"}, "id"=>"d14893fe-b499-328e-8296-75c766e3e8b8", "abstract"=>"Escherichia coli and other enteric bacteria survive exposure to extreme acid (pH 2 or lower) in gastric fluid. Aerated cultures survive via regulons expressing glutamate decarboxylase (Gad, activated by RpoS), cyclopropane fatty acid synthase (Cfa) and others. But extreme-acid survival is rarely tested under low oxygen, a condition found in the stomach and the intestinal tract. We observed survival of E. coli K-12 W3110 at pH 1.2-pH 2.0, conducting all manipulations (overnight culture at pH 5.5, extreme-acid exposure, dilution and plating) in a glove box excluding oxygen (10% H2, 5% CO2, balance N2). With dissolved O2 concentrations maintained below 6 µM, survival at pH 2 required Cfa but did not require GadC, RpoS, or hydrogenases. Extreme-acid survival in broth (containing tryptone and yeast extract) was diminished in media that had been autoclaved compared to media that had been filtered. The effect of autoclaved media on extreme-acid survival was most pronounced when oxygen was excluded. Exposure to H2O2 during extreme-acid treatment increased the death rate slightly for W3110 and to a greater extent for the rpoS deletion strain. Survival at pH 2 was increased in strains lacking the anaerobic regulator fnr. During anaerobic growth at pH 5.5, strains deleted for fnr showed enhanced transcription of acid-survival genes gadB, cfa, and hdeA, as well as catalase (katE). We show that E. coli cultured under oxygen exclusion (<6 µM O2) requires mechanisms different from those of aerated cultures. Extreme acid survival is more sensitive to autoclave products under oxygen exclusion.", "link"=>"http://www.mendeley.com/research/escherichia-coli-k12-survives-anaerobic-exposure-ph-2-without-rpos-gad-hydrogenases-shows-sensitivit", "reader_count"=>32, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>5, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>11, "Student > Master"=>8, "Other"=>1, "Student > Bachelor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>5, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>11, "Student > Master"=>8, "Other"=>1, "Student > Bachelor"=>3}, "reader_count_by_subject_area"=>{"Engineering"=>4, "Unspecified"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>18, "Chemistry"=>3, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>4}, "Chemistry"=>{"Chemistry"=>3}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>18}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Ireland"=>2, "Japan"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/982710"], "description"=>"<p>Overnight cultures were diluted 1∶200 into 100 ml of LBK at pH 7.0 (open circles) and pH 5.5 (solid circles). Cultures were incubated in a 37°C water bath rotating at 160 rpm in 250-ml baffled flasks. Optical density (λ = 600) and dissolved oxygen levels were recorded every 20 min after the first hour of incubation. Dissolved oxygen concentrations were plotted as a function of OD<sub>600</sub>.</p>", "links"=>[], "tags"=>["detection"], "article_id"=>648785, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Daniel P. Riggins", "Maria J. Narvaez", "Keith A. Martinez", "Mark M. Harden", "Joan L. Slonczewski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0056796.g005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Oxygen_levels_drop_below_levels_of_detection_by_OD_600_8202_8202_1_5_/648785", "title"=>"Oxygen levels drop below levels of detection by OD<sub>600</sub> = 1.5.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:19:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/982708"], "description"=>"<p>Overnight cultures of W3110 and our <i>rpoS</i> mutant were exposed to filter sterilized LBK pH 2.0, with and without 2 mM H<sub>2</sub>O<sub>2</sub> under both oxygen exclusion and aeration and were serially diluted to final dilutions of 1∶80,000 and 1∶400,000, respectively. Error bars indicate SEM (n = 5 or 6).</p>", "links"=>[], "tags"=>["mutant", "affected", "concentrations"], "article_id"=>648783, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Daniel P. Riggins", "Maria J. Narvaez", "Keith A. Martinez", "Mark M. Harden", "Joan L. Slonczewski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0056796.g003", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_rpoS_mutant_survival_is_affected_by_low_concentrations_of_H_2_O_2_/648783", "title"=>"<i>rpoS</i> mutant survival is affected by low concentrations of H<sub>2</sub>O<sub>2</sub>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:19:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/982709"], "description"=>"<p>Cultures of W3110 and JLS1115 (W3110 <i>fnr</i>) were grown in LBK buffered with 100 mM MES at pH 5.5. Bacterial cultures were exposed to LBK pH 2.0 for 2 hours. Exposure tubes were serially diluted 1∶400,000 and 1∶80,000 aerobically and anaerobically, respectively, and plated. Viable colonies on each of 6 replicate plates were counted and log transformed. The log ratios (pH 2.0– pH 7.0) were then used to calculate the percentage of cells surviving in comparison to a pH 7.0 exposure control. The survival response of W3110 and JLS1115 were compared in autoclaved medium (light bars) and filtered medium (dark bars). Error bars indicate SEM (n = 5 or 6).</p>", "links"=>[], "tags"=>["deletion", "anaerobic", "autoclaved"], "article_id"=>648784, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Daniel P. Riggins", "Maria J. Narvaez", "Keith A. Martinez", "Mark M. Harden", "Joan L. Slonczewski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0056796.g004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_FNR_deletion_enhances_anaerobic_acid_resistance_in_autoclaved_medium_/648784", "title"=>"FNR deletion enhances anaerobic acid resistance in autoclaved medium.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:19:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/982707"], "description"=>"<p>Overnight cultures of <i>E. coli</i> K-12 strain W3110 were grown in LBK 100 mM MES pH 5.0. These cultures were exposed to medium at pH 1.2; 1.6;and 2.0, respectively, for two hours. Dilutions from exposed cells were completed as in <b>Fig. 1</b>. Strains were exposed in autoclave-sterilized medium (light bars) and in filtered medium (dark bars). Error bars indicate SEM (n = 5 or 6).</p>", "links"=>[], "tags"=>["survives", "ph"], "article_id"=>648782, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Daniel P. Riggins", "Maria J. Narvaez", "Keith A. Martinez", "Mark M. Harden", "Joan L. Slonczewski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0056796.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_E_coli_survives_at_pH_lower_than_pH_2_0_/648782", "title"=>"<i>E. coli</i> survives at pH lower than pH 2.0.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:19:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/982704"], "description"=>"<p>Single-gene mutants of <i>E. coli</i> K-12 strain W3110 were constructed as described under <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056796#s2\" target=\"_blank\">Methods</a>. Strains defective for <i>gadC</i>, <i>rpoS</i>, <i>cfa</i>, <i>hypF</i>, and <i>fnr</i> were cultured overnight and exposed to pH 2.0 for 2 hours before being diluted 1∶80,000 and 1∶400,000 under anoxic and aerated conditions, respectively. Dilutions were then plated allowing colonies to grow up overnight at 37° C. The number of colonies per plate was log transformed and a ratio of acidic exposure – control (pH 7.0) and a percentage was calculated from that ratio. Extreme acid medium was autoclave sterilized (Light bars); or filter sterilized (dark bars). Error bars indicate SEM (n = 5 or 6). * denotes undetectable colony counts on dilution plates and a corresponding survival of <1%.</p>", "links"=>[], "tags"=>["mutant"], "article_id"=>648779, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Daniel P. Riggins", "Maria J. Narvaez", "Keith A. Martinez", "Mark M. Harden", "Joan L. Slonczewski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0056796.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Acid_survival_of_mutant_strains_/648779", "title"=>"Acid survival of mutant strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:18:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1012081"], "description"=>"<p>Primers used for qRT-PCR.</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology", "Biochemistry"], "article_id"=>672491, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Daniel P. Riggins", "Maria J. Narvaez", "Keith A. Martinez", "Mark M. Harden", "Joan L. Slonczewski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0056796.t002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Primers_used_for_qRT_PCR_/672491", "title"=>"Primers used for qRT-PCR.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-08 00:41:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/982711"], "description"=>"<p>RNA was isolated from anaerobic cultures of JLS1115 (W3110 <i>fnr</i>) (gray bars) grown to stationary phase at pH 5.5 in buffered LBK. qRT-PCR was used to measure the differential expression of mRNA levels for <i>cfa</i>, <i>gadB</i>, <i>hdeA katE</i>, <i>sdhC</i>, and <i>frdB</i> in the <i>fnr</i> mutant compared to the wild-type using primers listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056796#pone-0056796-t002\" target=\"_blank\">Table 2</a>. Positive values denote higher expression in the <i>fnr</i> mutant than in the wild-type and vice-versa. Error bars represent SEM, n = 3 (RNA from independent cultures). The expression profile for each gene was verified in triplicate.</p>", "links"=>[], "tags"=>["affected", "ph"], "article_id"=>648786, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Daniel P. Riggins", "Maria J. Narvaez", "Keith A. Martinez", "Mark M. Harden", "Joan L. Slonczewski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0056796.g006", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_expression_affected_by_fnr_during_growth_at_pH_5_5_/648786", "title"=>"Gene expression affected by <i>fnr</i> during growth at pH 5.5.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:19:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1012098"], "description"=>"<p>Statistical analysis of survival assays for <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056796#pone-0056796-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["assays"], "article_id"=>672511, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Daniel P. Riggins", "Maria J. Narvaez", "Keith A. Martinez", "Mark M. Harden", "Joan L. Slonczewski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0056796.t001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistical_analysis_of_survival_assays_for_Figure_1_/672511", "title"=>"Statistical analysis of survival assays for Figure 1.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-08 00:41:51"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"10", "full-text"=>"9", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"10", "full-text"=>"10", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"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"=>"2"}
  • {"unique-ip"=>"2", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"4", "full-text"=>"1", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

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/Biochemistry", "average_usage"=>[266, 468, 593, 703, 804, 903, 993, 1084, 1171, 1256, 1339, 1422, 1492]}, {"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/Neuroscience", "average_usage"=>[261, 444, 554, 655, 748, 834, 923, 1004, 1089, 1170, 1244, 1315, 1380]}, {"subject_area"=>"/Earth sciences", "average_usage"=>[296, 488, 620, 717, 828, 938, 1038, 1130, 1230, 1328, 1414, 1502, 1592]}, {"subject_area"=>"/Earth sciences/Marine and aquatic sciences", "average_usage"=>[299, 492, 619, 718, 826, 932, 1037, 1143, 1246, 1333, 1414, 1517, 1575]}, {"subject_area"=>"/Physical sciences", "average_usage"=>[254, 431, 547, 651, 748, 842, 932, 1017, 1098, 1178, 1259, 1336, 1404]}]}
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