Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12 View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2006-10-06

AUTHORS

Everett T Hayes, Jessica C Wilks, Piero Sanfilippo, Elizabeth Yohannes, Daniel P Tate, Brian D Jones, Michael D Radmacher, Sandra S BonDurant, Joan L Slonczewski

ABSTRACT

BackgroundIn Escherichia coli, pH regulates genes for amino-acid and sugar catabolism, electron transport, oxidative stress, periplasmic and envelope proteins. Many pH-dependent genes are co-regulated by anaerobiosis, but the overall intersection of pH stress and oxygen limitation has not been investigated.ResultsThe pH dependence of gene expression was analyzed in oxygen-limited cultures of E. coli K-12 strain W3110. E. coli K-12 strain W3110 was cultured in closed tubes containing LBK broth buffered at pH 5.7, pH 7.0, and pH 8.5. Affymetrix array hybridization revealed pH-dependent expression of 1,384 genes and 610 intergenic regions. A core group of 251 genes showed pH responses similar to those in a previous study of cultures grown with aeration. The highly acid-induced gene yagU was shown to be required for extreme-acid resistance (survival at pH 2). Acid also up-regulated fimbriae (fimAC), periplasmic chaperones (hdeAB), cyclopropane fatty acid synthase (cfa), and the "constitutive" Na+/H+ antiporter (nhaB). Base up-regulated core genes for maltodextrin transport (lamB, mal), ATP synthase (atp), and DNA repair (recA, mutL). Other genes showed opposite pH responses with or without aeration, for example ETS components (cyo,nuo, sdh) and hydrogenases (hya, hyb, hyc, hyf, hyp). A hypF strain lacking all hydrogenase activity showed loss of extreme-acid resistance. Under oxygen limitation only, acid down-regulated ribosome synthesis (rpl,rpm, rps). Acid up-regulated the catabolism of sugar derivatives whose fermentation minimized acid production (gnd, gnt, srl), and also a cluster of 13 genes in the gadA region. Acid up-regulated drug transporters (mdtEF, mdtL), but down-regulated penicillin-binding proteins (dacACD, mreBC). Intergenic regions containing regulatory sRNAs were up-regulated by acid (ryeA, csrB, gadY, rybC).ConclusionpH regulates a core set of genes independently of oxygen, including yagU, fimbriae, periplasmic chaperones, and nhaB. Under oxygen limitation, however, pH regulation is reversed for genes encoding electron transport components and hydrogenases. Extreme-acid resistance requires yagU and hydrogenase production. Ribosome synthesis is down-regulated at low pH under oxygen limitation, possibly due to the restricted energy yield of catabolism. Under oxygen limitation, pH regulates metabolism and transport so as to maximize alternative catabolic options while minimizing acidification or alkalinization of the cytoplasm. More... »

PAGES

89

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2180-6-89

DOI

http://dx.doi.org/10.1186/1471-2180-6-89

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1016974365

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/17026754


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0601", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biochemistry and Cell Biology", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Carrier Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Down-Regulation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Drug Resistance, Multiple, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Escherichia coli K12", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Escherichia coli Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Regulation, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genes, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Hydrogen-Ion Concentration", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Hydrogenase", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Oxygen", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Up-Regulation", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Department of Biology, Kenyon College, 43022, Gambier, OH, USA", 
          "id": "http://www.grid.ac/institutes/grid.258533.a", 
          "name": [
            "Department of Biology, Kenyon College, 43022, Gambier, OH, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hayes", 
        "givenName": "Everett T", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Biology, Kenyon College, 43022, Gambier, OH, USA", 
          "id": "http://www.grid.ac/institutes/grid.258533.a", 
          "name": [
            "Department of Biology, Kenyon College, 43022, Gambier, OH, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Wilks", 
        "givenName": "Jessica C", 
        "id": "sg:person.01113334210.18", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01113334210.18"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Biology, Kenyon College, 43022, Gambier, OH, USA", 
          "id": "http://www.grid.ac/institutes/grid.258533.a", 
          "name": [
            "Department of Biology, Kenyon College, 43022, Gambier, OH, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Sanfilippo", 
        "givenName": "Piero", 
        "id": "sg:person.0635250226.78", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0635250226.78"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Biology, Kenyon College, 43022, Gambier, OH, USA", 
          "id": "http://www.grid.ac/institutes/grid.258533.a", 
          "name": [
            "Department of Biology, Kenyon College, 43022, Gambier, OH, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Yohannes", 
        "givenName": "Elizabeth", 
        "id": "sg:person.01153432664.37", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01153432664.37"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Biology, Kenyon College, 43022, Gambier, OH, USA", 
          "id": "http://www.grid.ac/institutes/grid.258533.a", 
          "name": [
            "Department of Biology, Kenyon College, 43022, Gambier, OH, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Tate", 
        "givenName": "Daniel P", 
        "id": "sg:person.0726122053.08", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0726122053.08"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Mathematics, Kenyon College, 43022, Gambier, OH, USA", 
          "id": "http://www.grid.ac/institutes/grid.258533.a", 
          "name": [
            "Department of Mathematics, Kenyon College, 43022, Gambier, OH, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Jones", 
        "givenName": "Brian D", 
        "id": "sg:person.0646333007.16", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0646333007.16"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Mathematics, Kenyon College, 43022, Gambier, OH, USA", 
          "id": "http://www.grid.ac/institutes/grid.258533.a", 
          "name": [
            "Department of Mathematics, Kenyon College, 43022, Gambier, OH, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Radmacher", 
        "givenName": "Michael D", 
        "id": "sg:person.01347005633.05", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01347005633.05"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Gene Expression Center, University of Wisconsin, 53706, Madison, WI, USA", 
          "id": "http://www.grid.ac/institutes/grid.14003.36", 
          "name": [
            "Gene Expression Center, University of Wisconsin, 53706, Madison, WI, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "BonDurant", 
        "givenName": "Sandra S", 
        "id": "sg:person.0764515304.42", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0764515304.42"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Biology, Kenyon College, 43022, Gambier, OH, USA", 
          "id": "http://www.grid.ac/institutes/grid.258533.a", 
          "name": [
            "Department of Biology, Kenyon College, 43022, Gambier, OH, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Slonczewski", 
        "givenName": "Joan L", 
        "id": "sg:person.012564170647.70", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012564170647.70"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1038/nrmicro1181", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016619827", 
          "https://doi.org/10.1038/nrmicro1181"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/0-387-21679-0_5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030952091", 
          "https://doi.org/10.1007/0-387-21679-0_5"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg1749", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017349746", 
          "https://doi.org/10.1038/nrg1749"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1023/a:1015827908309", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052956580", 
          "https://doi.org/10.1023/a:1015827908309"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00284-002-3764-z", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011575678", 
          "https://doi.org/10.1007/s00284-002-3764-z"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrmicro1021", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024287184", 
          "https://doi.org/10.1038/nrmicro1021"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2180-5-59", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006121575", 
          "https://doi.org/10.1186/1471-2180-5-59"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1385/cbb:41:3:357", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004351009", 
          "https://doi.org/10.1385/cbb:41:3:357"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2006-10-06", 
    "datePublishedReg": "2006-10-06", 
    "description": "BackgroundIn Escherichia coli, pH regulates genes for amino-acid and sugar catabolism, electron transport, oxidative stress, periplasmic and envelope proteins. Many pH-dependent genes are co-regulated by anaerobiosis, but the overall intersection of pH stress and oxygen limitation has not been investigated.ResultsThe pH dependence of gene expression was analyzed in oxygen-limited cultures of E. coli K-12 strain W3110. E. coli K-12 strain W3110 was cultured in closed tubes containing LBK broth buffered at pH 5.7, pH 7.0, and pH 8.5. Affymetrix array hybridization revealed pH-dependent expression of 1,384 genes and 610 intergenic regions. A core group of 251 genes showed pH responses similar to those in a previous study of cultures grown with aeration. The highly acid-induced gene yagU was shown to be required for extreme-acid resistance (survival at pH 2). Acid also up-regulated fimbriae (fimAC), periplasmic chaperones (hdeAB), cyclopropane fatty acid synthase (cfa), and the \"constitutive\" Na+/H+ antiporter (nhaB). Base up-regulated core genes for maltodextrin transport (lamB, mal), ATP synthase (atp), and DNA repair (recA, mutL). Other genes showed opposite pH responses with or without aeration, for example ETS components (cyo,nuo, sdh) and hydrogenases (hya, hyb, hyc, hyf, hyp). A hypF strain lacking all hydrogenase activity showed loss of extreme-acid resistance. Under oxygen limitation only, acid down-regulated ribosome synthesis (rpl,rpm, rps). Acid up-regulated the catabolism of sugar derivatives whose fermentation minimized acid production (gnd, gnt, srl), and also a cluster of 13 genes in the gadA region. Acid up-regulated drug transporters (mdtEF, mdtL), but down-regulated penicillin-binding proteins (dacACD, mreBC). Intergenic regions containing regulatory sRNAs were up-regulated by acid (ryeA, csrB, gadY, rybC).ConclusionpH regulates a core set of genes independently of oxygen, including yagU, fimbriae, periplasmic chaperones, and nhaB. Under oxygen limitation, however, pH regulation is reversed for genes encoding electron transport components and hydrogenases. Extreme-acid resistance requires yagU and hydrogenase production. Ribosome synthesis is down-regulated at low pH under oxygen limitation, possibly due to the restricted energy yield of catabolism. Under oxygen limitation, pH regulates metabolism and transport so as to maximize alternative catabolic options while minimizing acidification or alkalinization of the cytoplasm.", 
    "genre": "article", 
    "id": "sg:pub.10.1186/1471-2180-6-89", 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.3033272", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1024253", 
        "issn": [
          "1471-2180"
        ], 
        "name": "BMC Microbiology", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "6"
      }
    ], 
    "keywords": [
      "extreme acid resistance", 
      "E. coli K", 
      "coli K", 
      "periplasmic chaperone", 
      "ribosome synthesis", 
      "intergenic region", 
      "oxygen limitation", 
      "strain W3110", 
      "cyclopropane fatty acid synthase", 
      "pH-dependent expression", 
      "Escherichia coli K", 
      "regulation of catabolism", 
      "electron transport components", 
      "regulatory sRNAs", 
      "fatty acid synthase", 
      "maltodextrin transport", 
      "ATP synthase", 
      "penicillin-binding proteins", 
      "sugar catabolism", 
      "DNA repair", 
      "core genes", 
      "array hybridization", 
      "gene expression", 
      "multidrug transporter", 
      "oxygen-limited cultures", 
      "hydrogenase activity", 
      "genes", 
      "acid synthase", 
      "Escherichia coli", 
      "chaperones", 
      "pH regulation", 
      "hydrogenases", 
      "envelope protein", 
      "W3110", 
      "transport components", 
      "catabolism", 
      "acid production", 
      "oxidative stress", 
      "protein", 
      "transporters", 
      "core set", 
      "synthase", 
      "drug transporters", 
      "regulation", 
      "electron transport", 
      "expression", 
      "sRNAs", 
      "antiporter", 
      "low pH", 
      "cytoplasm", 
      "ETS components", 
      "anaerobiosis", 
      "coli", 
      "core group", 
      "hybridization", 
      "transport", 
      "stress", 
      "region", 
      "production", 
      "metabolism", 
      "resistance", 
      "previous studies", 
      "acidification", 
      "culture", 
      "fimbriae", 
      "response", 
      "strains", 
      "sugar derivatives", 
      "alkalinization", 
      "synthesis", 
      "acid", 
      "repair", 
      "pH", 
      "broth", 
      "components", 
      "activity", 
      "aeration", 
      "clusters", 
      "composition", 
      "yield", 
      "loss", 
      "limitations", 
      "overall intersection", 
      "energy yield", 
      "oxygen", 
      "study", 
      "closed tube", 
      "derivatives", 
      "set", 
      "group", 
      "tube", 
      "dependence", 
      "options", 
      "intersection"
    ], 
    "name": "Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12", 
    "pagination": "89", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1016974365"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2180-6-89"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "17026754"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2180-6-89", 
      "https://app.dimensions.ai/details/publication/pub.1016974365"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-10-01T06:33", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20221001/entities/gbq_results/article/article_425.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1186/1471-2180-6-89"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1471-2180-6-89'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2180-6-89'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2180-6-89'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2180-6-89'


 

This table displays all metadata directly associated to this object as RDF triples.

296 TRIPLES      21 PREDICATES      139 URIs      122 LITERALS      18 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2180-6-89 schema:about N101335f3b826461783b5508f5ae3b18d
2 N2b7629c1dc2d4629b65cc809684f3d34
3 N360d2cde61f8454c8e6f9c5bd23dda5e
4 N3e537acdcb0441ea91c8e84ddc50aa6d
5 N41949b690c3f4cb0b1ca851703f50a1b
6 N7dcfd96d85bf4330b7aa2779d06283f3
7 N8728c29a2d3242e7b7c2923659072faf
8 Na5272d6919c248c6beb06246845e6e63
9 Nc0d62c6068754f74be4f7847da410db5
10 Ncb335cfa1c2148f8b4c9a0b0b1d6e185
11 Ne68a791656ba40c989b3cbec055287c2
12 anzsrc-for:06
13 anzsrc-for:0601
14 anzsrc-for:0604
15 schema:author Nd793d1909c3e42ac9a55c91ed8e7c544
16 schema:citation sg:pub.10.1007/0-387-21679-0_5
17 sg:pub.10.1007/s00284-002-3764-z
18 sg:pub.10.1023/a:1015827908309
19 sg:pub.10.1038/nrg1749
20 sg:pub.10.1038/nrmicro1021
21 sg:pub.10.1038/nrmicro1181
22 sg:pub.10.1186/1471-2180-5-59
23 sg:pub.10.1385/cbb:41:3:357
24 schema:datePublished 2006-10-06
25 schema:datePublishedReg 2006-10-06
26 schema:description BackgroundIn Escherichia coli, pH regulates genes for amino-acid and sugar catabolism, electron transport, oxidative stress, periplasmic and envelope proteins. Many pH-dependent genes are co-regulated by anaerobiosis, but the overall intersection of pH stress and oxygen limitation has not been investigated.ResultsThe pH dependence of gene expression was analyzed in oxygen-limited cultures of E. coli K-12 strain W3110. E. coli K-12 strain W3110 was cultured in closed tubes containing LBK broth buffered at pH 5.7, pH 7.0, and pH 8.5. Affymetrix array hybridization revealed pH-dependent expression of 1,384 genes and 610 intergenic regions. A core group of 251 genes showed pH responses similar to those in a previous study of cultures grown with aeration. The highly acid-induced gene yagU was shown to be required for extreme-acid resistance (survival at pH 2). Acid also up-regulated fimbriae (fimAC), periplasmic chaperones (hdeAB), cyclopropane fatty acid synthase (cfa), and the "constitutive" Na+/H+ antiporter (nhaB). Base up-regulated core genes for maltodextrin transport (lamB, mal), ATP synthase (atp), and DNA repair (recA, mutL). Other genes showed opposite pH responses with or without aeration, for example ETS components (cyo,nuo, sdh) and hydrogenases (hya, hyb, hyc, hyf, hyp). A hypF strain lacking all hydrogenase activity showed loss of extreme-acid resistance. Under oxygen limitation only, acid down-regulated ribosome synthesis (rpl,rpm, rps). Acid up-regulated the catabolism of sugar derivatives whose fermentation minimized acid production (gnd, gnt, srl), and also a cluster of 13 genes in the gadA region. Acid up-regulated drug transporters (mdtEF, mdtL), but down-regulated penicillin-binding proteins (dacACD, mreBC). Intergenic regions containing regulatory sRNAs were up-regulated by acid (ryeA, csrB, gadY, rybC).ConclusionpH regulates a core set of genes independently of oxygen, including yagU, fimbriae, periplasmic chaperones, and nhaB. Under oxygen limitation, however, pH regulation is reversed for genes encoding electron transport components and hydrogenases. Extreme-acid resistance requires yagU and hydrogenase production. Ribosome synthesis is down-regulated at low pH under oxygen limitation, possibly due to the restricted energy yield of catabolism. Under oxygen limitation, pH regulates metabolism and transport so as to maximize alternative catabolic options while minimizing acidification or alkalinization of the cytoplasm.
27 schema:genre article
28 schema:isAccessibleForFree true
29 schema:isPartOf N19dcdcd07a86476cb265bca471e2d359
30 Nae8505b6a70044369db5d6d5b950987e
31 sg:journal.1024253
32 schema:keywords ATP synthase
33 DNA repair
34 E. coli K
35 ETS components
36 Escherichia coli
37 Escherichia coli K
38 W3110
39 acid
40 acid production
41 acid synthase
42 acidification
43 activity
44 aeration
45 alkalinization
46 anaerobiosis
47 antiporter
48 array hybridization
49 broth
50 catabolism
51 chaperones
52 closed tube
53 clusters
54 coli
55 coli K
56 components
57 composition
58 core genes
59 core group
60 core set
61 culture
62 cyclopropane fatty acid synthase
63 cytoplasm
64 dependence
65 derivatives
66 drug transporters
67 electron transport
68 electron transport components
69 energy yield
70 envelope protein
71 expression
72 extreme acid resistance
73 fatty acid synthase
74 fimbriae
75 gene expression
76 genes
77 group
78 hybridization
79 hydrogenase activity
80 hydrogenases
81 intergenic region
82 intersection
83 limitations
84 loss
85 low pH
86 maltodextrin transport
87 metabolism
88 multidrug transporter
89 options
90 overall intersection
91 oxidative stress
92 oxygen
93 oxygen limitation
94 oxygen-limited cultures
95 pH
96 pH regulation
97 pH-dependent expression
98 penicillin-binding proteins
99 periplasmic chaperone
100 previous studies
101 production
102 protein
103 region
104 regulation
105 regulation of catabolism
106 regulatory sRNAs
107 repair
108 resistance
109 response
110 ribosome synthesis
111 sRNAs
112 set
113 strain W3110
114 strains
115 stress
116 study
117 sugar catabolism
118 sugar derivatives
119 synthase
120 synthesis
121 transport
122 transport components
123 transporters
124 tube
125 yield
126 schema:name Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12
127 schema:pagination 89
128 schema:productId N1289ebac068d49c0899c40f787a52807
129 N2f0d4883b89b47a4ab98eb469e93a657
130 Ned460e0cb6b74bc7a2c77df276b92407
131 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016974365
132 https://doi.org/10.1186/1471-2180-6-89
133 schema:sdDatePublished 2022-10-01T06:33
134 schema:sdLicense https://scigraph.springernature.com/explorer/license/
135 schema:sdPublisher N1f52156750e048288b485cdd725451e7
136 schema:url https://doi.org/10.1186/1471-2180-6-89
137 sgo:license sg:explorer/license/
138 sgo:sdDataset articles
139 rdf:type schema:ScholarlyArticle
140 N101335f3b826461783b5508f5ae3b18d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
141 schema:name Escherichia coli K12
142 rdf:type schema:DefinedTerm
143 N1289ebac068d49c0899c40f787a52807 schema:name dimensions_id
144 schema:value pub.1016974365
145 rdf:type schema:PropertyValue
146 N19dcdcd07a86476cb265bca471e2d359 schema:issueNumber 1
147 rdf:type schema:PublicationIssue
148 N1f52156750e048288b485cdd725451e7 schema:name Springer Nature - SN SciGraph project
149 rdf:type schema:Organization
150 N2b7629c1dc2d4629b65cc809684f3d34 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
151 schema:name Drug Resistance, Multiple, Bacterial
152 rdf:type schema:DefinedTerm
153 N2f0d4883b89b47a4ab98eb469e93a657 schema:name doi
154 schema:value 10.1186/1471-2180-6-89
155 rdf:type schema:PropertyValue
156 N2f83ddd18e5d4c6ab1b90b5daffa0372 rdf:first sg:person.0726122053.08
157 rdf:rest N76eae5d71ee94613bbc091c19fa57c06
158 N360d2cde61f8454c8e6f9c5bd23dda5e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
159 schema:name Oxygen
160 rdf:type schema:DefinedTerm
161 N3e537acdcb0441ea91c8e84ddc50aa6d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
162 schema:name Escherichia coli Proteins
163 rdf:type schema:DefinedTerm
164 N41949b690c3f4cb0b1ca851703f50a1b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
165 schema:name Gene Expression Regulation, Bacterial
166 rdf:type schema:DefinedTerm
167 N5e6f1bbbf25041a0b5a0b4ea9c6d5a61 rdf:first sg:person.0764515304.42
168 rdf:rest Nc32d16f02ceb4f718799762c8b5d5339
169 N76eae5d71ee94613bbc091c19fa57c06 rdf:first sg:person.0646333007.16
170 rdf:rest N9f0b333ec96a4c59acf983eabc283bed
171 N7dcfd96d85bf4330b7aa2779d06283f3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
172 schema:name Genes, Bacterial
173 rdf:type schema:DefinedTerm
174 N81873de5b1a24518bf1dd26b288333af rdf:first sg:person.01113334210.18
175 rdf:rest N8c3b0dd969444f4e814134a4092fa7a9
176 N85023dd572ca45d59ed0048d9b39dc45 schema:affiliation grid-institutes:grid.258533.a
177 schema:familyName Hayes
178 schema:givenName Everett T
179 rdf:type schema:Person
180 N8728c29a2d3242e7b7c2923659072faf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
181 schema:name Hydrogen-Ion Concentration
182 rdf:type schema:DefinedTerm
183 N8c3b0dd969444f4e814134a4092fa7a9 rdf:first sg:person.0635250226.78
184 rdf:rest Ndb5891ee66f54f728e13b9d9f84e9fac
185 N9f0b333ec96a4c59acf983eabc283bed rdf:first sg:person.01347005633.05
186 rdf:rest N5e6f1bbbf25041a0b5a0b4ea9c6d5a61
187 Na5272d6919c248c6beb06246845e6e63 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
188 schema:name Hydrogenase
189 rdf:type schema:DefinedTerm
190 Nae8505b6a70044369db5d6d5b950987e schema:volumeNumber 6
191 rdf:type schema:PublicationVolume
192 Nc0d62c6068754f74be4f7847da410db5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
193 schema:name Carrier Proteins
194 rdf:type schema:DefinedTerm
195 Nc32d16f02ceb4f718799762c8b5d5339 rdf:first sg:person.012564170647.70
196 rdf:rest rdf:nil
197 Ncb335cfa1c2148f8b4c9a0b0b1d6e185 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
198 schema:name Down-Regulation
199 rdf:type schema:DefinedTerm
200 Nd793d1909c3e42ac9a55c91ed8e7c544 rdf:first N85023dd572ca45d59ed0048d9b39dc45
201 rdf:rest N81873de5b1a24518bf1dd26b288333af
202 Ndb5891ee66f54f728e13b9d9f84e9fac rdf:first sg:person.01153432664.37
203 rdf:rest N2f83ddd18e5d4c6ab1b90b5daffa0372
204 Ne68a791656ba40c989b3cbec055287c2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
205 schema:name Up-Regulation
206 rdf:type schema:DefinedTerm
207 Ned460e0cb6b74bc7a2c77df276b92407 schema:name pubmed_id
208 schema:value 17026754
209 rdf:type schema:PropertyValue
210 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
211 schema:name Biological Sciences
212 rdf:type schema:DefinedTerm
213 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
214 schema:name Biochemistry and Cell Biology
215 rdf:type schema:DefinedTerm
216 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
217 schema:name Genetics
218 rdf:type schema:DefinedTerm
219 sg:grant.3033272 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2180-6-89
220 rdf:type schema:MonetaryGrant
221 sg:journal.1024253 schema:issn 1471-2180
222 schema:name BMC Microbiology
223 schema:publisher Springer Nature
224 rdf:type schema:Periodical
225 sg:person.01113334210.18 schema:affiliation grid-institutes:grid.258533.a
226 schema:familyName Wilks
227 schema:givenName Jessica C
228 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01113334210.18
229 rdf:type schema:Person
230 sg:person.01153432664.37 schema:affiliation grid-institutes:grid.258533.a
231 schema:familyName Yohannes
232 schema:givenName Elizabeth
233 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01153432664.37
234 rdf:type schema:Person
235 sg:person.012564170647.70 schema:affiliation grid-institutes:grid.258533.a
236 schema:familyName Slonczewski
237 schema:givenName Joan L
238 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012564170647.70
239 rdf:type schema:Person
240 sg:person.01347005633.05 schema:affiliation grid-institutes:grid.258533.a
241 schema:familyName Radmacher
242 schema:givenName Michael D
243 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01347005633.05
244 rdf:type schema:Person
245 sg:person.0635250226.78 schema:affiliation grid-institutes:grid.258533.a
246 schema:familyName Sanfilippo
247 schema:givenName Piero
248 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0635250226.78
249 rdf:type schema:Person
250 sg:person.0646333007.16 schema:affiliation grid-institutes:grid.258533.a
251 schema:familyName Jones
252 schema:givenName Brian D
253 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0646333007.16
254 rdf:type schema:Person
255 sg:person.0726122053.08 schema:affiliation grid-institutes:grid.258533.a
256 schema:familyName Tate
257 schema:givenName Daniel P
258 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0726122053.08
259 rdf:type schema:Person
260 sg:person.0764515304.42 schema:affiliation grid-institutes:grid.14003.36
261 schema:familyName BonDurant
262 schema:givenName Sandra S
263 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0764515304.42
264 rdf:type schema:Person
265 sg:pub.10.1007/0-387-21679-0_5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030952091
266 https://doi.org/10.1007/0-387-21679-0_5
267 rdf:type schema:CreativeWork
268 sg:pub.10.1007/s00284-002-3764-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1011575678
269 https://doi.org/10.1007/s00284-002-3764-z
270 rdf:type schema:CreativeWork
271 sg:pub.10.1023/a:1015827908309 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052956580
272 https://doi.org/10.1023/a:1015827908309
273 rdf:type schema:CreativeWork
274 sg:pub.10.1038/nrg1749 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017349746
275 https://doi.org/10.1038/nrg1749
276 rdf:type schema:CreativeWork
277 sg:pub.10.1038/nrmicro1021 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024287184
278 https://doi.org/10.1038/nrmicro1021
279 rdf:type schema:CreativeWork
280 sg:pub.10.1038/nrmicro1181 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016619827
281 https://doi.org/10.1038/nrmicro1181
282 rdf:type schema:CreativeWork
283 sg:pub.10.1186/1471-2180-5-59 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006121575
284 https://doi.org/10.1186/1471-2180-5-59
285 rdf:type schema:CreativeWork
286 sg:pub.10.1385/cbb:41:3:357 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004351009
287 https://doi.org/10.1385/cbb:41:3:357
288 rdf:type schema:CreativeWork
289 grid-institutes:grid.14003.36 schema:alternateName Gene Expression Center, University of Wisconsin, 53706, Madison, WI, USA
290 schema:name Gene Expression Center, University of Wisconsin, 53706, Madison, WI, USA
291 rdf:type schema:Organization
292 grid-institutes:grid.258533.a schema:alternateName Department of Biology, Kenyon College, 43022, Gambier, OH, USA
293 Department of Mathematics, Kenyon College, 43022, Gambier, OH, USA
294 schema:name Department of Biology, Kenyon College, 43022, Gambier, OH, USA
295 Department of Mathematics, Kenyon College, 43022, Gambier, OH, USA
296 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...