Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition inEscherichia coli K-12

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• 作者：Everett T Hayes (1)
  Jessica C Wilks (1)
  Piero Sanfilippo (1)
  Elizabeth Yohannes (1)
  Daniel P Tate (1)
  Brian D Jones (2)
  Michael D Radmacher (2)
  Sandra S BonDurant (3)
  Joan L Slonczewski (1)
  
• 刊名：BMC Microbiology
• 出版年：2006
• 出版时间：December 2006
• 年：2006
• 卷：6
• 期：1
• 全文大小：1118KB
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• 作者单位：Everett T Hayes (1)
  Jessica C Wilks (1)
  Piero Sanfilippo (1)
  Elizabeth Yohannes (1)
  Daniel P Tate (1)
  Brian D Jones (2)
  Michael D Radmacher (2)
  Sandra S BonDurant (3)
  Joan L Slonczewski (1)
  
  1. Department of Biology, Kenyon College, 43022, Gambier, OH, USA
  2. Department of Mathematics, Kenyon College, 43022, Gambier, OH, USA
  3. Gene Expression Center, University of Wisconsin, 53706, Madison, WI, USA
  
• ISSN：1471-2180

文摘

Background InEscherichia 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. Results The pH dependence of gene expression was analyzed in oxygen-limited cultures ofE. 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 geneyagU 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). AhypF 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 thegadA 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). Conclusion pH regulates a core set of genes independently of oxygen, includingyagU, fimbriae, periplasmic chaperones, andnhaB. Under oxygen limitation, however, pH regulation is reversed for genes encoding electron transport components and hydrogenases. Extreme-acid resistance requiresyagU 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.