Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12.
Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12.
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DOI：
10.1186/1471-2180-6-89
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发表时间：
2006-10-06
期刊：
影响因子：
4.2
通讯作者：
Slonczewski JL
中科院分区：
文献类型：
--
作者：
Hayes ET;Wilks JC;Sanfilippo P;Yohannes E;Tate DP;Jones BD;Radmacher MD;BonDurant SS;Slonczewski JL
在大肠杆菌中，pH 调节氨基酸和糖分解代谢、电子传递、氧化应激、周质和包膜蛋白的基因。许多 pH 依赖性基因受到厌氧作用的共同调节，但 pH 胁迫和氧限制的总体交叉点尚未得到研究。在大肠杆菌 K-12 菌株 W3110 的限氧培养物中分析了基因表达的 pH 依赖性。大肠杆菌 K-12 菌株 W3110 在含有缓冲至 pH 5.7、pH 7.0 和 pH 8.5 的 LBK 肉汤的封闭管中培养。 Affymetrix 阵列杂交揭示了 1,384 个基因和 610 个基因间区域的 pH 依赖性表达。由 251 个基因组成的核心组显示出与之前通气培养物研究中相似的 pH 响应。高度酸诱导的基因 yagU 被证明是极端酸性抵抗（在 pH 2 下生存）所必需的。酸还上调菌毛 (fimAC)、周质伴侣 (hdeAB)、环丙烷脂肪酸合酶 (cfa) 和“组成型”Na+/H+ 逆向转运蛋白 (nhaB)。麦芽糖糊精转运 (lamB、mal)、ATP 合酶 (atp) 和 DNA 修复 (recA、mutL) 的核心基因碱基上调。其他基因在通气或不通气的情况下表现出相反的 pH 响应，例如 ETS 成分（cyo、nuo、sdh）和氢化酶（hya、hyb、hyc、hyf、hyp）。缺乏所有氢化酶活性的 hypF 菌株显示出极端酸性耐受性的丧失。仅在氧限制下，酸下调核糖体合成（rpl、rpm、rps）。酸上调了糖衍生物的分解代谢，这些衍生物的发酵最大限度地减少了酸的产生（gnd、gnt、srl），并且还上调了 gadA 区域中的 13 个基因簇。酸上调药物转运蛋白（mdtEF、mdtL），但下调青霉素结合蛋白（dacACD、mreBC）。含有调节 sRNA 的基因间区域被酸上调（ryeA、csrB、gadY、rybC）。 pH 值独立于氧气调节一组核心基因，包括 yagU、菌毛、周质伴侣和 nhaB。然而，在氧气限制下，编码电子传递成分和氢化酶的基因的 pH 调节发生逆转。极端的耐酸性需要产生 yagU 和氢化酶。在氧限制下，核糖体合成在低 pH 值下下调，可能是由于分解代谢的能量产量有限。在氧气限制下，pH 值调节新陈代谢和运输，以最大限度地增加替代分解代谢选择，同时最大限度地减少细胞质的酸化或碱化。
In 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. The 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). pH 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.
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影响因子：
3.2
作者：
Arnold, CN;McElhanon, J;Siegele, DA
通讯作者：
Siegele, DA
影响因子：
3.2
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影响因子：
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影响因子：
3.6
作者：
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通讯作者：
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影响因子：
2.8
作者：
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通讯作者：
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