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Li G, Yao Y. TorR/TorS Two-Component system resists extreme acid environment by regulating the key response factor RpoS in Escherichia coli. Gene 2022; 821:146295. [PMID: 35181503 DOI: 10.1016/j.gene.2022.146295] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/26/2021] [Accepted: 02/04/2022] [Indexed: 01/23/2023]
Abstract
Response to acid stress is critical for Escherichia coli to successfully complete its life-cycle. Acid resistance is an indispensable mechanism that allows neutralophilic bacteria, such as E. coli, to survive in the gastrointestinal tract. Escherichia coli acid tolerance has been extensively studied over the past decades, and most studies have focused on mechanisms of gene regulation. Bacterial two-component signal transduction systems sense and respond to external environmental changes through regulating genes expression. However, there has been little research on the mechanism of the TorR/TorS system in acid resistance, and how TorR/TorS regulate the expression ofacid-resistantgenes is still unclear. We found that TorR/TorS deletion in E. coli cells led to a growth defect in extreme acid conditions,andthis defectmightdepend on the nutritional conditionsand growth phase.TorS/TorR sensed an extremely acidic environment, and this TorR phosphorylation process might not be entirely dependent on TorS.RNA-seqand RT-qPCR results suggested that TorR regulated expressions of gadB, gadC, hdeA, gadE, mdtE, mdtF, gadX, and slp acid-resistant genes. Compared with wild-type cells, the stress response factor RpoSlevels and itsexpressions were significantly decreased in Δ torR cellsstimulated by extreme acid. And under these circumstances, the expression of iraM was significantly reduced to 0.6-fold inΔ torR cells. Electrophoreticmobility shift assay showed that TorR-His6 could interact with the rpoS promoter sequence in vitro. β-galactosidase activity assayresultsapprovedthat TorR might bind the rpoS promoter region in vivo. After the mutation of the TorR-box in the rpoS promoter region, these interactions were no longer observed. Taken together, we propose thatTorS and potential Hanks model Ser/Thr kinase received an external acid stress signal and then phosphorylated TorR, which guided the expressions of a variety of acid resistance genes. Moreover,TorRcoped with extreme acid environmentsthroughRpoS, levels of which might be maintained byIraM. Finally,TorR may confer E. coli with the abilityto resist gastric acid, allowing the bacterium to reach the surface of the terminal ileum and large intestine mucosal epithelial cells through the gastric acid barrier, andestablishcolonization and pathogenicity.
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Affiliation(s)
- Guotao Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China.
| | - Yuan Yao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China; Department of Neurology, Inner Mongolia People's Hospital, Hohhot, China.
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Du B, Yang L, Lloyd CJ, Fang X, Palsson BO. Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli. PLoS Comput Biol 2019; 15:e1007525. [PMID: 31809503 PMCID: PMC6897400 DOI: 10.1371/journal.pcbi.1007525] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 11/01/2019] [Indexed: 12/20/2022] Open
Abstract
Response to acid stress is critical for Escherichia coli to successfully complete its life-cycle by passing through the stomach to colonize the digestive tract. To develop a fundamental understanding of this response, we established a molecular mechanistic description of acid stress mitigation responses in E. coli and integrated them with a genome-scale model of its metabolism and macromolecular expression (ME-model). We considered three known mechanisms of acid stress mitigation: 1) change in membrane lipid fatty acid composition, 2) change in periplasmic protein stability over external pH and periplasmic chaperone protection mechanisms, and 3) change in the activities of membrane proteins. After integrating these mechanisms into an established ME-model, we could simulate their responses in the context of other cellular processes. We validated these simulations using RNA sequencing data obtained from five E. coli strains grown under external pH ranging from 5.5 to 7.0. We found: i) that for the differentially expressed genes accounted for in the ME-model, 80% of the upregulated genes were correctly predicted by the ME-model, and ii) that these genes are mainly involved in translation processes (45% of genes), membrane proteins and related processes (18% of genes), amino acid metabolism (12% of genes), and cofactor and prosthetic group biosynthesis (8% of genes). We also demonstrated several intervention strategies on acid tolerance that can be simulated by the ME-model. We thus established a quantitative framework that describes, on a genome-scale, the acid stress mitigation response of E. coli that has both scientific and practical uses.
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Affiliation(s)
- Bin Du
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Laurence Yang
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Colton J. Lloyd
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Xin Fang
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Kongens, Lyngby, Denmark
- * E-mail:
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Du B, Olson CA, Sastry AV, Fang X, Phaneuf PV, Chen K, Wu M, Szubin R, Xu S, Gao Y, Hefner Y, Feist AM, Palsson BO. Adaptive laboratory evolution of Escherichia coli under acid stress. MICROBIOLOGY-SGM 2019; 166:141-148. [PMID: 31625833 DOI: 10.1099/mic.0.000867] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The ability of Escherichia coli to tolerate acid stress is important for its survival and colonization in the human digestive tract. Here, we performed adaptive laboratory evolution of the laboratory strain E. coli K-12 MG1655 at pH 5.5 in glucose minimal medium. After 800 generations, six independent populations under evolution had reached 18.0 % higher growth rates than their starting strain at pH 5.5, while maintaining comparable growth rates to the starting strain at pH 7. We characterized the evolved strains and found that: (1) whole genome sequencing of isolated clones from each evolved population revealed mutations in rpoC appearing in five of six sequenced clones; and (2) gene expression profiles revealed different strategies to mitigate acid stress, which are related to amino acid metabolism and energy production and conversion. Thus, a combination of adaptive laboratory evolution, genome resequencing and expression profiling revealed, on a genome scale, the strategies that E. coli uses to mitigate acid stress.
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Affiliation(s)
- Bin Du
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Connor A Olson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Anand V Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Xin Fang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Patrick V Phaneuf
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ke Chen
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Muyao Wu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Sibei Xu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ye Gao
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Adam M Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Bernhard O Palsson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
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Tchuenchieu A, Sylvain SK, Pop C, Jean‐Justin EN, Mudura E, Etoa F, Rotar A. Low thermal inactivation of
Escherichia coli
ATCC 25922 in pineapple, orange and watermelon juices: Effect of a prior acid‐adaptation and of carvacrol supplementation. J Food Saf 2017. [DOI: 10.1111/jfs.12415] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alex Tchuenchieu
- Department of MicrobiologyFaculty of Science, University of Yaoundé IYaoundé Cameroon
- Faculty of Food Science and TechnologyUniversity of Agricultural Science and Veterinary, MedicineCluj‐Napoca Romania
- Centre for Food and Nutrition Research, IMPMYaoundé Cameroon
| | - Sado Kamdem Sylvain
- Department of MicrobiologyFaculty of Science, University of Yaoundé IYaoundé Cameroon
| | - Carmen Pop
- Faculty of Food Science and TechnologyUniversity of Agricultural Science and Veterinary, MedicineCluj‐Napoca Romania
| | | | - Elena Mudura
- Faculty of Food Science and TechnologyUniversity of Agricultural Science and Veterinary, MedicineCluj‐Napoca Romania
| | - François‐Xavier Etoa
- Department of MicrobiologyFaculty of Science, University of Yaoundé IYaoundé Cameroon
| | - Ancuta Rotar
- Faculty of Food Science and TechnologyUniversity of Agricultural Science and Veterinary, MedicineCluj‐Napoca Romania
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Fate of Escherichia coli and Kluyveromyces marxianus contaminants during storage of Greek-style yogurt produced by centrifugation or ultrafiltration. Int Dairy J 2017. [DOI: 10.1016/j.idairyj.2017.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Zhou R, Li Y, Tian Y, Sun Q, Deng P, Wu L, Hou X. Simple fluorescence sensing of extreme acidity based on inner filter effect of ascorbic acid to fluorescent Au nanoclusters. NANOSCALE 2017; 9:10167-10172. [PMID: 28702587 DOI: 10.1039/c7nr03566g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
As acidic pH plays essential roles in several organelles, development of pH sensors for extreme acidity is of vital importance. Herein, on the basis of the inner filter effect (IFE) between ascorbic acid (AA) and Au nano-clusters (AuNCs), a simple extreme acidity fluorescence sensor was developed without complex organic synthesis. The as-prepared probe can be used to detect acidity within the pH range of 2.4-4.6. Moreover, the probe possesses high selectivity, good photostability, and excellent reversibility for monitoring extreme acidity in bacterial cells without the influence of autofluorescence.
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Affiliation(s)
- Ronghui Zhou
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yuqin Li
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, China.
| | - Yuanyuan Tian
- College of Life Science, Sichuan University, Chengdu, Sichuan 610064, China
| | - Qun Sun
- College of Life Science, Sichuan University, Chengdu, Sichuan 610064, China
| | - Pengchi Deng
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, China.
| | - Lan Wu
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, China.
| | - Xiandeng Hou
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China and Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, China.
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Inactivation and occurrence of sublethal injury of Salmonella Typhimurium under mild heat stress in broth. J Verbrauch Lebensm 2012. [DOI: 10.1007/s00003-012-0763-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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