1
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Zhu M, Mu H, Dai X. Integrated control of bacterial growth and stress response by (p)ppGpp in Escherichia coli: A seesaw fashion. iScience 2024; 27:108818. [PMID: 38299113 PMCID: PMC10828813 DOI: 10.1016/j.isci.2024.108818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/02/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
To thrive in nature, bacteria have to reproduce efficiently under favorable conditions and persist during stress. The global strategy that integrates the growth control and stress response remains to be explored. Here, we find that a moderate induction of (p)ppGpp reduces growth rate but significantly enhances the stress tolerance of E. coli, resulting from a global resource re-allocation from ribosome synthesis to the synthesis of stress-responsive proteins. Strikingly, the activation of stress response by (p)ppGpp is still largely retained in the absence of RpoS. In addition, (p)ppGpp induction could activate the catabolism of alanine and arginine, facilitating the adaption of bacteria to nutrient downshift. Our work demonstrates that the activation of stress response by (p)ppGpp could occur in an RpoS-independent manner and (p)ppGpp enables bacteria to integrate the control of growth and stress response in a seesaw fashion, thus acting as an important global regulator of the bacterial fitness landscape.
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Affiliation(s)
- Manlu Zhu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences & National Key Laboratory of Green Pesticides, Central China Normal University, Wuhan, China
| | - Haoyan Mu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences & National Key Laboratory of Green Pesticides, Central China Normal University, Wuhan, China
| | - Xiongfeng Dai
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences & National Key Laboratory of Green Pesticides, Central China Normal University, Wuhan, China
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2
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Lim JY, Choi YJ, Yu H, Choi JY, Yang JH, Chung YB, Park SH, Min SG, Lee MA. Investigation of Metabolite Differences in Salted Shrimp Varieties during Fermentation. ACS OMEGA 2023; 8:47735-47745. [PMID: 38144087 PMCID: PMC10733927 DOI: 10.1021/acsomega.3c06046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 12/26/2023]
Abstract
Fermentation of salted shrimp involves the interaction of multiple factors. However, studies of the effects of shrimp variety and fermentation temperature on metabolites generated during fermentation are limited. Therefore, we investigated the effects of the shrimp variety, fermentation temperature, and fermentation period on the composition of fermented salted shrimp. Four different varieties of salted shrimp, namely, Detteugijeot (SSA), Red shrimp jeot (SSB), Chujeot (SSC), and Yukjeot (SSD), were prepared and stored at 5 and 10 °C for 5 months. The pH values ranged from 6.71 to 6.99, with SSD showing the lowest pH at both temperatures. Although total nitrogen content remained relatively constant, amino nitrogen exhibited an upward trend after 2 months and was particularly increased at 10 °C. This increase was attributed to variations in microorganisms and enzymes in the salted shrimp. Except for proline, citrulline, and ornithine, amino acid levels increased during fermentation with the highest amounts detected in SSA. Additionally, the levels of glutamic acid and branched-chain amino acids were found to be sensitive to fermentation temperature. Amino acid levels were apparently affected by species-specific metabolic pathways of the microorganisms present in each salted shrimp. Compared to the other varieties, SSB had significantly higher contents of adenosine triphosphate and hypoxanthine. A high hypoxanthine content could contribute to increased bitterness and an umami taste profile. Furthermore, the correlation between salted shrimp and metabolites was unique in SSB, whereas partial clustering was observed between the SSA and SSC.
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Affiliation(s)
- Ju-Young Lim
- World
Institute of Kimchi, Gwangju 61755, Republic
of Korea
- Department
of Food and Nutrition, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Yun-Jeong Choi
- World
Institute of Kimchi, Gwangju 61755, Republic
of Korea
| | - Hyejin Yu
- World
Institute of Kimchi, Gwangju 61755, Republic
of Korea
| | - Ji-Young Choi
- World
Institute of Kimchi, Gwangju 61755, Republic
of Korea
| | - Ji-Hee Yang
- World
Institute of Kimchi, Gwangju 61755, Republic
of Korea
| | | | - Sung-Hee Park
- World
Institute of Kimchi, Gwangju 61755, Republic
of Korea
| | - Sung Gi Min
- World
Institute of Kimchi, Gwangju 61755, Republic
of Korea
| | - Mi-Ai Lee
- . Tel.: +82 62 610 1733.
Fax: +82 62 610 1850
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3
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Wang X, Zou Y, Wang Y, Niu J, Li H. Metabolic insights into the interaction between nitrogen removal and 4-chlorophenol reduction of anammox consortia. ENVIRONMENTAL RESEARCH 2023; 231:116192. [PMID: 37201701 DOI: 10.1016/j.envres.2023.116192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/01/2023] [Accepted: 05/16/2023] [Indexed: 05/20/2023]
Abstract
The response characteristic and performance stabilization of anammox process under the stress of the potential organic pollutants support the application of ammonia-nitrogen wastewater treatment. In the present study, nitrogen removal performance was significantly suppressed with the addition of 4-chlorophenol. The activity of anammox process was inhibited by 14.23% (0.1 mg/L), 20.54% (1 mg/L) and 78.15% (10 mg/L), respectively. Metagenomic analysis revealed a significant decrease in the abundance of KEGG pathways associated with carbohydrate and amino acid metabolism with increasing 4-chlorophenol concentration. Metabolic pathway profiles suggest that putrescine is down-regulated at high 4-chlorophenol stress due to inhibition of nitrogen metabolism processes, while it is up-regulated to reduce oxidative damage. In addition, the presence of 4-chlorophenol induced an enhancement of EPS and bacterial debris decomposition, and a partial conversion of 4-chlorophenol to p-nitrophenol. This study unravels the mechanism of effect on anammox consortia in response to 4-CP, which could provide supplementary to facilitate its full-scale application.
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Affiliation(s)
- Xiaojing Wang
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Yu Zou
- Shansuyouke (Shenzhen) New Materials Co., Ltd., Shenzhen, 518081, China
| | - Yameng Wang
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Junfeng Niu
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
| | - Haibo Li
- Shansuyouke (Shenzhen) New Materials Co., Ltd., Shenzhen, 518081, China
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4
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Chen W, Lv X, Cao X, Yuan Z, Wang S, Getachew T, Mwacharo JM, Haile A, Quan K, Li Y, Sun W. Integration of the Microbiome, Metabolome and Transcriptome Reveals Escherichia coli F17 Susceptibility of Sheep. Animals (Basel) 2023; 13:ani13061050. [PMID: 36978593 PMCID: PMC10044122 DOI: 10.3390/ani13061050] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023] Open
Abstract
Escherichia coli (E. coli) F17 is one of the most common pathogens causing diarrhea in farm livestock. In the previous study, we accessed the transcriptomic and microbiomic profile of E. coli F17-antagonism (AN) and -sensitive (SE) lambs; however, the biological mechanism underlying E. coli F17 infection has not been fully elucidated. Therefore, the present study first analyzed the metabolite data obtained with UHPLC-MS/MS. A total of 1957 metabolites were profiled in the present study, and 11 differential metabolites were identified between E. coli F17 AN and SE lambs (i.e., FAHFAs and propionylcarnitine). Functional enrichment analyses showed that most of the identified metabolites were related to the lipid metabolism. Then, we presented a machine-learning approach (Random Forest) to integrate the microbiome, metabolome and transcriptome data, which identified subsets of potential biomarkers for E. coli F17 infection (i.e., GlcADG 18:0-18:2, ethylmalonic acid and FBLIM1); furthermore, the PCCs were calculated and the interaction network was constructed to gain insight into the crosstalk between the genes, metabolites and bacteria in E. coli F17 AN/SE lambs. By combing classic statistical approaches and a machine-learning approach, our results revealed subsets of metabolites, genes and bacteria that could be potentially developed as candidate biomarkers for E. coli F17 infection in lambs.
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Affiliation(s)
- Weihao Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyang Lv
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Shanhe Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Tesfaye Getachew
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Joram M. Mwacharo
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Aynalem Haile
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Kai Quan
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economics, Zhengzhou 450046, China
| | - Yutao Li
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Wei Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- “Innovative China” “Belt and Road” International Agricultural Technology Innovation Institute for Evaluation, Protection, and Improvement on Sheep Genetic Resource, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-13952750912
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5
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Priya P, Aneesh B, Sivakumar KC, Harikrishnan K. Comparative proteomic analysis of saline tolerant, phosphate solubilizing endophytic Pantoea sp., and Pseudomonas sp. isolated from Eichhornia rhizosphere. Microbiol Res 2022; 265:127217. [DOI: 10.1016/j.micres.2022.127217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 02/07/2023]
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6
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Li R, Panxianzhi N, Ye S, Yuan T, Fan Y, Zhang X. A simple, safe and easily accessible polyvinyl alcohol hydrogel for wound cleaning. J Biomater Appl 2022; 36:1737-1747. [PMID: 35244481 DOI: 10.1177/08853282211058944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Acute wounds are often contaminated by some kind of filth, and fluids are usually used to wash away the dirt, but the force of the fluid may cause secondary injury at the wound site or even increase the risk of infection. Hydrogels have several advantages over liquid scouring since they are less intense, more portable, and easier to control. In this study, poly(vinyl alcohol) was used to prepared a series of hydrogels, which were tested in terms of their properties and abilities to clean simulated dirty wounds. Simulated dirt and bacterial (Serratia marcescens) adhesion experiments demonstrated that they could effectively adhere to a certain amount of dirt or bacteria to achieve the purpose of wound cleaning. In addition to the bacterial adhesion, the antibacterial experiments also proved that the hydrogels have a certain inhibitory effect on the proliferation of E.coli and S.aureus. The hydrogels could change shape freely and exhibited excellent biocompatibility, ductility, and self-healing capabilities, which increase their service life and make them more suitable for treating wounds or acting as protection buffers. Based on all these characteristics, the developed hydrogel may be a potentially valuable material for wound cleaning.
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Affiliation(s)
- Renpeng Li
- 12530National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan, China
| | - Ni Panxianzhi
- 12530National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan, China
| | - Sheng Ye
- 12530National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan, China
| | - Tun Yuan
- 12530National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan, China
| | - Yujiang Fan
- 12530National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan, China
| | - XingDong Zhang
- 12530National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan, China
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7
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Tang R, Sun W, Zhang JC, Mao L, Quanquin N, Wu D, Sun Y. Expression of Human Uncoupling Protein-1 in Escherichia coli Decreases its Survival Under Extremely Acidic Conditions. Curr Microbiol 2022; 79:77. [DOI: 10.1007/s00284-022-02762-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 01/08/2022] [Indexed: 11/03/2022]
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8
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Comparison of the metabolic responses of eight Escherichia coli strains including the “big six” in pea sprouts to low concentration electrolysed water by NMR spectroscopy. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108458] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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9
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Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli. Commun Biol 2021; 4:991. [PMID: 34413462 PMCID: PMC8376909 DOI: 10.1038/s42003-021-02516-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/21/2021] [Indexed: 01/26/2023] Open
Abstract
Many genes in bacterial genomes are of unknown function, often referred to as y-genes. Recently, the analytic methods have divided bacterial transcriptomes into independently modulated sets of genes (iModulons). Functionally annotated iModulons that contain y-genes lead to testable hypotheses to elucidate y-gene function. The inversely correlated expression of a putative transporter gene, ydhC, relative to purine biosynthetic genes, has led to the hypothesis that it encodes a purine-related transporter and revealed a LysR-family regulator, YdhB, with a predicted 23-bp palindromic binding motif. RNA-Seq analysis of a ydhB knockout mutant confirmed the YdhB-dependent activation of ydhC in the presence of adenosine. The deletion of either the ydhC or the ydhB gene led to a substantially decreased growth rate for E. coli in minimal medium with adenosine, inosine, or guanosine as the nitrogen source. Taken together, we provide clear evidence that YdhB activates the expression of the ydhC gene that encodes a purine transporter in E. coli. We propose that the genes ydhB and ydhC be re-named as punR and punC, respectively. Rodionova et al. find that the putative transporter gene, ydhC and its regulator ydhB are involved in purine transportation and that the expression of the ydhC gene is activated by the YdhB in E. coli. The authors suggest renaming the regulator PunR and the transporter PunC, respectively.
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10
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Kalam S, Basu A, Ahmad I, Sayyed RZ, El-Enshasy HA, Dailin DJ, Suriani NL. Recent Understanding of Soil Acidobacteria and Their Ecological Significance: A Critical Review. Front Microbiol 2020; 11:580024. [PMID: 33193209 PMCID: PMC7661733 DOI: 10.3389/fmicb.2020.580024] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/08/2020] [Indexed: 11/13/2022] Open
Abstract
Acidobacteria represents an underrepresented soil bacterial phylum whose members are pervasive and copiously distributed across nearly all ecosystems. Acidobacterial sequences are abundant in soils and represent a significant fraction of soil microbial community. Being recalcitrant and difficult-to-cultivate under laboratory conditions, holistic, polyphasic approaches are required to study these refractive bacteria extensively. Acidobacteria possesses an inventory of genes involved in diverse metabolic pathways, as evidenced by their pan-genomic profiles. Because of their preponderance and ubiquity in the soil, speculations have been made regarding their dynamic roles in vital ecological processes viz., regulation of biogeochemical cycles, decomposition of biopolymers, exopolysaccharide secretion, and plant growth promotion. These bacteria are expected to have genes that might help in survival and competitive colonization in the rhizosphere, leading to the establishment of beneficial relationships with plants. Exploration of these genetic attributes and more in-depth insights into the belowground mechanics and dynamics would lead to a better understanding of the functions and ecological significance of this enigmatic phylum in the soil-plant environment. This review is an effort to provide a recent update into the diversity of genes in Acidobacteria useful for characterization, understanding ecological roles, and future biotechnological perspectives.
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Affiliation(s)
- Sadaf Kalam
- Department of Biochemistry, St. Ann's College for Women, Hyderabad, India
| | - Anirban Basu
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Iqbal Ahmad
- Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India
| | - R Z Sayyed
- Department of Microbiology, PSGVP Mandal's, Arts, Science and Commerce College, Shahada, India
| | - Hesham Ali El-Enshasy
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,City of Scientific Research and Technological Applications, New Borg El-Arab, Egypt
| | - Daniel Joe Dailin
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia
| | - Ni Luh Suriani
- Biology Department, Faculty of Mathematics and Natural Science, Udayana University, Bali, Indonesia
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Kornspan D, Zahavi T, Salmon-Divon M. The Acidic Stress Response of the Intracellular Pathogen Brucella melitensis: New Insights from a Comparative, Genome-Wide Transcriptome Analysis. Genes (Basel) 2020; 11:genes11091016. [PMID: 32872264 PMCID: PMC7563570 DOI: 10.3390/genes11091016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 11/30/2022] Open
Abstract
The intracellular pathogenic bacteria belonging to the genus Brucella must cope with acidic stress as they penetrate the host via the gastrointestinal route, and again during the initial stages of intracellular infection. A transcription-level regulation has been proposed to explain this but the specific molecular mechanisms are yet to be determined. We recently reported a comparative transcriptomic analysis of the attenuated vaccine Brucella melitensis strain Rev.1 against the virulent strain 16M in cultures grown under either neutral or acidic conditions. Here, we re-analyze the RNA-seq data of 16M from our previous study and compare it to published transcriptomic data of this strain from both an in cellulo and an in vivo model. We identify 588 genes that are exclusively differentially expressed in 16M grown under acidic versus neutral pH conditions, including 286 upregulated genes and 302 downregulated genes that are not differentially expressed in either the in cellulo or the in vivo model. Of these, we highlight 13 key genes that are known to be associated with a bacterial response to acidic stress and, in our study, were highly upregulated under acidic conditions. These genes provide new molecular insights into the mechanisms underlying the acid-resistance of Brucella within its host.
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Affiliation(s)
- David Kornspan
- Department of Bacteriology, Kimron Veterinary Institute, Bet Dagan 50250, Israel
- Correspondence: ; Tel.: +972-3-968-1745
| | - Tamar Zahavi
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel 40700, Israel; (T.Z.); (M.S.-D.)
| | - Mali Salmon-Divon
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel 40700, Israel; (T.Z.); (M.S.-D.)
- Adelson School of Medicine, Ariel University, Ariel 40700, Israel
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12
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Zhang W, Chen X, Sun W, Nie T, Quanquin N, Sun Y. Escherichia Coli Increases its ATP Concentration in Weakly Acidic Environments Principally through the Glycolytic Pathway. Genes (Basel) 2020; 11:genes11090991. [PMID: 32854287 PMCID: PMC7563387 DOI: 10.3390/genes11090991] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 12/23/2022] Open
Abstract
Acid resistance is an intrinsic characteristic of intestinal bacteria in order to survive passage through the stomach. Adenosine triphosphate (ATP), the ubiquitous chemical used to power metabolic reactions, activate signaling cascades, and form precursors of nucleic acids, was also found to be associated with the survival of Escherichia coli (E. coli) in acidic environments. The metabolic pathway responsible for elevating the level of ATP inside these bacteria during acid adaptation has been unclear. E. coli uses several mechanisms of ATP production, including oxidative phosphorylation, glycolysis and the oxidation of organic compounds. To uncover which is primarily used during adaptation to acidic conditions, we broadly analyzed the levels of gene transcription of multiple E. coli metabolic pathway components. Our findings confirmed that the primary producers of ATP in E. coli undergoing mild acidic stress are the glycolytic enzymes Glk, PykF and Pgk, which are also essential for survival under markedly acidic conditions. By contrast, the transcription of genes related to oxidative phosphorylation was downregulated, despite it being the major producer of ATP in neutral pH environments.
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Affiliation(s)
- Wenbin Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510640, China;
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (W.S.); (T.N.)
| | - Xin Chen
- Guangdong Key Laboratory of IoT Information Technology, School of Automation, Guangdong University of Technology, Guangzhou 510006, China;
| | - Wei Sun
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (W.S.); (T.N.)
| | - Tao Nie
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (W.S.); (T.N.)
| | - Natalie Quanquin
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA;
| | - Yirong Sun
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (W.S.); (T.N.)
- Correspondence:
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13
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Guan N, Liu L. Microbial response to acid stress: mechanisms and applications. Appl Microbiol Biotechnol 2020; 104:51-65. [PMID: 31773206 PMCID: PMC6942593 DOI: 10.1007/s00253-019-10226-1] [Citation(s) in RCA: 232] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/23/2019] [Accepted: 10/27/2019] [Indexed: 02/07/2023]
Abstract
Microorganisms encounter acid stress during multiple bioprocesses. Microbial species have therefore developed a variety of resistance mechanisms. The damage caused by acidic environments is mitigated through the maintenance of pH homeostasis, cell membrane integrity and fluidity, metabolic regulation, and macromolecule repair. The acid tolerance mechanisms can be used to protect probiotics against gastric acids during the process of food intake, and can enhance the biosynthesis of organic acids. The combination of systems and synthetic biology technologies offers new and wide prospects for the industrial applications of microbial acid tolerance mechanisms. In this review, we summarize acid stress response mechanisms of microbial cells, illustrate the application of microbial acid tolerance in industry, and prospect the introduction of systems and synthetic biology to further explore the acid tolerance mechanisms and construct a microbial cell factory for valuable chemicals.
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Affiliation(s)
- Ningzi Guan
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China.
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
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14
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Salmon-Divon M, Kornspan D. Transcriptomic analysis of smooth versus rough Brucella melitensis Rev.1 vaccine strains reveals insights into virulence attenuation. Int J Med Microbiol 2019; 310:151363. [PMID: 31699441 DOI: 10.1016/j.ijmm.2019.151363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/10/2019] [Accepted: 10/16/2019] [Indexed: 12/20/2022] Open
Abstract
Brucella melitensis Rev.1 is the live attenuated Elberg-originated vaccine strain of the facultative intracellular Brucella species, and is widely used to control brucellosis in small ruminants. However, Rev.1 may cause abortions in small ruminants that have been vaccinated during the last trimester of gestation, it is pathogenic to humans, and it induces antibodies directed at the O-polysaccharide (O-PS) of the smooth lipopolysaccharide, thus making it difficult to distinguish between vaccinated and infected animals. Rough Brucella strains, which lack O-PS and are considered less pathogenic, have been introduced to address these drawbacks; however, as Rev.1 confers a much better immunity than the rough mutants, it is still considered the reference vaccine for the prophylaxis of brucellosis in small ruminants. Therefore, developing an improved vaccine strain, which lacks the Rev.1 drawbacks, is a highly evaluated task, which requires a better understanding of the molecular mechanisms underlying the virulence attenuation of Rev.1 smooth strains and of natural Rev.1 rough strains, which are currently only partly understood. As the acidification of the Brucella-containing vacuole during the initial stages of infection is crucial for their survival, identifying the genes that contribute to their survival in an acidic environment versus a normal environment will greatly assist our understanding of the molecular pathogenic mechanisms and the attenuated virulence of the Rev.1 strain. Here, we compared the transcriptomes of the smooth and natural rough Rev.1 strains, each grown under either normal or acidic conditions. We found 12 key genes that are significantly downregulated in the Rev.1 rough strains under normal pH, as compared with Rev.1 smooth strains, and six highly important genes that are significantly upregulated in the smooth strains under acidic conditions, as compared with Rev.1 rough strains. All 18 differentially expressed genes are associated with bacterial virulence and survival and may explain the attenuated virulence of the rough Rev.1 strains versus smooth Rev.1 strains, thus providing new insights into the virulence attenuation mechanisms of Brucella. These highly important candidate genes may facilitate the design of new and improved brucellosis vaccines.
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Affiliation(s)
- Mali Salmon-Divon
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel; Adelson School of Medicine, Ariel University, Israel.
| | - David Kornspan
- Department of Bacteriology, Kimron Veterinary Institute, Bet Dagan, Israel.
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Moore JP, Li H, Engmann ML, Bischof KM, Kunka KS, Harris ME, Tancredi AC, Ditmars FS, Basting PJ, George NS, Bhagwat AA, Slonczewski JL. Inverted Regulation of Multidrug Efflux Pumps, Acid Resistance, and Porins in Benzoate-Evolved Escherichia coli K-12. Appl Environ Microbiol 2019; 85:e00966-19. [PMID: 31175192 PMCID: PMC6677852 DOI: 10.1128/aem.00966-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 05/30/2019] [Indexed: 01/23/2023] Open
Abstract
Benzoic acid, a partial uncoupler of the proton motive force (PMF), selects for sensitivity to chloramphenicol and tetracycline during the experimental evolution of Escherichia coli K-12. Transcriptomes of E. coli isolates evolved with benzoate showed the reversal of benzoate-dependent regulation, including the downregulation of multidrug efflux pump genes, the gene for the Gad acid resistance regulon, the nitrate reductase genes narHJ, and the gene for the acid-consuming hydrogenase Hyd-3. However, the benzoate-evolved strains had increased expression of OmpF and other large-hole porins that admit fermentable substrates and antibiotics. Candidate genes identified from benzoate-evolved strains were tested for their roles in benzoate tolerance and in chloramphenicol sensitivity. Benzoate or salicylate tolerance was increased by deletion of the Gad activator ariR or of the acid fitness island from slp to the end of the gadX gene encoding Gad regulators and the multidrug pump genes mdtEF Benzoate tolerance was also increased by deletion of multidrug component gene emrA, RpoS posttranscriptional regulator gene cspC, adenosine deaminase gene add, hydrogenase gene hyc (Hyd-3), and the RNA chaperone/DNA-binding regulator gene hfq Chloramphenicol resistance was decreased by mutations in genes for global regulators, such as RNA polymerase alpha subunit gene rpoA, the Mar activator gene rob, and hfq Deletion of lipopolysaccharide biosynthetic kinase gene rfaY decreased the rate of growth in chloramphenicol. Isolates from experimental evolution with benzoate had many mutations affecting aromatic biosynthesis and catabolism, such as aroF (encoding tyrosine biosynthesis) and apt (encoding adenine phosphoribosyltransferase). Overall, benzoate or salicylate exposure selects for the loss of multidrug efflux pumps and of hydrogenases that generate a futile cycle of PMF and upregulates porins that admit fermentable nutrients and antibiotics.IMPORTANCE Benzoic acid is a common food preservative, and salicylic acid (2-hydroxybenzoic acid) is the active form of aspirin. At high concentrations, benzoic acid conducts a proton across the membrane, depleting the proton motive force. In the absence of antibiotics, benzoate exposure selects against proton-driven multidrug efflux pumps and upregulates porins that admit fermentable substrates but that also allow the entry of antibiotics. Thus, evolution with benzoate and related molecules, such as salicylates, requires a trade-off for antibiotic sensitivity, a trade-off that could help define a stable gut microbiome. Benzoate and salicylate are naturally occurring plant signal molecules that may modulate the microbiomes of plants and animal digestive tracts so as to favor fermenters and exclude drug-resistant pathogens.
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Affiliation(s)
- Jeremy P Moore
- Department of Biology, Kenyon College, Gambier, Ohio, USA
| | - Haofan Li
- Department of Biology, Kenyon College, Gambier, Ohio, USA
| | | | | | - Karina S Kunka
- Department of Biology, Kenyon College, Gambier, Ohio, USA
| | - Mary E Harris
- Department of Biology, Kenyon College, Gambier, Ohio, USA
| | | | | | | | - Nadja S George
- Environmental Microbiology and Food Safety Laboratory, Beltsville Agricultural Research Center, U.S. Department of Agriculture, Beltsville, Maryland, USA
| | - Arvind A Bhagwat
- Environmental Microbiology and Food Safety Laboratory, Beltsville Agricultural Research Center, U.S. Department of Agriculture, Beltsville, Maryland, USA
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16
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Li L, Li J, Peng J, Wu W, Guo Y. Identification ofatpDas an optimal reference gene to explore antibiotic resistance and stress tolerance inRahnella aquatilis. J Appl Microbiol 2019; 126:1096-1107. [DOI: 10.1111/jam.14215] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/06/2018] [Accepted: 01/24/2019] [Indexed: 11/28/2022]
Affiliation(s)
- L. Li
- Department of Ecological Science and Engineering College of Resources and Environmental Sciences, China Agricultural University Beijing China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing China
| | - J. Li
- Department of Plant Pathology College of Plant Protection, China Agricultural University Beijing China
| | - J. Peng
- Department of Ecological Science and Engineering College of Resources and Environmental Sciences, China Agricultural University Beijing China
| | - W. Wu
- Department of Ecological Science and Engineering College of Resources and Environmental Sciences, China Agricultural University Beijing China
| | - Y. Guo
- Department of Ecological Science and Engineering College of Resources and Environmental Sciences, China Agricultural University Beijing China
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17
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Chen X, Ma A, McDermaid A, Zhang H, Liu C, Cao H, Ma Q. RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis. Genes (Basel) 2018; 9:genes9060278. [PMID: 29849014 PMCID: PMC6027394 DOI: 10.3390/genes9060278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/19/2018] [Accepted: 05/25/2018] [Indexed: 11/16/2022] Open
Abstract
Regulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, regulon identification based on comparative genomics and transcriptomics analysis (RECTA), for regulon prediction related to the gene regulatory network under certain conditions. To demonstrate the effectiveness of this tool, we implemented RECTA on Lactococcus lactis MG1363 data to elucidate acid-response regulons. A total of 51 regulons were identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to be connected with acid stress response. Validated by literature, 33 genes in Lactococcus lactis MG1363 were found to have orthologous genes which were associated with six regulons. An acid response related regulatory network was constructed, involving two trans-membrane proteins, eight regulons (llrA, llrC, hllA, ccpA, NHP6A, rcfB, regulons #8 and #39), nine functional modules, and 33 genes with orthologous genes known to be associated with acid stress. The predicted response pathways could serve as promising candidates for better acid tolerance engineering in Lactococcus lactis. Our RECTA pipeline provides an effective way to construct a reliable gene regulatory network through regulon elucidation, and has strong application power and can be effectively applied to other bacterial genomes where the elucidation of the transcriptional regulation network is needed.
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Affiliation(s)
- Xin Chen
- Center for Applied Mathematics, Tianjin University, Tianjin 300072, China.
| | - Anjun Ma
- Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57006, USA.
- Department of Mathematics and Statistics, South Dakota State University, Brookings, SD 57006, USA.
| | - Adam McDermaid
- Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57006, USA.
- Department of Mathematics and Statistics, South Dakota State University, Brookings, SD 57006, USA.
| | - Hanyuan Zhang
- College of Computer Science and Engineering, University of Nebraska Lincoln, Lincoln, NE 68588, USA.
| | - Chao Liu
- Shandong Provincial Hospital affiliated to Shandong University, Jinan 250021, China.
| | - Huansheng Cao
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Qin Ma
- Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57006, USA.
- Department of Mathematics and Statistics, South Dakota State University, Brookings, SD 57006, USA.
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18
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Kobayashi H. Cancer Chemotherapy Specific to Acidic Nests. Cancers (Basel) 2017; 9:cancers9040036. [PMID: 28425953 PMCID: PMC5406711 DOI: 10.3390/cancers9040036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 04/17/2017] [Accepted: 04/18/2017] [Indexed: 12/15/2022] Open
Abstract
The realization of cancer therapeutics specific to cancer cells with less of an effect on normal tissues is our goal. Many trials have been carried out for this purpose, but this goal is still far from being realized. It was found more than 80 years ago that solid cancer nests are acidified, but in vitro studies under acidic conditions have not been extensively studied. Recently, in vitro experiments under acidic conditions were started and anti-cancer drugs specific to acidic areas have been identified. Many genes have been reported to be expressed at a high level under acidic conditions, and such genes may be potent targets for anti-cancer drugs specific to acidic nests. In this review article, recent in vitro, in vivo, and clinical achievements in anti-cancer drugs with marked efficacy under acidic conditions are summarized, and the clinical use of anti-cancer drugs specific to acidic nests is discussed.
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Affiliation(s)
- Hiroshi Kobayashi
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan.
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19
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Noisy Response to Antibiotic Stress Predicts Subsequent Single-Cell Survival in an Acidic Environment. Cell Syst 2017; 4:393-403.e5. [PMID: 28342718 DOI: 10.1016/j.cels.2017.03.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/14/2016] [Accepted: 03/01/2017] [Indexed: 11/23/2022]
Abstract
Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to "cross-protect" bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors.
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20
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Sun Y, Zhang W, Ma J, Pang H, Wang H. Overproduction of α-Lipoic Acid by Gene Manipulated Escherichia coli. PLoS One 2017; 12:e0169369. [PMID: 28068366 PMCID: PMC5222372 DOI: 10.1371/journal.pone.0169369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/15/2016] [Indexed: 11/23/2022] Open
Abstract
Alpha-lipoic acid (LA) is an important enzyme cofactor widely used by organisms and is also a natural antioxidant for the treatment of pathologies driven by low levels of endogenous antioxidants. In order to establish a safer and more efficient process for LA production, we developed a new biological method for LA synthesis based on the emerging knowledge of lipoic acid biosynthesis. We first cloned the lipD gene, which encodes the lipoyl domain of the E2 subunit of pyruvate dehydrogenase, allowing high levels of LipD production. Plasmids containing genes for the biosynthesis of LA were subsequently constructed utilizing various vectors and promotors to produce high levels of LA. These plasmids were transformed into the Escherichia coli strain BL21. Octanoic acid (OA) was used as the substrate for LA synthesis. One transformant, YS61, which carried lipD, lplA, and lipA, produced LA at levels over 200-fold greater than the wild-type strain, showing that LA could be produced efficiently in E. coli using genetic engineering methods.
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Affiliation(s)
- Yirong Sun
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, P. R. China
- * E-mail: (YS); (HW)
| | - Wenbin Zhang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Jincheng Ma
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Hongshen Pang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
- Shenzhen University, Shenzhen, Guangdong, P.R.China
| | - Haihong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
- * E-mail: (YS); (HW)
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21
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Vivijs B, Aertsen A, Michiels CW. Identification of Genes Required for Growth of Escherichia coli MG1655 at Moderately Low pH. Front Microbiol 2016; 7:1672. [PMID: 27826291 PMCID: PMC5078493 DOI: 10.3389/fmicb.2016.01672] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/06/2016] [Indexed: 01/27/2023] Open
Abstract
The survival of some pathotypes of Escherichia coli in very low pH environments like highly acidic foods and the stomach has been well documented and contributes to their success as foodborne pathogens. In contrast, the ability of E. coli to grow at moderately low pH has received less attention, although this property can be anticipated to be also very important for the safety of mildly acidic foods. Therefore, the objective of this study was to identify cellular functions required for growth of the non-pathogenic strain E. coli MG1655 at low pH. First, the role of the four E. coli amino acid decarboxylase systems, which are the major cellular mechanisms allowing extreme acid survival, was investigated using mutants defective in each of the systems. Only the lysine decarboxylase (CadA) was required for low pH growth. Secondly, a screening of 8544 random transposon insertion mutants resulted in the identification of six genes affecting growth in LB broth acidified to pH 4.50 with HCl. Two of the genes, encoding the transcriptional regulator LeuO and the elongation factor P-β-lysine ligase EpmA, can be linked to CadA production. Two other genes, encoding the diadenosine tetraphosphatase ApaH and the tRNA modification GTPase MnmE, have been previously implicated in the bacterial response to stresses other than low pH. A fifth gene encodes the LPS heptosyltransferase WaaC, and its mutant has a deep rough colony phenotype, which has been linked to reduced acid tolerance in earlier work. Finally, tatC encodes a secA-independent protein translocase that exports a few dozen proteins and thus is likely to have a pleiotropic phenotype. For mnmE, apaH, epmA, and waaC, de novo in frame deletion and genetic complementation confirmed their role in low pH growth, and these deletion mutants were also affected in growth in apple juice and tomato juice. However, the mutants were not affected in survival in gastric simulation medium at pH 2.5, indicating that growth at moderately low pH and survival of extremely low pH depend mostly on different cellular functions.
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Affiliation(s)
| | | | - Chris W. Michiels
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, and Leuven Food Science and Nutrition Research Centre (LFoRCe), KU LeuvenLeuven, Belgium
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22
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Lund P, Tramonti A, De Biase D. Coping with low pH: molecular strategies in neutralophilic bacteria. FEMS Microbiol Rev 2014; 38:1091-125. [PMID: 24898062 DOI: 10.1111/1574-6976.12076] [Citation(s) in RCA: 272] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 02/26/2014] [Accepted: 03/14/2014] [Indexed: 12/31/2022] Open
Abstract
As part of their life cycle, neutralophilic bacteria are often exposed to varying environmental stresses, among which fluctuations in pH are the most frequent. In particular, acid environments can be encountered in many situations from fermented food to the gastric compartment of the animal host. Herein, we review the current knowledge of the molecular mechanisms adopted by a range of Gram-positive and Gram-negative bacteria, mostly those affecting human health, for coping with acid stress. Because organic and inorganic acids have deleterious effects on the activity of the biological macromolecules to the point of significantly reducing growth and even threatening their viability, it is not unexpected that neutralophilic bacteria have evolved a number of different protective mechanisms, which provide them with an advantage in otherwise life-threatening conditions. The overall logic of these is to protect the cell from the deleterious effects of a harmful level of protons. Among the most favoured mechanisms are the pumping out of protons, production of ammonia and proton-consuming decarboxylation reactions, as well as modifications of the lipid content in the membrane. Several examples are provided to describe mechanisms adopted to sense the external acidic pH. Particular attention is paid to Escherichia coli extreme acid resistance mechanisms, the activity of which ensure survival and may be directly linked to virulence.
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Affiliation(s)
- Peter Lund
- School of Biosciences, University of Birmingham, Birmingham, UK
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23
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Sun Y, Fukamachi T, Saito H, Kobayashi H. Respiration and the F₁Fo-ATPase enhance survival under acidic conditions in Escherichia coli. PLoS One 2012; 7:e52577. [PMID: 23300708 PMCID: PMC3534200 DOI: 10.1371/journal.pone.0052577] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 11/20/2012] [Indexed: 11/20/2022] Open
Abstract
Besides amino acid decarboxylation, the ADP biosynthetic pathway was reported to
enhance survival under extremely acidic conditions in Escherichia
coli (Sun et al., J. Bacteriol. 193∶
3072–3077, 2011). E. coli has two pathways for ATP synthesis
from ADP: glycolysis and oxidative phosphorylation. We found in this study that the
deletion of the F1Fo-ATPase, which catalyzes the synthesis of ATP from ADP
and inorganic phosphate using the electro-chemical gradient of protons generated by
respiration in E. coli, decreased the survival at pH 2.5. A mutant
deficient in hemA encoding the glutamyl tRNA reductase, which
synthesizes glutamate 1-semialdehyde also showed the decreased survival of E.
coli at pH 2.5. Glutamate 1-semialdehyde is a precursor of heme synthesis
that is an essential component of the respiratory chain. The ATP content decreased
rapidly at pH 2.5 in these mutants as compared with that of their parent strain. The
internal pH was lowered by the deletion of these genes at pH 2.5. These results
suggest that respiration and the F1Fo-ATPase are still working at pH 2.5
to enhance the survival under such extremely acidic conditions.
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Affiliation(s)
- Yirong Sun
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China.
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