1
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Liu Y, Van Horn AM, Pham MTN, Dinh BNN, Chen R, Raphael SDR, Paulino A, Thaker K, Somadder A, Frost DJ, Menke CC, Slimak ZC, Slonczewski JL. Fitness trade-offs of multidrug efflux pumps in Escherichia coli K-12 in acid or base, and with aromatic phytochemicals. Appl Environ Microbiol 2024; 90:e0209623. [PMID: 38289137 PMCID: PMC10880634 DOI: 10.1128/aem.02096-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 12/14/2023] [Indexed: 02/22/2024] Open
Abstract
Multidrug efflux pumps are the frontline defense mechanisms of Gram-negative bacteria, yet little is known of their relative fitness trade-offs under gut conditions such as low pH and the presence of antimicrobial food molecules. Low pH contributes to the proton-motive force (PMF) that drives most efflux pumps. We show how the PMF-dependent pumps AcrAB-TolC, MdtEF-TolC, and EmrAB-TolC undergo selection at low pH and in the presence of membrane-permeant phytochemicals. Competition assays were performed by flow cytometry of co-cultured Escherichia coli K-12 strains possessing or lacking a given pump complex. All three pumps showed negative selection under conditions that deplete PMF (pH 5.5 with carbonyl cyanide 3-chlorophenylhydrazone or at pH 8.0). At pH 5.5, selection against AcrAB-TolC was increased by aromatic acids, alcohols, and related phytochemicals such as methyl salicylate. The degree of fitness cost for AcrA was correlated with the phytochemical's lipophilicity (logP). Methyl salicylate and salicylamide selected strongly against AcrA, without genetic induction of drug resistance regulons. MdtEF-TolC and EmrAB-TolC each had a fitness cost at pH 5.5, but salicylate or benzoate made the fitness contribution positive. Pump fitness effects were not explained by gene expression (measured by digital PCR). Between pH 5.5 and 8.0, acrA and emrA were upregulated in the log phase, whereas mdtE expression was upregulated in the transition-to-stationary phase and at pH 5.5 in the log phase. Methyl salicylate did not affect pump gene expression. Our results suggest that lipophilic non-acidic molecules select against a major efflux pump without inducing antibiotic resistance regulons.IMPORTANCEFor drugs that are administered orally, we need to understand how ingested phytochemicals modulate drug resistance in our gut microbiome. Bacteria maintain low-level resistance by proton-motive force (PMF)-driven pumps that efflux many different antibiotics and cell waste products. These pumps play a key role in bacterial defense by conferring resistance to antimicrobial agents at first exposure while providing time for a pathogen to evolve resistance to higher levels of the antibiotic exposed. Nevertheless, efflux pumps confer energetic costs due to gene expression and pump energy expense. The bacterial PMF includes the transmembrane pH difference (ΔpH), which may be depleted by permeant acids and membrane disruptors. Understanding the fitness costs of efflux pumps may enable us to develop resistance breakers, that is, molecules that work together with antibiotics to potentiate their effect. Non-acidic aromatic molecules have the advantage that they avoid the Mar-dependent induction of regulons conferring other forms of drug resistance. We show that different pumps have distinct selection criteria, and we identified non-acidic aromatic molecules as promising candidates for drug resistance breakers.
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Affiliation(s)
- Yangyang Liu
- Department of Biology, Kenyon College, Gambier, Ohio, USA
| | | | | | | | - Rachel Chen
- Department of Biology, Kenyon College, Gambier, Ohio, USA
| | | | | | - Kavya Thaker
- Department of Biology, Kenyon College, Gambier, Ohio, USA
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2
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Zhang R, Wang Y. EvgS/EvgA, the unorthodox two-component system regulating bacterial multiple resistance. Appl Environ Microbiol 2023; 89:e0157723. [PMID: 38019025 PMCID: PMC10734491 DOI: 10.1128/aem.01577-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE EvgS/EvgA, one of the five unorthodox two-component systems in Escherichia coli, plays an essential role in adjusting bacterial behaviors to adapt to the changing environment. Multiple resistance regulated by EvgS/EvgA endows bacteria to survive in adverse conditions such as acidic pH, multidrug, and heat. In this minireview, we summarize the specific structures and regulation mechanisms of EvgS/EvgA and its multiple resistance. By discussing several unresolved issues and proposing our speculations, this review will be helpful and enlightening for future directions about EvgS/EvgA.
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Affiliation(s)
- Ruizhen Zhang
- MoE Key Laboratory of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yan Wang
- MoE Key Laboratory of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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3
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Tanudjaja E, Hoshi N, Yamamoto K, Ihara K, Furuta T, Tsujii M, Ishimaru Y, Uozumi N. Two Trk/Ktr/HKT-type potassium transporters, TrkG and TrkH, perform distinct functions in Escherichia coli K-12. J Biol Chem 2022; 299:102846. [PMID: 36586436 PMCID: PMC9898762 DOI: 10.1016/j.jbc.2022.102846] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Escherichia coli K-12 possesses two versions of Trk/Ktr/HKT-type potassium ion (K+) transporters, TrkG and TrkH. The current paradigm is that TrkG and TrkH have largely identical characteristics, and little information is available regarding their functional differences. Here, we show using cation uptake experiments with K+ transporter knockout mutants that TrkG and TrkH have distinct ion transport activities and physiological roles. K+-transport by TrkG required Na+, whereas TrkH-mediated K+ uptake was not affected by Na+. An aspartic acid located five residues away from a critical glycine in the third pore-forming region might be involved in regulation of Na+-dependent activation of TrkG. In addition, we found that TrkG but not TrkH had Na+ uptake activity. Our analysis of K+ transport mutants revealed that TrkH supported cell growth more than TrkG; however, TrkG was able to complement loss of TrkH-mediated K+ uptake in E. coli. Furthermore, we determined that transcription of trkG in E. coli was downregulated but not completely silenced by the xenogeneic silencing factor H-NS (histone-like nucleoid structuring protein or heat-stable nucleoid-structuring protein). Taken together, the transport function of TrkG is clearly distinct from that of TrkH, and TrkG seems to have been accepted by E. coli during evolution as a K+ uptake system that coexists with TrkH.
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Affiliation(s)
- Ellen Tanudjaja
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Naomi Hoshi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | | | - Kunio Ihara
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Tadaomi Furuta
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Masaru Tsujii
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Yasuhiro Ishimaru
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Nobuyuki Uozumi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan.
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4
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Fu D, Wu J, Wu X, Shao Y, Song X, Tu J, Qi K. The two-component system histidine kinase EnvZ contributes to Avian pathogenic Escherichia coli pathogenicity by regulating biofilm formation and stress responses. Poult Sci 2022; 102:102388. [PMID: 36586294 PMCID: PMC9811210 DOI: 10.1016/j.psj.2022.102388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 11/24/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
EnvZ, the histidine kinase (HK) of OmpR/EnvZ, transduces osmotic signals in Escherichia coli K12 and affects the pathogenicity of Shigella flexneri and Vibrio cholera. Avian pathogenic E. coli (APEC) is an extra-intestinal pathogenic E. coli (ExPEC), causing acute and sudden death in poultry and leading to severe economic losses to the global poultry industry. How the functions of EnvZ correlate with APEC pathogenicity was still unknown. In this study, we successfully constructed the envZ mutant strain AE17ΔenvZ and the inactivation of envZ significantly reduced biofilms and altered red, dry, and rough (rdar) morphology. In addition, AE17ΔenvZ was significantly less resistant to acid, alkali, osmotic, and oxidative stress conditions. Deletion of envZ significantly enhanced sensitivity to specific pathogen-free (SPF) chicken serum and increased adhesion to chicken embryonic fibroblast DF-1 cells and elevated inflammatory cytokine IL-1β, IL6, and IL8 expression levels. Also, when compared with the WT strain, AE17ΔenvZ attenuated APEC pathogenicity in chickens. To explore the molecular mechanisms underpinning envZ in APEC17, we compared the WT and envZ-deletion strains using transcriptome analyses. RNA-Seq results identified 711 differentially expressed genes (DEGs) in the envZ mutant strain and DEGs were mainly enriched in outer membrane proteins, stress response systems, and TCSs. Quantitative real-time reverse transcription PCR (RT-qPCR) showed that EnvZ influenced the expression of biofilms and stress responses genes, including ompC, ompT, mlrA, basR, hdeA, hdeB, adiY, and uspB. We provided compelling evidence showing EnvZ contributed to APEC pathogenicity by regulating biofilms and stress response expression.
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Affiliation(s)
- Dandan Fu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China,Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Jianmei Wu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China,Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Xiaoyan Wu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China,Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Ying Shao
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China,Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Xiangjun Song
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China,Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Jian Tu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China,Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Kezong Qi
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China,Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China,Corresponding author:
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5
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Wang W, Yue Y, Zhang M, Song N, Jia H, Dai Y, Zhang F, Li C, Li B. Host acid signal controls Salmonella flagella biogenesis through CadC-YdiV axis. Gut Microbes 2022; 14:2146979. [PMID: 36456534 PMCID: PMC9728131 DOI: 10.1080/19490976.2022.2146979] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Upon entering host cells, Salmonella quickly turns off flagella biogenesis to avoid recognition by the host immune system. However, it is not clear which host signal(s) Salmonella senses to initiate flagellum control. Here, we demonstrate that the acid signal can suppress flagella synthesis and motility of Salmonella, and this occurs after the transcription of master flagellar gene flhDC and depends on the anti-FlhDC factor YdiV. YdiV expression is activated after acid treatment. A global screen with ydiV promoter DNA and total protein from acid-treated Salmonella revealed a novel regulator of YdiV, the acid-related transcription factor CadC. Further studies showed that CadCC, the DNA binding domain of CadC, directly binds to a 33 nt region of the ydiV promoter with a 0.2 μM KD affinity. Furthermore, CadC could separate H-NS-ydiV promoter DNA complex to form CadC-DNA complex at a low concentration. Structural simulation and mutagenesis assays revealed that H43 and W106 of CadC are essential for ydiV promoter binding. No acid-induced flagellum control phenotype was observed in cadC mutant or ydiV mutant strains, suggesting that flagellum control during acid adaption is dependent on CadC and YdiV. The intracellular survival ability of cadC mutant strain decreased significantly compared with WT strain while the flagellin expression could not be effectively controlled in the cadC mutant strain when surviving within host cells. Together, our results demonstrated that acid stress acts as an important host signal to trigger Salmonella flagellum control through the CadC-YdiV-FlhDC axis, allowing Salmonella to sense a hostile environment and regulate flagellar synthesis during infection.
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Affiliation(s)
- Weiwei Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yingying Yue
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Min Zhang
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Nannan Song
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Haihong Jia
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yuanji Dai
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Fengyu Zhang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, China
| | - Cuiling Li
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Bingqing Li
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China,Shandong First Medical University, Key Lab for Biotech-Drugs of National Health Commission, Jinan, China,KeyLaboratory for Rare & Uncommon Diseases of Shandong Province, Jinan, China,CONTACT Bingqing Li Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan250021Shandong, China
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6
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A genetic platform to investigate the functions of bacterial drug efflux pumps. Nat Chem Biol 2022; 18:1399-1409. [PMID: 36065018 DOI: 10.1038/s41589-022-01119-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 07/21/2022] [Indexed: 11/08/2022]
Abstract
Efflux pumps are a serious challenge for the development of antibacterial agents. Overcoming efflux requires an in-depth understanding of efflux pump functions, specificities and the development of inhibitors. However, the complexities of efflux networks have limited such studies. To address these challenges, we generated Efflux KnockOut-35 (EKO-35), a highly susceptible Escherichia coli strain lacking 35 efflux pumps. We demonstrate the use of this strain by constructing an efflux platform comprising EKO-35 strains individually producing efflux pumps forming tripartite complexes with TolC. This platform was profiled against a curated diverse compound collection, which enabled us to define physicochemical properties that contribute to transport. We also show the E. coli drug efflux network is conditionally essential for growth, and that the platform can be used to investigate efflux pump inhibitor specificities and efflux pump interplay. We believe EKO-35 and the efflux platform will have widespread application for the study of drug efflux.
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7
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Lin WF, Hu RY, Chang HY, Lin FY, Kuo CH, Su LH, Peng HL. The role of urease in the acid stress response and fimbriae expression in Klebsiella pneumoniae CG43. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:620-633. [PMID: 35367140 DOI: 10.1016/j.jmii.2022.02.002] [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: 08/23/2021] [Revised: 01/26/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND/PURPOSE Two urease operons were identified in Klebsiella pneumoniae CG43, ure-1 and ure-2. This study investigates whether a differential regulation of the expression of ure-1 and ure-2 exists and how urease activity influences the acid stress response and expression of type 1 and type 3 fimbriae. METHODS The ureA1 and ureA2 gene specific deletion mutants were constructed. Promoter activity was assessed using a LacZ reporter system. The sensitivity to acid stress was determined by assessing the survival after pH 2.5 treatment. The influence on type 1 and type 3 fimbriae expression was assessed using western blotting and mannose-sensitive yeast agglutination and biofilm formation assay, respectively. RESULTS Bacterial growth analysis in mM9-U or modified Stuart broth revealed that ure-1 was the principal urease system, and ure-2 had a negative effect on ure-1 activity. Deletion of the fur or nac gene had no apparent effect on the activity of Pure1, Pure2-1, and Pure2-2. The Pure2-2 activity was enhanced by deletion of the hns gene. ureA1 deletion increased acid stress sensitivity, whereas the deleting effect of ureA2 was notable without hns. Deletion of ureA1 or ureA2 significantly induced the expression of type 1 fimbriae but decreased MrkA production and biofilm formation. CONCLUSION ure-1 is the primary expression system in K. pneumoniae CG43, while ure-2 is active in the absence of hns. Impairment of urease activity increases the sensitivity to acid stress, and the accumulation of urea induces the expression of type 1 fimbriae but represses type 3 fimbriae expression.
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Affiliation(s)
- Wei-Feng Lin
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsin Chu, Taiwan
| | - Rong-Yu Hu
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsin Chu, Taiwan
| | - Hwan-You Chang
- Institute of Molecular Medicine, National Tsing Hua University, Hsin Chu, Taiwan
| | - Fang-Yu Lin
- Institute of Molecular Medicine, National Tsing Hua University, Hsin Chu, Taiwan
| | - Chih-Hao Kuo
- Department of Biological Science and Technology, School of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsin Chu, Taiwan
| | - Li-Hsin Su
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsin Chu, Taiwan
| | - Hwei-Ling Peng
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsin Chu, Taiwan; Department of Biological Science and Technology, School of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsin Chu, Taiwan.
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8
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Gagarinova A, Hosseinnia A, Rahmatbakhsh M, Istace Z, Phanse S, Moutaoufik MT, Zilocchi M, Zhang Q, Aoki H, Jessulat M, Kim S, Aly KA, Babu M. Auxotrophic and prototrophic conditional genetic networks reveal the rewiring of transcription factors in Escherichia coli. Nat Commun 2022; 13:4085. [PMID: 35835781 PMCID: PMC9283627 DOI: 10.1038/s41467-022-31819-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 07/05/2022] [Indexed: 11/25/2022] Open
Abstract
Bacterial transcription factors (TFs) are widely studied in Escherichia coli. Yet it remains unclear how individual genes in the underlying pathways of TF machinery operate together during environmental challenge. Here, we address this by applying an unbiased, quantitative synthetic genetic interaction (GI) approach to measure pairwise GIs among all TF genes in E. coli under auxotrophic (rich medium) and prototrophic (minimal medium) static growth conditions. The resulting static and differential GI networks reveal condition-dependent GIs, widespread changes among TF genes in metabolism, and new roles for uncharacterized TFs (yjdC, yneJ, ydiP) as regulators of cell division, putrescine utilization pathway, and cold shock adaptation. Pan-bacterial conservation suggests TF genes with GIs are co-conserved in evolution. Together, our results illuminate the global organization of E. coli TFs, and remodeling of genetic backup systems for TFs under environmental change, which is essential for controlling the bacterial transcriptional regulatory circuits. The bacterium E. coli has around 300 transcriptional factors, but the functions of many of them, and the interactions between their respective regulatory networks, are unclear. Here, the authors study genetic interactions among all transcription factor genes in E. coli, revealing condition-dependent interactions and roles for uncharacterized transcription factors.
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Affiliation(s)
- Alla Gagarinova
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Ali Hosseinnia
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | | | - Zoe Istace
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | | | - Mara Zilocchi
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Qingzhou Zhang
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Hiroyuki Aoki
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Matthew Jessulat
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Sunyoung Kim
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Khaled A Aly
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, Canada.
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9
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Youn J, Rai N, Tagkopoulos I. Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes. Nat Commun 2022; 13:2360. [PMID: 35487919 PMCID: PMC9055065 DOI: 10.1038/s41467-022-29993-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 03/04/2022] [Indexed: 11/09/2022] Open
Abstract
We present a machine learning framework to automate knowledge discovery through knowledge graph construction, inconsistency resolution, and iterative link prediction. By incorporating knowledge from 10 publicly available sources, we construct an Escherichia coli antibiotic resistance knowledge graph with 651,758 triples from 23 triple types after resolving 236 sets of inconsistencies. Iteratively applying link prediction to this graph and wet-lab validation of the generated hypotheses reveal 15 antibiotic resistant E. coli genes, with 6 of them never associated with antibiotic resistance for any microbe. Iterative link prediction leads to a performance improvement and more findings. The probability of positive findings highly correlates with experimentally validated findings (R2 = 0.94). We also identify 5 homologs in Salmonella enterica that are all validated to confer resistance to antibiotics. This work demonstrates how evidence-driven decisions are a step toward automating knowledge discovery with high confidence and accelerated pace, thereby substituting traditional time-consuming and expensive methods.
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Affiliation(s)
- Jason Youn
- Department of Computer Science, University of California, Davis, CA, 95616, USA
- Genome Center, University of California, Davis, CA, 95616, USA
- USDA/NSF AI Institute for Next Generation Food Systems (AIFS), University of California, Davis, CA, 95616, USA
| | - Navneet Rai
- Department of Computer Science, University of California, Davis, CA, 95616, USA
- Genome Center, University of California, Davis, CA, 95616, USA
- USDA/NSF AI Institute for Next Generation Food Systems (AIFS), University of California, Davis, CA, 95616, USA
| | - Ilias Tagkopoulos
- Department of Computer Science, University of California, Davis, CA, 95616, USA.
- Genome Center, University of California, Davis, CA, 95616, USA.
- USDA/NSF AI Institute for Next Generation Food Systems (AIFS), University of California, Davis, CA, 95616, USA.
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10
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Dong H, Zhao Y, Bi C, Han Y, Zhang J, Bai X, Zhai G, Zhang H, Tian S, Hu D, Xu L, Zhang K. TmcA functions as a lysine 2-hydroxyisobutyryltransferase to regulate transcription. Nat Chem Biol 2022; 18:142-151. [PMID: 34903851 DOI: 10.1038/s41589-021-00906-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 09/23/2021] [Indexed: 02/05/2023]
Abstract
Protein lysine 2-hydroxyisobutyrylation (Khib) has recently been shown to play a critical role in the regulation of cellular processes. However, the mechanism and functional consequence of Khib in prokaryotes remain unclear. Here we report that TmcA, an RNA acetyltransferase, functions as a lysine 2-hydroxyisobutyryltransferase in the regulation of transcription. We show that TmcA can effectively catalyze Khib both in vitro and intracellularly, and that R502 is a key site for the Khib catalytic activity of TmcA. Using quantitative proteomics, we identified 467 endogenous candidates targeted by TmcA for Khib in Escherichia coli. Interestingly, we demonstrate that TmcA can specifically modulate the DNA-binding activity of H-NS, a nucleoid-associated protein, by catalysis of Khib at K121. Furthermore, this TmcA-targeted Khib regulates transcription of acid-resistance genes and enhances E. coli survival under acid stress. Our study reveals transcription regulation mediated by TmcA-catalyzed Khib for bacterial acid resistance.
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Affiliation(s)
- Hanyang Dong
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Yujie Zhao
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Changfen Bi
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, China
| | - Yue Han
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Jianji Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Xue Bai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Guijin Zhai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Hui Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Shanshan Tian
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Deqing Hu
- Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - Liyan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China.
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11
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Wang W, Yue Y, Zhang M, Song N, Jia H, Dai Y, Zhang F, Li C, Li B. Host acid signal controls Salmonella flagella biogenesis through CadC-YdiV axis. Gut Microbes 2022. [PMID: 36456534 DOI: 10.1080/194909762125747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Upon entering host cells, Salmonella quickly turns off flagella biogenesis to avoid recognition by the host immune system. However, it is not clear which host signal(s) Salmonella senses to initiate flagellum control. Here, we demonstrate that the acid signal can suppress flagella synthesis and motility of Salmonella, and this occurs after the transcription of master flagellar gene flhDC and depends on the anti-FlhDC factor YdiV. YdiV expression is activated after acid treatment. A global screen with ydiV promoter DNA and total protein from acid-treated Salmonella revealed a novel regulator of YdiV, the acid-related transcription factor CadC. Further studies showed that CadCC, the DNA binding domain of CadC, directly binds to a 33 nt region of the ydiV promoter with a 0.2 μM KD affinity. Furthermore, CadC could separate H-NS-ydiV promoter DNA complex to form CadC-DNA complex at a low concentration. Structural simulation and mutagenesis assays revealed that H43 and W106 of CadC are essential for ydiV promoter binding. No acid-induced flagellum control phenotype was observed in cadC mutant or ydiV mutant strains, suggesting that flagellum control during acid adaption is dependent on CadC and YdiV. The intracellular survival ability of cadC mutant strain decreased significantly compared with WT strain while the flagellin expression could not be effectively controlled in the cadC mutant strain when surviving within host cells. Together, our results demonstrated that acid stress acts as an important host signal to trigger Salmonella flagellum control through the CadC-YdiV-FlhDC axis, allowing Salmonella to sense a hostile environment and regulate flagellar synthesis during infection.
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Affiliation(s)
- Weiwei Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yingying Yue
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Min Zhang
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Nannan Song
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Haihong Jia
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yuanji Dai
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Fengyu Zhang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, China
| | - Cuiling Li
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Bingqing Li
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- Shandong First Medical University, Key Lab for Biotech-Drugs of National Health Commission, Jinan, China
- KeyLaboratory for Rare & Uncommon Diseases of Shandong Province, Jinan, China
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12
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Bessaiah H, Anamalé C, Sung J, Dozois CM. What Flips the Switch? Signals and Stress Regulating Extraintestinal Pathogenic Escherichia coli Type 1 Fimbriae (Pili). Microorganisms 2021; 10:5. [PMID: 35056454 PMCID: PMC8777976 DOI: 10.3390/microorganisms10010005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 12/18/2022] Open
Abstract
Pathogens are exposed to a multitude of harmful conditions imposed by the environment of the host. Bacterial responses against these stresses are pivotal for successful host colonization and pathogenesis. In the case of many E. coli strains, type 1 fimbriae (pili) are an important colonization factor that can contribute to diseases such as urinary tract infections and neonatal meningitis. Production of type 1 fimbriae in E. coli is dependent on an invertible promoter element, fimS, which serves as a phase variation switch determining whether or not a bacterial cell will produce type 1 fimbriae. In this review, we present aspects of signaling and stress involved in mediating regulation of type 1 fimbriae in extraintestinal E. coli; in particular, how certain regulatory mechanisms, some of which are linked to stress response, can influence production of fimbriae and influence bacterial colonization and infection. We suggest that regulation of type 1 fimbriae is potentially linked to environmental stress responses, providing a perspective for how environmental cues in the host and bacterial stress response during infection both play an important role in regulating extraintestinal pathogenic E. coli colonization and virulence.
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Affiliation(s)
- Hicham Bessaiah
- Institut National de Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (H.B.); (C.A.); (J.S.)
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Saint-Hyacinthe, QC J2S 2M2, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 0B1, Canada
| | - Carole Anamalé
- Institut National de Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (H.B.); (C.A.); (J.S.)
| | - Jacqueline Sung
- Institut National de Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (H.B.); (C.A.); (J.S.)
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 0B1, Canada
| | - Charles M. Dozois
- Institut National de Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (H.B.); (C.A.); (J.S.)
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Saint-Hyacinthe, QC J2S 2M2, Canada
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13
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Groisman EA, Duprey A, Choi J. How the PhoP/PhoQ System Controls Virulence and Mg 2+ Homeostasis: Lessons in Signal Transduction, Pathogenesis, Physiology, and Evolution. Microbiol Mol Biol Rev 2021; 85:e0017620. [PMID: 34191587 PMCID: PMC8483708 DOI: 10.1128/mmbr.00176-20] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The PhoP/PhoQ two-component system governs virulence, Mg2+ homeostasis, and resistance to a variety of antimicrobial agents, including acidic pH and cationic antimicrobial peptides, in several Gram-negative bacterial species. Best understood in Salmonella enterica serovar Typhimurium, the PhoP/PhoQ system consists o-regulated gene products alter PhoP-P amounts, even under constant inducing conditions. PhoP-P controls the abundance of hundreds of proteins both directly, by having transcriptional effects on the corresponding genes, and indirectly, by modifying the abundance, activity, or stability of other transcription factors, regulatory RNAs, protease regulators, and metabolites. The investigation of PhoP/PhoQ has uncovered novel forms of signal transduction and the physiological consequences of regulon evolution.
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Affiliation(s)
- Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
| | - Alexandre Duprey
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Jeongjoon Choi
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
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14
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Arcari T, Feger ML, Guerreiro DN, Wu J, O’Byrne CP. Comparative Review of the Responses of Listeria monocytogenes and Escherichia coli to Low pH Stress. Genes (Basel) 2020; 11:genes11111330. [PMID: 33187233 PMCID: PMC7698193 DOI: 10.3390/genes11111330] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023] Open
Abstract
Acidity is one of the principal physicochemical factors that influence the behavior of microorganisms in any environment, and their response to it often determines their ability to grow and survive. Preventing the growth and survival of pathogenic bacteria or, conversely, promoting the growth of bacteria that are useful (in biotechnology and food production, for example), might be improved considerably by a deeper understanding of the protective responses that these microorganisms deploy in the face of acid stress. In this review, we survey the molecular mechanisms used by two unrelated bacterial species in their response to low pH stress. We chose to focus on two well-studied bacteria, Escherichia coli (phylum Proteobacteria) and Listeria monocytogenes (phylum Firmicutes), that have both evolved to be able to survive in the mammalian gastrointestinal tract. We review the mechanisms that these species use to maintain a functional intracellular pH as well as the protective mechanisms that they deploy to prevent acid damage to macromolecules in the cells. We discuss the mechanisms used to sense acid in the environment and the regulatory processes that are activated when acid is encountered. We also highlight the specific challenges presented by organic acids. Common themes emerge from this comparison as well as unique strategies that each species uses to cope with acid stress. We highlight some of the important research questions that still need to be addressed in this fascinating field.
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15
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Nguyen-Vo TP, Ko S, Ryu H, Kim JR, Kim D, Park S. Systems evaluation reveals novel transporter YohJK renders 3-hydroxypropionate tolerance in Escherichia coli. Sci Rep 2020; 10:19064. [PMID: 33149261 PMCID: PMC7642389 DOI: 10.1038/s41598-020-76120-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/22/2020] [Indexed: 11/09/2022] Open
Abstract
Previously, we have reported that 3-hydroxypropionate (3-HP) tolerance in Escherichia coli W is improved by deletion of yieP, a less-studied transcription factor. Here, through systems analyses along with physiological and functional studies, we suggest that the yieP deletion improves 3-HP tolerance by upregulation of yohJK, encoding putative 3-HP transporter(s). The tolerance improvement by yieP deletion was highly specific to 3-HP, among various C2-C4 organic acids. Mapping of YieP binding sites (ChIP-exo) coupled with transcriptomic profiling (RNA-seq) advocated seven potential genes/operons for further functional analysis. Among them, the yohJK operon, encoding for novel transmembrane proteins, was the most responsible for the improved 3-HP tolerance; deletion of yohJK reduced 3-HP tolerance regardless of yieP deletion, and their subsequent complementation fully restored the tolerance in both the wild-type and yieP deletion mutant. When determined by 3-HP-responsive biosensor, a drastic reduction of intracellular 3-HP was observed upon yieP deletion or yohJK overexpression, suggesting that yohJK encodes for novel 3-HP exporter(s).
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Affiliation(s)
- Thuan Phu Nguyen-Vo
- School of Energy and Chemical Engineering, UNIST, Ulsan, 44919, Republic of Korea
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Seyoung Ko
- School of Energy and Chemical Engineering, UNIST, Ulsan, 44919, Republic of Korea
| | - Huichang Ryu
- School of Energy and Chemical Engineering, UNIST, Ulsan, 44919, Republic of Korea
| | - Jung Rae Kim
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, UNIST, Ulsan, 44919, Republic of Korea.
| | - Sunghoon Park
- School of Energy and Chemical Engineering, UNIST, Ulsan, 44919, Republic of Korea.
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, 46241, Republic of Korea.
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16
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Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community. ISME JOURNAL 2020; 14:2816-2828. [PMID: 32788711 DOI: 10.1038/s41396-020-00737-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/24/2020] [Accepted: 08/03/2020] [Indexed: 01/12/2023]
Abstract
Interactive microbial communities are ubiquitous, influencing biogeochemical cycles and host health. One widespread interaction is nutrient exchange, or cross-feeding, wherein metabolites are transferred between microbes. Some cross-fed metabolites, such as vitamins, amino acids, and ammonium (NH4+), are communally valuable and impose a cost on the producer. The mechanisms that enforce cross-feeding of communally valuable metabolites are not fully understood. Previously we engineered a cross-feeding coculture between N2-fixing Rhodopseudomonas palustris and fermentative Escherichia coli. Engineered R. palustris excretes essential nitrogen as NH4+ to E. coli, while E. coli excretes essential carbon as fermentation products to R. palustris. Here, we sought to determine whether a reciprocal cross-feeding relationship would evolve spontaneously in cocultures with wild-type R. palustris, which is not known to excrete NH4+. Indeed, we observed the emergence of NH4+ cross-feeding, but driven by adaptation of E. coli alone. A missense mutation in E. coli NtrC, a regulator of nitrogen scavenging, resulted in constitutive activation of an NH4+ transporter. This activity likely allowed E. coli to subsist on the small amount of leaked NH4+ and better reciprocate through elevated excretion of fermentation products from a larger E. coli population. Our results indicate that enhanced nutrient uptake by recipients, rather than increased excretion by producers, is an underappreciated yet possibly prevalent mechanism by which cross-feeding can emerge.
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Tn-Seq Analysis Identifies Genes Important for Yersinia pestis Adherence during Primary Pneumonic Plague. mSphere 2020; 5:5/4/e00715-20. [PMID: 32759339 PMCID: PMC7407073 DOI: 10.1128/msphere.00715-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Colonization of the lung by Yersinia pestis is a critical first step in establishing infection during primary pneumonic plague, a disease characterized by high lethality. However, the mechanisms by which Y. pestis adheres in the lung after inhalation remain elusive. Here, we used Tn-seq to identify Y. pestis genes important for adherence early during primary pneumonic plague. Our mutant enrichment strategy resulted in the identification of genes important for regulation and assembly of genes and proteins rather than adhesin genes themselves. These results reveal that there may be multiple Y. pestis adhesins or redundancy among adhesins. Identifying the adhesins regulated by the genes identified in our enrichment screen may reveal novel therapeutic targets for preventing Y. pestis adherence and the subsequent development of pneumonic plague. Following inhalation, Yersinia pestis rapidly colonizes the lung to establish infection during primary pneumonic plague. Although several adhesins have been identified in Yersinia spp., the factors mediating early Y. pestis adherence in the lung remain unknown. To identify genes important for Y. pestis adherence during primary pneumonic plague, we used transposon insertion sequencing (Tn-seq). Wild-type and capsule mutant (Δcaf1) Y. pestis transposon mutant libraries were serially passaged in vivo to enrich for nonadherent mutants in the lung using a mouse model of primary pneumonic plague. Sequencing of the passaged libraries revealed six mutants that were significantly enriched in both the wild-type and Δcaf1Y. pestis backgrounds. The enriched mutants had insertions in genes that encode transcriptional regulators, chaperones, an endoribonuclease, and YPO3903, a hypothetical protein. Using single-strain infections and a transcriptional analysis, we identified a significant role for YPO3903 in Y. pestis adherence in the lung and showed that YPO3903 regulated transcript levels of psaA, which encodes a fimbria previously implicated in Y. pestis adherence in vitro. Deletion of psaA had a minor effect on Y. pestis adherence in the lung, suggesting that YPO3903 regulates other adhesins in addition to psaA. By enriching for mutations in genes that regulate the expression or assembly of multiple genes or proteins, we obtained screen results indicating that there may be not just one dominant adhesin but rather several factors that contribute to early Y. pestis adherence during primary pneumonic plague. IMPORTANCE Colonization of the lung by Yersinia pestis is a critical first step in establishing infection during primary pneumonic plague, a disease characterized by high lethality. However, the mechanisms by which Y. pestis adheres in the lung after inhalation remain elusive. Here, we used Tn-seq to identify Y. pestis genes important for adherence early during primary pneumonic plague. Our mutant enrichment strategy resulted in the identification of genes important for regulation and assembly of genes and proteins rather than adhesin genes themselves. These results reveal that there may be multiple Y. pestis adhesins or redundancy among adhesins. Identifying the adhesins regulated by the genes identified in our enrichment screen may reveal novel therapeutic targets for preventing Y. pestis adherence and the subsequent development of pneumonic plague.
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Dual Function of Aar, a Member of the New AraC Negative Regulator Family, in Escherichia coli Gene Expression. Infect Immun 2020; 88:IAI.00100-20. [PMID: 32253248 DOI: 10.1128/iai.00100-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/30/2020] [Indexed: 11/20/2022] Open
Abstract
Enteroaggregative Escherichia coli (EAEC) is an E. coli pathotype associated with diarrhea and growth faltering. EAEC virulence gene expression is controlled by the autoactivated AraC family transcriptional regulator, AggR. AggR activates transcription of a large number of virulence genes, including Aar, which in turn acts as a negative regulator of AggR itself. Aar has also been shown to affect expression of E. coli housekeeping genes, including H-NS, a global regulator that acts at multiple promoters and silences AT-rich genes (such as those in the AggR regulon). Although Aar has been shown to bind both AggR and H-NS in vitro, functional significance of these interactions has not been shown in vivo In order to dissect this regulatory network, we removed the complex interdependence of aggR and aar by placing the genes under the control of titratable promoters. We measured phenotypic and genotypic changes on downstream genes in EAEC strain 042 and E. coli K-12 strain DH5α, which lacks the AggR regulon. In EAEC, we found that low expression of aar increases aafA fimbrial gene expression via H-NS; however, when aar is more highly expressed, it acts as a negative regulator via AggR. In DH5α, aar affected expression of E. coli genes in some cases via H-NS and in some cases independent of H-NS. Our data support the model that Aar interacts in concert with AggR, H-NS, and possibly other regulators and that these interactions are likely to be functionally significant in vivo.
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Four LysR-type transcriptional regulator family proteins (LTTRs) involved in antibiotic resistance in Aeromonas hydrophila. World J Microbiol Biotechnol 2019; 35:127. [DOI: 10.1007/s11274-019-2700-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 07/22/2019] [Indexed: 01/21/2023]
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Gawade P, Gunjal G, Sharma A, Ghosh P. Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome-wide data analysis. Genomics 2019; 112:1264-1272. [PMID: 31356968 DOI: 10.1016/j.ygeno.2019.07.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/29/2022]
Abstract
Fis (Factor for inversion stimulation) and H-NS (Histone-like nucleoid-structuring protein) are two well-known nucleoid-associated proteins (NAPs) in proteobacteria, which play crucial roles in genome organization and transcriptional regulation. We performed RNA-sequencing to identify genes regulated by these NAPs. Study reveals that Fis and H-NS affect expression of 462 and 88 genes respectively in Escherichia coli at mid-exponential growth phase. By integrating available ChIP-seq data, we identified direct and indirect regulons of Fis and H-NS proteins. Functional analysis reveals that Fis controls expression of genes involved in translation, oxidative phosphorylation, sugar metabolism and transport, amino acid metabolism, bacteriocin transport, cell division, two-component system, biofilm formation, pilus organization and lipopolysaccharide biosynthesis pathways. However, H-NS represses expression of genes in cell adhesion, recombination, biofilm formation and lipopolysaccharide biosynthesis pathways under mid-exponential growth condition. The current regulatory networks thus provide a global glimpse of coordinated regulatory roles for these two important NAPs.
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Affiliation(s)
- Priyanka Gawade
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India
| | - Gaurav Gunjal
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Anamika Sharma
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Payel Ghosh
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India.
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Wu H, Chen S, Ji M, Chen Q, Shi J, Sun J. Activation of colanic acid biosynthesis linked to heterologous expression of the polyhydroxybutyrate pathway in Escherichia coli. Int J Biol Macromol 2019; 128:752-760. [DOI: 10.1016/j.ijbiomac.2019.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/01/2019] [Accepted: 02/02/2019] [Indexed: 01/31/2023]
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22
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Identification of novel genes involved in high hydrostatic pressure resistance of Escherichia coli. Food Microbiol 2019; 78:171-178. [DOI: 10.1016/j.fm.2018.10.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/19/2018] [Accepted: 10/21/2018] [Indexed: 12/16/2022]
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23
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Liu CJ, Lin CT, Chiang JD, Lin CY, Tay YX, Fan LC, Peng KN, Lin CH, Peng HL. RcsB regulation of the YfdX-mediated acid stress response in Klebsiella pneumoniae CG43S3. PLoS One 2019; 14:e0212909. [PMID: 30818355 PMCID: PMC6394985 DOI: 10.1371/journal.pone.0212909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/12/2019] [Indexed: 12/31/2022] Open
Abstract
In Klebsiella pneumoniae CG43S3, deletion of the response regulator gene rcsB reduced the capsular polysaccharide amount and survival on exposure to acid stress. A comparison of the pH 4.4-induced proteomes between CG43S3 and CG43S3ΔrcsB revealed numerous differentially expressed proteins and one of them, YfdX, which has recently been reported as a periplasmic protein, was absent in CG43S3ΔrcsB. Acid survival analysis was then conducted to determine its role in the acid stress response. Deletion of yfdX increased the sensitivity of K. pneumoniae CG43S3 to a pH of 2.5, and transforming the mutant with a plasmid carrying yfdX restored the acid resistance (AR) levels. In addition, the effect of yfdX deletion was cross-complemented by the expression of the periplasmic chaperone HdeA. Furthermore, the purified recombinant protein YfdX reduced the acid-induced protein aggregation, suggesting that YfdX as well as HdeA functions as a chaperone. The following promoter activity measurement revealed that rcsB deletion reduced the expression of yfdX after the bacteria were subjected to pH 4.4 adaptation. Western blot analysis also revealed that YfdX production was inhibited by rcsB deletion and only the plasmid expressing RcsB or the nonphosphorylated form of RcsB, RcsBD56A, could restore the YfdX production, and the RcsB-mediated complementation was no longer observed when the sensor kinase RcsD gene was deleted. In conclusion, this is the first study demonstrating that YfdX may be involved in the acid stress response as a periplasmic chaperone and that RcsB positively regulates the acid stress response partly through activation of yfdX expression. Moreover, the phosphorylation status of RcsB may affect the YfdX expression under acidic conditions.
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Affiliation(s)
- Chia-Jui Liu
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Ching-Ting Lin
- School of Chinese Medicine, China Medical University, Taichung, Taiwan, Republic of China
| | - Jo-Di Chiang
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Chen-Yi Lin
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Yen-Xi Tay
- Institute of Molecular Medicine and Biological Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Li-Cheng Fan
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Kuan-Nan Peng
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Chih-Huan Lin
- Institute of Molecular Medicine and Biological Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Hwei-Ling Peng
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
- Institute of Molecular Medicine and Biological Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
- * E-mail:
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24
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Zupok A, Iobbi-Nivol C, Méjean V, Leimkühler S. The regulation of Moco biosynthesis and molybdoenzyme gene expression by molybdenum and iron in bacteria. Metallomics 2019; 11:1602-1624. [DOI: 10.1039/c9mt00186g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The regulation of the operons involved in Moco biosynthesis is dependent on the availability of Fe–S clusters in the cell.
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Affiliation(s)
- Arkadiusz Zupok
- University of Potsdam
- Institute of Biochemistry and Biology
- Molecular Enzymology
- Potsdam-Golm
- Germany
| | - Chantal Iobbi-Nivol
- Aix-Marseille Université
- Institut de Microbiologie de la Méditerranée
- Laboratoire de Bioénergétique et Ingénierie des Protéines
- Centre National de la Recherche Scientifique
- Marseille
| | - Vincent Méjean
- Aix-Marseille Université
- Institut de Microbiologie de la Méditerranée
- Laboratoire de Bioénergétique et Ingénierie des Protéines
- Centre National de la Recherche Scientifique
- Marseille
| | - Silke Leimkühler
- University of Potsdam
- Institute of Biochemistry and Biology
- Molecular Enzymology
- Potsdam-Golm
- Germany
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25
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Leistra AN, Curtis NC, Contreras LM. Regulatory non-coding sRNAs in bacterial metabolic pathway engineering. Metab Eng 2018; 52:190-214. [PMID: 30513348 DOI: 10.1016/j.ymben.2018.11.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/31/2018] [Accepted: 11/29/2018] [Indexed: 12/11/2022]
Abstract
Non-coding RNAs (ncRNAs) are versatile and powerful controllers of gene expression that have been increasingly linked to cellular metabolism and phenotype. In bacteria, identified and characterized ncRNAs range from trans-acting, multi-target small non-coding RNAs to dynamic, cis-encoded regulatory untranslated regions and riboswitches. These native regulators have inspired the design and construction of many synthetic RNA devices. In this work, we review the design, characterization, and impact of ncRNAs in engineering both native and exogenous metabolic pathways in bacteria. We also consider the opportunities afforded by recent high-throughput approaches for characterizing sRNA regulators and their corresponding networks to showcase their potential applications and impact in engineering bacterial metabolism.
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Affiliation(s)
- Abigail N Leistra
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA
| | - Nicholas C Curtis
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA.
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26
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Gao X, Yang X, Li J, Zhang Y, Chen P, Lin Z. Engineered global regulator H-NS improves the acid tolerance of E. coli. Microb Cell Fact 2018; 17:118. [PMID: 30053876 PMCID: PMC6064147 DOI: 10.1186/s12934-018-0966-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 07/19/2018] [Indexed: 11/25/2022] Open
Abstract
Background Acid stress is often encountered during industrial fermentation as a result of the accumulation of acidic metabolites. Acid stress increases the intracellular acidity and can cause DNA damage and denaturation of essential enzymes, thus leading to a decrease of growth and fermentation yields. Although acid stress can be relieved by addition of a base to the medium, fermentations with acid-tolerant strains are generally considered much more efficient and cost-effective. Results In this study, the global regulator H-NS was found to have significant influence on the acid tolerance of E. coli. The final OD600 of strains overexpressing H-NS increased by 24% compared to control, when cultured for 24 h at pH 4.5 using HCl as an acid agent. To further improve the acid tolerance, a library of H-NS was constructed by error-prone PCR and subjected to selection. Five mutants that conferred a significant growth advantage compared to the control strain were obtained. The final OD600 of strains harboring the five H-NS mutants was enhanced by 26–53%, and their survival rate was increased by 10- to 100-fold at pH 2.5. Further investigation showed that the improved acid tolerance of H-NS mutants coincides with the activation of multiple acid resistance mechanisms, in particular the glutamate- and glutamine-dependent acid resistance system (AR2). The improved acid tolerance of H-NS mutants was also demonstrated in media acidified by acetic acid and succinic acid, which are common acidic fermentation by-products or products. Conclusions The results obtained in this work demonstrate that the engineering of H-NS can enhance the acid tolerance of E. coli. More in general, this study shows the potential of the engineering of global regulators acting as repressors, such as H-NS, as a promising method to obtain phenotypes of interest. This approach could expand the spectrum of application of global transcription machinery engineering. Electronic supplementary material The online version of this article (10.1186/s12934-018-0966-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xianxing Gao
- Department of Chemical Engineering, Tsinghua University, One Tsinghua Garden Road, Beijing, 100084, China
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, Guangdong, China
| | - Jiahui Li
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, Guangdong, China
| | - Yan Zhang
- Department of Chemical Engineering, Tsinghua University, One Tsinghua Garden Road, Beijing, 100084, China.,Shenzhen Agricultural Genomics Institute, China Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng District, Shenzhen, 518120, Guangdong, China
| | - Ping Chen
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, Guangdong, China.
| | - Zhanglin Lin
- Department of Chemical Engineering, Tsinghua University, One Tsinghua Garden Road, Beijing, 100084, China. .,School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, Guangdong, China.
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27
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Yamanaka Y, Winardhi RS, Yamauchi E, Nishiyama SI, Sowa Y, Yan J, Kawagishi I, Ishihama A, Yamamoto K. Dimerization site 2 of the bacterial DNA-binding protein H-NS is required for gene silencing and stiffened nucleoprotein filament formation. J Biol Chem 2018; 293:9496-9505. [PMID: 29695505 DOI: 10.1074/jbc.ra117.001425] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/20/2018] [Indexed: 11/06/2022] Open
Abstract
The bacterial nucleoid-associated protein H-NS is a DNA-binding protein, playing a major role in gene regulation. To regulate transcription, H-NS silences genes, including horizontally acquired foreign genes. Escherichia coli H-NS is 137 residues long and consists of two discrete and independent structural domains: an N-terminal oligomerization domain and a C-terminal DNA-binding domain, joined by a flexible linker. The N-terminal oligomerization domain is composed of two dimerization sites, dimerization sites 1 and 2, which are both required for H-NS oligomerization, but the exact role of dimerization site 2 in gene silencing is unclear. To this end, we constructed a whole set of single amino acid substitution variants spanning residues 2 to 137. Using a well-characterized H-NS target, the slp promoter of the glutamic acid-dependent acid resistance (GAD) cluster promoters, we screened for any variants defective in gene silencing. Focusing on the function of dimerization site 2, we analyzed four variants, I70C/I70A and L75C/L75A, which all could actively bind DNA but are defective in gene silencing. Atomic force microscopy analysis of DNA-H-NS complexes revealed that all of these four variants formed condensed complexes on DNA, whereas WT H-NS formed rigid and extended nucleoprotein filaments, a conformation required for gene silencing. Single-molecule stretching experiments confirmed that the four variants had lost the ability to form stiffened filaments. We conclude that dimerization site 2 of H-NS plays a key role in the formation of rigid H-NS nucleoprotein filament structures required for gene silencing.
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Affiliation(s)
- Yuki Yamanaka
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan.,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan.,the Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore, and
| | - Ricksen S Winardhi
- the Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore, and.,the Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542, Singapore
| | - Erika Yamauchi
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan
| | - So-Ichiro Nishiyama
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan.,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan
| | - Yoshiyuki Sowa
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan.,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan
| | - Jie Yan
- the Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore, and.,the Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542, Singapore
| | - Ikuro Kawagishi
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan.,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan
| | - Akira Ishihama
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan.,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan
| | - Kaneyoshi Yamamoto
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan, .,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan
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28
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Shin J, Cho H, Kim S, Kim KS. Role of acid responsive genes in the susceptibility of Escherichia coli to ciclopirox. Biochem Biophys Res Commun 2018; 500:296-301. [PMID: 29654752 DOI: 10.1016/j.bbrc.2018.04.063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 04/10/2018] [Indexed: 10/17/2022]
Abstract
Antibiotic resistance poses a huge threat to the effective treatment of bacterial infections. To circumvent the limitations in developing new antibiotics, researchers are attempting to repurpose pre-developed drugs that are known to be safe. Ciclopirox, an off-patent antifungal agent, inhibits the growth of Gram-negative bacteria, and genes involved in galactose metabolism and lipopolysaccharide (LPS) biosynthesis are plausible antibacterial targets for ciclopirox, since their expression levels partially increase susceptibility at restrictive concentrations. In the present study, to identify new target genes involved in the susceptibility of Escherichia coli to ciclopirox, genome-wide mRNA profiling was performed following ciclopirox addition at sublethal concentrations, and glutamate-dependent acid resistance (GDAR) genes were differentially regulated. Additional susceptibility testing, growth analyses and viability assays of GDAR regulatory genes revealed that down-regulation of evgS or hns strongly enhanced susceptibility to ciclopirox. Further microscopy and phenotypic analyses revealed that down-regulation of these genes increased cell size and decreased motility. Our findings could help to maximise the efficacy of ciclopirox against hard-to-treat Gram-negative pathogens.
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Affiliation(s)
- Jonghoon Shin
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Hyejin Cho
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Suran Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Kwang-Sun Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea.
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29
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Reynolds TS, Courtney CM, Erickson KE, Wolfe LM, Chatterjee A, Nagpal P, Gill RT. ROS mediated selection for increased NADPH availability in Escherichia coli. Biotechnol Bioeng 2017; 114:2685-2689. [PMID: 28710857 DOI: 10.1002/bit.26385] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 06/21/2017] [Accepted: 07/12/2017] [Indexed: 11/10/2022]
Abstract
The economical production of chemicals and fuels by microbial processes remains an intense area of interest in biotechnology. A key limitation in such efforts concerns the availability of key co-factors, in this case NADPH, required for target pathways. Many of the strategies pursued for increasing NADPH availability in Escherichia coli involve manipulations to the central metabolism, which can create redox imbalances and overall growth defects. In this study we used a reactive oxygen species based selection to search for novel methods of increasing NADPH availability. We report a loss of function mutation in the gene hdfR appears to increase NADPH availability in E. coli. Additionally, we show this excess NADPH can be used to improve the production of 3HP in E. coli.
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Affiliation(s)
- Thomas S Reynolds
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado
| | - Colleen M Courtney
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado
| | - Keesha E Erickson
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado
| | - Lisa M Wolfe
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, Colorado
| | - Anushree Chatterjee
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado.,BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Prashant Nagpal
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado.,BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado.,Materials Science and Engineering, University of Colorado, Boulder, Boulder, Colorado
| | - Ryan T Gill
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado.,Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado
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30
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The Long Hunt for pssR-Looking for a Phospholipid Synthesis Transcriptional Regulator, Finding the Ribosome. J Bacteriol 2017; 199:JB.00202-17. [PMID: 28484043 DOI: 10.1128/jb.00202-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 04/26/2017] [Indexed: 11/20/2022] Open
Abstract
The phospholipid (PL) composition of bacterial membranes varies as a function of growth rate and in response to changes in the environment. While growth adaptation can be explained by biochemical feedback in the PL synthesis pathway, recent transcriptome studies have revealed that the expression of PL synthesis genes can also be tuned in response to various stresses. We previously showed that the BasRS two-component pathway controls the expression of the diacylglycerol kinase gene, dgkA, in Escherichia coli (A. Wahl, L. My, R. Dumoulin, J. N. Sturgis, and E. Bouveret, Mol Microbiol, 80:1260-1275, 2011, https://doi.org/10.1111/j.1365-2958.2011.07641.x). In this study, we set up a strategy to identify the mutation responsible for the upregulation of pssA observed in the historical pssR1 mutant and supposedly corresponding to a transcriptional repressor (C. P. Sparrow and J. Raetz, J Biol Chem, 258:9963-9967, 1983). pssA encodes phosphatidylserine synthase, the first step of phosphatidylethanolamine synthesis. We showed that this mutation corresponded to a single nucleotide change in the anti-Shine-Dalgarno sequence of the 16S rRNA encoded by the rrnC operon. We further demonstrated that this mutation enhanced the translation of pssA Though this effect appeared to be restricted to PssA among phospholipid synthesis enzymes, it was not specific, as evidenced by a global effect on the production of unrelated proteins.IMPORTANCE Bacteria adjust the phospholipid composition of their membranes to the changing environment. In addition to enzymatic regulation, stress response regulators control specific steps of the phospholipid synthesis pathway. We wanted to identify a potential regulator controlling the expression of the phosphatidylserine synthase gene. We showed that it was not the previously suggested hdfR gene and instead that a mutation in the anti-Shine-Dalgarno sequence of 16S RNA was responsible for an increase in pssA translation. This example underlines the fact that gene expression can be modulated by means other than specific regulatory processes.
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31
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Structure-function analysis of the DNA-binding domain of a transmembrane transcriptional activator. Sci Rep 2017; 7:1051. [PMID: 28432336 PMCID: PMC5430869 DOI: 10.1038/s41598-017-01031-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/23/2017] [Indexed: 11/08/2022] Open
Abstract
The transmembrane DNA-binding protein CadC of E. coli, a representative of the ToxR-like receptor family, combines input and effector domains for signal sensing and transcriptional activation, respectively, in a single protein, thus representing one of the simplest signalling systems. At acidic pH in a lysine-rich environment, CadC activates the transcription of the cadBA operon through recruitment of the RNA polymerase (RNAP) to the two cadBA promoter sites, Cad1 and Cad2, which are directly bound by CadC. However, the molecular details for its interaction with DNA have remained elusive. Here, we present the crystal structure of the CadC DNA-binding domain (DBD) and show that it adopts a winged helix-turn-helix fold. The interaction with the cadBA promoter site Cad1 is studied by using nuclear magnetic resonance (NMR) spectroscopy, biophysical methods and functional assays and reveals a preference for AT-rich regions. By mutational analysis we identify amino acids within the CadC DBD that are crucial for DNA-binding and functional activity. Experimentally derived structural models of the CadC-DNA complex indicate that the CadC DBD employs mainly non-sequence-specific over a few specific contacts. Our data provide molecular insights into the CadC-DNA interaction and suggest how CadC dimerization may provide high-affinity binding to the Cad1 promoter.
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32
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Milosavljevic V, Jelinkova P, Jimenez Jimenez AM, Moulick A, Haddad Y, Buchtelova H, Krizkova S, Heger Z, Kalina L, Richtera L, Kopel P, Adam V. Alternative Synthesis Route of Biocompatible Polyvinylpyrrolidone Nanoparticles and Their Effect on Pathogenic Microorganisms. Mol Pharm 2016; 14:221-233. [PMID: 27943679 DOI: 10.1021/acs.molpharmaceut.6b00807] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein we describe a novel alternative synthesis route of polyvinylpyrrolidone nanoparticles using salting-out method at a temperature close to polyvinylpyrrolidone decomposition. At elevated temperatures, the stability of polyvinylpyrrolidone decreases and the opening of pyrrolidone ring fractions occurs. This leads to cross-linking process, where separate units of polyvinylpyrrolidone interact among themselves and rearrange to form nanoparticles. The formation/stability of these nanoparticles was confirmed by transmission electron microscopy, X-ray photoelectron spectroscopy, mass spectrometry, infrared spectroscopy, and spectrophotometry. The obtained nanoparticles possess exceptional biocompatibility. No toxicity and genotoxicity was found in normal human prostate epithelium cells (PNT1A) together with their high hemocompatibility. The antimicrobial effects of polyvinylpyrrolidone nanoparticles were tested on bacterial strains isolated from the wounds of patients suffering from hard-to-heal infections. Molecular analysis (qPCR) confirmed that the treatment can induce the regulation of stress-related survival genes. Our results strongly suggest that the polyvinylpyrrolidone nanoparticles have great potential to be developed into a novel antibacterial compound.
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Affiliation(s)
- Vedran Milosavljevic
- Department of Chemistry and Biochemistry, Mendel University in Brno , Zemedelska 1, CZ-613 00 Brno, Czech Republic
| | - Pavlina Jelinkova
- Department of Chemistry and Biochemistry, Mendel University in Brno , Zemedelska 1, CZ-613 00 Brno, Czech Republic
| | - Ana Maria Jimenez Jimenez
- Department of Chemistry and Biochemistry, Mendel University in Brno , Zemedelska 1, CZ-613 00 Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology , Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Amitava Moulick
- Department of Chemistry and Biochemistry, Mendel University in Brno , Zemedelska 1, CZ-613 00 Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology , Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Yazan Haddad
- Department of Chemistry and Biochemistry, Mendel University in Brno , Zemedelska 1, CZ-613 00 Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology , Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Hana Buchtelova
- Department of Chemistry and Biochemistry, Mendel University in Brno , Zemedelska 1, CZ-613 00 Brno, Czech Republic
| | - Sona Krizkova
- Department of Chemistry and Biochemistry, Mendel University in Brno , Zemedelska 1, CZ-613 00 Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology , Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno , Zemedelska 1, CZ-613 00 Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology , Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Lukas Kalina
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology , Purkynova 118, Brno CZ-612 00, Czech Republic
| | - Lukas Richtera
- Department of Chemistry and Biochemistry, Mendel University in Brno , Zemedelska 1, CZ-613 00 Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology , Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Pavel Kopel
- Department of Chemistry and Biochemistry, Mendel University in Brno , Zemedelska 1, CZ-613 00 Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology , Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno , Zemedelska 1, CZ-613 00 Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology , Technicka 3058/10, CZ-616 00 Brno, Czech Republic
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Woo JM, Kim JW, Song JW, Blank LM, Park JB. Activation of the Glutamic Acid-Dependent Acid Resistance System in Escherichia coli BL21(DE3) Leads to Increase of the Fatty Acid Biotransformation Activity. PLoS One 2016; 11:e0163265. [PMID: 27681369 PMCID: PMC5040553 DOI: 10.1371/journal.pone.0163265] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 09/05/2016] [Indexed: 01/29/2023] Open
Abstract
The biosynthesis of carboxylic acids including fatty acids from biomass is central in envisaged biorefinery concepts. The productivities are often, however, low due to product toxicity that hamper whole-cell biocatalyst performance. Here, we have investigated factors that influence the tolerance of Escherichia coli to medium chain carboxylic acid (i.e., n-heptanoic acid)-induced stress. The metabolic and genomic responses of E. coli BL21(DE3) and MG1655 grown in the presence of n-heptanoic acid indicated that the GadA/B-based glutamic acid-dependent acid resistance (GDAR) system might be critical for cellular tolerance. The GDAR system, which is responsible for scavenging intracellular protons by catalyzing decarboxylation of glutamic acid, was inactive in E. coli BL21(DE3). Activation of the GDAR system in this strain by overexpressing the rcsB and dsrA genes, of which the gene products are involved in the activation of GadE and RpoS, respectively, resulted in acid tolerance not only to HCl but also to n-heptanoic acid. Furthermore, activation of the GDAR system allowed the recombinant E. coli BL21(DE3) expressing the alcohol dehydrogenase of Micrococcus luteus and the Baeyer-Villiger monooxygenase of Pseudomonas putida to reach 60% greater product concentration in the biotransformation of ricinoleic acid (i.e., 12-hydroxyoctadec-9-enoic acid (1)) into n-heptanoic acid (5) and 11-hydroxyundec-9-enoic acid (4). This study may contribute to engineering E. coli-based biocatalysts for the production of carboxylic acids from renewable biomass.
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Affiliation(s)
- Ji-Min Woo
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Ji-Won Kim
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Ji-Won Song
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Lars M. Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Jin-Byung Park
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 120-750, Republic of Korea
- * E-mail:
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34
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Liu X, Hu W, An Z, Bai Z, Dai X, Yang Y. Exploration of cell lysis in a bioreactor using Escherichia coli expressing single-chain variable-domain antibody fragments. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-016-1202-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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35
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Global Regulator of Virulence A (GrvA) Coordinates Expression of Discrete Pathogenic Mechanisms in Enterohemorrhagic Escherichia coli through Interactions with GadW-GadE. J Bacteriol 2015; 198:394-409. [PMID: 26527649 DOI: 10.1128/jb.00556-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/28/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Global regulator of virulence A (GrvA) is a ToxR-family transcriptional regulator that activates locus of enterocyte effacement (LEE)-dependent adherence in enterohemorrhagic Escherichia coli (EHEC). LEE activation by GrvA requires the Rcs phosphorelay response regulator RcsB and is sensitive to physiologically relevant concentrations of bicarbonate, a known stimulant of virulence systems in intestinal pathogens. This study determines the genomic scale of GrvA-dependent regulation and uncovers details of the molecular mechanism underlying GrvA-dependent regulation of pathogenic mechanisms in EHEC. In a grvA-null background of EHEC strain TW14359, RNA sequencing analysis revealed the altered expression of over 700 genes, including the downregulation of LEE- and non-LEE-encoded effectors and the upregulation of genes for glutamate-dependent acid resistance (GDAR). Upregulation of GDAR genes corresponded with a marked increase in acid resistance. GrvA-dependent regulation of GDAR and the LEE required gadE, the central activator of GDAR genes and a direct repressor of the LEE. Control of gadE by GrvA was further determined to occur through downregulation of the gadE activator GadW. This interaction of GrvA with GadW-GadE represses the acid resistance phenotype, while it concomitantly activates the LEE-dependent adherence and secretion of immune subversion effectors. The results of this study significantly broaden the scope of GrvA-dependent regulation and its role in EHEC pathogenesis. IMPORTANCE Enterohemorrhagic Escherichia coli (EHEC) is an intestinal human pathogen causing acute hemorrhagic colitis and life-threatening hemolytic-uremic syndrome. For successful transmission and gut colonization, EHEC relies on the glutamate-dependent acid resistance (GDAR) system and a type III secretion apparatus, encoded on the LEE pathogenicity island. This study investigates the mechanism whereby the DNA-binding regulator GrvA coordinates activation of the LEE with repression of GDAR. Investigating how these systems are regulated leads to an understanding of pathogenic behavior and novel strategies aimed at disease prevention and control.
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Seo SW, Kim D, O'Brien EJ, Szubin R, Palsson BO. Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli. Nat Commun 2015; 6:7970. [PMID: 26258987 PMCID: PMC4918353 DOI: 10.1038/ncomms8970] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 07/01/2015] [Indexed: 12/27/2022] Open
Abstract
The regulators GadE, GadW and GadX (which we refer to as GadEWX) play a critical role in the transcriptional regulation of the glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the genome-wide regulatory role of GadEWX is still unknown. Here we comprehensively reconstruct the genome-wide GadEWX transcriptional regulatory network and RpoS involvement in E. coli K-12 MG1655 under acidic stress. Integrative data analysis reveals that GadEWX regulons consist of 45 genes in 31 transcription units and 28 of these genes were associated with RpoS-binding sites. We demonstrate that GadEWX directly and coherently regulate several proton-generating/consuming enzymes with pairs of negative-feedback loops for pH homeostasis. In addition, GadEWX regulate genes with assorted functions, including molecular chaperones, acid resistance, stress response and other regulatory activities. These results show how GadEWX simultaneously coordinate many cellular processes to produce the overall response of E. coli to acid stress. GadEWX regulons play a critical role in transcription regulation in response to acid stress. By reconstructing genome-wide GadEWX transcriptional network, here the authors show how GadEWX simultaneously coordinates many other cellular processes to produce the overall response of E. coli to acid stress.
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Affiliation(s)
- Sang Woo Seo
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - Donghyuk Kim
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - Edward J O'Brien
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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Yamamoto K, Watanabe H, Ishihama A. Expression levels of transcription factors in Escherichia coli: growth phase- and growth condition-dependent variation of 90 regulators from six families. Microbiology (Reading) 2014; 160:1903-1913. [DOI: 10.1099/mic.0.079889-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The expression pattern of the genome in Escherichia coli is controlled by regulating the utilization of a limited number of RNA polymerases between a total of 4600 genes on its genome. The distribution pattern of RNA polymerase on the genome changes after two steps of protein–protein interaction with seven sigma subunits and about 300 transcription factors (TFs). Based on a systematic search for the regulation target promoters recognized by each TF, we propose two novel concepts: each TF regulates a number of target promoters; and each promoter is regulated by many TFs. In parallel, attempts have been made to determine the intracellular concentrations of all TFs using two systems: quantitative immunoblot analysis using TF-specific antibodies; and reporter assay of TF promoter activities. The direct measurement of TF protein level has so far been published for a set of 60 regulators with known functions. This study describes the determination of growth phase-dependent expression levels of 90 TFs using the reporter assay system. The translational fusion vector was constructed from the TF promoter sequence including an N-terminal proximal TF segment and the reporter GFP. At the beginning of cell growth, high-level expression was observed only for a small number of TFs. In the exponential phase, approximately 80 % TFs are expressed, but the expressed TF species change upon transfer to the stationary phase. Significant changes in the pattern of TF expression were observed between aerobic and anaerobic conditions. The list of intracellular levels of TFs provides further understanding to the transcription regulation of the E. coli genome under various stressful conditions.
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Affiliation(s)
- Kaneyoshi Yamamoto
- Research Institute of Micro-Nano Technology, Hosei University, Koganei, Tokyo 185-8584, Japan
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 185-8584, Japan
| | - Hiroki Watanabe
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 185-8584, Japan
| | - Akira Ishihama
- Research Institute of Micro-Nano Technology, Hosei University, Koganei, Tokyo 185-8584, Japan
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 185-8584, Japan
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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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An H, Douillard FP, Wang G, Zhai Z, Yang J, Song S, Cui J, Ren F, Luo Y, Zhang B, Hao Y. Integrated transcriptomic and proteomic analysis of the bile stress response in a centenarian-originated probiotic Bifidobacterium longum BBMN68. Mol Cell Proteomics 2014; 13:2558-72. [PMID: 24965555 DOI: 10.1074/mcp.m114.039156] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bifidobacteria are natural inhabitants of the human gastrointestinal tract and well known for their health-promoting effects. Tolerance to bile stress is crucial for bifidobacteria to survive in the colon and to exert their beneficial actions. In this work, RNA-Seq transcriptomic analysis complemented with proteomic analysis was used to investigate the cellular response to bile in Bifidobacterium longum BBMN68. The transcript levels of 236 genes were significantly changed (≥ threefold, p < 0.001) and 44 proteins were differentially abundant (≥1.6-fold, p < 0.01) in B. longum BBMN68 when exposed to 0.75 g l(-1) ox-bile. The hemolysin-like protein and bile efflux systems were significantly over produced, which might prevent bile adsorption and exclude bile, respectively. The cell membrane composition was modified probably by an increase of cyclopropane fatty acid and a decrease of transmembrane proteins, resulting in a cell membrane more impermeable to bile salts. Our hypothesis was later confirmed by surface hydrophobicity assay. The transcription of genes related to xylose utilization and bifid shunt were up-regulated, which increased the production of ATP and reducing equivalents to cope with bile-induced damages in a xylan-rich colon environment. Bile salts signal the B. longum BBMN68 to gut entrance and enhance the expression of esterase and sortase associated with adhesion and colonization in intestinal tract, which was supported by a fivefold increased adhesion ability to HT-29 cells by BBMN68 upon bile exposure. Notably, bacterial one-hybrid and EMSA assay revealed that the two-component system senX3-regX3 controlled the expression of pstS in bifidobacteria and the role of this target gene in bile resistance was further verified by heterologous expression in Lactococcus lactis. Taken altogether, this study established a model for global response mechanisms in B. longum to bile.
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Affiliation(s)
- Haoran An
- From the ‡Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - François P Douillard
- §Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Guohong Wang
- From the ‡Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zhengyuan Zhai
- From the ‡Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jin Yang
- ¶Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuhui Song
- ¶Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianyun Cui
- From the ‡Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Fazheng Ren
- From the ‡Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- From the ‡Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Bing Zhang
- ¶Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanling Hao
- From the ‡Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China;
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Bi H, Zhang C. Integration Host Factor is Required for the Induction of Acid Resistance in Escherichia coli. Curr Microbiol 2014; 69:218-24. [DOI: 10.1007/s00284-014-0595-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 03/05/2014] [Indexed: 10/25/2022]
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Gaida SM, Al-Hinai MA, Indurthi DC, Nicolaou SA, Papoutsakis ET. Synthetic tolerance: three noncoding small RNAs, DsrA, ArcZ and RprA, acting supra-additively against acid stress. Nucleic Acids Res 2013; 41:8726-37. [PMID: 23892399 PMCID: PMC3794604 DOI: 10.1093/nar/gkt651] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 06/30/2013] [Accepted: 07/02/2013] [Indexed: 12/31/2022] Open
Abstract
Synthetic acid tolerance, especially during active cell growth, is a desirable phenotype for many biotechnological applications. Natively, acid resistance in Escherichia coli is largely a stationary-phase phenotype attributable to mechanisms mostly under the control of the stationary-phase sigma factor RpoS. We show that simultaneous overexpression of noncoding small RNAs (sRNAs), DsrA, RprA and ArcZ, which are translational RpoS activators, increased acid tolerance (based on a low-pH survival assay) supra-additively up to 8500-fold during active cell growth, and provided protection against carboxylic acid and oxidative stress. Overexpression of rpoS without its regulatory 5'-UTR resulted in inferior acid tolerance. The supra-additive effect of overexpressing the three sRNAs results from the impact their expression has on RpoS-protein levels, and the beneficial perturbation of the interconnected RpoS and H-NS networks, thus leading to superior tolerance during active growth. Unlike the overexpression of proteins, overexpression of sRNAs imposes hardly any metabolic burden on cells, and constitutes a more effective strain engineering strategy.
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Affiliation(s)
- Stefan M. Gaida
- Department Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA, Molecular Biotechnology Laboratory, Department of Chemical and Biomolecular Engineering, The Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA, Department of Biological Sciences, University of Delaware, Newark, DE 19711, USA and Department of Biology, Sultan Qaboos University, Muscat, 123, Oman
| | - Mohab A. Al-Hinai
- Department Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA, Molecular Biotechnology Laboratory, Department of Chemical and Biomolecular Engineering, The Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA, Department of Biological Sciences, University of Delaware, Newark, DE 19711, USA and Department of Biology, Sultan Qaboos University, Muscat, 123, Oman
| | - Dinesh C. Indurthi
- Department Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA, Molecular Biotechnology Laboratory, Department of Chemical and Biomolecular Engineering, The Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA, Department of Biological Sciences, University of Delaware, Newark, DE 19711, USA and Department of Biology, Sultan Qaboos University, Muscat, 123, Oman
| | - Sergios A. Nicolaou
- Department Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA, Molecular Biotechnology Laboratory, Department of Chemical and Biomolecular Engineering, The Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA, Department of Biological Sciences, University of Delaware, Newark, DE 19711, USA and Department of Biology, Sultan Qaboos University, Muscat, 123, Oman
| | - Eleftherios T. Papoutsakis
- Department Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA, Molecular Biotechnology Laboratory, Department of Chemical and Biomolecular Engineering, The Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA, Department of Biological Sciences, University of Delaware, Newark, DE 19711, USA and Department of Biology, Sultan Qaboos University, Muscat, 123, Oman
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Wiles TJ, Norton JP, Russell CW, Dalley BK, Fischer KF, Mulvey MA. Combining quantitative genetic footprinting and trait enrichment analysis to identify fitness determinants of a bacterial pathogen. PLoS Genet 2013; 9:e1003716. [PMID: 23990803 PMCID: PMC3749937 DOI: 10.1371/journal.pgen.1003716] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 06/26/2013] [Indexed: 01/03/2023] Open
Abstract
Strains of Extraintestinal Pathogenic Escherichia c oli (ExPEC) exhibit an array of virulence strategies and are a major cause of urinary tract infections, sepsis and meningitis. Efforts to understand ExPEC pathogenesis are challenged by the high degree of genetic and phenotypic variation that exists among isolates. Determining which virulence traits are widespread and which are strain-specific will greatly benefit the design of more effective therapies. Towards this goal, we utilized a quantitative genetic footprinting technique known as transposon insertion sequencing (Tn-seq) in conjunction with comparative pathogenomics to functionally dissect the genetic repertoire of a reference ExPEC isolate. Using Tn-seq and high-throughput zebrafish infection models, we tracked changes in the abundance of ExPEC variants within saturated transposon mutant libraries following selection within distinct host niches. Nine hundred and seventy bacterial genes (18% of the genome) were found to promote pathogen fitness in either a niche-dependent or independent manner. To identify genes with the highest therapeutic and diagnostic potential, a novel Trait Enrichment Analysis (TEA) algorithm was developed to ascertain the phylogenetic distribution of candidate genes. TEA revealed that a significant portion of the 970 genes identified by Tn-seq have homologues more often contained within the genomes of ExPEC and other known pathogens, which, as suggested by the first axiom of molecular Koch's postulates, is considered to be a key feature of true virulence determinants. Three of these Tn-seq-derived pathogen-associated genes--a transcriptional repressor, a putative metalloendopeptidase toxin and a hypothetical DNA binding protein--were deleted and shown to independently affect ExPEC fitness in zebrafish and mouse models of infection. Together, the approaches and observations reported herein provide a resource for future pathogenomics-based research and highlight the diversity of factors required by a single ExPEC isolate to survive within varying host environments.
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Affiliation(s)
- Travis J. Wiles
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - J. Paul Norton
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Colin W. Russell
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Brian K. Dalley
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Kael F. Fischer
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- ARUP Laboratories, Salt Lake City, Utah, United States of America
| | - Matthew A. Mulvey
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- * E-mail:
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Al Mamun AAM, Lombardo MJ, Shee C, Lisewski AM, Gonzalez C, Lin D, Nehring RB, Saint-Ruf C, Gibson JL, Frisch RL, Lichtarge O, Hastings PJ, Rosenberg SM. Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 2012; 338:1344-8. [PMID: 23224554 PMCID: PMC3782309 DOI: 10.1126/science.1226683] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mechanisms of DNA repair and mutagenesis are defined on the basis of relatively few proteins acting on DNA, yet the identities and functions of all proteins required are unknown. Here, we identify the network that underlies mutagenic repair of DNA breaks in stressed Escherichia coli and define functions for much of it. Using a comprehensive screen, we identified a network of ≥93 genes that function in mutation. Most operate upstream of activation of three required stress responses (RpoS, RpoE, and SOS, key network hubs), apparently sensing stress. The results reveal how a network integrates mutagenic repair into the biology of the cell, show specific pathways of environmental sensing, demonstrate the centrality of stress responses, and imply that these responses are attractive as potential drug targets for blocking the evolution of pathogens.
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Affiliation(s)
- Abu Amar M. Al Mamun
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Mary-Jane Lombardo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Chandan Shee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Andreas M. Lisewski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Caleb Gonzalez
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Dongxu Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Ralf B. Nehring
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Claude Saint-Ruf
- U1001 INSERM, Université Paris, Descartes, Sorbonne Paris cité, site Necker, 156 rue de Vaugirard, 75730 Paris Cedex 15, France
| | - Janet L. Gibson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Ryan L. Frisch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - P. J. Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Susan M. Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
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RcsB contributes to the distinct stress fitness among Escherichia coli O157:H7 curli variants of the 1993 hamburger-associated outbreak strains. Appl Environ Microbiol 2012; 78:7706-19. [PMID: 22923406 DOI: 10.1128/aem.02157-12] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Curli are adhesive fimbriae of Enterobactericaeae and are involved in surface attachment, cell aggregation, and biofilm formation. We reported previously that curli-producing (C(+)) variants of E. coli O157:H7 (EcO157) were much more acid sensitive than their corresponding curli-deficient (C(-)) variants; however, this difference was not linked to the curli fimbriae per se. Here, we investigated the underlying molecular basis of this phenotypic divergence. We identified large deletions in the rcsB gene of C(+) variants isolated from the 1993 U.S. hamburger-associated outbreak strains. rcsB encodes the response regulator of the RcsCDB two-component signal transduction system, which regulates curli biogenesis negatively but acid resistance positively. Further comparison of stress fitness revealed that C(+) variants were also significantly more sensitive to heat shock but were resistant to osmotic stress and oxidative damage, similar to C(-) variants. Transcriptomics analysis uncovered a large number of differentially expressed genes between the curli variants, characterized by enhanced expression in C(+) variants of genes related to biofilm formation, virulence, catabolic activity, and nutrient uptake but marked decreases in transcription of genes related to various types of stress resistance. Supplying C(+) variants with a functional rcsB restored resistance to heat shock and acid challenge in cells but blocked curli production, confirming that inactivation of RcsB in C(+) variants was the basis of fitness segregation within the EcO157 population. This study provides an example of how genome instability of EcO157 promotes intrapopulation diversification, generating subpopulations carrying an array of distinct phenotypes that may confer the pathogen with survival advantages in diverse environments.
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Uchiyama J, Asakura R, Kimura M, Moriyama A, Tahara H, Kobayashi Y, Kubo Y, Yoshihara T, Ohta H. Slr0967 and Sll0939 induced by the SphR response regulator in Synechocystis sp. PCC 6803 are essential for growth under acid stress conditions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1270-6. [PMID: 22497796 DOI: 10.1016/j.bbabio.2012.03.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 03/24/2012] [Accepted: 03/24/2012] [Indexed: 11/24/2022]
Abstract
Two-component signal transduction is the primary signaling mechanism for global regulation of the cellular response to environmental changes. We used DNA microarray analysis to identify genes that were upregulated by acid stress in the cyanobacterium Synechocystis sp. PCC 6803. Several of these genes may be response regulators that are directly involved in this type of stress response. We constructed deletion mutants for the response regulator genes and compared the growth rates of cells transfected with mutant and wild-type genes in a low pH medium. Of these mutants, deletion of sphR affected the growth rate under acid stress (pH 6.0) conditions. We examined genome-wide expression in ΔsphR mutant cells using DNA microarray to determine whether SphR was involved in the regulation of other acid stress responsive genes. Microarray and real-time quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analyses of wild-type cells showed that the expression of phoA, pstS1, and pstS2, which are upregulated under phosphate-limiting conditions, increased (2.48-, 1.88-, and 5.07-fold, respectively) after acid stress treatment for 0.5h. In contrast, pstS2 expression did not increase in the ΔsphR mutant cells after acid stress, whereas the phoA and sphX mRNA levels increased. Furthermore, qRT-PCR and northern blot analysis indicated that downregulation of the acid-responsive genes slr0967 and sll0939 occurred with the deletion of sphR. Indeed, mutants of these genes were more sensitive to acid stress than the wild-type cells. Thus, induction of Slr0967 and Sll0939 by SphR may be essential for growth under acid stress conditions. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.
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Mika F, Busse S, Possling A, Berkholz J, Tschowri N, Sommerfeldt N, Pruteanu M, Hengge R. Targeting of csgD by the small regulatory RNA RprA links stationary phase, biofilm formation and cell envelope stress in Escherichia coli. Mol Microbiol 2012; 84:51-65. [PMID: 22356413 PMCID: PMC3465796 DOI: 10.1111/j.1365-2958.2012.08002.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RprA is a small regulatory RNA known to weakly affect the translation of σS (RpoS) in Escherichia coli. Here we demonstrate that csgD, which encodes a stationary phase-induced biofilm regulator, as well as ydaM, which encodes a diguanylate cyclase involved in activating csgD transcription, are novel negatively controlled RprA targets. As shown by extensive mutational analysis, direct binding of RprA to the 5′-untranslated and translational initiation regions of csgD mRNA inhibits translation and reduces csgD mRNA levels. In the case of ydaM mRNA, RprA base-pairs directly downstream of the translational start codon. In a feedforward loop, RprA can thus downregulate > 30 YdaM/CsgD-activated genes including those for adhesive curli fimbriae. However, during early stationary phase, when csgD transcription is strongly activated, the synthesis of csgD mRNA exceeds that of RprA, which allows the accumulation of CsgD protein. This situation is reversed when csgD transcription is shut off – for instance, later in stationary phase or during biofilm formation – or by conditions that further activate RprA expression via the Rcs two-component system. Thus, antagonistic regulation of csgD and RprA at the mRNA level integrates cell envelope stress signals with global gene expression during stationary phase and biofilm formation.
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Affiliation(s)
- Franziska Mika
- Institut für Biologie - Mikrobiologie, Freie Universität Berlin, 14195 Berlin, Germany
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Hancock T, Wicker N, Takigawa I, Mamitsuka H. Identifying neighborhoods of coordinated gene expression and metabolite profiles. PLoS One 2012; 7:e31345. [PMID: 22355360 PMCID: PMC3280297 DOI: 10.1371/journal.pone.0031345] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 01/06/2012] [Indexed: 11/19/2022] Open
Abstract
In this paper we investigate how metabolic network structure affects any coordination between transcript and metabolite profiles. To achieve this goal we conduct two complementary analyses focused on the metabolic response to stress. First, we investigate the general size of any relationship between metabolic network gene expression and metabolite profiles. We find that strongly correlated transcript-metabolite profiles are sustained over surprisingly long network distances away from any target metabolite. Secondly, we employ a novel pathway mining method to investigate the structure of this transcript-metabolite relationship. The objective of this method is to identify a minimum set of metabolites which are the target of significantly correlated gene expression pathways. The results reveal that in general, a global regulation signature targeting a small number of metabolites is responsible for a large scale metabolic response. However, our method also reveals pathway specific effects that can degrade this global regulation signature and complicates the observed coordination between transcript-metabolite profiles.
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Nguyen TM, Sparks-Thissen RL. The inner membrane protein, YhiM, is necessary for Escherichia coli (E. coli) survival in acidic conditions. Arch Microbiol 2012; 194:637-41. [DOI: 10.1007/s00203-012-0798-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 01/18/2012] [Accepted: 01/27/2012] [Indexed: 10/14/2022]
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Abstract
In their stressful natural environments, bacteria often are in stationary phase and use their limited resources for maintenance and stress survival. Underlying this activity is the general stress response, which in Escherichia coli depends on the σS (RpoS) subunit of RNA polymerase. σS is closely related to the vegetative sigma factor σ70 (RpoD), and these two sigmas recognize similar but not identical promoter sequences. During the postexponential phase and entry into stationary phase, σS is induced by a fine-tuned combination of transcriptional, translational, and proteolytic control. In addition, regulatory "short-cuts" to high cellular σS levels, which mainly rely on the rapid inhibition of σS proteolysis, are triggered by sudden starvation for various nutrients and other stressful shift conditons. σS directly or indirectly activates more than 500 genes. Additional signal input is integrated by σS cooperating with various transcription factors in complex cascades and feedforward loops. Target gene products have stress-protective functions, redirect metabolism, affect cell envelope and cell shape, are involved in biofilm formation or pathogenesis, or can increased stationary phase and stress-induced mutagenesis. This review summarizes these diverse functions and the amazingly complex regulation of σS. At the molecular level, these processes are integrated with the partitioning of global transcription space by sigma factor competition for RNA polymerase core enzyme and signaling by nucleotide second messengers that include cAMP, (p)ppGpp, and c-di-GMP. Physiologically, σS is the key player in choosing between a lifestyle associated with postexponential growth based on nutrient scavenging and motility and a lifestyle focused on maintenance, strong stress resistance, and increased adhesiveness. Finally, research with other proteobacteria is beginning to reveal how evolution has further adapted function and regulation of σS to specific environmental niches.
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Wang D, Calla B, Vimolmangkang S, Wu X, Korban SS, Huber SC, Clough SJ, Zhao Y. The orphan gene ybjN conveys pleiotropic effects on multicellular behavior and survival of Escherichia coli. PLoS One 2011; 6:e25293. [PMID: 21980417 PMCID: PMC3181261 DOI: 10.1371/journal.pone.0025293] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 08/31/2011] [Indexed: 11/19/2022] Open
Abstract
YbjN, encoding an enterobacteria-specific protein, is a multicopy suppressor of temperature sensitivity in the ts9 mutant strain of Escherichia coli. In this study, we further explored the role(s) of ybjN. First, we demonstrated that the ybjN transcript was about 10-fold lower in the ts9 strain compared to that of E. coli strain BW25113 (BW). Introduction of multiple copies of ybjN in the ts9 strain resulted in over-expression of ybjN by about 10-fold as compared to that of BW. These results suggested that temperature sensitivity of the ts9 mutant of E. coli may be related to expression levels of ybjN. Characterization of E. coli ybjN mutant revealed that ybjN mutation resulted in pleiotropic phenotypes, including increased motility, fimbriation (auto-aggregation), exopolysaccharide production, and biofilm formation. In contrast, over-expression of ybjN (in terms of multiple copies) resulted in reduced motility, fimbriation, exopolysaccharide production, biofilm formation and acid resistance. In addition, our results indicate that a ybjN-homolog gene from Erwinia amylovora, a plant enterobacterial pathogen, is functionally conserved with that of E. coli, suggesting similar evolution of the YbjN family proteins in enterobacteria. A microarray study revealed that the expression level of ybjN was inversely correlated with the expression of flagellar, fimbrial and acid resistance genes. Over-expression of ybjN significantly down-regulated genes involved in citric acid cycle, glycolysis, the glyoxylate shunt, oxidative phosphorylation, amino acid and nucleotide metabolism. Furthermore, over-expression of ybjN up-regulated toxin-antitoxin modules, the SOS response pathway, cold shock and starvation induced transporter genes. Collectively, these results suggest that YbjN may play important roles in regulating bacterial multicellular behavior, metabolism, and survival under stress conditions in E. coli. These results also suggest that ybjN over-expression-related temperature rescue of the ts9 mutant may be due to down-regulation of metabolic activity and activation of stress response genes in the ts9 mutant.
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Affiliation(s)
- Dongping Wang
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Bernarda Calla
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Sornkanok Vimolmangkang
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Xia Wu
- Program in Physiological and Molecular Plant Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Schuyler S. Korban
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Steven C. Huber
- Program in Physiological and Molecular Plant Biology, University of Illinois, Urbana, Illinois, United States of America
- Agricultural Research Service, United States Department of Agriculture (USDA), Urbana, Illinois, United States of America
| | - Steven J. Clough
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
- Agricultural Research Service, United States Department of Agriculture (USDA), Urbana, Illinois, United States of America
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
- Program in Physiological and Molecular Plant Biology, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
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