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Qiu J, Gasperotti A, Sisattana N, Zacharias M, Jung K. The LytS-type histidine kinase BtsS is a 7-transmembrane receptor that binds pyruvate. mBio 2023; 14:e0108923. [PMID: 37655896 PMCID: PMC10653868 DOI: 10.1128/mbio.01089-23] [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: 05/02/2023] [Accepted: 07/17/2023] [Indexed: 09/02/2023] Open
Abstract
IMPORTANCE Here, we studied the LytS-type histidine kinase BtsS of E. coli and identified the pyruvate binding site within the membrane-spanning domains. It is a small cavity, and pyruvate forms interactions with the side chains of Arg72, Arg99, Cys110, and Ser113 located in transmembrane helices III, IV, and V, respectively. Our results can serve as a starting point to convert BtsS into a sensor for structurally similar ligands such as lactate, which can be used as biosensor in medicine.
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Affiliation(s)
- Jin Qiu
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Ana Gasperotti
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Nathalie Sisattana
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Martin Zacharias
- Center of Functional Protein Assemblies, Technical University of Munich, Garching, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
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2
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Serine Deamination Is a New Acid Tolerance Mechanism Observed in Uropathogenic Escherichia coli. mBio 2022; 13:e0296322. [PMID: 36468870 PMCID: PMC9765748 DOI: 10.1128/mbio.02963-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
Escherichia coli associates with humans early in life and can occupy several body niches either as a commensal in the gut and vagina, or as a pathogen in the urinary tract. As such, E. coli has an arsenal of acid response mechanisms that allow it to withstand the different levels of acid stress encountered within and outside the host. Here, we report the discovery of an additional acid response mechanism that involves the deamination of l-serine to pyruvate by the conserved l-serine deaminases SdaA and SdaB. l-serine is the first amino acid to be imported in E. coli during growth in laboratory media. However, there remains a lack in knowledge as to how l-serine is utilized. Using a uropathogenic strain of E. coli, UTI89, we show that in acidified media, l-serine is brought into the cell via the SdaC transporter. We further demonstrate that deletion of the l-serine deaminases SdaA and SdaB renders E. coli susceptible to acid stress, similar to other acid stress deletion mutants. The pyruvate produced by l-serine deamination activates the pyruvate sensor BtsS, which in concert with the noncognate response regulator YpdB upregulates the putative transporter YhjX. Based on these observations, we propose that l-serine deamination constitutes another acid response mechanism in E. coli. IMPORTANCE The observation that l-serine uptake occurs as E. coli cultures grow is well established, yet the benefit E. coli garners from this uptake remains unclear. Here, we report a novel acid tolerance mechanism where l-serine is deaminated to pyruvate and ammonia, promoting survival of E. coli under acidic conditions. This study is important as it provides evidence of the use of l-serine as an acid response strategy, not previously reported for E. coli.
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Paulini S, Fabiani FD, Weiss AS, Moldoveanu AL, Helaine S, Stecher B, Jung K. The Biological Significance of Pyruvate Sensing and Uptake in Salmonella enterica Serovar Typhimurium. Microorganisms 2022; 10:microorganisms10091751. [PMID: 36144354 PMCID: PMC9504724 DOI: 10.3390/microorganisms10091751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Pyruvate (CH3COCOOH) is the simplest of the alpha-keto acids and is at the interface of several metabolic pathways both in prokaryotes and eukaryotes. In an amino acid-rich environment, fast-growing bacteria excrete pyruvate instead of completely metabolizing it. The role of pyruvate uptake in pathological conditions is still unclear. In this study, we identified two pyruvate-specific transporters, BtsT and CstA, in Salmonella enterica serovar Typhimurium (S. Typhimurium). Expression of btsT is induced by the histidine kinase/response regulator system BtsS/BtsR upon sensing extracellular pyruvate, whereas expression of cstA is maximal in the stationary phase. Both pyruvate transporters were found to be important for the uptake of this compound, but also for chemotaxis to pyruvate, survival under oxidative and nitrosative stress, and persistence of S. Typhimurium in response to gentamicin. Compared with the wild-type cells, the ΔbtsTΔcstA mutant has disadvantages in antibiotic persistence in macrophages, as well as in colonization and systemic infection in gnotobiotic mice. These data demonstrate the surprising complexity of the two pyruvate uptake systems in S. Typhimurium.
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Affiliation(s)
- Stephanie Paulini
- Department of Microbiology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Florian D. Fabiani
- Department of Microbiology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Anna S. Weiss
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, Ludwig-Maximilians-University Munich, 80336 Munich, Germany
| | - Ana Laura Moldoveanu
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2DD, UK
| | - Sophie Helaine
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2DD, UK
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, Ludwig-Maximilians-University Munich, 80336 Munich, Germany
- German Center for Infection Research (DZIF), Partner Site LMU Munich, 80337 Munich, Germany
| | - Kirsten Jung
- Department of Microbiology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
- Correspondence: ; Tel.: +49-(0)89/2180-74500
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First insights into a pyruvate sensing and uptake system in Vibrio campbellii and its importance for virulence. J Bacteriol 2021; 203:e0029621. [PMID: 34339295 DOI: 10.1128/jb.00296-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyruvate is a key metabolite in living cells and has been shown to play a crucial role in the virulence of several bacterial pathogens. The bioluminescent Vibrio campbellii, a severe infectious burden for marine aquaculture, excretes extraordinarily large amounts of pyruvate during growth and rapidly retrieves it by an as-yet unknown mechanism. We have now identified the responsible pyruvate transporter, here named BtsU, and our results show that it is the only pyruvate transporter in V. campbellii. Expression of btsU is tightly regulated by the membrane-integrated LytS-type histidine kinase BtsS, a sensor for extracellular pyruvate, and the LytTR-type response regulator BtsR. Cells lacking either the pyruvate transporter or sensing system show no chemotactic response towards pyruvate, indicating that intracellular pyruvate is required to activate the chemotaxis system. Moreover, pyruvate sensing and uptake were found to be important for the resuscitation of V. campbellii from the viable but nonculturable (VBNC) state and the bacterium's virulence against brine shrimp larvae. IMPORTANCE Bacterial infections are a serious threat to marine aquaculture, one of the fastest growing food sectors on earth. Therefore, it is extremely important to learn more about the pathogens responsible, one of which is Vibrio campbellii. This study sheds light on the importance of pyruvate sensing and uptake for V. campbellii, and reveals that the bacterium possesses only one pyruvate transporter, which is activated by a pyruvate-responsive histidine kinase/response regulator system. Without the ability to sense or take up pyruvate, the virulence of V. campbellii towards gnotobiotic brine shrimp larvae is strongly reduced.
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Virus-Host Interaction Gets Curiouser and Curiouser. PART II: Functional Transcriptomics of the E. coli DksA-Deficient Cell upon Phage P1 vir Infection. Int J Mol Sci 2021; 22:ijms22116159. [PMID: 34200430 PMCID: PMC8201110 DOI: 10.3390/ijms22116159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
The virus–host interaction requires a complex interplay between the phage strategy of reprogramming the host machinery to produce and release progeny virions, and the host defense against infection. Using RNA sequencing, we investigated the phage–host interaction to resolve the phenomenon of improved lytic development of P1vir phage in a DksA-deficient E. coli host. Expression of the ant1 and kilA P1vir genes in the wild-type host was the highest among all and most probably leads to phage virulence. Interestingly, in a DksA-deficient host, P1vir genes encoding lysozyme and holin are downregulated, while antiholins are upregulated. Gene expression of RepA, a protein necessary for replication initiating at the phage oriR region, is increased in the dksA mutant; this is also true for phage genes responsible for viral morphogenesis and architecture. Still, it seems that P1vir is taking control of the bacterial protein, sugar, and lipid metabolism in both, the wild type and dksA− hosts. Generally, bacterial hosts are reacting by activating their SOS response or upregulating the heat shock proteins. However, only DksA-deficient cells upregulate their sulfur metabolism and downregulate proteolysis upon P1vir infection. We conclude that P1vir development is enhanced in the dksA mutant due to several improvements, including replication and virion assembly, as well as a less efficient lysis.
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Gasperotti A, Göing S, Fajardo-Ruiz E, Forné I, Jung K. Function and Regulation of the Pyruvate Transporter CstA in Escherichia coli. Int J Mol Sci 2020; 21:ijms21239068. [PMID: 33260635 PMCID: PMC7730263 DOI: 10.3390/ijms21239068] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/02/2022] Open
Abstract
Pyruvate is a central metabolite that connects many metabolic pathways in living organisms. To meet the cellular pyruvate requirements, the enterobacterium Escherichia coli has at least three pyruvate uptake systems—the H+/pyruvate symporter BtsT, and two thus far less well-characterized transporters, YhjX and CstA. BtsT and CstA belong to the putative carbon starvation (CstA) family (transporter classification TC# 2.A.114). We have created an E. coli mutant that cannot grow on pyruvate as the sole carbon source and used it to characterize CstA as a pyruvate transporter. Transport studies in intact cells confirmed that CstA is a highly specific pyruvate transporter with moderate affinity and is energized by a proton gradient. When cells of a reporter strain were cultured in complex medium, cstA expression was maximal only in stationary phase. A DNA affinity-capture assay combined with mass spectrometry and an in-vivo reporter assay identified Fis as a repressor of cstA expression, in addition to the known activator cAMP-CRP. The functional characterization and regulation of this second pyruvate uptake system provides valuable information for understanding the complexity of pyruvate sensing and uptake in E. coli.
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Affiliation(s)
- Ana Gasperotti
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany; (A.G.); (S.G.); (E.F.-R.)
| | - Stephanie Göing
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany; (A.G.); (S.G.); (E.F.-R.)
| | - Elena Fajardo-Ruiz
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany; (A.G.); (S.G.); (E.F.-R.)
| | - Ignasi Forné
- Protein Analysis Unit, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany;
| | - Kirsten Jung
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany; (A.G.); (S.G.); (E.F.-R.)
- Correspondence:
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He H, Peng S, Yuan S, Tang J, Liu Z, Rang J, Xia Z, Hu J, Chen J, Ding X, Hu S, Sun Y, Xia L. Effects of lytS-L on the primary metabolism and butenyl-spinosyn biosynthesis in Saccharopolyspora pogona. Gene 2020; 766:145130. [PMID: 32911030 DOI: 10.1016/j.gene.2020.145130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 07/31/2020] [Accepted: 09/01/2020] [Indexed: 12/11/2022]
Abstract
The LytTR family two-component system widely exists in bacterial cells and plays an important role in metabolic regulation. The lytS-L gene that encodes for a LytTR family sensor kinase was knocked out to study its influence on the growth, phenotype, and the biosynthesis of the insecticidal polyketide butenyl-spinosyn in Saccharopolyspora pogona NRRL 30141 (S. pogona). High performance liquid chromatography (HPLC) results showed that the butenyl-spinosyn yield of the lytS-L knockout mutant decreased by 58.9% compared with that of the parental strain. This is manifested by a weak toxicity of the mutant against the insect Helicoverpa assulta (H. armigera). Comparative proteomic analysis revealed the expression characteristics of the proteins in S. pogona and S. pogona-ΔlytS-L: a total of 14 proteins involved in energy metabolism were down-regulated, 9 proteins related to carbon metabolism such as glycolysis, and tricarboxylic acid cycle (TCA) were up-regulated, while 13 proteins involved in the biosynthesis of butenyl-spinosyn were down-regulated (fold change >1.2 or< 0.83). The qRT-PCR (Quantitative Real-time PCR) analysis illustrated that the changes in the expression levels of transcription and translation of the identified genes were consistent. This study explores the function of the two-component system of the LytTR family in S. pogona and shows that the lytS-L gene has an important influence on regulating primary metabolism and butenyl-spinosyn biosynthesis of S. pogona.
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Affiliation(s)
- Haocheng He
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Shengnan Peng
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Shuangqin Yuan
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jianli Tang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Zhudong Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jie Rang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Ziyuan Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jinjuan Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jianming Chen
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Shengbiao Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Yunjun Sun
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China.
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China.
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8
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Ogasawara H, Ishizuka T, Yamaji K, Kato Y, Shimada T, Ishihama A. Regulatory role of pyruvate-sensing BtsSR in biofilm formation by Escherichia coli K-12. FEMS Microbiol Lett 2019; 366:5675631. [PMID: 31834370 DOI: 10.1093/femsle/fnz251] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/12/2019] [Indexed: 12/29/2022] Open
Abstract
Pyruvate, the key regulator in connection of a variety of metabolic pathways, influences transcription of the Escherichia coli genome through controlling the activity of two pyruvate-sensing two-component systems (TCSs), BtsSR and PyrSR. Previously, we identified the whole set of regulatory targets of PyrSR with low-affinity to pyruvate. Using gSELEX screening system, we found here that BtsSR with high-affinity to pyruvate regulates more than 100 genes including as many as 13 transcription factors genes including the csgD gene encoding the master regulator of biofilm formation. CsgD regulates more than 20 target genes including the csg operons encoding the Curli fimbriae. In addition, we identified the csgBAC as one of the regulatory targets of BtsR, thus indicating the involvement of two pyruvate-dependent regulatory pathways of the curli formation: indirect regulation by CsgD; and direct regulation by BtsR. Based on the findings of the whole set of regulatory targets by two pyruvate-sensing BtsR and PyrR, we further propose an innovative concept that the pyruvate level-dependent regulation of different gene sets takes place through two pyruvate-sensing TCS systems, high-affinity BtsSR and low-affinity PyrSR to pyruvate.
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Affiliation(s)
- Hiroshi Ogasawara
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Tokida 3-15-1, Ueda, Nagano 386-8567, Japan.,Research Center for Fungal and Microbial Dynamism, Shinshu University, Minamiminowa 8304, Kamiina, Nagano 399-4598, Japan.,Academic Assembly School of Humanities and Social Sciences Institute of Humanities, Shinshu University, Asahi 3-1-1, Matsumoto, 390-8621, Japan
| | - Toshiyuki Ishizuka
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Tokida 3-15-1, Ueda, Nagano 386-8567, Japan
| | - Kotaro Yamaji
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Tokida 3-15-1, Ueda, Nagano 386-8567, Japan
| | - Yuki Kato
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Tokida 3-15-1, Ueda, Nagano 386-8567, Japan
| | - Tomohiro Shimada
- School of Agriculture, Meiji University, 1-1-1 Higashi Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan
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Gasperotti A, Brameyer S, Fabiani F, Jung K. Phenotypic heterogeneity of microbial populations under nutrient limitation. Curr Opin Biotechnol 2019; 62:160-167. [PMID: 31698311 DOI: 10.1016/j.copbio.2019.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/16/2022]
Abstract
Phenotypic heterogeneity is a phenomenon in which genetically identical individuals have different characteristics. This behavior can also be found in bacteria, even if they grow as monospecies in well-mixed environments such as bioreactors. Here it is discussed how phenotypic heterogeneity is generated by internal factors and how it is promoted under nutrient-limited growth conditions. A better understanding of the molecular levels that control phenotypic heterogeneity could improve biotechnological production processes.
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Affiliation(s)
- Ana Gasperotti
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Florian Fabiani
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Kirsten Jung
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany.
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Jung K, Brameyer S, Fabiani F, Gasperotti A, Hoyer E. Phenotypic Heterogeneity Generated by Histidine Kinase-Based Signaling Networks. J Mol Biol 2019; 431:4547-4558. [DOI: 10.1016/j.jmb.2019.03.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/26/2019] [Accepted: 03/29/2019] [Indexed: 01/16/2023]
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Jung K, Fabiani F, Hoyer E, Lassak J. Bacterial transmembrane signalling systems and their engineering for biosensing. Open Biol 2019; 8:rsob.180023. [PMID: 29695618 PMCID: PMC5936718 DOI: 10.1098/rsob.180023] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/03/2018] [Indexed: 12/27/2022] Open
Abstract
Every living cell possesses numerous transmembrane signalling systems that receive chemical and physical stimuli from the environment and transduce this information into an intracellular signal that triggers some form of cellular response. As unicellular organisms, bacteria require these systems for survival in rapidly changing environments. The receptors themselves act as ‘sensory organs’, while subsequent signalling circuits can be regarded as forming a ‘neural network’ that is involved in decision making, adaptation and ultimately in ensuring survival. Bacteria serve as useful biosensors in industry and clinical diagnostics, in addition to producing drugs for therapeutic purposes. Therefore, there is a great demand for engineered bacterial strains that contain transmembrane signalling systems with high molecular specificity, sensitivity and dose dependency. In this review, we address the complexity of transmembrane signalling systems and discuss principles to rewire receptors and their signalling outputs.
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Affiliation(s)
- Kirsten Jung
- Munich Center for Integrated Protein Science (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Florian Fabiani
- Munich Center for Integrated Protein Science (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Elisabeth Hoyer
- Munich Center for Integrated Protein Science (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Jürgen Lassak
- Munich Center for Integrated Protein Science (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
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Importance of Pyruvate Sensing and Transport for the Resuscitation of Viable but Nonculturable Escherichia coli K-12. J Bacteriol 2019; 201:JB.00610-18. [PMID: 30420452 DOI: 10.1128/jb.00610-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 10/29/2018] [Indexed: 12/21/2022] Open
Abstract
Escherichia coli and many other bacterial species can enter into a viable but nonculturable (VBNC) state, which is a survival strategy adopted by cells exposed to adverse environmental conditions. Pyruvate is known to be one factor that promotes resuscitation of VBNC cells. Here we studied the role of a pyruvate-sensing network, composed of the histidine kinase-response regulator systems BtsS/BtsR and YpdA/YpdB and the target gene btsT, encoding the high-affinity pyruvate/H+ symporter BtsT, in the resuscitation of VBNC E. coli K-12 cells after exposure to cold for 120 days. Analysis of the proteome of VBNC cells revealed upregulation, relative to exponentially growing cells, of BtsT and other proteins involved in pyruvate metabolism. Provision of pyruvate stimulated protein and DNA biosynthesis, and thus resuscitation, in wild-type but not btsSR ypdAB mutant VBNC cells. This result was corroborated by time-dependent tracking of the resuscitation of individual VBNC E. coli cells observed in a microfluidic system. Finally, transport assays revealed that 14C-labeled pyruvate was rapidly taken up into VBNC cells by BtsT. These results provide the first evidence that pyruvate is taken up as a carbon source for the resuscitation of VBNC E. coli cells.IMPORTANCE Viable but nonculturable (VBNC) bacteria do not form colonies in standard medium but otherwise retain their metabolic activity and can express toxic proteins. Many bacterial genera, including Escherichia, Vibrio, and Listeria, have been shown to enter the VBNC state upon exposure to adverse conditions, such as low temperature, radiation, and starvation. Ultimately, these organisms pose a public health risk with potential implications for the pharmaceutical and food industries, as dormant organisms are especially difficult to selectively eliminate and VBNC bacteria can be resuscitated if placed in an environment with appropriate nutrition and temperature. Here we used a microfluidic system to monitor the resuscitation of single VBNC cells over time. We provide new molecular insights into the initiation of resuscitation by demonstrating that VBNC E. coli cells rapidly take up pyruvate with an inducible high-affinity transporter, whose expression is triggered by the BtsSR-YpdAB sensing network.
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Miyake Y, Inaba T, Watanabe H, Teramoto J, Yamamoto K, Ishihama A. Regulatory roles of pyruvate-sensing two-component system PyrSR (YpdAB) inEscherichia coliK-12. FEMS Microbiol Lett 2019; 366:5281236. [DOI: 10.1093/femsle/fnz009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/08/2019] [Indexed: 01/14/2023] Open
Affiliation(s)
- Yukari Miyake
- Department of Frontier Bioscience, Hosei University, Kajino-cho 3-7-2, Koganei 184-8584, Tokyo, Japan
| | - Tatsuya Inaba
- Department of Frontier Bioscience, Hosei University, Kajino-cho 3-7-2, Koganei 184-8584, Tokyo, Japan
| | - Hiroki Watanabe
- Department of Frontier Bioscience, Hosei University, Kajino-cho 3-7-2, Koganei 184-8584, Tokyo, Japan
| | - Jun Teramoto
- Department of Frontier Bioscience, Hosei University, Kajino-cho 3-7-2, Koganei 184-8584, Tokyo, Japan
| | - Kaneyoshi Yamamoto
- Department of Frontier Bioscience, Hosei University, Kajino-cho 3-7-2, Koganei 184-8584, Tokyo, Japan
- Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Kogagnei 184-0003, Tokyo, Japan
| | - Akira Ishihama
- Department of Frontier Bioscience, Hosei University, Kajino-cho 3-7-2, Koganei 184-8584, Tokyo, Japan
- Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Kogagnei 184-0003, Tokyo, Japan
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Rosenberg T, Salam BB, Burdman S. Association Between Loss of Type IV Pilus Synthesis Ability and Phenotypic Variation in the Cucurbit Pathogenic Bacterium Acidovorax citrulli. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:548-559. [PMID: 29298127 DOI: 10.1094/mpmi-12-17-0324-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Acidovorax citrulli is the causal agent of bacterial fruit blotch of cucurbits. We have shown that functional type IV pili (T4P) are required for full virulence of this bacterium. To identify A. citrulli genes required for T4P activity, we screened a library of about 10,000 transposon mutants of A. citrulli M6 for altered T4P-mediated twitching motility. This screen led to the identification of 50 mutants impaired in twitching ability due to transposon insertions into 20 different genes. Representative mutants with disruptions in these genes were further characterized. All mutants were compromised in their virulence in seed transmission and stem inoculation assays and had reduced biofilm formation ability relative to wild-type M6. When grown on nutrient agar, most mutants produced colonies with a translucent and fuzzy appearance, in contrast to the opaque and smooth appearance of wild-type colonies. The colony morphology of these mutants was identical to that of previously reported phenotypic variants of strain M6. The exceptions were M6 mutants disrupted in genes tonB, pilT, pilW, and pilX that exhibited typical wild-type colony morphology, although lacking twitching haloes surrounding the colony. Transmission electron microscopy revealed that most mutants lacked the ability to produce T4P. The exceptions were mutants with disruptions in tonB, pilT, pilW, and pilX genes that were shown to produce these appendages. These findings support the idea that colony phenotypic variation in A. citrulli is determined by the lack of ability to synthesize T4P but not by lack of T4P functionality.
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Affiliation(s)
- Tally Rosenberg
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Bolaji Babajide Salam
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Saul Burdman
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
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Hwang S, Choe D, Yoo M, Cho S, Kim SC, Cho S, Cho BK. Peptide Transporter CstA Imports Pyruvate in Escherichia coli K-12. J Bacteriol 2018; 200:e00771-17. [PMID: 29358499 PMCID: PMC5847655 DOI: 10.1128/jb.00771-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 01/17/2018] [Indexed: 12/01/2022] Open
Abstract
Pyruvate is an important intermediate of central carbon metabolism and connects a variety of metabolic pathways in Escherichia coli Although the intracellular pyruvate concentration is dynamically altered and tightly balanced during cell growth, the pyruvate transport system remains unclear. Here, we identified a pyruvate transporter in E. coli using high-throughput transposon sequencing. The transposon mutant library (a total of 5 × 105 mutants) was serially grown with a toxic pyruvate analog (3-fluoropyruvate [3FP]) to enrich for transposon mutants lacking pyruvate transport function. A total of 52 candidates were selected on the basis of a stringent enrichment level of transposon insertion frequency in response to 3FP treatment. Subsequently, their pyruvate transporter function was examined by conventional functional assays, such as those measuring growth inhibition by the toxic pyruvate analog and pyruvate uptake activity. The pyruvate transporter system comprises CstA and YbdD, which are known as a peptide transporter and a conserved protein, respectively, whose functions are associated with carbon starvation conditions. In addition to the presence of more than one endogenous pyruvate importer, it has been suggested that the E. coli genome encodes constitutive and inducible pyruvate transporters. Our results demonstrated that CstA and YbdD comprise the constitutive pyruvate transporter system in E. coli, which is consistent with the tentative genomic locus previously suggested and the functional relationship with the extracellular pyruvate sensing system. The identification of this pyruvate transporter system provides valuable genetic information for understanding the complex process of pyruvate metabolism in E. coliIMPORTANCE Pyruvate is an important metabolite as a central node in bacterial metabolism, and its intracellular levels are tightly regulated to maintain its functional roles in highly interconnected metabolic pathways. However, an understanding of the mechanism of how bacterial cells excrete and transport pyruvate remains elusive. Using high-throughput transposon sequencing followed by pyruvate uptake activity testing of the selected candidate genes, we found that a pyruvate transporter system comprising CstA and YbdD, currently annotated as a peptide transporter and a conserved protein, respectively, constitutively transports pyruvate. The identification of the physiological role of the pyruvate transporter system provides valuable genetic information for understanding the complex pyruvate metabolism in Escherichia coli.
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Affiliation(s)
- Soonkyu Hwang
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Donghui Choe
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Minseob Yoo
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Sanghyuk Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Sun Chang Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- Intelligent Synthetic Biology Center, Daejeon, South Korea
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- Intelligent Synthetic Biology Center, Daejeon, South Korea
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Steiner BD, Eberly AR, Hurst MN, Zhang EW, Green HD, Behr S, Jung K, Hadjifrangiskou M. Evidence of Cross-Regulation in Two Closely Related Pyruvate-Sensing Systems in Uropathogenic Escherichia coli. J Membr Biol 2018; 251:65-74. [PMID: 29374286 DOI: 10.1007/s00232-018-0014-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 11/08/2017] [Indexed: 11/27/2022]
Abstract
Two-component systems (TCSs) dictate many bacterial responses to environmental change via the activation of a membrane-embedded sensor kinase, which has molecular specificity for a cognate response regulator protein. However, although the majority of TCSs operate through seemingly strict cognate protein-protein interactions, there have been several reports of TCSs that violate this classical model of signal transduction. Our group has recently demonstrated that some of these cross-interacting TCSs function in a manner that imparts a fitness advantage to bacterial pathogens. In this study, we describe interconnectivity between the metabolite-sensing TCSs YpdA/YpdB and BtsS/BtsR in uropathogenic Escherichia coli (UPEC). The YpdA/YpdB and BtsS/BtsR TCSs have been previously reported to interact in K12 E. coli, where they alter the expression of putative transporter genes yhjX and yjiY, respectively. These target genes are both upregulated in UPEC during acute and chronic murine models of urinary tract infection, as well as in response to pyruvate and serine added to growth media in vitro. Here, we show that proper regulation of yhjX in UPEC requires the presence of all components from both of these TCSs. By utilizing plasmid-encoded luciferase reporters tracking the activity of the yhjX and yjiY promoters, we demonstrate that deletions in one TCS substantially alter transcriptional activity of the opposing system's target gene. However, unlike in K12 E. coli, single gene deletions in the YpdA/YpdB system do not alter yjiY gene expression in UPEC, suggesting that niche and lifestyle-specific pressures may be selecting for differential cross-regulation of TCSs in pathogenic and non-pathogenic E. coli.
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Affiliation(s)
- Bradley D Steiner
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Allison R Eberly
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, MCN A5225A, Nashville, TN, 37232, USA
| | - Melanie N Hurst
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, MCN A5225A, Nashville, TN, 37232, USA
| | - Ellisa W Zhang
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, MCN A5225A, Nashville, TN, 37232, USA
| | | | - Stefan Behr
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
- Roche Diagnostics GmbH, Nonnenwald 2, 82377, Penzberg, Germany
| | - Kirsten Jung
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Maria Hadjifrangiskou
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, MCN A5225A, Nashville, TN, 37232, USA.
- Department of Urologic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt Institute for Infection, Immunology & Inflammation, Nashville, TN, USA.
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17
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Chandra K, Garai P, Chatterjee J, Chakravortty D. Peptide transporter YjiY influences the expression of the virulence gene mgtC to regulate biofilm formation in Salmonella. FEMS Microbiol Lett 2017; 364:4590042. [PMID: 29112725 DOI: 10.1093/femsle/fnx236] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 11/02/2017] [Indexed: 09/19/2023] Open
Abstract
Formation of a biofilm is one of the coping strategies of Salmonella against antimicrobial environmental stresses including nutrient starvation. However, the channeling of the starvation cue towards biofilm formation is not well understood. Our study shows that a carbon starvation gene, yjiY, coding for a peptide transporter, influences the expression of a virulence-associated gene mgtC in Salmonella to regulate biofilm formation. We demonstrate here that the mutant strain ΔyjiY is unable to form a biofilm due to the increased expression of mgtC. The upregulation of mgtC in the ΔyjiY strain correlates with the downregulation of the biofilm master regulator gene, csgD, and reduced levels of ATP. Our work further indicates that a yjiY-encoded peptide transporter may regulate the expression of mgtC by transporting proline peptides.
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Affiliation(s)
- Kasturi Chandra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Preeti Garai
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Jayanta Chatterjee
- Department of Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Center for Biosystem Science and Engineering, Indian Institute of Science, Bangalore, India
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BtsT, a Novel and Specific Pyruvate/H + Symporter in Escherichia coli. J Bacteriol 2017; 200:JB.00599-17. [PMID: 29061664 DOI: 10.1128/jb.00599-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 10/12/2017] [Indexed: 01/11/2023] Open
Abstract
The peptide transporter carbon starvation (CstA) family (transporter classification [TC] 2.A.114) belongs to the second largest superfamily of secondary transporters, the amino acid/polyamine/organocation (APC) superfamily. No representative of the CstA family has previously been characterized either biochemically or structurally, but we have now identified the function of one of its members, the transport protein YjiY of Escherichia coli Expression of the yjiY gene is regulated by the LytS-like histidine kinase BtsS, a sensor of extracellular pyruvate, together with the LytTR-like response regulator BtsR. YjiY consists of 716 amino acids, which form 18 putative transmembrane helices. Transport studies with intact cells provided evidence that YjiY is a specific and high-affinity transporter for pyruvate (Km , 16 μM). Furthermore, reconstitution of the purified YjiY into proteoliposomes revealed that YjiY is a pyruvate/H+ symporter. It has long been assumed that E. coli possesses a transporter(s) for pyruvate, but the present study is the first to definitively identify such a protein. Based on its function, we propose to change the name of the uncharacterized gene yjiY to btsT for Brenztraubensäure (the German word for pyruvate) transporter.IMPORTANCE BtsT (formerly known as YjiY) is found in many commensal and pathogenic representatives of the Enterobacteriaceae This study for the first time characterizes a pyruvate transporter in E. coli, BtsT, as a specific pyruvate/H+ symporter. When nutrients are limiting, BtsT takes up pyruvate from the medium, thus enabling it to be used as a carbon source for the growth and survival of E. coli.
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A Single-Cell View of the BtsSR/YpdAB Pyruvate Sensing Network in Escherichia coli and Its Biological Relevance. J Bacteriol 2017; 200:JB.00536-17. [PMID: 29038258 DOI: 10.1128/jb.00536-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/09/2017] [Indexed: 12/16/2022] Open
Abstract
Fluctuating environments and individual physiological diversity force bacteria to constantly adapt and optimize the uptake of substrates. We focus here on two very similar two-component systems (TCSs) of Escherichia coli belonging to the LytS/LytTR family: BtsS/BtsR (formerly YehU/YehT) and YpdA/YpdB. Both TCSs respond to extracellular pyruvate, albeit with different affinities, typically during postexponential growth, and each system regulates expression of a single transporter gene, yjiY and yhjX, respectively. To obtain insights into the biological significance of these TCSs, we analyzed the activation of the target promoters at the single-cell level. We found unimodal cell-to-cell variability; however, the degree of variance was strongly influenced by the available nutrients and differed between the two TCSs. We hypothesized that activation of either of the TCSs helps individual cells to replenish carbon resources. To test this hypothesis, we compared wild-type cells with the btsSR ypdAB mutant under two metabolically modulated conditions: protein overproduction and persister formation. Although all wild-type cells were able to overproduce green fluorescent protein (GFP), about half of the btsSR ypdAB population was unable to overexpress GFP. Moreover, the percentage of persister cells, which tolerate antibiotic stress, was significantly lower in the wild-type cells than in the btsSR ypdAB population. Hence, we suggest that the BtsS/BtsR and YpdA/YpdB network contributes to a balancing of the physiological state of all cells within a population.IMPORTANCE Histidine kinase/response regulator (HK/RR) systems enable bacteria to respond to environmental and physiological fluctuations. Escherichia coli and other members of the Enterobacteriaceae possess two similar LytS/LytTR-type HK/RRs, BtsS/BtsR (formerly YehU/YehT) and YpdA/YpdB, which form a functional network. Both systems are activated in response to external pyruvate, typically when cells face overflow metabolism during post-exponential growth. Single-cell analysis of the activation of their respective target genes yjiY and yhjX revealed cell-to-cell variability, and the range of variation was strongly influenced by externally available nutrients. Based on the phenotypic characterization of a btsSR ypdAB mutant compared to the parental strain, we suggest that this TCS network supports an optimization of the physiological state of the individuals within the population.
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20
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Comparative analysis of LytS/LytTR-type histidine kinase/response regulator systems in γ-proteobacteria. PLoS One 2017; 12:e0182993. [PMID: 28796832 PMCID: PMC5552118 DOI: 10.1371/journal.pone.0182993] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 07/27/2017] [Indexed: 11/19/2022] Open
Abstract
Bacterial histidine kinase/response regulator systems operate at the interface between environmental cues and physiological states. Escherichia coli contains two LytS/LytTR-type histidine kinase/response regulator systems, BtsS/BtsR (formerly YehU/YehT) and YpdA/YpdB, which have been identified as pyruvate-responsive two-component systems. Since they exhibit remarkable similarity, we analyzed their phylogenetic distribution within the γ-proteobacteria, and experimentally characterized them in a set of representative species. We found that BtsS/BtsR is the predominant LytS/LytTR-type two-component system among γ-proteobacteria, whereas YpdA/YpdB primarily appears in a supplementary role. Based on our observations in E. coli, we used the highly conserved DNA-binding motifs to test the in vivo functionality of both systems in various genera, including Salmonella, Enterobacter, Citrobacter, Xenorhabdus, Yersinia, Aeromonas and Vibrio. The results suggest that, in all cases tested, BtsS/BtsR and YpdA/YpdB respond to different levels of pyruvate in the environment.
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Behr S, Kristoficova I, Witting M, Breland EJ, Eberly AR, Sachs C, Schmitt-Kopplin P, Hadjifrangiskou M, Jung K. Identification of a High-Affinity Pyruvate Receptor in Escherichia coli. Sci Rep 2017; 7:1388. [PMID: 28469239 PMCID: PMC5431176 DOI: 10.1038/s41598-017-01410-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 03/28/2017] [Indexed: 11/09/2022] Open
Abstract
Two-component systems are crucial for signal perception and modulation of bacterial behavior. Nevertheless, to date, very few ligands have been identified that directly interact with histidine kinases. The histidine kinase/response regulator system YehU/YehT of Escherichia coli is part of a nutrient-sensing network. Here we demonstrate that this system senses the onset of nutrient limitation in amino acid rich media and responds to extracellular pyruvate. Binding of radiolabeled pyruvate was found for full-length YehU in right-side-out membrane vesicles as well as for a truncated, membrane-integrated variant, confirming that YehU is a high-affinity receptor for extracellular pyruvate. Therefore we propose to rename YehU/YehT as BtsS/BtsR, after "Brenztraubensäure", the name given to pyruvic acid when it was first synthesized. The function of BtsS/BtsR was also assessed in a clinically relevant uropathogenic E. coli strain. Quantitative transcriptional analysis revealed BtsS/BtsR importance during acute and chronic urinary-tract infections.
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Affiliation(s)
- Stefan Behr
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Microbiology, Ludwig-Maximilians-Universität München, 82152, Martinsried, Germany
| | - Ivica Kristoficova
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Microbiology, Ludwig-Maximilians-Universität München, 82152, Martinsried, Germany
| | - Michael Witting
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Research Unit Analytical BioGeoChemistry, 85764, Neuherberg, Germany
| | - Erin J Breland
- Departments of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Allison R Eberly
- Departments of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Corinna Sachs
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Microbiology, Ludwig-Maximilians-Universität München, 82152, Martinsried, Germany
| | - Philippe Schmitt-Kopplin
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Research Unit Analytical BioGeoChemistry, 85764, Neuherberg, Germany
| | - Maria Hadjifrangiskou
- Departments of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Departments of Urologic Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kirsten Jung
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Microbiology, Ludwig-Maximilians-Universität München, 82152, Martinsried, Germany.
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Garai P, Chandra K, Chakravortty D. Bacterial peptide transporters: Messengers of nutrition to virulence. Virulence 2016; 8:297-309. [PMID: 27589415 DOI: 10.1080/21505594.2016.1221025] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bacteria possess numerous peptide transporters for importing peptides as nutrients. However, these peptide transporters are now consistently reported to play a role in the virulence of various bacterial pathogens. Their ability to transport peptides has implications in antibacterial therapy as well. Therefore, it would be instrumental to have complete knowledge about the role of peptide transporters in mediating this cross connection between metabolism and pathogenesis. Studies on various peptide transporters in bacterial pathogens have improved our understanding of this field. In this review, we have given an overview of the functioning of bacterial peptide transporters and their contribution in virulence of major bacterial pathogens.
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Affiliation(s)
- Preeti Garai
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India
| | - Kasturi Chandra
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India
| | - Dipshikha Chakravortty
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India
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Insights into the DNA-binding mechanism of a LytTR-type transcription regulator. Biosci Rep 2016; 36:BSR20160069. [PMID: 27013338 PMCID: PMC4847170 DOI: 10.1042/bsr20160069] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 03/24/2016] [Indexed: 12/25/2022] Open
Abstract
A combination of surface plasmon resonance (SPR) spectroscopy and interaction map® (IM) analysis was used to characterize binding of the LytTR-type response regulator YpdB to promoter DNA. YpdB follows an ‘AB-BA’ mechanism involving sequential and cooperative DNA binding followed by rapid successive promoter clearance. Most bacterial response regulators (RRs) make contact with DNA through a recognition α-helix in their DNA-binding domains. An emerging class of RRs interacts with DNA via a relatively novel type of binding domain, called the LytTR domain, which is mainly composed of β-strands. YpdB belongs to this latter class, is part of a nutrient-sensing network in Escherichia coli and triggers expression of its only target gene, yhjX, in response to extracellular pyruvate. Expression of yhjX mainly occurs in the late exponential growth phase, and in a pulsed manner. Although the DNA-binding sites for YpdB are well defined, exactly how YpdB initiates pulsed gene expression has remained elusive. To address this question, we measured the binding kinetics of wild-type YpdB and the phosphomimetic variant YpdB-D53E to the yhjX promoter region (PyhjX) using surface plasmon resonance (SPR) spectroscopy combined with interaction map® (IM) analysis. Both YpdB and YpdB-D53E bound as monomers to the tandem-repeat sequences in the promoter, with YpdB-D53E displaying a higher maximal binding rate than YpdB. Furthermore, we identified a high-affinity (A-site) and a low-affinity binding site (B-site) within the yhjX promoter. Only YpdB-D53E utilizes an ‘AB-BA’ DNA-binding mechanism, involving sequential and cooperative promoter binding, and rapid, successive promoter clearance. We propose that response regulator phosphorylation, in combination with the cycle of cooperative DNA binding and rapid promoter clearance just described, can account for pulsed gene expression.
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Comparative genomics and experimental evolution of Escherichia coli BL21(DE3) strains reveal the landscape of toxicity escape from membrane protein overproduction. Sci Rep 2015; 5:16076. [PMID: 26531007 PMCID: PMC4632034 DOI: 10.1038/srep16076] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 10/08/2015] [Indexed: 11/08/2022] Open
Abstract
Achieving sufficient yields of proteins in their functional form represents the first bottleneck in contemporary bioscience and biotechnology. To accomplish successful overexpression of membrane proteins in a workhorse organism such as E. coli, defined and rational optimization strategies based on an understanding of the genetic background of the toxicity-escape mechanism are desirable. To this end, we sequenced the genomes of E. coli C41(DE3) and its derivative C43(DE3), which were developed for membrane protein production. Comparative analysis of their genomes with those of their ancestral strain E. coli BL21(DE3) revealed various genetic changes in both strains. A series of E. coli variants that are able to tolerate transformation with or overexpression of membrane proteins were generated by in vitro evolution. Targeted sequencing of the evolved strains revealed the mutational hotspots among the acquired genetic changes. By these combinatorial approaches, we found non-synonymous changes in the lac repressor gene of the lac operon as well as nucleotide substitutions in the lacUV5 promoter of the DE3 region, by which the toxic effect to the host caused by overexpression of membrane proteins could be relieved. A mutation in lacI was demonstrated to be crucial for conferring tolerance to membrane protein overexpression.
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Borland S, Oudart A, Prigent-Combaret C, Brochier-Armanet C, Wisniewski-Dyé F. Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum. BMC Genomics 2015; 16:833. [PMID: 26489830 PMCID: PMC4618731 DOI: 10.1186/s12864-015-1962-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/29/2015] [Indexed: 01/05/2023] Open
Abstract
Background Two-component systems (TCS) play critical roles in sensing and responding to environmental cues. Azospirillum is a plant growth-promoting rhizobacterium living in the rhizosphere of many important crops. Despite numerous studies about its plant beneficial properties, little is known about how the bacterium senses and responds to its rhizospheric environment. The availability of complete genome sequenced from four Azospirillum strains (A. brasilense Sp245 and CBG 497, A. lipoferum 4B and Azospirillum sp. B510) offers the opportunity to conduct a comprehensive comparative analysis of the TCS gene family. Results Azospirillum genomes harbour a very large number of genes encoding TCS, and are especially enriched in hybrid histidine kinases (HyHK) genes compared to other plant-associated bacteria of similar genome sizes. We gained further insight into HyHK structure and architecture, revealing an intriguing complexity of these systems. An unusual proportion of TCS genes were orphaned or in complex clusters, and a high proportion of predicted soluble HKs compared to other plant-associated bacteria are reported. Phylogenetic analyses of the transmitter and receiver domains of A. lipoferum 4B HyHK indicate that expansion of this family mainly arose through horizontal gene transfer but also through gene duplications all along the diversification of the Azospirillum genus. By performing a genome-wide comparison of TCS, we unraveled important ‘genus-defining’ and ‘plant-specifying’ TCS. Conclusions This study shed light on Azospirillum TCS which may confer important regulatory flexibility. Collectively, these findings highlight that Azospirillum genomes have broad potential for adaptation to fluctuating environments. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1962-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stéphanie Borland
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Laboratoire d'Ecologie Microbienne, 43 7 boulevard du 11 novembre 1918, F-69622, Villeurbanne, France.
| | - Anne Oudart
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918, F-69622, Villeurbanne, France.
| | - Claire Prigent-Combaret
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Laboratoire d'Ecologie Microbienne, 43 7 boulevard du 11 novembre 1918, F-69622, Villeurbanne, France.
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918, F-69622, Villeurbanne, France.
| | - Florence Wisniewski-Dyé
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Laboratoire d'Ecologie Microbienne, 43 7 boulevard du 11 novembre 1918, F-69622, Villeurbanne, France.
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Garai P, Lahiri A, Ghosh D, Chatterjee J, Chakravortty D. Peptide utilizing carbon starvation gene yjiY is required for flagella mediated infection caused by Salmonella. MICROBIOLOGY-SGM 2015; 162:100-116. [PMID: 26497384 DOI: 10.1099/mic.0.000204] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Peptide metabolism forms an important part of the metabolic network of Salmonella and to acquire these peptides the pathogen possesses a number of peptide transporters. While various peptide transporters known in Salmonella are well studied, very little is known about the carbon starvation (cst) genes, cstA and yjiY, which are also predicted to be involved in peptide metabolism. We investigated the role of these genes in the metabolism and pathogenesis of Salmonella and demonstrated for the first time that cst genes actually participate in transport of specific peptides in Salmonella. Further, we established that the carbon starvation gene yjiY affects the expression of flagella leading to poor adhesion of the bacterium to host cells. In contrast with the previously reported role of the gene cstA in virulence of Salmonella in C. elegans, we showed that yjiY is required for successful colonization of Salmonella in the mouse gut. Thus, cst genes not only contribute to the metabolism of Salmonella but also influence its virulence.
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Affiliation(s)
- Preeti Garai
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Amit Lahiri
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Dipan Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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Dual-Color Monitoring Overcomes the Limitations of Single Bioluminescent Reporters in Fast-Growing Microbes and Reveals Phase-Dependent Protein Productivity during the Metabolic Rhythms of Saccharomyces cerevisiae. Appl Environ Microbiol 2015; 81:6484-95. [PMID: 26162874 DOI: 10.1128/aem.01631-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/06/2015] [Indexed: 01/19/2023] Open
Abstract
Luciferase is a useful, noninvasive reporter of gene regulation that can be continuously monitored over long periods of time; however, its use is problematic in fast-growing microbes like bacteria and yeast because rapidly changing cell numbers and metabolic states also influence bioluminescence, thereby confounding the reporter's signal. Here we show that these problems can be overcome in the budding yeast Saccharomyces cerevisiae by simultaneously monitoring bioluminescence from two different colors of beetle luciferase, where one color (green) reports activity of a gene of interest, while a second color (red) is stably expressed and used to continuously normalize green bioluminescence for fluctuations in signal intensity that are unrelated to gene regulation. We use this dual-luciferase strategy in conjunction with a light-inducible promoter system to test whether different phases of yeast respiratory oscillations are more suitable for heterologous protein production than others. By using pulses of light to activate production of a green luciferase while normalizing signal variation to a red luciferase, we show that the early reductive phase of the yeast metabolic cycle produces more luciferase than other phases.
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De-convoluting the Genetic Adaptations of E. coli C41(DE3) in Real Time Reveals How Alleviating Protein Production Stress Improves Yields. Cell Rep 2015; 10:1758-1766. [DOI: 10.1016/j.celrep.2015.02.029] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/29/2015] [Accepted: 02/08/2015] [Indexed: 11/20/2022] Open
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Soufi B, Krug K, Harst A, Macek B. Characterization of the E. coli proteome and its modifications during growth and ethanol stress. Front Microbiol 2015; 6:103. [PMID: 25741329 PMCID: PMC4332353 DOI: 10.3389/fmicb.2015.00103] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 01/27/2015] [Indexed: 12/31/2022] Open
Abstract
We set out to provide a resource to the microbiology community especially with respect to systems biology based endeavors. To this end, we generated a comprehensive dataset monitoring the changes in protein expression, copy number, and post translational modifications in a systematic fashion during growth and ethanol stress in E. coli. We utilized high-resolution mass spectrometry (MS) combined with the Super-SILAC approach. In a single experiment, we have identified over 2300 proteins, which represent approximately 88% of the estimated expressed proteome of E. coli and estimated protein copy numbers using the Intensity Based Absolute Quantitation (iBAQ). The dynamic range of protein expression spanned up to six orders of magnitude, with the highest protein copy per cell estimated at approximately 300,000. We focused on the proteome dynamics involved during stationary phase growth. A global up-regulation of proteins related to stress response was detected in later stages of growth. We observed the down-regulation of the methyl directed mismatch repair system containing MutS and MutL of E. coli growing in long term growth cultures, confirming that higher incidence of mutations presents an important mechanism in the increase in genetic diversity and stationary phase survival in E. coli. During ethanol stress, known markers such as alcohol dehydrogenase and aldehyde dehydrogenase were induced, further validating the dataset. Finally, we performed unbiased protein modification detection and revealed changes of many known and unknown protein modifications in both experimental conditions. Data are available via ProteomeXchange with identifier PXD001648.
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Affiliation(s)
- Boumediene Soufi
- Proteome Center Tuebingen, University of Tuebingen Tuebingen, Germany
| | - Karsten Krug
- Proteome Center Tuebingen, University of Tuebingen Tuebingen, Germany
| | - Andreas Harst
- Proteome Center Tuebingen, University of Tuebingen Tuebingen, Germany
| | - Boris Macek
- Proteome Center Tuebingen, University of Tuebingen Tuebingen, Germany
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Soufi B, Krug K, Harst A, Macek B. Characterization of the E. coli proteome and its modifications during growth and ethanol stress. Front Microbiol 2015. [PMID: 25741329 DOI: 10.3389/fpls.2018.0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
We set out to provide a resource to the microbiology community especially with respect to systems biology based endeavors. To this end, we generated a comprehensive dataset monitoring the changes in protein expression, copy number, and post translational modifications in a systematic fashion during growth and ethanol stress in E. coli. We utilized high-resolution mass spectrometry (MS) combined with the Super-SILAC approach. In a single experiment, we have identified over 2300 proteins, which represent approximately 88% of the estimated expressed proteome of E. coli and estimated protein copy numbers using the Intensity Based Absolute Quantitation (iBAQ). The dynamic range of protein expression spanned up to six orders of magnitude, with the highest protein copy per cell estimated at approximately 300,000. We focused on the proteome dynamics involved during stationary phase growth. A global up-regulation of proteins related to stress response was detected in later stages of growth. We observed the down-regulation of the methyl directed mismatch repair system containing MutS and MutL of E. coli growing in long term growth cultures, confirming that higher incidence of mutations presents an important mechanism in the increase in genetic diversity and stationary phase survival in E. coli. During ethanol stress, known markers such as alcohol dehydrogenase and aldehyde dehydrogenase were induced, further validating the dataset. Finally, we performed unbiased protein modification detection and revealed changes of many known and unknown protein modifications in both experimental conditions. Data are available via ProteomeXchange with identifier PXD001648.
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Affiliation(s)
- Boumediene Soufi
- Proteome Center Tuebingen, University of Tuebingen Tuebingen, Germany
| | - Karsten Krug
- Proteome Center Tuebingen, University of Tuebingen Tuebingen, Germany
| | - Andreas Harst
- Proteome Center Tuebingen, University of Tuebingen Tuebingen, Germany
| | - Boris Macek
- Proteome Center Tuebingen, University of Tuebingen Tuebingen, Germany
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Yamanaka Y, Oshima T, Ishihama A, Yamamoto K. Characterization of the YdeO regulon in Escherichia coli. PLoS One 2014; 9:e111962. [PMID: 25375160 PMCID: PMC4222967 DOI: 10.1371/journal.pone.0111962] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 10/09/2014] [Indexed: 11/23/2022] Open
Abstract
Enterobacteria are able to survive under stressful conditions within animals, such as acidic conditions in the stomach, bile salts during transfer to the intestine and anaerobic conditions within the intestine. The glutamate-dependent (GAD) system plays a major role in acid resistance in Escherichia coli, and expression of the GAD system is controlled by the regulatory cascade consisting of EvgAS > YdeO > GadE. To understand the YdeO regulon in vivo, we used ChIP-chip to interrogate the E. coli genome for candidate YdeO binding sites. All of the seven operons identified by ChIP-chip as being potentially regulated by YdeO were confirmed as being under the direct control of YdeO using RT-qPCR, EMSA, DNaseI-footprinting and reporter assays. Within this YdeO regulon, we identified four stress-response transcription factors, DctR, NhaR, GadE, and GadW and enzymes for anaerobic respiration. Both GadE and GadW are involved in regulation of the GAD system and NhaR is an activator for the sodium/proton antiporter gene. In conjunction with co-transcribed Slp, DctR is involved in protection against metabolic endoproducts under acidic conditions. Taken all together, we suggest that YdeO is a key regulator of E. coli survival in both acidic and anaerobic conditions.
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Affiliation(s)
- Yuki Yamanaka
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
| | - Taku Oshima
- Graduate School of Information Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Akira Ishihama
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
- Micro-Nano Technology Research Center, Hosei University, Koganei, Tokyo, Japan
| | - Kaneyoshi Yamamoto
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
- Micro-Nano Technology Research Center, Hosei University, Koganei, Tokyo, Japan
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Okkotsu Y, Little AS, Schurr MJ. The Pseudomonas aeruginosa AlgZR two-component system coordinates multiple phenotypes. Front Cell Infect Microbiol 2014; 4:82. [PMID: 24999454 PMCID: PMC4064291 DOI: 10.3389/fcimb.2014.00082] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/02/2014] [Indexed: 01/28/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes a multitude of infections. These infections can occur at almost any site in the body and are usually associated with a breach of the innate immune system. One of the prominent sites where P. aeruginosa causes chronic infections is within the lungs of cystic fibrosis patients. P. aeruginosa uses two-component systems that sense environmental changes to differentially express virulence factors that cause both acute and chronic infections. The P. aeruginosa AlgZR two component system is one of its global regulatory systems that affects the organism's fitness in a broad manner. This two-component system is absolutely required for two P. aeruginosa phenotypes: twitching motility and alginate production, indicating its importance in both chronic and acute infections. Additionally, global transcriptome analyses indicate that it regulates the expression of many different genes, including those associated with quorum sensing, type IV pili, type III secretion system, anaerobic metabolism, cyanide and rhamnolipid production. This review examines the complex AlgZR regulatory network, what is known about the structure and function of each protein, and how it relates to the organism's ability to cause infections.
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Affiliation(s)
- Yuta Okkotsu
- Department of Microbiology, University of Colorado School of Medicine Aurora, CO, USA
| | - Alexander S Little
- Department of Microbiology, University of Colorado School of Medicine Aurora, CO, USA
| | - Michael J Schurr
- Department of Microbiology, University of Colorado School of Medicine Aurora, CO, USA
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Yamamoto K. The hierarchic network of metal-response transcription factors in Escherichia coli. Biosci Biotechnol Biochem 2014; 78:737-47. [PMID: 25035972 DOI: 10.1080/09168451.2014.915731] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Enterobacteria such as Escherichia coli are able to survive under various environments within host animals by changes of the expression pattern of its genome. The selective expression of genes in its genome takes place by controlling the promoter recognition properties of RNA polymerase by protein-protein interplays with transcription factors. In this review, I describe the regulatory network formed by the metal-sensing transcription factors in E. coli. Comprehensive analyses identify the set of regulation targets for a total of 13 metal-response transcription factors, indicating that nine species of transcription factors are local regulators while four species of transcription factors are global regulators. The signal transduction pathways for these metal-response regulons show not only the complex cross-talks but also the hierarchic multi-regulatory network. This regulatory network seems to play a role for E. coli survival to colonize in a large intestine within host animals.
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Affiliation(s)
- Kaneyoshi Yamamoto
- a Department of Frontier Bioscience and Micro-Nano Technology Research Center , Hosei University , Koganei, Tokyo , Japan
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Vergara-Irigaray M, Fookes MC, Thomson NR, Tang CM. RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri. BMC Genomics 2014; 15:438. [PMID: 24907032 PMCID: PMC4229854 DOI: 10.1186/1471-2164-15-438] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 05/23/2014] [Indexed: 01/03/2023] Open
Abstract
Background Shigella flexneri is an important human pathogen that has to adapt to the anaerobic environment in the gastrointestinal tract to cause dysentery. To define the influence of anaerobiosis on the virulence of Shigella, we performed deep RNA sequencing to identify transcriptomic differences that are induced by anaerobiosis and modulated by the anaerobic Fumarate and Nitrate Reduction regulator, FNR. Results We found that 528 chromosomal genes were differentially expressed in response to anaerobic conditions; of these, 228 genes were also influenced by FNR. Genes that were up-regulated in anaerobic conditions are involved in carbon transport and metabolism (e.g. ptsG, manX, murQ, cysP, cra), DNA topology and regulation (e.g. ygiP, stpA, hns), host interactions (e.g. yciD, nmpC, slyB, gapA, shf, msbB) and survival within the gastrointestinal tract (e.g. shiA, ospI, adiY, cysP). Interestingly, there was a marked effect of available oxygen on genes involved in Type III secretion system (T3SS), which is required for host cell invasion and pathogenesis. These genes, located on the large Shigella virulence plasmid, were down regulated in anaerobiosis in an FNR-dependent manner. We also confirmed anaerobic induction of csrB and csrC small RNAs in an FNR-independent manner. Conclusions Anaerobiosis promotes survival and adaption strategies of Shigella, while modulating virulence plasmid genes involved in T3SS-mediated host cell invasion. The influence of FNR on this process is more extensive than previously appreciated, although aside from the virulence plasmid, this transcriptional regulator does not govern expression of genes on other horizontally acquired sequences on the chromosome such as pathogenicity islands. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-438) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Christoph M Tang
- Sir William Dunn School of Pathology, Oxford University, Oxford, United Kingdom.
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Identification of a novel nutrient-sensing histidine kinase/response regulator network in Escherichia coli. J Bacteriol 2014; 196:2023-9. [PMID: 24659770 DOI: 10.1128/jb.01554-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
When carbon sources become limiting for growth, bacteria must choose which of the remaining nutrients should be used first. We have identified a nutrient-sensing signaling network in Escherichia coli that is activated at the transition to stationary phase. The network is composed of the two histidine kinase/response regulator systems YehU/YehT and YpdA/YpdB and their target proteins, YjiY and YhjX (both of which are membrane-integrated transporters). The peptide/amino acid-responsive YehU/YehT system was found to have a negative effect on expression of the target gene, yhjX, of the pyruvate-responsive YpdA/YpdB system, while the YpdA/YpdB system stimulated expression of yjiY, the target of the YehU/YehT system. These effects were confirmed in mutants lacking any of the genes for the three primary components of either system. Furthermore, an in vivo interaction assay based on bacterial adenylate cyclase detected heteromeric interactions between the membrane-bound components of the two systems, specifically, between the two histidine kinases and the two transporters, which is compatible with the formation of a larger signaling unit. Finally, the carbon storage regulator A (CsrA) was shown to be involved in posttranscriptional regulation of both yjiY and yhjX.
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New Insights into the Interplay Between the Lysine Transporter LysP and the pH Sensor CadC in Escherichia Coli. J Mol Biol 2014; 426:215-29. [DOI: 10.1016/j.jmb.2013.09.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/12/2013] [Accepted: 09/15/2013] [Indexed: 11/20/2022]
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Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium. PLoS One 2013; 8:e84567. [PMID: 24386394 PMCID: PMC3875573 DOI: 10.1371/journal.pone.0084567] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 11/24/2013] [Indexed: 12/29/2022] Open
Abstract
Proteins exhibiting hyper-variable sequences within a bacterial pathogen may be associated with host adaptation. Several lineages of the monophyletic pathogen Salmonella enterica serovar Typhi (S. Typhi) have accumulated non-synonymous mutations in the putative two-component regulatory system yehUT. Consequently we evaluated the function of yehUT in S. Typhi BRD948 and S. Typhimurium ST4/74. Transcriptome analysis identified the cstA gene, encoding a carbon starvation protein as the predominantly yehUT regulated gene in both these serovars. Deletion of yehUT had no detectable effect on the ability of these mutant Salmonella to invade cultured epithelial cells (S. Typhi and S. Typhimurium) or induce colitis in a murine model (S. Typhimurium only). Growth, metabolic and antimicrobial susceptibility tests identified no obvious influences of yehUT on these phenotypes.
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Deangelis KM, Sharma D, Varney R, Simmons B, Isern NG, Markilllie LM, Nicora C, Norbeck AD, Taylor RC, Aldrich JT, Robinson EW. Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1. Front Microbiol 2013; 4:280. [PMID: 24065962 PMCID: PMC3777014 DOI: 10.3389/fmicb.2013.00280] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/29/2013] [Indexed: 01/05/2023] Open
Abstract
Lignocellulosic biofuels are promising as sustainable alternative fuels, but lignin inhibits access of enzymes to cellulose, and by-products of lignin degradation can be toxic to cells. The fast growth, high efficiency and specificity of enzymes employed in the anaerobic litter deconstruction carried out by tropical soil bacteria make these organisms useful templates for improving biofuel production. The facultative anaerobe Enterobacter lignolyticus SCF1 was initially cultivated from Cloud Forest soils in the Luquillo Experimental Forest in Puerto Rico, based on anaerobic growth on lignin as sole carbon source. The source of the isolate was tropical forest soils that decompose litter rapidly with low and fluctuating redox potentials, where bacteria using oxygen-independent enzymes likely play an important role in decomposition. We have used transcriptomics and proteomics to examine the observed increased growth of SCF1 grown on media amended with lignin compared to unamended growth. Proteomics suggested accelerated xylose uptake and metabolism under lignin-amended growth, with up-regulation of proteins involved in lignin degradation via the 4-hydroxyphenylacetate degradation pathway, catalase/peroxidase enzymes, and the glutathione biosynthesis and glutathione S-transferase (GST) proteins. We also observed increased production of NADH-quinone oxidoreductase, other electron transport chain proteins, and ATP synthase and ATP-binding cassette (ABC) transporters. This suggested the use of lignin as terminal electron acceptor. We detected significant lignin degradation over time by absorbance, and also used metabolomics to demonstrate moderately significant decreased xylose concentrations as well as increased metabolic products acetate and formate in stationary phase in lignin-amended compared to unamended growth conditions. Our data show the advantages of a multi-omics approach toward providing insights as to how lignin may be used in nature by microorganisms coping with poor carbon availability.
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Affiliation(s)
- Kristen M Deangelis
- Department of Microbiology, University of Massachusetts Amherst Amherst, MA, USA
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Identification of a target gene and activating stimulus for the YpdA/YpdB histidine kinase/response regulator system in Escherichia coli. J Bacteriol 2012; 195:807-15. [PMID: 23222720 DOI: 10.1128/jb.02051-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli contains 30 two-component systems (TCSs), each consisting of a histidine kinase and a response regulator. Whereas most TCSs are well characterized in this model organism, little is known about the YpdA/YpdB system. To identify YpdB-regulated genes, we compared the transcriptomes of E. coli cells overproducing either YpdB or a control protein. Expression levels of 15 genes differed by more than 1.9-fold between the two strains. A comprehensive evaluation of these genes identified yhjX as the sole target of YpdB. Electrophoretic mobility shift assays with purified YpdB confirmed its interaction with the yhjX promoter. Specifically, YpdB binds to two direct repeats of the motif GGCATTTCAT separated by an 11-bp spacer in the yhjX promoter. yhjX encodes a cytoplasmic membrane protein of unknown function that belongs to the major facilitator superfamily of transporters. Finally, we characterized the pattern of yhjX expression and identified extracellular pyruvate as a stimulus for the YpdA/YpdB system. It is suggested that YpdA/YpdB contributes to nutrient scavenging before entry into stationary phase.
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