1
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Kang X, Zhou X, Tang Y, Jiang Z, Chen J, Mohsin M, Yue M. Characterization of Two-Component System CitB Family in Salmonella Pullorum. Int J Mol Sci 2022; 23:ijms231710201. [PMID: 36077599 PMCID: PMC9456408 DOI: 10.3390/ijms231710201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Salmonella enterica, serovar Gallinarum, biovar Pullorum, is an avian-specific pathogen which has caused considerable economic losses to the poultry industry worldwide. Two-component systems (TCSs) play an essential role in obtaining nutrients, detecting the presence of neighboring bacteria and regulating the expression of virulence factors. The genome analysis of S. Pullorum strain S06004 suggesting the carriage of 22 pairs of TCSs, which belong to five families named CitB, OmpR, NarL, Chemotaxis and LuxR. In the CitB family, three pairs of TCSs, namely CitA-CitB, DcuS-DcuR and DpiB-DpiA, remain unaddressed in S. Pullorum. To systematically investigate the function of the CitB family in S. Pullorum, four mutants, ΔcitAB (abbreviated as Δcit), ΔdcuSR (Δdcu), ΔdpiBA (Δdpi) and ΔcitABΔdcuSRΔdpiBA (Δ3), were made using the CRISPR/Cas9 system. The results demonstrated that the CitB family did not affect the growth of bacteria, the results of biochemical tests, invasion and proliferation in chicken macrophage HD-11 cells and the expression of fimbrial protein. But the mutants showed thicker biofilm formation, higher resistance to antimicrobial agents, enhanced tolerance to inhibition by egg albumen and increased virulence in chicken embryos. Moreover, the deletion of Dpi TCS was detrimental to survival after exposure to hyperosmotic and oxidative environments, as well as the long-term colonization of the small intestine of chickens. Collectively, we provided new knowledge regarding the possible role of the CitB family involved in the pathogenic processes of S. Pullorum.
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Affiliation(s)
- Xiamei Kang
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Xiao Zhou
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Yanting Tang
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Zhijie Jiang
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Jiaqi Chen
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Muhammad Mohsin
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Min Yue
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572025, China
- Zhejiang Provincial Key Laboratory, Preventive Veterinary Medicine, Hangzhou 310058, China
- Correspondence: ; Tel./Fax: +86-571-88982832
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2
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Wang P, Li M, Dong L, Zhang C, Xie W. Comparative Genomics of Thaumarchaeota From Deep-Sea Sponges Reveal Their Niche Adaptation. Front Microbiol 2022; 13:869834. [PMID: 35859738 PMCID: PMC9289680 DOI: 10.3389/fmicb.2022.869834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
Thaumarchaeota account for a large portion of microbial symbionts in deep-sea sponges and are even dominant in some cases. In this study, we investigated three new sponge-associated Thaumarchaeota from the deep West Pacific Ocean. Thaumarchaeota were found to be the most dominant phylum in this sponge by both prokaryotic 16S rRNA amplicons and metagenomic sequencing. Fifty-seven published Thaumarchaeota genomes from sponges and other habitats were included for genomic comparison. Similar to shallow sponge-associated Thaumarchaeota, those Thaumarchaeota in deep-sea sponges have extended genome sizes and lower coding density compared with their free-living lineages. Thaumarchaeota in deep-sea sponges were specifically enriched in genes related to stress adapting, symbiotic adhesion and stability, host–microbe interaction and protein transportation. The genes involved in defense mechanisms, such as the restriction-modification system, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system, and toxin-antitoxin system were commonly enriched in both shallow and deep sponge-associated Thaumarchaeota. Our study demonstrates the significant effects of both depth and symbiosis on forming genomic characteristics of Thaumarchaeota, and provides novel insights into their niche adaptation in deep-sea sponges.
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Affiliation(s)
- Peng Wang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Minchun Li
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Liang Dong
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Cheng Zhang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- *Correspondence: Wei Xie,
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3
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Hu X, Tang Y, Liu Y, Pei X, Huang Z, Song F, Zhang H. Comprehensive Genomic Analysis of Marine Strain Streptomyces sp. 891, an Excellent Producer of Chrysomycin A with Therapeutic Potential. Mar Drugs 2022; 20:287. [PMID: 35621938 PMCID: PMC9144908 DOI: 10.3390/md20050287] [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: 03/27/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/29/2022] Open
Abstract
Chrysomycin A is one of the most promising therapeutic candidates for treating infections caused by multidrug-resistant Gram-positive bacteria. By hybridizing next-step generation (Illumina) and third-generation (PacBio) sequencing technologies, a high-quality chromosome-level genome together with a plasmid was firstly assembled for chrysomycin A-producing marine strain 891. Phylogenetic analysis of the 16S rRNA gene and genome sequences revealed that this strain unambiguously belonged to the genus Streptomyces, and its genomic features and functional genes were comprehensively analyzed and annotated. AntiSMASH analysis of this strain unveiled one key biosynthetic gene cluster, T2PKS, responsible for the biosynthesis of chrysomycin, the biosynthesis pathway of which was putatively proposed. These findings definitely shed light on further investigation for construction of a robust industrial strain with high-yield chrysomycin A production using genetic engineering techniques and combinatorial biology approaches.
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Affiliation(s)
- Xu Hu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuqi Tang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
| | - Yuanyuan Liu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
| | - Xinwei Pei
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
| | - Ziwei Huang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
| | - Fuhang Song
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China;
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
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4
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Guffey AA, Loll PJ. Regulation of Resistance in Vancomycin-Resistant Enterococci: The VanRS Two-Component System. Microorganisms 2021; 9:2026. [PMID: 34683347 PMCID: PMC8541618 DOI: 10.3390/microorganisms9102026] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 01/20/2023] Open
Abstract
Vancomycin-resistant enterococci (VRE) are a serious threat to human health, with few treatment options being available. New therapeutics are urgently needed to relieve the health and economic burdens presented by VRE. A potential target for new therapeutics is the VanRS two-component system, which regulates the expression of vancomycin resistance in VRE. VanS is a sensor histidine kinase that detects vancomycin and in turn activates VanR; VanR is a response regulator that, when activated, directs expression of vancomycin-resistance genes. This review of VanRS examines how the expression of vancomycin resistance is regulated, and provides an update on one of the field's most pressing questions: How does VanS sense vancomycin?
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Affiliation(s)
| | - Patrick J. Loll
- Department of Biochemistry & Molecular Biology, College of Medicine, Drexel University, Philadelphia, PA 19102, USA;
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5
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Matilla MA, Velando F, Martín-Mora D, Monteagudo-Cascales E, Krell T. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. FEMS Microbiol Rev 2021; 46:6356564. [PMID: 34424339 DOI: 10.1093/femsre/fuab043] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria have evolved many different signal transduction systems that sense signals and generate a variety of responses. Generally, most abundant are transcriptional regulators, sensor histidine kinases and chemoreceptors. Typically, these systems recognize their signal molecules with dedicated ligand-binding domains (LBDs), which, in turn, generate a molecular stimulus that modulates the activity of the output module. There are an enormous number of different LBDs that recognize a similarly diverse set of signals. To give a global perspective of the signals that interact with transcriptional regulators, sensor kinases and chemoreceptors, we manually retrieved information on the protein-ligand interaction from about 1,200 publications and 3D structures. The resulting 811 proteins were classified according to the Pfam family into 127 groups. These data permit a delineation of the signal profiles of individual LBD families as well as distinguishing between families that recognize signals in a promiscuous manner and those that possess a well-defined ligand range. A major bottleneck in the field is the fact that the signal input of many signaling systems is unknown. The signal repertoire reported here will help the scientific community design experimental strategies to identify the signaling molecules for uncharacterised sensor proteins.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Elizabet Monteagudo-Cascales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
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6
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Meng F, Lu F, Du H, Nie T, Zhu X, Connerton IF, Zhao H, Bie X, Zhang C, Lu Z, Lu Y. Acetate and auto-inducing peptide are independent triggers of quorum sensing in Lactobacillus plantarum. Mol Microbiol 2021; 116:298-310. [PMID: 33660340 DOI: 10.1111/mmi.14709] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/12/2021] [Accepted: 02/27/2021] [Indexed: 01/26/2023]
Abstract
The synthesis of plantaricin in Lactobacillus plantarum is regulated by quorum sensing. However, the nature of the extra-cytoplasmic (EC) sensing domain of the histidine kinase (PlnB1) and the ability to recognize the auto-inducing peptide PlnA1 is not known. We demonstrate the key motif Ile-Ser-Met-Leu of auto-inducing peptide PlnA1 binds to the hydrophobic region Phe-Ala-Ser-Gln-Phe of EC loop 2 of PlnB1 via hydrophobic interactions and hydrogen bonding. Moreover, we identify a new inducer, acetate, that regulates the synthesis of plantaricin by binding to a positively charged region (Arg-Arg-Tyr-Ser-His-Lys) in loop 4 of PlnB1 via electrostatic interaction. The side chain of Phe143 on loop 4 determined the specificity and affinity of PlnB1 to recognize acetate. PlnA1 activates quorum sensing in log phase growth and acetate in stationary phase to maintain the synthesis of plantaricin under conditions of reduced growth. Acetate activation of PlnB was also evident in four types of PlnB present in different Lb. plantarum strains. Finally, we proposed a model to explain the developmental regulation of plantaricin synthesis by PlnA and acetate. These results have potential applications in improving food fermentation and bacteriocin production.
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Affiliation(s)
- Fanqiang Meng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Hechao Du
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ting Nie
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaoyu Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ian F Connerton
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, UK
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Chong Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yingjian Lu
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, China
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7
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Jiang F, Huang X, Barbieri NL, Logue CM, Nolan LK, Li G. Citrate utilization under anaerobic environment in Escherichia coli is under direct control of Fnr and indirect control of ArcA and Fnr via CitA-CitB system. Environ Microbiol 2020; 23:1496-1509. [PMID: 33325149 DOI: 10.1111/1462-2920.15357] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/12/2020] [Indexed: 11/29/2022]
Abstract
Most Escherichia coli (E. coli) strains do not cause disease, naturally living in the lower intestine and is expelled into the environment within faecal matter. Escherichia coli can utilize citrate under anaerobic conditions but not aerobic conditions. However, the underlying regulatory mechanisms are poorly understood. In this study, we explored regulatory mechanisms of citrate fermentation genes by global regulators ArcA and Fnr under anaerobic conditions. A gel mobility shift assay showed that the regulator proteins ArcA and Fnr binded to the promoter region localized between the citAB and citCDEFXGT operons. Subsequent assays confirmed that ArcA indirectly controled the expression of citrate fermentation genes via regulating CitA-CitB system, while Fnr directly regulated but also indirectly modulated citrate fermentation genes via controling CitA-CitB system. Deletions of arcA and fnr significantly reduced the growth of Escherichia coli in M9 medium with a citrate carbon source. We conclude that both ArcA and Fnr can indirectly control the citrate utilization via CitA-CitB system, while Fnr can also directly regulate the expression of citrate fermentation genes in E. coli under anaerobic conditions.
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Affiliation(s)
- Fengwei Jiang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.,Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Xinxin Huang
- Technical Centre for Animal, Plant, and Food Inspection and Quarantine of Shanghai Customs, Shanghai, China
| | - Nicolle L Barbieri
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Catherine M Logue
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Lisa K Nolan
- Department of Infectious Disease, College of Veterinary Medicine, University of Georgia, Athens, Georgia, 30602, USA
| | - Ganwu Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.,Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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8
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Olivieri FA, Burastero O, Drusin SI, Defelipe LA, Wetzler DE, Turjanski A, Marti M. Conformational and Reaction Dynamic Coupling in Histidine Kinases: Insights from Hybrid QM/MM Simulations. J Chem Inf Model 2020; 60:833-842. [PMID: 31923359 DOI: 10.1021/acs.jcim.9b00806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Histidine kinases (HK) of bacterial two-component systems represent a hallmark of allosterism in proteins, being able to detect a signal through the sensor domain and transmit this information through the protein matrix to the kinase domain which, once active, autophosphorylates a specific histidine residue. Inactive-to-active transition results in a large conformational change that moves the kinase on top of the histidine. In the present work, we use several molecular simulation techniques (Molecular Dynamics, Hybrid QM/MM, and constant pH molecular dynamics) to study the activation and autophosphorylation reactions in L. plantarum WalK, a cis-acting HK. In agreement with previous results, we show that the chemical step requires tight coupling with the conformational step in order to maintain the histidine phosphoacceptor in the correct tautomeric state, with a reactive δ-nitrogen. During the conformational transition, the kinase domain is never released and walks along the HK helix axis, breaking and forming several conserved residue-based contacts. The phosphate transfer reaction is concerted in the transition state region and is catalyzed through the stabilization of the negative developing charge of transferring phosphate along the reaction.
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Affiliation(s)
- Federico A Olivieri
- Departamento de Quı́mica Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,Instituto de Quı́mica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET , Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina
| | - Osvaldo Burastero
- Departamento de Quı́mica Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,Instituto de Quı́mica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET , Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina
| | - Salvador I Drusin
- Departamento de Quı́mica Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,Instituto de Quı́mica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET , Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,Área Fı́sica, Departamento de Quı́mico-Fı́sica, Facultad de Ciencias Bioquı́micas y Farmacéuticas , Universidad Nacional de Rosario , Suipacha 531 , S2002LRK Rosario , Santa Fe , Argentina
| | - Lucas A Defelipe
- Departamento de Quı́mica Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,Instituto de Quı́mica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET , Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,European Molecular Biology Laboratory Hamburg , Notkestrasse 85 , D-22607 Hamburg , Germany
| | - Diana E Wetzler
- Departamento de Quı́mica Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,Instituto de Quı́mica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET , Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina
| | - Adrián Turjanski
- Departamento de Quı́mica Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,Instituto de Quı́mica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET , Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina
| | - Marcelo Marti
- Departamento de Quı́mica Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,Instituto de Quı́mica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET , Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina
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9
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Samanta S, Biswas P, Banerjee A, Bose A, Siddiqui N, Nambi S, Saini DK, Visweswariah SS. A universal stress protein in Mycobacterium smegmatis sequesters the cAMP-regulated lysine acyltransferase and is essential for biofilm formation. J Biol Chem 2020; 295:1500-1516. [PMID: 31882539 PMCID: PMC7008380 DOI: 10.1074/jbc.ra119.011373] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/19/2019] [Indexed: 01/08/2023] Open
Abstract
Universal stress proteins (USPs) are present in many bacteria, and their expression is enhanced under various environmental stresses. We have previously identified a USP in Mycobacterium smegmatis that is a product of the msmeg_4207 gene and is a substrate for a cAMP-regulated protein lysine acyltransferase (KATms; MSMEG_5458). Here, we explored the role of this USP (USP4207) in M. smegmatis and found that its gene is present in an operon that also contains genes predicted to encode a putative tripartite tricarboxylate transporter (TTT). Transcription of the TTT-usp4207 operon was induced in the presence of citrate and tartrate, perhaps by the activity of a divergent histidine kinase-response regulator gene pair. A usp4207-deleted strain had rough colony morphology and reduced biofilm formation compared with the WT strain; however, both normal colony morphology and biofilm formation were restored in a Δusp4207Δkatms strain. We identified several proteins whose acetylation was lost in the Δkatms strain, and whose transcript levels increased in M. smegmatis biofilms along with that of USP4207, suggesting that USP4207 insulates KATms from its other substrates in the cell. We propose that USP4207 sequesters KATms from diverse substrates whose activities are down-regulated by acylation but are required for biofilm formation, thus providing a defined role for this USP in mycobacterial physiology and stress responses.
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Affiliation(s)
- Sintu Samanta
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Priyanka Biswas
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Arka Banerjee
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Avipsa Bose
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Nida Siddiqui
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Subhalaxmi Nambi
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Deepak Kumar Saini
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Sandhya S Visweswariah
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India.
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10
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Sevilla E, Bes MT, González A, Peleato ML, Fillat MF. Redox-Based Transcriptional Regulation in Prokaryotes: Revisiting Model Mechanisms. Antioxid Redox Signal 2019; 30:1651-1696. [PMID: 30073850 DOI: 10.1089/ars.2017.7442] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
SIGNIFICANCE The successful adaptation of microorganisms to ever-changing environments depends, to a great extent, on their ability to maintain redox homeostasis. To effectively maintain the redox balance, cells have developed a variety of strategies mainly coordinated by a battery of transcriptional regulators through diverse mechanisms. Recent Advances: This comprehensive review focuses on the main mechanisms used by major redox-responsive regulators in prokaryotes and their relationship with the different redox signals received by the cell. An overview of the corresponding regulons is also provided. CRITICAL ISSUES Some regulators are difficult to classify since they may contain several sensing domains and respond to more than one signal. We propose a classification of redox-sensing regulators into three major groups. The first group contains one-component or direct regulators, whose sensing and regulatory domains are in the same protein. The second group comprises the classical two-component systems involving a sensor kinase that transduces the redox signal to its DNA-binding partner. The third group encompasses a heterogeneous group of flavin-based photosensors whose mechanisms are not always fully understood and are often involved in more complex regulatory networks. FUTURE DIRECTIONS Redox-responsive transcriptional regulation is an intricate process as identical signals may be sensed and transduced by different transcription factors, which often interplay with other DNA-binding proteins with or without regulatory activity. Although there is much information about some key regulators, many others remain to be fully characterized due to the instability of their clusters under oxygen. Understanding the mechanisms and the regulatory networks operated by these regulators is essential for the development of future applications in biotechnology and medicine.
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Affiliation(s)
- Emma Sevilla
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - María Teresa Bes
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - Andrés González
- 2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain.,4 Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - María Luisa Peleato
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - María F Fillat
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
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11
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CitAB Two-Component System-Regulated Citrate Utilization Contributes to Vibrio cholerae Competitiveness with the Gut Microbiota. Infect Immun 2019; 87:IAI.00746-18. [PMID: 30559220 DOI: 10.1128/iai.00746-18] [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: 09/30/2018] [Accepted: 12/09/2018] [Indexed: 01/05/2023] Open
Abstract
Citrate is a ubiquitous compound and can be utilized by many bacterial species, including enteric pathogens, as a carbon and energy source. Genes involved in citrate utilization have been extensively studied in some enteric bacteria, such as Klebsiella pneumoniae; however, their role in pathogenesis is still not clear. In this study, we investigated citrate utilization and regulation in Vibrio cholerae, the causative agent of cholera. The putative anaerobic citrate fermentation genes in V. cholerae, consisting of citCDEFXG, citS-oadGAB, and the two-component system (TCS) genes citAB, are highly homologous to those in K. pneumoniae Deletion analysis shows that these cit genes are essential for V. cholerae growth when citrate is the sole carbon source. The expression of citC and citS operons was dependent on citrate and CitAB, whose transcription was autorepressed and regulated by another TCS regulator, ArcA. In addition, citrate fermentation was under the control of catabolite repression. Mouse colonization experiments showed that V. cholerae can utilize citrate in vivo using the citrate fermentation pathway and that V. cholerae likely needs to compete with other members of the gut microbiota to access citrate in the gut.
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12
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Cormann KU, Baumgart M, Bott M. Structure-Based Design of Versatile Biosensors for Small Molecules Based on the PAS Domain of a Thermophilic Histidine Kinase. ACS Synth Biol 2018; 7:2888-2897. [PMID: 30525476 DOI: 10.1021/acssynbio.8b00348] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of biosensors for in vitro quantification of small molecules such as metabolites or man-made chemicals is still a major challenge. Here we show that engineered variants of the sensory PAS domain of the histidine kinase CitA of the thermophilic bacterium Geobacillus thermoleovorans represent promising alternatives to established biorecognition elements. By combining binding site grafting and rational design we constructed protein variants binding l-malate, ethylmalonate, or the aromatic compound phthalate instead of the native ligand citrate. Due to more favorable entropy contributions, the wild-type protein and its engineered variants exhibited increased (nano- to micromolar) affinities and improved enantioselectivity compared to CitA homologues of mesophilic organisms. Ligand binding was directly converted into an optical signal that was preserved after immobilization of the protein. A fluorescently labeled variant was used to quantify ethylmalonate, an urinary biomarker for ethylmalonic encephalopathy, in synthetic urine, thereby demonstrating the applicability of the sensor in complex samples.
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Affiliation(s)
- Kai U. Cormann
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Meike Baumgart
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany
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13
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Sensory domain contraction in histidine kinase CitA triggers transmembrane signaling in the membrane-bound sensor. Proc Natl Acad Sci U S A 2017; 114:3115-3120. [PMID: 28265100 DOI: 10.1073/pnas.1620286114] [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] [Indexed: 11/18/2022] Open
Abstract
Bacteria use membrane-integral sensor histidine kinases (HK) to perceive stimuli and transduce signals from the environment to the cytosol. Information on how the signal is transmitted across the membrane by HKs is still scarce. Combining both liquid- and solid-state NMR, we demonstrate that structural rearrangements in the extracytoplasmic, citrate-sensing Per-Arnt-Sim (PAS) domain of HK CitA are identical for the isolated domain in solution and in a longer construct containing the membrane-embedded HK and lacking only the kinase core. We show that upon citrate binding, the PAS domain contracts, resulting in a shortening of the C-terminal β-strand. We demonstrate that this contraction of the PAS domain, which is well characterized for the isolated domain, is the signal transmitted to the transmembrane (TM) helices in a CitA construct in liposomes. Putting the extracytoplasmic PAS domain into context of the membrane-embedded CitA construct slows down citrate-binding kinetics by at least a factor of 60, confirming that TM helix motions are linked to the citrate-binding event. Our results are confirmation of a hallmark of the HK signal transduction mechanism with atomic resolution on a full-length construct lacking only the kinase core domain.
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14
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Kaschner M, Schillinger O, Fettweiss T, Nutschel C, Krause F, Fulton A, Strodel B, Stadler A, Jaeger KE, Krauss U. A combination of mutational and computational scanning guides the design of an artificial ligand-binding controlled lipase. Sci Rep 2017; 7:42592. [PMID: 28218303 PMCID: PMC5316958 DOI: 10.1038/srep42592] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/11/2017] [Indexed: 11/09/2022] Open
Abstract
Allostery, i.e. the control of enzyme activity by a small molecule at a location distant from the enzyme’s active site, represents a mechanism essential for sustaining life. The rational design of allostery is a non-trivial task but can be achieved by fusion of a sensory domain, which responds to environmental stimuli with a change in its structure. Hereby, the site of domain fusion is difficult to predict. We here explore the possibility to rationally engineer allostery into the naturally not allosterically regulated Bacillus subtilis lipase A, by fusion of the citrate-binding sensor-domain of the CitA sensory-kinase of Klebsiella pneumoniae. The site of domain fusion was rationally determined based on whole-protein site-saturation mutagenesis data, complemented by computational evolutionary-coupling analyses. Functional assays, combined with biochemical and biophysical studies suggest a mechanism for control, similar but distinct to the one of the parent CitA protein, with citrate acting as an indirect modulator of Triton-X100 inhibition of the fusion protein. Our study demonstrates that the introduction of ligand-dependent regulatory control by domain fusion is surprisingly facile, suggesting that the catalytic mechanism of some enzymes may be evolutionary optimized in a way that it can easily be perturbed by small conformational changes.
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Affiliation(s)
- Marco Kaschner
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Oliver Schillinger
- Institute of Complex Systems ICS-6: Structural Biochemistry, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Timo Fettweiss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Christina Nutschel
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Frank Krause
- Nanolytics, Gesellschaft für Kolloidanalytik GmbH, Am Mühlenberg 11, 14476 Potsdam, Germany
| | - Alexander Fulton
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems ICS-6: Structural Biochemistry, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Andreas Stadler
- Jülich Centre for Neutron Science JCNS and Institute for Complex Systems ICS, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
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15
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Kallscheuer N, Vogt M, Bott M, Marienhagen J. Functional expression of plant-derived O-methyltransferase, flavanone 3-hydroxylase, and flavonol synthase in Corynebacterium glutamicum for production of pterostilbene, kaempferol, and quercetin. J Biotechnol 2017; 258:190-196. [PMID: 28143765 DOI: 10.1016/j.jbiotec.2017.01.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/16/2017] [Accepted: 01/24/2017] [Indexed: 01/02/2023]
Abstract
Plant polyphenols receive significant attention due to their anti-oxidative and health-promoting properties, and several microorganisms are currently engineered towards producing these valuable compounds. Previously, Corynebacterium glutamicum has been engineered for synthesizing polyphenol core structures such as the stilbene resveratrol and the (2S)-flavanone naringenin. Decoration of these compounds by O-methylation or hydroxylation would provide access to polyphenols of even higher commercial interest. In this study, introduction of a heterologous O-methyltransferase into a resveratrol-producing C. glutamicum strain allowed synthesis of 42mg/L (0.16mM) of the di-O-methylated pterostilbene from p-coumaric acid. A prerequisite for reaching this product titer was a fusion of O-methyltransferase with the maltose-binding protein of Escherichia coli lacking its signal peptide, thereby increasing the solubility of the O-methyltransferase. Furthermore, expression of heterologous dioxygenase genes in (2S)-flavanone-producing C. glutamicum strains enabled the production of flavanonols and flavonols starting from the phenylpropanoids p-coumaric acid and caffeic acid. For the flavonols kaempferol and quercetin, maximum product titers of 23mg/L (0.08mM) and 10mg/L (0.03mM) could be achieved, respectively. The obtained results demonstrate that C. glutamicum is a suitable host organism for the production of more complex plant polyphenols.
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Affiliation(s)
- Nicolai Kallscheuer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Michael Vogt
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany.
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16
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Adams FG. A key regulatory mechanism of antimicrobial resistance in pathogenic Acinetobacter baumannii. MICROBIOLOGY AUSTRALIA 2017. [DOI: 10.1071/ma17046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Acinetobacter baumannii is a Gram-negative bacterial pathogen that has become a pressing global health issue in recent decades. Although virulence factors for this pathogen have been identified, details of how they are regulated are largely unknown. One widely employed regulatory mechanism that bacteria, such as A. baumannii, have adopted is through two component signal transduction systems (TCS). TCS consist of two proteins; a histidine kinase and response regulator. The histidine kinase allows the bacterium to sense alterations in the extracellular milieu, transmitting the information to the response regulator which prompts the cell to modify gene expression levels accordingly. Bacteria can encode multiple TCS, where each system can mediate specific responses to particular conditions or stressors. Identifying those conditions in which these TCS are expressed, and the genes they regulate known as their ‘regulon', is vital for understanding how A. baumannii survives and persists within the hospital environment or the human host during infection. As we enter the post-antibiotic era, knowledge of TCS could prove to be invaluable, as they offer an alternative target for the treatment of multidrug resistant bacterial infections.
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17
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Unden G, Strecker A, Kleefeld A, Kim OB. C4-Dicarboxylate Utilization in Aerobic and Anaerobic Growth. EcoSal Plus 2016; 7. [PMID: 27415771 DOI: 10.1128/ecosalplus.esp-0021-2015] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Indexed: 06/06/2023]
Abstract
C4-dicarboxylates and the C4-dicarboxylic amino acid l-aspartate support aerobic and anaerobic growth of Escherichia coli and related bacteria. In aerobic growth, succinate, fumarate, D- and L-malate, L-aspartate, and L-tartrate are metabolized by the citric acid cycle and associated reactions. Because of the interruption of the citric acid cycle under anaerobic conditions, anaerobic metabolism of C4-dicarboxylates depends on fumarate reduction to succinate (fumarate respiration). In some related bacteria (e.g., Klebsiella), utilization of C4-dicarboxylates, such as tartrate, is independent of fumarate respiration and uses a Na+-dependent membrane-bound oxaloacetate decarboxylase. Uptake of the C4-dicarboxylates into the bacteria (and anaerobic export of succinate) is achieved under aerobic and anaerobic conditions by different sets of secondary transporters. Expression of the genes for C4-dicarboxylate metabolism is induced in the presence of external C4-dicarboxylates by the membrane-bound DcuS-DcuR two-component system. Noncommon C4-dicarboxylates like l-tartrate or D-malate are perceived by cytoplasmic one-component sensors/transcriptional regulators. This article describes the pathways of aerobic and anaerobic C4-dicarboxylate metabolism and their regulation. The citric acid cycle, fumarate respiration, and fumarate reductase are covered in other articles and discussed here only in the context of C4-dicarboxylate metabolism. Recent aspects of C4-dicarboxylate metabolism like transport, sensing, and regulation will be treated in more detail. This article is an updated version of an article published in 2004 in EcoSal Plus. The update includes new literature, but, in particular, the sections on the metabolism of noncommon C4-dicarboxylates and their regulation, on the DcuS-DcuR regulatory system, and on succinate production by engineered E. coli are largely revised or new.
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Affiliation(s)
- Gottfried Unden
- Institute for Microbiology und Wine Research, Johannes Gutenberg-University, 55099 Mainz, Germany
| | - Alexander Strecker
- Institute for Microbiology und Wine Research, Johannes Gutenberg-University, 55099 Mainz, Germany
| | - Alexandra Kleefeld
- Institute for Microbiology und Wine Research, Johannes Gutenberg-University, 55099 Mainz, Germany
| | - Ok Bin Kim
- Department of Life Sciences, Ewha Womans University, 120-750 Seoul, Korea
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18
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Unden G, Wörner S, Monzel C. Cooperation of Secondary Transporters and Sensor Kinases in Transmembrane Signalling: The DctA/DcuS and DcuB/DcuS Sensor Complexes of Escherichia coli. Adv Microb Physiol 2016; 68:139-67. [PMID: 27134023 DOI: 10.1016/bs.ampbs.2016.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many membrane-bound sensor kinases require accessory proteins for function. The review describes functional control of membrane-bound sensors by transporters. The C4-dicarboxylate sensor kinase DcuS requires the aerobic or anaerobic C4-dicarboxylate transporters DctA or DcuB, respectively, for function and forms DctA/DcuS or DcuB/DcuS sensor complexes. Free DcuS is in the permanent (ligand independent) ON state. The DctA/DcuS and DcuB/DcuS complexes, on the other hand, control expression in response to C4-dicarboxylates. In DctA/DcuS, helix 8b of DctA and the PASC domain of DcuS are involved in interaction. The stimulus is perceived by the extracytoplasmic sensor domain (PASP) of DcuS. The signal is transmitted across the membrane by a piston-type movement of TM2 of DcuS which appears to be pulled (by analogy to the homologous citrate sensor CitA) by compaction of PASP after C4-dicarboxylate binding. In the cytoplasm, the signal is perceived by the PASC domain of DcuS. PASC inhibits together with DctA the kinase domain of DcuS which is released after C4-dicarboxylate binding. DcuS exhibits two modes for regulating expression of target genes. At higher C4-dicarboxylate levels, DcuS is part of the DctA/DcuS complex and in the C4-dicarboxylate-responsive form which stimulates expression of target genes in response to the concentration of the C4-dicarboxylates (catabolic use of C4-dicarboxylates, mode I regulation). At limiting C4-dicarboxylate concentrations (≤0.05mM), expression of DctA drops and free DcuS appears. Free DcuS is in the permanent ON state (mode II regulation) and stimulates low level (C4-dicarboxylate independent) DctA synthesis for DctA/DcuS complex formation and anabolic C4-dicarboxylate uptake.
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Affiliation(s)
- G Unden
- Institute for Microbiology and Wine Research, University of Mainz, Mainz, Germany.
| | - S Wörner
- Institute for Microbiology and Wine Research, University of Mainz, Mainz, Germany
| | - C Monzel
- Institute for Microbiology and Wine Research, University of Mainz, Mainz, Germany
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19
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Abstract
Environmental citrate or malonate is degraded by a variety of aerobic or anaerobic bacteria. For selected examples, the genes encoding the specific enzymes of the degradation pathway are described together with the encoded proteins and their catalytic mechanisms. Aerobic bacteria degrade citrate readily by the basic enzyme equipment of the cell if a specific transporter for citrate is available. Anaerobic degradation of citrate in Klebsiella pneumoniae requires the so-called substrate activation module to convert citrate into its thioester with the phosphoribosyl dephospho-CoA prosthetic group of citrate lyase. The citryl thioester is subsequently cleaved into oxaloacetate and the acetyl thioester, from which a new citryl thioester is formed as the turnover continues. The degradation of malonate likewise includes a substrate activation module with a phosphoribosyl dephospho-CoA prosthetic group. The machinery gets ready for turnover after forming the acetyl thioester with the prosthetic group. The acetyl residue is then exchanged by a malonyl residue, which is easily decarboxylated with the regeneration of the acetyl thioester. This equipment suffices for aerobic growth on malonate, since ATP is produced via the oxidation of acetate. Anaerobic growth on citrate or malonate, however, depends on additional enzymes of a so-called energy conservation module. This allows the conversion of decarboxylation energy into an electrochemical gradient of Na+ ions. In citrate-fermenting K. pneumoniae, the Na+ gradient is formed by the oxaloacetate decarboxylase and mainly used to drive the active transport of citrate into the cell. To use this energy source for this purpose is possible, since ATP is generated by substrate phosphorylation in the well-known sequence from pyruvate to acetate. In the malonate-fermenting bacterium Malonomonas rubra, however, no reactions for substrate level phosphorylation are available and the Na+ gradient formed in the malonate decarboxylation reaction must therefore be used as the driving force for ATP synthesis.
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20
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Graf S, Broll C, Wissig J, Strecker A, Parowatkin M, Unden G. CitA (citrate) and DcuS (C4-dicarboxylate) sensor kinases in thermophilic Geobacillus kaustophilus and Geobacillus thermodenitrificans. MICROBIOLOGY-SGM 2015; 162:127-137. [PMID: 26346610 DOI: 10.1099/mic.0.000171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The thermophilic Geobacillus thermodenitrificans and Geobacillus kaustophilus are able to use citrate or C4-dicarboxylates like fumarate or succinate as the substrates for growth. The genomes of the sequenced Geobacillus strains (nine strains) each encoded a two-component system of the CitA family. The sensor kinase of G. thermodenitrificans (termed CitAGt) was able to replace CitA of Escherichia coli (CitAEc) in a heterologous complementation assay restoring expression of the CitAEc-dependent citC-lacZ reporter gene and anaerobic growth on citrate. Complementation was specific for citrate. The sensor kinase of G. kaustophilus (termed DcuSGk) was able to replace DcuSEc of E. coli. It responded in the heterologous expression system to C4-dicarboxylates and to citrate, suggesting that DcuSGk is, like DcuSEc, a C4-dicarboxylate sensor with a side-activity for citrate. DcuSGk, unlike the homologous DctS from Bacillus subtilis, required no binding protein for function in the complementation assay. Thus, the thermophilic G. thermodenitrificans and G. kaustophilus contain citrate and C4-dicarboxylate sensor kinases of the CitA and DcuS type, respectively, and retain function and substrate specificity under mesophilic growth conditions in E. coli.
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Affiliation(s)
- Sabrina Graf
- Institute for Microbiology and Wine Research, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Constanze Broll
- Institute for Microbiology and Wine Research, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Juliane Wissig
- Institute for Microbiology and Wine Research, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Alexander Strecker
- Institute for Microbiology and Wine Research, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Maria Parowatkin
- Institute for Microbiology and Wine Research, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Gottfried Unden
- Institute for Microbiology and Wine Research, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
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21
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Otten A, Brocker M, Bott M. Metabolic engineering of Corynebacterium glutamicum for the production of itaconate. Metab Eng 2015; 30:156-165. [DOI: 10.1016/j.ymben.2015.06.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/23/2015] [Accepted: 06/11/2015] [Indexed: 10/23/2022]
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22
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Bhate MP, Molnar KS, Goulian M, DeGrado WF. Signal transduction in histidine kinases: insights from new structures. Structure 2015; 23:981-94. [PMID: 25982528 DOI: 10.1016/j.str.2015.04.002] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 03/22/2015] [Accepted: 03/30/2015] [Indexed: 10/23/2022]
Abstract
Histidine kinases (HKs) are major players in bacterial signaling. There has been an explosion of new HK crystal structures in the last 5 years. We globally analyze the structures of HKs to yield insights into the mechanisms by which signals are transmitted to and across protein structures in this family. We interpret known enzymological data in the context of new structural data to show how asymmetry across the dimer interface is a key feature of signal transduction in HKs, and discuss how different HK domains undergo asymmetric to symmetric transitions during signal transduction and catalysis. A thermodynamic framework for signaling that encompasses these various properties is presented, and the consequences of weak thermodynamic coupling are discussed. The synthesis of observations from enzymology, structural biology, protein engineering, and thermodynamics paves the way for a deeper molecular understanding of HK signal transduction.
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Affiliation(s)
- Manasi P Bhate
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, 555 Mission Bay Boulevard South, Box 3122, San Francisco, CA 94158, USA
| | - Kathleen S Molnar
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, 555 Mission Bay Boulevard South, Box 3122, San Francisco, CA 94158, USA; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark Goulian
- Department of Biology and Department of Physics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, 555 Mission Bay Boulevard South, Box 3122, San Francisco, CA 94158, USA.
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23
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Molnar KS, Bonomi M, Pellarin R, Clinthorne GD, Gonzalez G, Goldberg SD, Goulian M, Sali A, DeGrado WF. Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ. Structure 2014; 22:1239-1251. [PMID: 25087511 PMCID: PMC4322757 DOI: 10.1016/j.str.2014.04.019] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 04/17/2014] [Accepted: 04/29/2014] [Indexed: 01/16/2023]
Abstract
Bacteria transduce signals across the membrane using two-component systems (TCSs), consisting of a membrane-spanning sensor histidine kinase and a cytoplasmic response regulator. In gram-negative bacteria, the PhoPQ TCS senses cations and antimicrobial peptides, yet little is known about the structural changes involved in transmembrane signaling. We construct a model of PhoQ signal transduction using Bayesian inference, based on disulfide crosslinking data and homologous crystal structures. The data are incompatible with a single conformation but are instead consistent with two interconverting structures. These states differ in membrane depth of the periplasmic acidic patch and the reciprocal displacement of diagonal helices along the dimer interface. Studies of multiple histidine kinases suggest this repacking might be a common mode of signal transduction in sensor His-kinase receptors. Because a similar scissors model has been ruled out in CheA-linked chemoreceptors, the evidence suggests that sensor His-kinase and CheA-linked receptors possess different signaling mechanisms.
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Affiliation(s)
- Kathleen S Molnar
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group19104, USA, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Massimiliano Bonomi
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Riccardo Pellarin
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Graham D Clinthorne
- Pharmacological Sciences Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gabriel Gonzalez
- Biochemistry and Molecular Biophysics Graduate Group19104, USA, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Shalom D Goldberg
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
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Guo Y, Li Y, Su L, Chang D, Liu W, Wang T, Yuan Y, Fang X, Wang J, Li T, Fang C, Dai W, Liu C. Comparative genomic analysis of Klebsiella pneumonia (LCT-KP214) and a mutant strain (LCT-KP289) obtained after spaceflight. BMC Genomics 2014; 15:589. [PMID: 25015528 PMCID: PMC4226956 DOI: 10.1186/1471-2164-15-589] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 07/07/2014] [Indexed: 01/07/2023] Open
Abstract
Background With the development of space science, it is important to analyze the relationship between the space environment and genome variations that might cause phenotypic changes in microbes. Klebsiella pneumoniae is commonly found on the human body and is resistant to multiple drugs. To study space-environment-induced genome variations and drug resistance changes, K. pneumoniae was carried into outer space by the Shenzhou VIII spacecraft. Results The K. pneumoniae strain LCT-KP289 was selected after spaceflight based on its phenotypic differences compared to the ground-control strain. Analysis of genomic structural variations revealed one inversion, 25 deletions, fifty-nine insertions, two translocations and six translocations with inversions. In addition, 155 and 400 unique genes were observed in LCT-KP214 and LCT-KP289, respectively, including the gene encoding dihydroxyacetone kinase, which generates the ATP and NADH required for microbial growth. Furthermore, a large number of mutant genes were related to transport and metabolism. Phylogenetic analysis revealed that most genes in these two strains had a dN/dS value greater than 1, indicating that the strain diversity increased after spaceflight. Analysis of drug-resistance phenotypes revealed that the K. pneumoniae strain LCT-KP289 was resistant to sulfamethoxazole, whereas the control strain, LCT-KP214, was not; both strains were resistant to benzylpenicillin, ampicillin, lincomycin, vancomycin, chloramphenicol and streptomycin. The sulfamethoxazole resistance may be associated with sequences in Scaffold7 in LCT-KP289, which were not observed in LCT-K214; this scaffold contained the gene sul1. In the strain LCT-KP289, we also observed a drug-resistance integron containing emrE (confers multidrug resistance) and ant (confers resistance to spectinomycin, streptomycin, tobramycin, kanamycin, sisomicin, dibekacin, and gentamicin). The gene ampC (confers resistance to penicillin, cephalosporin-ii and cephalosporin-i) was present near the integron. In addition, 30 and 26 drug-resistance genes were observed in LCT-KP289 and LCT-KP214, respectively. Conclusions Comparison of a K. pneumoniae strain obtained after spaceflight with the ground-control strain revealed genome variations and phenotypic changes and elucidated the genomic basis of the acquired drug resistance. These data pave the way for future studies on the effects of spaceflight.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Wenkui Dai
- Nanlou Respiratory Diseases Department, Chinese PLA General Hospital, Beijing 100853, China.
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Gudipaty SA, McEvoy MM. The histidine kinase CusS senses silver ions through direct binding by its sensor domain. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1656-61. [PMID: 24948475 DOI: 10.1016/j.bbapap.2014.06.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 06/01/2014] [Indexed: 01/27/2023]
Abstract
The Cus system of Escherichia coli aids in protection of cells from high concentrations of Ag(I) and Cu(I). The histidine kinase CusS of the CusRS two-component system functions as a Ag(I)/Cu(I)-responsive sensor kinase and is essential for induction of the genes encoding the CusCFBA efflux pump. In this study, we have examined the molecular features of the sensor domain of CusS in order to understand how a metal-responsive histidine kinase senses specific metal ions. We find that the predicted periplasmic sensor domain of CusS directly interacts with Ag(I) ions and undergoes a conformational change upon metal binding. Metal binding also enhances the tendency of the domain to dimerize. These findings suggest a model for activation of the histidine kinase through metal binding events in the periplasmic sensor domain.
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Affiliation(s)
- Swapna A Gudipaty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Megan M McEvoy
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA; Department of Soil, Water and Environmental Sciences, University of Arizona, Tucson, AZ 85721, USA.
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26
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Honda Y, Kirimura K. Generation of circularly permuted fluorescent-protein-based indicators for in vitro and in vivo detection of citrate. PLoS One 2013; 8:e64597. [PMID: 23717638 PMCID: PMC3661591 DOI: 10.1371/journal.pone.0064597] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/15/2013] [Indexed: 11/30/2022] Open
Abstract
Indicators for citrate, particularly those applicable to its in vivo detection and quantitation, have attracted much interest in both biochemical studies and industrial applications since citrate is a key metabolic intermediate playing important roles in living cells. We generated novel fluorescence indicators for citrate by fusing the circularly permuted fluorescent protein (cpFP) and the periplasmic domain of the bacterial histidine kinase CitA, which can bind to citrate with high specificity. The ratiometric fluorescent signal change was observed with one of these cpFP-based indicators, named CF98: upon addition of citrate, the excitation peak at 504 nm increased proportionally to the decrease in the peak at 413 nm, suitable for build-in quantitative estimation of the binding compound. We confirmed that CF98 can be used for detecting citrate in vitro at millimolar levels in the range of 0.1 to 50 mM with high selectivity; even in the presence of other organic acids such as isocitrate and malate, the fluorescence intensity of CF98 remains unaffected. We finally demonstrated the in vivo applicability of CF98 to estimation of the intracellular citrate concentration in Escherichia coli co-expressing the genes encoding CF98 and the citrate carrier CitT. The novel indicator CF98 can be a specific and simple detection tool for citrate in vitro and a non-invasive tool for real-time estimation of intracellular concentrations of the compound in vivo.
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Affiliation(s)
- Yuki Honda
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Kohtaro Kirimura
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
- * E-mail:
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Bott M, Eikmanns BJ. TCA Cycle and Glyoxylate Shunt of Corynebacterium glutamicum. CORYNEBACTERIUM GLUTAMICUM 2013. [DOI: 10.1007/978-3-642-29857-8_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Bott M, Brocker M. Two-component signal transduction in Corynebacterium glutamicum and other corynebacteria: on the way towards stimuli and targets. Appl Microbiol Biotechnol 2012; 94:1131-50. [PMID: 22539022 PMCID: PMC3353115 DOI: 10.1007/s00253-012-4060-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/26/2012] [Accepted: 03/27/2012] [Indexed: 11/30/2022]
Abstract
In bacteria, adaptation to changing environmental conditions is often mediated by two-component signal transduction systems. In the prototypical case, a specific stimulus is sensed by a membrane-bound histidine kinase and triggers autophosphorylation of a histidine residue. Subsequently, the phosphoryl group is transferred to an aspartate residue of the cognate response regulator, which then becomes active and mediates a specific response, usually by activating and/or repressing a set of target genes. In this review, we summarize the current knowledge on two-component signal transduction in Corynebacterium glutamicum. This Gram-positive soil bacterium is used for the large-scale biotechnological production of amino acids and can also be applied for the synthesis of a wide variety of other products, such as organic acids, biofuels, or proteins. Therefore, C. glutamicum has become an important model organism in industrial biotechnology and in systems biology. The type strain ATCC 13032 possesses 13 two-component systems and the role of five has been elucidated in recent years. They are involved in citrate utilization (CitAB), osmoregulation and cell wall homeostasis (MtrAB), adaptation to phosphate starvation (PhoSR), adaptation to copper stress (CopSR), and heme homeostasis (HrrSA). As C. glutamicum does not only face changing conditions in its natural environment, but also during cultivation in industrial bioreactors of up to 500 m(3) volume, adaptability can also be crucial for good performance in biotechnological production processes. Detailed knowledge on two-component signal transduction and regulatory networks therefore will contribute to both the application and the systemic understanding of C. glutamicum and related species.
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Affiliation(s)
- Michael Bott
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany.
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Signal perception by the secretion stress-responsive CssRS two-component system in Bacillus subtilis. J Bacteriol 2012; 194:1800-14. [PMID: 22307758 DOI: 10.1128/jb.05767-11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The CssRS two-component system responds to heat and secretion stresses in Bacillus subtilis by controlling expression of HtrA and HtrB chaperone-type proteases and positively autoregulating its own expression. Here we report on the features of the CssS extracellular loop domain that are involved in signal perception and on CssS subcellular localization. Individual regions of the CssS extracellular loop domain contribute differently to signal perception and activation. The conserved hydrophilic 26-amino-acid segment juxtaposed to transmembrane helix 1 is involved in the switch between the deactivated and activated states, while the conserved 19-amino-acid hydrophobic segment juxtaposed to transmembrane 2 is required for signal perception and/or transduction. Perturbing the size of the extracellular loop domain increases CssS kinase activity and makes it unresponsive to secretion stress. CssS is localized primarily at the septum but is also found in a punctate pattern with lower intensity throughout the cell cylinder. Moreover, the CssRS-controlled HtrA and HtrB proteases are randomly distributed in foci throughout the cell surface, with more HtrB than HtrA foci in unstressed cells.
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30
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Silva-Jiménez H, García-Fontana C, Cadirci BH, Ramos-González MI, Ramos JL, Krell T. Study of the TmoS/TmoT two-component system: towards the functional characterization of the family of TodS/TodT like systems. Microb Biotechnol 2011; 5:489-500. [PMID: 22212183 PMCID: PMC3815326 DOI: 10.1111/j.1751-7915.2011.00322.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The two‐component system TmoS/TmoT controls the expression of the toluene‐4‐monooxygenase pathway in Pseudomonas mendocina RK1 via modulation of PtmoX activity. The TmoS/TmoT system belongs to the family of TodS/TodT like proteins. The sensor kinase TmoS is a 108 kDa protein composed of seven different domains. Using isothermal titration calorimetry we show that purified TmoS binds a wide range of aromatic compounds with high affinities. Tightest ligand binding was observed for toluene (KD = 150 nM), which corresponds to the highest affinity measured between an effector and a sensor kinase. Other compounds with affinities in the nanomolar range include benzene, the 3 xylene isomers, styrene, nitrobenzene or p‐chlorotoluene. We demonstrate that only part of the ligands that bind to TmoS increase protein autophosphorylation in vitro and consequently pathway expression in vivo. These compounds are referred to as agonists. Other TmoS ligands, termed antagonists, failed to increase TmoS autophosphorylation, which resulted in their incapacity to stimulate gene expression in vivo. We also show that TmoS saturated with different agonists differs in their autokinase activities. The effector screening of gene expression showed that promoter activity of PtmoX and PtodX (controlled by the TodS/TodT system) is mediated by the same set of 22 compounds. The common structural feature of these compounds is the presence of a single aromatic ring. Among these ligands, toluene was the most potent inducer of both promoter activities. Information on the TmoS/TmoT and TodS/TodT system combined with a sequence analysis of family members permits to identify distinct features that define this protein family.
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Affiliation(s)
- Hortencia Silva-Jiménez
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda 1, Granada, Spain.
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Ewald JC, Reich S, Baumann S, Frommer WB, Zamboni N. Engineering genetically encoded nanosensors for real-time in vivo measurements of citrate concentrations. PLoS One 2011; 6:e28245. [PMID: 22164251 PMCID: PMC3229521 DOI: 10.1371/journal.pone.0028245] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 11/04/2011] [Indexed: 11/19/2022] Open
Abstract
Citrate is an intermediate in catabolic as well as biosynthetic pathways and is an important regulatory molecule in the control of glycolysis and lipid metabolism. Mass spectrometric and NMR based metabolomics allow measuring citrate concentrations, but only with limited spatial and temporal resolution. Methods are so far lacking to monitor citrate levels in real-time in-vivo. Here, we present a series of genetically encoded citrate sensors based on Förster resonance energy transfer (FRET). We screened databases for citrate-binding proteins and tested three candidates in vitro. The citrate binding domain of the Klebsiella pneumoniae histidine sensor kinase CitA, inserted between the FRET pair Venus/CFP, yielded a sensor highly specific for citrate. We optimized the peptide linkers to achieve maximal FRET change upon citrate binding. By modifying residues in the citrate binding pocket, we were able to construct seven sensors with different affinities spanning a concentration range of three orders of magnitude without losing specificity. In a first in vivo application we show that E. coli maintains the capacity to take up glucose or acetate within seconds even after long-term starvation.
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Affiliation(s)
- Jennifer C. Ewald
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- PhD Program in Systems Biology of Complex Diseases, ETH Zurich, Zurich, Switzerland
| | - Sabrina Reich
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Stephan Baumann
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Wolf B. Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- * E-mail:
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Lacal J, García-Fontana C, Callejo-García C, Ramos JL, Krell T. Physiologically relevant divalent cations modulate citrate recognition by the McpS chemoreceptor. J Mol Recognit 2011; 24:378-85. [PMID: 21360620 DOI: 10.1002/jmr.1101] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The McpS chemoreceptor of Pseudomonas putida KT2440 recognizes six different tricarboxylic acid (TCA) cycle intermediates. However, the magnitude of the chemotactic response towards these compounds differs largely, which has led to distinguish between strong attractants (malate, succinate, fumarate, oxaloacetate) and weak attractants (citrate, isocitrate). Citrate is abundantly present in plant tissues and root exudates and can serve as the only carbon source for growth. Citrate is known to form complexes with divalent cations which are also abundantly present in natural habitats of this bacterium. We have used isothermal titration calorimetry to study the formation of citrate-metal ion complexes. In all cases binding was entropy driven but significant differences in affinity were observed ranging from K(D)=157 µM (for Mg(2+)) to 3 µM (for Ni(2+)). Complex formation occurred over a range of pH and ionic strength. The ligand binding domain of McpS (McpS-LBD) was found to bind free citrate, but not complexes with physiologically relevant Mg(2+) and Ca(2+). In contrast, complexes with divalent cations which are present as trace elements (Co(2+), Cd(2+) and Ni(2+)) were recognized by McpS-LBD. This discrimination differs from other citrate sensing proteins. These results are discussed in the context of the three dimensional structure of free citrate and its complex with Mg(2+). Chemotaxis assays using P. putida revealed that taxis towards the strong attractant malate is strongly reduced in the presence of free citrate. However, this reduction is much less important in the presence of citrate-Mg(2+) complexes. The physiological relevance of these findings is discussed.
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Affiliation(s)
- Jesús Lacal
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda, 1, Granada 18008, Spain
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Perry J, Koteva K, Wright G. Receptor domains of two-component signal transduction systems. MOLECULAR BIOSYSTEMS 2011; 7:1388-98. [PMID: 21347487 DOI: 10.1039/c0mb00329h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Two-component signal transduction systems are found ubiquitously in prokaryotes, and in archaea, fungi, yeast and some plants, where they regulate physiologic and molecular processes at both transcriptional and post-transcriptional levels. Two-component systems sense changes in environmental conditions when a specific ligand binds to the receptor domain of the histidine kinase sensory component. The structures of many histidine kinase receptors are known, including those which sense extracellular and cytoplasmic signals. In this review, we discuss the basic architecture of two-component signalling circuits, including known system ligands, structure and function of both receptor and signalling domains, the chemistry of phosphotransfer, and cross-talk between different two-component pathways. Given the importance of these systems in regulating cellular responses, many biochemical techniques have been developed for their study and analysis. We therefore also review current methods used to study two-component signalling, including a new affinity-based proteomics approach used to study inducible resistance to the antibiotic vancomycin through the VanSR two-component signal transduction system.
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Affiliation(s)
- Julie Perry
- MG DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1200 Main St W, Hamilton, Ontario, Canada
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Target genes, consensus binding site, and role of phosphorylation for the response regulator MtrA of Corynebacterium glutamicum. J Bacteriol 2010; 193:1237-49. [PMID: 21183673 DOI: 10.1128/jb.01032-10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The two-component signal transduction system consisting of the sensor kinase MtrB and the response regulator MtrA is highly conserved in corynebacteria and mycobacteria. Whereas mtrA of Mycobacterium tuberculosis was reported to be essential, we recently succeeded in creating ΔmtrAB and ΔmtrA deletion mutants of Corynebacterium glutamicum and provided evidence that mepA and nlpC, both encoding putative cell wall peptidases, are directly repressed by MtrA, whereas proP and betP, both encoding carriers for compatible solutes, are directly activated by MtrA. In the present study, novel MtrA target genes were identified, including mepB, encoding another putative cell wall peptidase. The repressor or activator functions of MtrA correlate with the distance between the MtrA binding site and the transcriptional start site. From the identified binding sites within 20 target promoters, a 19-bp MtrA consensus motif was derived which represents a direct repeat of 8 base pairs separated by 3 base pairs. Gene expression of a strain containing MtrA with a D53N mutation instead of wild-type MtrA resembled that of a ΔmtrA mutant, indicating that MtrA is active in its phosphorylated form. This result was confirmed by electrophoretic mobility shift assays with phosphorylated MtrA which showed an increased binding affinity.
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Krell T, Lacal J, Busch A, Silva-Jiménez H, Guazzaroni ME, Ramos JL. Bacterial sensor kinases: diversity in the recognition of environmental signals. Annu Rev Microbiol 2010; 64:539-59. [PMID: 20825354 DOI: 10.1146/annurev.micro.112408.134054] [Citation(s) in RCA: 255] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteria sense and respond to a wide range of physical and chemical signals. Central to sensing and responding to these signals are two-component systems, which have a sensor histidine kinase (SK) and a response regulator (RR) as basic components. Here we review the different molecular mechanisms by which these signals are integrated and modulate the phosphorylation state of SKs. Apart from the basic mechanism, which consists of signal recognition by the SK that leads to an alteration of its autokinase activity and subsequently a change in the RR phosphorylation state, a variety of alternative modes have evolved. The biochemical data available on SKs, particularly their molecular interactions with signals, nucleotides, and their cognate RRs, are also reviewed.
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Affiliation(s)
- Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
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Scheu PD, Kim OB, Griesinger C, Unden G. Sensing by the membrane-bound sensor kinase DcuS: exogenous versus endogenous sensing of C4-dicarboxylates in bacteria. Future Microbiol 2010; 5:1383-402. [DOI: 10.2217/fmb.10.103] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bacteria are able to grow at the expense of both common (succinate, L-malate, fumarate and aspartate) and uncommon (L-tartrate and D-malate) C4-dicarboxylates, which are components of central metabolism. Two types of sensors/regulators responding to the C4-dicarboxylates function in Escherichia coli, Bacillus, Lactobacillus and related bacteria. The first type represents membrane-integral two-component systems, while the second includes cytoplasmic LysR-type transcriptional regulators. The difference in location and substrate specificity allows the exogenous induction of metabolic genes by common C4-dicarboxylates, and endogenous induction by uncommon C4-dicarboxylates. The two-component sensors, DcuS and CitA, are composed of an extracellular Per-Arnt-Sim (PAS) domain, two transmembrane helices, a cytoplasmic PAS and the kinase domain. The structures of the extracellular PAS domains of DcuS and CitA have been determined in the ligand-bound and the apo form. Binding of the ligand results in closing and compaction of the binding site, and the structural change gives rise to piston-type movement of the adjacent membrane-spanning helix-2, and signal transmission to the cytoplasmic side. For DcuS, a membrane-embedded construct has been developed that suggests (by experimentation and modeling) that plasticity of the cytoplasmic PAS domain is central to signal transduction from the membrane to the kinase. Sensor kinase DcuS of E. coli requires the C4-dicarboxylate transporters DctA or DcuB as co-sensors for function under aerobic and anaerobic conditions, respectively. DcuB contains a regulatory site that controls the function of DcuS and is independent from the transport region. Therefore, DcuS senses C4-dicarboxylates in two independent modes, responding to the effector concentration and the metabolic flux of extracellular C4-dicarboxylates.
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Affiliation(s)
- Patrick D Scheu
- Institute for Microbiology & Wine Research, University of Mainz, 55099 Mainz, Germany
| | - Ok Bin Kim
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Christian Griesinger
- Max-Planck-Institute for Biophysical Chemistry, Department of NMR-Based Structural Biology, Göttingen, Germany
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Transmembrane polar interactions are required for signaling in the Escherichia coli sensor kinase PhoQ. Proc Natl Acad Sci U S A 2010; 107:8141-6. [PMID: 20404199 DOI: 10.1073/pnas.1003166107] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PhoQ is the transmembrane sensor histidine kinase of the bacterial phoPQ two-component system, which detects and responds to divalent cations and to antimicrobial peptides, and can trigger virulence. Despite their ubiquitous importance in bacterial signaling, the structure and mechanism of the sensor kinases are not fully understood. In particular, the mechanism by which the signal is propagated through the transmembrane (TM) region remains unclear. We have identified a critical asparagine residue in the second TM helix of PhoQ. Replacement of this Asn202 with a variety of hydrophobic amino acids results in a protein that is blind to signal, fails to activate transcription of PhoQ-dependent genes, and abrogates transcription when coexpressed with wild-type PhoQ. Analysis of other two-component kinase sequences indicated that many such proteins contain similarly conserved polar residues, and the structure of one such domain shows a polar residue proximal to an extended cavity near the center of the TM bundle. We therefore examined the role of Asn202 in PhoQ. Our analysis indicated that its kinase function is dependent on the polarity of Asn202, rather than its precise structure or position in the TM region; it can be displaced up or down one turn of TM helix 2, or even moved to the adjacent TM helix 1. The presence of polar TM amino acids among many diverse sensor kinases suggest a widespread mechanism of two-component signal transduction; we speculate that they might stabilize underpacked water-containing cavities that can accommodate conformational changes required for switching from phosphatase to kinase-competent conformations.
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Nan B, Liu X, Zhou Y, Liu J, Zhang L, Wen J, Zhang X, Su XD, Wang YP. From signal perception to signal transduction: ligand-induced dimeric switch of DctB sensory domain in solution. Mol Microbiol 2010; 75:1484-94. [PMID: 20149110 DOI: 10.1111/j.1365-2958.2010.07069.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Sinorhizobium meliloti DctB is a typical transmembrane sensory histidine kinase, which senses C(4)-dicarboxylic acids (DCA) and regulates the expression of DctA, the DCA transporter. We previously reported the crystal structures of its periplasmic sensory domain (DctBp) in apo and succinate-bound states, and these structures showed dramatic conformational changes at dimeric level. Here we show a ligand-induced dimeric switch in solution and a strong correlation between DctBp's dimerization states and the in vivo activities of DctB. Using site-directed mutagenesis, we identify important determinants for signal perception and transduction. Specifically, we show that the ligand-binding pocket is essential for DCA-induced 'on' activity of DctB. Mutations at different sections of DctBp's dimerization interface can lock full-length DctB at either 'on' or 'off' state, independent of ligand binding. Taken together, these results suggest that DctBp's signal perception and transduction occur through a 'ligand-induced dimeric switch', in which the changes in the dimeric conformations upon ligand binding are responsible for the signal transduction in DctB.
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Affiliation(s)
- Beiyan Nan
- National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
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Chen YT, Liao TL, Wu KM, Lauderdale TL, Yan JJ, Huang IW, Lu MC, Lai YC, Liu YM, Shu HY, Wang JT, Su IJ, Tsai SF. Genomic diversity of citrate fermentation in Klebsiella pneumoniae. BMC Microbiol 2009; 9:168. [PMID: 19682387 PMCID: PMC2735749 DOI: 10.1186/1471-2180-9-168] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Accepted: 08/15/2009] [Indexed: 11/16/2022] Open
Abstract
Background It has long been recognized that Klebsiella pneumoniae can grow anaerobically on citrate. Genes responsible for citrate fermentation of K. pneumoniae were known to be located in a 13-kb gene cluster on the chromosome. By whole genome comparison of the available K. pneumoniae sequences (MGH 78578, 342, and NTUH-K2044), however, we discovered that the fermentation gene cluster was present in MGH 78578 and 342, but absent in NTUH-K2044. In the present study, the previously unknown genome diversity of citrate fermentation among K. pneumoniae clinical isolates was investigated. Results Using a genomic microarray containing probe sequences from multiple K. pneumoniae strains, we investigated genetic diversity among K. pneumoniae clinical isolates and found that a genomic region containing the citrate fermentation genes was not universally present in all strains. We confirmed by PCR analysis that the gene cluster was detectable in about half of the strains tested. To demonstrate the metabolic function of the genomic region, anaerobic growth of K. pneumoniae in artificial urine medium (AUM) was examined for ten strains with different clinical histories and genomic backgrounds, and the citrate fermentation potential was found correlated with the genomic region. PCR detection of the genomic region yielded high positive rates among a variety of clinical isolates collected from urine, blood, wound infection, and pneumonia. Conserved genetic organizations in the vicinity of the citrate fermentation gene clusters among K. pneumoniae, Salmonella enterica, and Escherichia coli suggest that the13-kb genomic region were not independently acquired. Conclusion Not all, but nearly half of the K. pneumoniae clinical isolates carry the genes responsible for anaerobic growth on citrate. Genomic variation of citrate fermentation genes in K. pneumoniae may contribute to metabolic diversity and adaptation to variable nutrient conditions in different environments.
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Affiliation(s)
- Ying-Tsong Chen
- Division of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan, Republic of China.
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Perozzo R, Folkers G, Scapozza L. Thermodynamics of Protein–Ligand Interactions: History, Presence, and Future Aspects. J Recept Signal Transduct Res 2009; 24:1-52. [PMID: 15344878 DOI: 10.1081/rrs-120037896] [Citation(s) in RCA: 266] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The understanding of molecular recognition processes of small ligands and biological macromolecules requires a complete characterization of the binding energetics and correlation of thermodynamic data with interacting structures involved. A quantitative description of the forces that govern molecular associations requires determination of changes of all thermodynamic parameters, including free energy of binding (deltaG), enthalpy (deltaH), and entropy (deltaS) of binding and the heat capacity change (deltaCp). A close insight into the binding process is of significant and practical interest, since it provides the fundamental know-how for development of structure-based molecular design-strategies. The only direct method to measure the heat change during complex formation at constant temperature is provided by isothermal titration calorimetry (ITC). With this method one binding partner is titrated into a solution containing the interaction partner, thereby generating or absorbing heat. This heat is the direct observable that can be quantified by the calorimeter. The use of ITC has been limited due to the lack of sensitivity, but recent developments in instrument design permit to measure heat effects generated by nanomol (typically 10-100) amounts of reactants. ITC has emerged as the primary tool for characterizing interactions in terms of thermodynamic parameters. Because heat changes occur in almost all chemical and biochemical processes, ITC can be used for numerous applications, e.g., binding studies of antibody-antigen, protein-peptide, protein-protein, enzyme-inhibitor or enzyme-substrate, carbohydrate-protein, DNA-protein (and many more) interactions as well as enzyme kinetics. Under appropriate conditions data analysis from a single experiment yields deltaH, K(B), the stoichiometry (n), deltaG and deltaS of binding. Moreover, ITC experiments performed at different temperatures yield the heat capacity change (deltaCp). The informational content of thermodynamic data is large, and it has been shown that it plays an important role in the elucidation of binding mechanisms and, through the link to structural data, also in rational drug design. In this review we will present a comprehensive overview to ITC by giving some historical background to calorimetry, outline some critical experimental and data analysis aspects, discuss the latest developments, and give three recent examples of studies published with respect to macromolecule-ligand interactions that have utilized ITC technology.
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Affiliation(s)
- Remo Perozzo
- Department of Chemistry and Applied BioSciences, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland.
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Grose JH, Sundwall E, Rutter J. Regulation and function of yeast PAS kinase: a role in the maintenance of cellular integrity. Cell Cycle 2009; 8:1824-32. [PMID: 19440050 DOI: 10.4161/cc.8.12.8799] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The inability to coordinate cellular metabolic processes with the cellular and organismal nutrient environment leads to a variety of disorders, including diabetes and obesity. Nutrient-sensing protein kinases, such as AMPK and mTOR, play a pivotal role in metabolic regulation and are promising therapeutic targets for the treatment of disease. In this Extra View, we describe another member of the nutrient-sensing protein kinase group, PAS kinase, which plays a role in the regulation of glucose utilization in both mammals and yeast. PAS kinase deficient mice are resistant to high fat diet-induced weight gain, insulin resistance and hepatic triglyceride hyperaccumulation, suggesting a role for PAS kinase in the regulation of glucose and lipid metabolism in mammals. Likewise, PAS kinase deficient yeast display altered glucose partitioning, favoring glycogen biosynthesis at the expense of cell wall biosynthesis. As a result, PAS kinase deficient yeast are sensitive to cell wall perturbing agents. This partitioning of glucose in response to PAS kinase activation is due to phosphorylation of Ugp1, the enzyme primarily responsible for UDP-glucose production. The two yeast PAS kinase homologs, Psk1 and Psk2, are activated by two stimuli, cell integrity stress and nonfermentative carbon sources. We review what is known about yeast PAS kinase and describe a genetic screen that may help elucidate pathways involved in PAS kinase activation and function.
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Affiliation(s)
- Julianne H Grose
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA.
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Citrate utilization by Corynebacterium glutamicum is controlled by the CitAB two-component system through positive regulation of the citrate transport genes citH and tctCBA. J Bacteriol 2009; 191:3869-80. [PMID: 19376865 DOI: 10.1128/jb.00113-09] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this work, the molecular basis of aerobic citrate utilization by the gram-positive bacterium Corynebacterium glutamicum was studied. Genome analysis revealed the presence of two putative citrate transport systems. The permease encoded by citH belongs to the citrate-Mg(2+):H(+)/citrate-Ca(2+):H(+) symporter family, whereas the permease encoded by the tctCBA operon is a member of the tripartite tricarboxylate transporter family. The expression of citH or tctCBA in Escherichia coli enabled this species to utilize citrate aerobically, indicating that both CitH and TctABC are functional citrate transporters. Growth tests with the recombinant E. coli strains indicated that CitH is active with Ca(2+) or Sr(2+) but not with Mg(2+) and that TctABC is active with Ca(2+) or Mg(2+) but not with Sr(2+). We could subsequently show that, with 50 mM citrate as the sole carbon and energy source, the C. glutamicum wild type grew best when the minimal medium was supplemented with CaCl(2) but that MgCl(2) and SrCl(2) also supported growth. Each of the two transporters alone was sufficient for growth on citrate. The expression of citH and tctCBA was activated by citrate in the growth medium, independent of the presence or absence of glucose. This activation was dependent on the two-component signal transduction system CitAB, composed of the sensor kinase CitA and the response regulator CitB. CitAB belongs to the CitAB/DcuSR family of two-component systems, whose members control the expression of genes that are involved in the transport and catabolism of tricarboxylates or dicarboxylates. C. glutamicum CitAB is the first member of this family studied in Actinobacteria.
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Characterization of CitA-CitB signal transduction activating genes involved in anaerobic citrate catabolism in Escherichia coli. Biosci Biotechnol Biochem 2009; 73:346-50. [PMID: 19202292 DOI: 10.1271/bbb.80586] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In Escherichia coli, CitA is a membrane-associated sensor histidine kinase that phosphorylates CitB, the response regulator. It is predicated to play a key role in anaerobic citrate catabolism. The citrate-binding site in CitA is located within its periplasmic domain, while the cytoplasmic domain (CitA-C) is involved in autophosphorylation. We found that autophosphorylation in vitro of CitA-C was induced by DTT. Using the whole set of CitA-C derivatives containing Cys-Ala substitution(s), Cys at 529 was found to be essential to the redox-sensing of autophosphorylation. The phosphorylated CitA-C transferred a phosphate to CitB. DNase-I footprinting assay indicated that CitB specifically bound on the intergenic region between the citA and citC genes. These results characterize the molecular mechanism of the CitA-CitB signal transduction system in E. coli.
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44
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Emami K, Topakas E, Nagy T, Henshaw J, Jackson KA, Nelson KE, Mongodin EF, Murray JW, Lewis RJ, Gilbert HJ. Regulation of the xylan-degrading apparatus of Cellvibrio japonicus by a novel two-component system. J Biol Chem 2008; 284:1086-96. [PMID: 18922794 DOI: 10.1074/jbc.m805100200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The microbial degradation of lignocellulose biomass is not only an important biological process but is of increasing industrial significance in the bioenergy sector. The mechanism by which the plant cell wall, an insoluble composite structure, activates the extensive repertoire of microbial hydrolytic enzymes required to catalyze its degradation is poorly understood. Here we have used a transposon mutagenesis strategy to identify a genetic locus, consisting of two genes that modulate the expression of xylan side chain-degrading enzymes in the saprophytic bacterium Cellvibrio japonicus. Significantly, the locus encodes a two-component signaling system, designated AbfS (sensor histidine kinase) and AbfR (response regulator). The AbfR/S two-component system is required to activate the expression of the suite of enzymes that remove the numerous side chains from xylan, but not the xylanases that hydrolyze the beta1,4-linked xylose polymeric backbone of this polysaccharide. Studies on the recombinant sensor domain of AbfS (AbfS(SD)) showed that it bound to decorated xylans and arabinoxylo-oligosaccharides, but not to undecorated xylo-oligosaccharides or other plant structural polysaccharides/oligosaccharides. The crystal structure of AbfS(SD) was determined to a resolution of 2.6A(.) The overall fold of AbfS(SD) is that of a classical Per Arndt Sim domain with a central antiparallel four-stranded beta-sheet flanked by alpha-helices. Our data expand the number of molecules known to bind to the sensor domain of two-component histidine kinases to include complex carbohydrates. The biological rationale for a regulatory system that induces enzymes that remove the side chains of xylan, but not the hydrolases that cleave the backbone of the polysaccharide, is discussed.
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Affiliation(s)
- Kaveh Emami
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Framlington Place, Newcastle-upon-Tyne, NE2 4HH, United Kingdom
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Scheu P, Sdorra S, Liao YF, Wegner M, Basché T, Unden G, Erker W. Polar accumulation of the metabolic sensory histidine kinases DcuS and CitA in Escherichia coli. Microbiology (Reading) 2008; 154:2463-2472. [DOI: 10.1099/mic.0.2008/018614-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Patrick Scheu
- Institute of Microbiology and Wine Research, Johannes Gutenberg University, Mainz, Becherweg 15, 55099 Mainz, Germany
| | - Sven Sdorra
- Institute of Physical Chemistry, Johannes Gutenberg University, Mainz, Welderweg 11, 55099 Mainz, Germany
| | - Yun-Feng Liao
- Institute of Physical Chemistry, Johannes Gutenberg University, Mainz, Welderweg 11, 55099 Mainz, Germany
| | - Maria Wegner
- Institute of Physical Chemistry, Johannes Gutenberg University, Mainz, Welderweg 11, 55099 Mainz, Germany
| | - Thomas Basché
- Institute of Physical Chemistry, Johannes Gutenberg University, Mainz, Welderweg 11, 55099 Mainz, Germany
| | - Gottfried Unden
- Institute of Microbiology and Wine Research, Johannes Gutenberg University, Mainz, Becherweg 15, 55099 Mainz, Germany
| | - Wolfgang Erker
- Institute of Physical Chemistry, Johannes Gutenberg University, Mainz, Welderweg 11, 55099 Mainz, Germany
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The vibrio cholerae hybrid sensor kinase VieS contributes to motility and biofilm regulation by altering the cyclic diguanylate level. J Bacteriol 2008; 190:6439-47. [PMID: 18676667 DOI: 10.1128/jb.00541-08] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phosphorelay systems are important mediators of signal transduction during bacterial adaptation to new environments. Previously we described the vieSAB operon, encoding a putative three-protein component phosphorelay involved in regulating Vibrio cholerae virulence gene expression. At least part of the regulatory activity of VieSAB is exerted through the cyclic diguanylate (c-di-GMP)-degrading activity of the putative response regulator VieA. So far no direct evidence that VieSAB encodes a phosphorelay system exists. In addition, the role VieS plays in modulating VieA activity remains unclear. To address these questions, we expressed and purified VieA and a soluble cytoplasmic portion of VieS and used them in autophosphorylation and phosphotransfer assays. These assays showed that VieS has kinase activity in vitro and is able to selectively phosphorylate VieA. A phenotypic comparison revealed that deletion of vieS results in increased biofilm production comparable to that seen for deletion of vieA, whereas motility was decreased only slightly in the DeltavieS mutant compared to the profound defect observed in a DeltavieA mutant. We also found that the DeltavieS strain has a lower level of vieA transcript and, similar to a DeltavieA mutant, an increased intracellular level of c-di-GMP. Further analysis using site-directed vieA mutants showed that some of the phenotypes observed were due to the phosphorylation status of VieA. The evidence presented in this report is the first to link VieS and VieA biochemically and genetically, lending support to the hypothesis that these proteins function together in a signaling system.
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Cheung J, Bingman CA, Reyngold M, Hendrickson WA, Waldburger CD. Crystal structure of a functional dimer of the PhoQ sensor domain. J Biol Chem 2008; 283:13762-70. [PMID: 18348979 PMCID: PMC2376233 DOI: 10.1074/jbc.m710592200] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2007] [Revised: 03/17/2008] [Indexed: 11/14/2022] Open
Abstract
The PhoP-PhoQ two-component system is a well studied bacterial signaling system that regulates virulence and stress response. Catalytic activity of the histidine kinase sensor protein PhoQ is activated by low extracellular concentrations of divalent cations such as Mg2+, and subsequently the response regulator PhoP is activated in turn through a classic phosphotransfer pathway that is typical in such systems. The PhoQ sensor domains of enteric bacteria contain an acidic cluster of residues (EDDDDAE) that has been implicated in direct binding to divalent cations. We have determined crystal structures of the wild-type Escherichia coli PhoQ periplasmic sensor domain and of a mutant variant in which the acidic cluster was neutralized to conservative uncharged residues (QNNNNAQ). The PhoQ domain structure is similar to that of DcuS and CitA sensor domains, and this PhoQ-DcuS-CitA (PDC) sensor fold is seen to be distinct from the superficially similar PAS domain fold. Analysis of the wild-type structure reveals a dimer that allows for the formation of a salt bridge across the dimer interface between Arg-50' and Asp-179 and with nickel ions bound to aspartate residues in the acidic cluster. The physiological importance of the salt bridge to in vivo PhoQ function has been confirmed by mutagenesis. The mutant structure has an alternative, non-physiological dimeric association.
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Affiliation(s)
- Jonah Cheung
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York 10032, USA
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Determination of the physiological dimer interface of the PhoQ sensor domain. J Mol Biol 2008; 379:656-65. [PMID: 18468622 DOI: 10.1016/j.jmb.2008.04.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Revised: 04/02/2008] [Accepted: 04/03/2008] [Indexed: 11/22/2022]
Abstract
PhoQ is the transmembrane sensor kinase of the phoPQ two-component system, which detects and responds to divalent cations and antimicrobial peptides and can trigger bacterial virulence. Despite their ubiquity and importance in bacterial signaling, the structure and molecular mechanism of the sensor kinases is not fully understood. Frequently, signals are transmitted from a periplasmic domain in these proteins to the cytoplasmic kinase domains via an extended dimeric interface, and the PhoQ protein would appear to follow this paradigm. However, the isolated truncated periplasmic domain of PhoQ dimerizes poorly, so it has been difficult to distinguish the relevant interface in crystal structures of the PhoQ periplasmic domain. Thus, to determine the arrangement of the periplasmic domains of Escherichia coli PhoQ in the physiological homodimer, disulfide-scanning mutagenesis was used. Single cysteine substitutions were introduced along the N-terminal helix of the periplasmic region, and the degree of cross-linking in each protein variant was determined by Western blotting and immunodetection. The results were subjected to periodicity analysis to generate a profile that provides information concerning the C(beta) distances between corresponding residues at the interface. This profile, together with a rigid-body search procedure, side-chain placement, and energy minimization, was used to build a model of the dimer arrangement. The final model proved to be highly compatible with one of the PhoQ crystal structures, 3BQ8, indicating that 3BQ8 is representative of the physiological arrangement. The model of the periplasmic region is also compatible with a full-length PhoQ protein in which a four-helix bundle forms in the membrane. The membrane four-helix bundle has been proposed for other sensor kinases and is thought to have a role in the mechanism of signal transduction; our model supports the idea that signaling through a membrane four-helix bundle is a widespread mechanism in the transmembrane sensor kinases.
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Sevvana M, Vijayan V, Zweckstetter M, Reinelt S, Madden DR, Herbst-Irmer R, Sheldrick GM, Bott M, Griesinger C, Becker S. A ligand-induced switch in the periplasmic domain of sensor histidine kinase CitA. J Mol Biol 2008; 377:512-23. [PMID: 18258261 DOI: 10.1016/j.jmb.2008.01.024] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2007] [Revised: 01/08/2008] [Accepted: 01/10/2008] [Indexed: 11/26/2022]
Abstract
Sensor histidine kinases of two-component signal-transduction systems are essential for bacteria to adapt to variable environmental conditions. However, despite their prevalence, it is not well understood how extracellular signals such as ligand binding regulate the activity of these sensor kinases. CitA is the sensor histidine kinase in Klebsiella pneumoniae that regulates the transport and anaerobic metabolism of citrate in response to its extracellular concentration. We report here the X-ray structures of the periplasmic sensor domain of CitA in the citrate-free and citrate-bound states. A comparison of the two structures shows that ligand binding causes a considerable contraction of the sensor domain. This contraction may represent the molecular switch that activates transmembrane signaling in the receptor.
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Affiliation(s)
- Madhumati Sevvana
- Department of Structural Chemistry, University of Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
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Krämer J, Fischer JD, Zientz E, Vijayan V, Griesinger C, Lupas A, Unden G. Citrate sensing by the C4-dicarboxylate/citrate sensor kinase DcuS of Escherichia coli: binding site and conversion of DcuS to a C4-dicarboxylate- or citrate-specific sensor. J Bacteriol 2007; 189:4290-8. [PMID: 17416661 PMCID: PMC1913419 DOI: 10.1128/jb.00168-07] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Accepted: 03/19/2007] [Indexed: 11/20/2022] Open
Abstract
The histidine protein kinase DcuS of Escherichia coli senses C(4)-dicarboxylates and citrate by a periplasmic domain. The closely related sensor kinase CitA binds citrate, but no C(4)-dicarboxylates, by a homologous periplasmic domain. CitA is known to bind the three carboxylate and the hydroxyl groups of citrate by sites C1, C2, C3, and H. DcuS requires the same sites for C(4)-dicarboxylate sensing, but only C2 and C3 are highly conserved. It is shown here that sensing of citrate by DcuS required the same sites. Binding of citrate to DcuS, therefore, was similar to binding of C(4)-dicarboxylates but different from that of citrate binding in CitA. DcuS could be converted to a C(4)-dicarboxylate-specific sensor (DcuS(DC)) by mutating residues of sites C1 and C3 or of some DcuS-subtype specific residues. Mutations around site C1 aimed at increasing the size and accessibility of the site converted DcuS to a citrate-specific sensor (DcuS(Cit)). DcuS(DC) and DcuS(Cit) had complementary effector specificities and responded either to C(4)-dicarboxylates or to citrate and mesaconate. The results imply that DcuS binds citrate (similar to the C(4)-dicarboxylates) via the C(4)-dicarboxylate part of the molecule. Sites C2 and C3 are essential for binding of two carboxylic groups of citrate or of C(4)-dicarboxylates; sites C1 and H are required for other essential purposes.
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Affiliation(s)
- J Krämer
- Institut für Mikrobiologie und Weinforschung, Johannes Gutenberg-Universität Mainz, Becherweg 15, 55099 Mainz, Germany
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