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Liang Q, Chen N, Wang W, Zhang B, Luo J, Zhong Y, Zhang F, Zhang Z, Martín-Rodríguez AJ, Wang Y, Xiang L, Xiong X, Hu R, Zhou Y. Co-occurrence of ST412 Klebsiella pneumoniae isolates with hypermucoviscous and non-mucoviscous phenotypes in a short-term hospitalized patient. mSystems 2024:e0026224. [PMID: 38904378 DOI: 10.1128/msystems.00262-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/10/2024] [Indexed: 06/22/2024] Open
Abstract
Hypermucoviscosity (HMV) is a phenotype that is commonly associated with hypervirulence in Klebsiella pneumoniae. The factors that contribute to the emergence of HMV subpopulations remain unclear. In this study, eight K. pneumoniae strains were recovered from an inpatient who had been hospitalized for 20 days. Three of the isolates exhibited a non-HMV phenotype, which was concomitant with higher biofilm formation than the other five HMV isolates. All eight isolates were highly susceptible to serum killing, albeit HMV strains were remarkably more infective than non-HMV counterparts in a mouse model of infection. Whole genome sequencing (WGS) showed that the eight isolates belonged to the K57-ST412 lineage. Average nucleotide identity (FastANIb) analysis indicated that eight isolates share 99.96% to 99.99% similarity and were confirmed to be the same clone. Through comparative genomics analysis, 12 non-synonymous mutations were found among these isolates, eight of which in the non-HMV variants, including rmpA (c.285delG) and wbaP (c.1305T > A), which are assumed to be associated with the non-HMV phenotype. Mutations in manB (c.1318G > A), dmsB (c.577C > T) and tkt (c.1928C > A) occurred in HMV isolates only. RNA-Seq revealed transcripts of genes involved in energy metabolism, carbohydrate metabolism and membrane transport, including cysP, cydA, narK, tktA, pduQ, aceB, metN, and lsrA, to be significantly dysregulated in the non-HMV strains, suggesting a contribution to HMV phenotype development. This study suggests that co-occurrence of HMV and non-HMV phenotypes in the same clonal population may be mediated by mutational mechanisms as well as by certain genes involved in membrane transport and central metabolism. IMPORTANCE K. pneumoniae with a hypermucoviscosity (HMV) phenotype is a community-acquired pathogen that is associated with increased invasiveness and pathogenicity, and underlying diseases are the most common comorbid risk factors inducing metastatic complications. HMV was earlier attributed to the overproduction of capsular polysaccharide, and more data point to the possibility of several causes contributing to this bacterial phenotype. Here, we describe a unique event in which the same clonal population showed both HMV and non-HMV characteristics. Studies have demonstrated that this process is influenced by mutational processes and genes related to transport and central metabolism. These findings provide fresh insight into the mechanisms behind co-occurrence of HMV and non-HMV phenotypes in monoclonal populations as well as potentially being critical in developing strategies to control the further spread of HMV K. pneumoniae.
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Affiliation(s)
- Qinghua Liang
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
- Department of Laboratory Medicine, Yilong County People's Hospital, Nanchong, China
| | - Nan Chen
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Wei Wang
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Biying Zhang
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Jinjing Luo
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Ying Zhong
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Feiyang Zhang
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Zhikun Zhang
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Alberto J Martín-Rodríguez
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Ying Wang
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Li Xiang
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Xia Xiong
- Department of Dermatology, The Affiliated Hospital,Southwest Medical University, Luzhou, China
| | - Renjing Hu
- Department of Laboratory Medicine, Jiangnan University Medical Center, Wuxi, China
| | - Yingshun Zhou
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
- Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medicine University, Luzhou, China
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Magalon A. History of Maturation of Prokaryotic Molybdoenzymes-A Personal View. Molecules 2023; 28:7195. [PMID: 37894674 PMCID: PMC10609526 DOI: 10.3390/molecules28207195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
In prokaryotes, the role of Mo/W enzymes in physiology and bioenergetics is widely recognized. It is worth noting that the most diverse family of Mo/W enzymes is exclusive to prokaryotes, with the probable existence of several of them from the earliest forms of life on Earth. The structural organization of these enzymes, which often include additional redox centers, is as diverse as ever, as is their cellular localization. The most notable observation is the involvement of dedicated chaperones assisting with the assembly and acquisition of the metal centers, including Mo/W-bisPGD, one of the largest organic cofactors in nature. This review seeks to provide a new understanding and a unified model of Mo/W enzyme maturation.
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Affiliation(s)
- Axel Magalon
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13402 Marseille, France
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Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia coli. mSystems 2023; 8:e0090422. [PMID: 36537814 PMCID: PMC9948699 DOI: 10.1128/msystems.00904-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
There is an urgent need for strategies to discover secondary drugs to prevent or disrupt antimicrobial resistance (AMR), which is causing >700,000 deaths annually. Here, we demonstrate that tetracycline-resistant (TetR) Escherichia coli undergoes global transcriptional and metabolic remodeling, including downregulation of tricarboxylic acid cycle and disruption of redox homeostasis, to support consumption of the proton motive force for tetracycline efflux. Using a pooled genome-wide library of single-gene deletion strains, at least 308 genes, including four transcriptional regulators identified by our network analysis, were confirmed as essential for restoring the fitness of TetR E. coli during treatment with tetracycline. Targeted knockout of ArcA, identified by network analysis as a master regulator of this new compensatory physiological state, significantly compromised fitness of TetR E. coli during tetracycline treatment. A drug, sertraline, which generated a similar metabolome profile as the arcA knockout strain, also resensitized TetR E. coli to tetracycline. We discovered that the potentiating effect of sertraline was eliminated upon knocking out arcA, demonstrating that the mechanism of potential synergy was through action of sertraline on the tetracycline-induced ArcA network in the TetR strain. Our findings demonstrate that therapies that target mechanistic drivers of compensatory physiological states could resensitize AMR pathogens to lost antibiotics. IMPORTANCE Antimicrobial resistance (AMR) is projected to be the cause of >10 million deaths annually by 2050. While efforts to find new potent antibiotics are effective, they are expensive and outpaced by the rate at which new resistant strains emerge. There is desperate need for a rational approach to accelerate the discovery of drugs and drug combinations that effectively clear AMR pathogens and even prevent the emergence of new resistant strains. Using tetracycline-resistant (TetR) Escherichia coli, we demonstrate that gaining resistance is accompanied by loss of fitness, which is restored by compensatory physiological changes. We demonstrate that transcriptional regulators of the compensatory physiologic state are promising drug targets because their disruption increases the susceptibility of TetR E. coli to tetracycline. Thus, we describe a generalizable systems biology approach to identify new vulnerabilities within AMR strains to rationally accelerate the discovery of therapeutics that extend the life span of existing antibiotics.
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Cruz E, Haeberle AL, Westerman TL, Durham ME, Suyemoto MM, Knodler LA, Elfenbein JR. Nonredundant Dimethyl Sulfoxide Reductases Influence Salmonella enterica Serotype Typhimurium Anaerobic Growth and Virulence. Infect Immun 2023; 91:e0057822. [PMID: 36722978 PMCID: PMC9933680 DOI: 10.1128/iai.00578-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 02/02/2023] Open
Abstract
Facultative anaerobic enteric pathogens can utilize a diverse array of alternate electron acceptors to support anaerobic metabolism and thrive in the hypoxic conditions within the mammalian gut. Dimethyl sulfoxide (DMSO) is produced by methionine catabolism and can act as an alternate electron acceptor to support anaerobic respiration. The DMSO reductase complex consists of three subunits, DmsA, DmsB, and DmsC, and allows bacteria to grow anaerobically with DMSO as an electron acceptor. The genomes of nontyphoidal Salmonella enterica encode three putative dmsABC operons, but the impact of the apparent genetic redundancy in DMSO reduction on the fitness of nontyphoidal S. enterica during infection remains unknown. We hypothesized that DMSO reduction would be needed for S. enterica serotype Typhimurium to colonize the mammalian gut. We demonstrate that an S. Typhimurium mutant with loss of function in all three putative DMSO reductases (ΔdmsA3) poorly colonizes the mammalian intestine when the microbiota is intact and when inflammation is absent. DMSO reduction enhances anaerobic growth through nonredundant contributions of two of the DMSO reductases. Furthermore, DMSO reduction influences virulence by increasing expression of the type 3 secretion system 2 and reducing expression of the type 3 secretion system 1. Collectively, our data demonstrate that the DMSO reductases of S. Typhimurium are functionally nonredundant and suggest DMSO is a physiologically relevant electron acceptor that supports S. enterica fitness in the gut.
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Affiliation(s)
- E. Cruz
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - A. L. Haeberle
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - T. L. Westerman
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - M. E. Durham
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - M. M. Suyemoto
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - L. A. Knodler
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - J. R. Elfenbein
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
- Food Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
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5
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Rosenbaum FP, Poehlein A, Daniel R, Müller V. Energy‐conserving dimethyl sulfoxide reduction in the acetogenic bacterium
Moorella thermoacetica. Environ Microbiol 2022; 24:2000-2012. [DOI: 10.1111/1462-2920.15971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Florian P. Rosenbaum
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences Johann Wolfgang Goethe University Frankfurt Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics Georg‐August University Göttingen Göttingen 37077 Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics Georg‐August University Göttingen Göttingen 37077 Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences Johann Wolfgang Goethe University Frankfurt Germany
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Leimkühler S. The biosynthesis of the molybdenum cofactors in Escherichia coli. Environ Microbiol 2020; 22:2007-2026. [PMID: 32239579 DOI: 10.1111/1462-2920.15003] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 12/29/2022]
Abstract
The biosynthesis of the molybdenum cofactor (Moco) is highly conserved among all kingdoms of life. In all molybdoenzymes containing Moco, the molybdenum atom is coordinated to a dithiolene group present in the pterin-based 6-alkyl side chain of molybdopterin (MPT). In general, the biosynthesis of Moco can be divided into four steps in in bacteria: (i) the starting point is the formation of the cyclic pyranopterin monophosphate (cPMP) from 5'-GTP, (ii) in the second step the two sulfur atoms are inserted into cPMP leading to the formation of MPT, (iii) in the third step the molybdenum atom is inserted into MPT to form Moco and (iv) in the fourth step bis-Mo-MPT is formed and an additional modification of Moco is possible with the attachment of a nucleotide (CMP or GMP) to the phosphate group of MPT, forming the dinucleotide variants of Moco. This review presents an update on the well-characterized Moco biosynthesis in the model organism Escherichia coli including novel discoveries from the recent years.
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Affiliation(s)
- Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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Kappler U, Nasreen M, McEwan A. New insights into the molecular physiology of sulfoxide reduction in bacteria. Adv Microb Physiol 2019; 75:1-51. [PMID: 31655735 DOI: 10.1016/bs.ampbs.2019.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Sulfoxides occur in biology as products of the S-oxygenation of small molecules as well as in peptides and proteins and their formation is often associated with oxidative stress and can affect biological function. In bacteria, sulfoxide damage can be reversed by different types of enzymes. Thioredoxin-dependent peptide methionine sulfoxide reductases (MSR proteins) repair oxidized methionine residues and are found in all Domains of life. In bacteria MSR proteins are often found in the cytoplasm but in some bacteria, including pathogenic Neisseria, Streptococci, and Haemophilus they are extracytoplasmic. Mutants lacking MSR proteins are often sensitive to oxidative stress and in pathogens exhibit decreased virulence as indicated by reduced survival in host cell or animal model systems. Molybdenum enzymes are also known to reduce S-oxides and traditionally their physiological role was considered to be in anaerobic respiration using dimethylsulfoxide (DMSO) as an electron acceptor. However, it now appears that some enzymes (MtsZ) of the DMSO reductase family of Mo enzymes use methionine sulfoxide as preferred physiological substrate and thus may be involved in scavenging/recycling of this amino acid. Similarly, an enzyme (MsrP/YedY) of the sulfite oxidase family of Mo enzymes has been shown to be involved in repair of methionine sulfoxides in periplasmic proteins. Again, some mutants deficient in Mo-dependent sulfoxide reductases exhibit reduced virulence, and there is evidence that these Mo enzymes and some MSR systems are induced by hypochlorite produced by the innate immune system. This review describes recent advances in the understanding of the molecular microbiology of MSR systems and the broadening of the role of Mo-dependent sulfoxide reductase to encompass functions beyond anaerobic respiration.
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Affiliation(s)
- Ulrike Kappler
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Marufa Nasreen
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Alastair McEwan
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
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8
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Xiong L, Jian H, Xiao X. Deep-Sea Bacterium Shewanella piezotolerans WP3 Has Two Dimethyl Sulfoxide Reductases in Distinct Subcellular Locations. Appl Environ Microbiol 2017; 83:e01262-17. [PMID: 28687647 PMCID: PMC5583501 DOI: 10.1128/aem.01262-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 06/30/2017] [Indexed: 11/20/2022] Open
Abstract
Dimethyl sulfoxide (DMSO) acts as a substantial sink for dimethyl sulfide (DMS) in deep waters and is therefore considered a potential electron acceptor supporting abyssal ecosystems. Shewanella piezotolerans WP3 was isolated from west Pacific deep-sea sediments, and two functional DMSO respiratory subsystems are essential for maximum growth of WP3 under in situ conditions (4°C/20 MPa). However, the relationship between these two subsystems and the electron transport pathway underlying DMSO reduction by WP3 remain unknown. In this study, both DMSO reductases (type I and type VI) in WP3 were found to be functionally independent despite their close evolutionary relationship. Moreover, immunogold labeling of DMSO reductase subunits revealed that the type I DMSO reductase was localized on the outer leaflet of the outer membrane, whereas the type VI DMSO reductase was located within the periplasmic space. CymA, a cytoplasmic membrane-bound tetraheme c-type cytochrome, served as a preferential electron transport protein for the type I and type VI DMSO reductases, in which type VI accepted electrons from CymA in a DmsE- and DmsF-independent manner. Based on these results, we proposed a core electron transport model of DMSO reduction in the deep-sea bacterium S. piezotolerans WP3. These results collectively suggest that the possession of two sets of DMSO reductases with distinct subcellular localizations may be an adaptive strategy for WP3 to achieve maximum DMSO utilization in deep-sea environments.IMPORTANCE As the dominant methylated sulfur compound in deep oceanic water, dimethyl sulfoxide (DMSO) has been suggested to play an important role in the marine biogeochemical cycle of the volatile anti-greenhouse gas dimethyl sulfide (DMS). Two sets of DMSO respiratory systems in the deep-sea bacterium Shewanella piezotolerans WP3 have previously been identified to mediate DMSO reduction under in situ conditions (4°C/20 MPa). Here, we report that the two DMSO reductases (type I and type VI) in WP3 have distinct subcellular localizations, in which type I DMSO reductase is localized to the exterior surface of the outer membrane and type VI DMSO reductase resides in the periplasmic space. A core electron transport model of DMSO reduction in WP3 was constructed based on genetic and physiological data. These results will contribute to a comprehensive understanding of the adaptation mechanisms of anaerobic respiratory systems in benthic microorganisms.
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Affiliation(s)
- Lei Xiong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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Connelly KRS, Stevenson C, Kneuper H, Sargent F. Biosynthesis of selenate reductase in Salmonella enterica: critical roles for the signal peptide and DmsD. MICROBIOLOGY-SGM 2016; 162:2136-2146. [PMID: 27902441 PMCID: PMC5203670 DOI: 10.1099/mic.0.000381] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Salmonella enterica serovar Typhimurium is a Gram-negative bacterium with a flexible respiratory capability. Under anaerobic conditions, S. enterica can utilize a range of terminal electron acceptors, including selenate, to sustain respiratory electron transport. The S. enterica selenate reductase is a membrane-bound enzyme encoded by the ynfEFGH-dmsD operon. The active enzyme is predicted to comprise at least three subunits where YnfE is a molybdenum-containing catalytic subunit. The YnfE protein is synthesized with an N-terminal twin-arginine signal peptide and biosynthesis of the enzyme is coordinated by a signal peptide binding chaperone called DmsD. In this work, the interaction between S. enterica DmsD and the YnfE signal peptide has been studied by chemical crosslinking. These experiments were complemented by genetic approaches, which identified the DmsD binding epitope within the YnfE signal peptide. YnfE signal peptide residues L24 and A28 were shown to be important for assembly of an active selenate reductase. Conversely, a random genetic screen identified the DmsD V16 residue as being important for signal peptide recognition and selenate reductase assembly.
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Affiliation(s)
| | - Calum Stevenson
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Holger Kneuper
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Frank Sargent
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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10
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Xiong L, Jian H, Zhang Y, Xiao X. The Two Sets of DMSO Respiratory Systems of Shewanella piezotolerans WP3 Are Involved in Deep Sea Environmental Adaptation. Front Microbiol 2016; 7:1418. [PMID: 27656177 PMCID: PMC5013071 DOI: 10.3389/fmicb.2016.01418] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/26/2016] [Indexed: 12/04/2022] Open
Abstract
Dimethyl sulfoxide (DMSO) is an abundant methylated sulfur compound in deep sea ecosystems. However, the mechanism underlying DMSO-induced reduction in benthic microorganisms is unknown. Shewanella piezotolerans WP3, which was isolated from a west Pacific deep sea sediment, can utilize DMSO as the terminal electron acceptor. In this study, two putative dms gene clusters [type I (dmsEFA1B1G1H1) and type II (dmsA2B2G2H2)] were identified in the WP3 genome. Genetic and physiological analyses demonstrated that both dms gene clusters were functional and the transcription of both gene clusters was affected by changes in pressure and temperature. Notably, the type I system is essential for WP3 to thrive under in situ conditions (4°C/20 MPa), whereas the type II system is more important under high pressure or low temperature conditions (20°C/20 MPa, 4°C/0.1 MPa). Additionally, DMSO-dependent growth conferred by the presence of both dms gene clusters was higher than growth conferred by either of the dms gene clusters alone. These data collectively suggest that the possession of two sets of DMSO respiratory systems is an adaptive strategy for WP3 survival in deep sea environments. We propose, for the first time, that deep sea microorganisms might be involved in global DMSO/DMS cycling.
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Affiliation(s)
- Lei Xiong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Yuxia Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong UniversityShanghai, China
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11
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The Aerobic and Anaerobic Respiratory Chain of Escherichia coli and Salmonella enterica: Enzymes and Energetics. EcoSal Plus 2015; 6. [PMID: 26442941 DOI: 10.1128/ecosalplus.esp-0005-2013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Escherichia coli contains a versatile respiratory chain that oxidizes 10 different electron donor substrates and transfers the electrons to terminal reductases or oxidases for the reduction of six different electron acceptors. Salmonella is able to use two more electron acceptors. The variation is further increased by the presence of isoenzymes for some substrates. A large number of respiratory pathways can be established by combining different electron donors and acceptors. The respiratory dehydrogenases use quinones as the electron acceptors that are oxidized by the terminal reductase and oxidases. The enzymes vary largely with respect to their composition, architecture, membrane topology, and the mode of energy conservation. Most of the energy-conserving dehydrogenases (FdnGHI, HyaABC, HybCOAB, and others) and the terminal reductases (CydAB, NarGHI, and others) form a proton potential (Δp) by a redox-loop mechanism. Two enzymes (NuoA-N and CyoABCD) couple the redox energy to proton translocation by proton pumping. A large number of dehydrogenases and terminal reductases do not conserve the redox energy in a proton potential. For most of the respiratory enzymes, the mechanism of proton potential generation is known or can be predicted. The H+/2e- ratios for most respiratory chains are in the range from 2 to 6 H+/2e-. The energetics of the individual redox reactions and the respiratory chains is described and related to the H+/2e- ratios.
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12
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Wang J, Rennie W, Liu C, Carmack CS, Prévost K, Caron MP, Massé E, Ding Y, Wade JT. Identification of bacterial sRNA regulatory targets using ribosome profiling. Nucleic Acids Res 2015; 43:10308-20. [PMID: 26546513 PMCID: PMC4666370 DOI: 10.1093/nar/gkv1158] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 10/19/2015] [Indexed: 12/30/2022] Open
Abstract
Bacteria express large numbers of non-coding, regulatory RNAs known as ‘small RNAs’ (sRNAs). sRNAs typically regulate expression of multiple target messenger RNAs (mRNAs) through base-pairing interactions. sRNA:mRNA base-pairing often results in altered mRNA stability and/or altered translation initiation. Computational identification of sRNA targets is challenging due to the requirement for only short regions of base-pairing that can accommodate mismatches. Experimental approaches have been applied to identify sRNA targets on a genomic scale, but these focus only on those targets regulated at the level of mRNA stability. Here, we utilize ribosome profiling (Ribo-seq) to experimentally identify regulatory targets of the Escherichia coli sRNA RyhB. We not only validate a majority of known RyhB targets using the Ribo-seq approach, but also discover many novel ones. We further confirm regulation of a selection of known and novel targets using targeted reporter assays. By mutating nucleotides in the mRNA of a newly discovered target, we demonstrate direct regulation of this target by RyhB. Moreover, we show that Ribo-seq distinguishes between mRNAs regulated at the level of RNA stability and those regulated at the level of translation. Thus, Ribo-seq represents a powerful approach for genome-scale identification of sRNA targets.
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Affiliation(s)
- Jing Wang
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - William Rennie
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Chaochun Liu
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Charles S Carmack
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Karine Prévost
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Quebec, J1H 5N4, Canada
| | - Marie-Pier Caron
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Quebec, J1H 5N4, Canada
| | - Eric Massé
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Quebec, J1H 5N4, Canada
| | - Ye Ding
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA Department of Biomedical Sciences, University at Albany, Albany, NY 12201, USA
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA Department of Biomedical Sciences, University at Albany, Albany, NY 12201, USA
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Leimkühler S, Iobbi-Nivol C. Bacterial molybdoenzymes: old enzymes for new purposes. FEMS Microbiol Rev 2015; 40:1-18. [PMID: 26468212 DOI: 10.1093/femsre/fuv043] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2015] [Indexed: 02/06/2023] Open
Abstract
Molybdoenzymes are widespread in eukaryotic and prokaryotic organisms where they play crucial functions in detoxification reactions in the metabolism of humans and bacteria, in nitrate assimilation in plants and in anaerobic respiration in bacteria. To be fully active, these enzymes require complex molybdenum-containing cofactors, which are inserted into the apoenzymes after folding. For almost all the bacterial molybdoenzymes, molybdenum cofactor insertion requires the involvement of specific chaperones. In this review, an overview on the molybdenum cofactor biosynthetic pathway is given together with the role of specific chaperones dedicated for molybdenum cofactor insertion and maturation. Many bacteria are involved in geochemical cycles on earth and therefore have an environmental impact. The roles of molybdoenzymes in bioremediation and for environmental applications are presented.
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Affiliation(s)
- Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, 14476 Potsdam, Germany
| | - Chantal Iobbi-Nivol
- The Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS, Aix Marseille Université, 13402 Marseille cedex 20, France
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Abstract
The transition element molybdenum (Mo) is of primordial importance for biological systems as it is required by enzymes catalyzing key reactions in global carbon, sulfur, and nitrogen metabolism. In order to gain biological activity, Mo has to be complexed by a special cofactor. With the exception of bacterial nitrogenase, all Mo-dependent enzymes contain a unique pyranopterin-based cofactor coordinating a Mo atom at their catalytic site. Various types of reactions are catalyzed by Mo enzymes in prokaryotes, including oxygen atom transfer, sulfur or proton transfer, hydroxylation, or even nonredox ones. Mo enzymes are widespread in prokaryotes, and many of them were likely present in LUCA. To date, more than 50-mostly bacterial-Mo enzymes are described in nature. In a few eubacteria and in many archaea, Mo is replaced by tungsten bound to the same unique pyranopterin. How Moco is synthesized in bacteria is reviewed as well as the way until its insertion into apo-Mo-enzymes.
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The Aerobic and Anaerobic Respiratory Chain of Escherichia coli and Salmonella enterica: Enzymes and Energetics. EcoSal Plus 2015; 3. [PMID: 26443736 DOI: 10.1128/ecosalplus.3.2.2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Escherichia coli contains a versatile respiratory chain which oxidizes ten different electron donor substrates and transfers the electrons to terminal reductases or oxidases for the reduction of six different electron acceptors. Salmonella is able to use even two more electron acceptors. The variation is further increased by the presence of isoenzymes for some substrates. Various respiratory pathways can be established by combining the oxidation of different electron donors and acceptors which are linked by respiratory quinones. The enzymes vary largely with respect to architecture, membrane topology, and mode of energy conservation. Most of the energy-conserving dehydrogenases (e.g., FdnGHI, HyaABC, and HybCOAB) and of the terminal reductases (CydAB, NarGHI, and others) form a proton potential (Δp) by a redox loop mechanism. Only two enzymes (NuoA-N and CyoABCD) couple the redox energy to proton translocation by proton pumping. A large number of dehydrogenases (e.g., Ndh, SdhABCD, and GlpD) and of terminal reductases (e.g., FrdABCD and DmsABC) do not conserve the redox energy in a proton potential. For most of the respiratory enzymes, the mechanism of proton potential generation is known from structural and biochemical studies or can be predicted from sequence information. The H+/2e- ratios of proton translocation for most respiratory chains are in the range from 2 to 6 H+/2e-. The energetics of the individual redox reactions and of the respiratory chains is described. In contrast to the knowledge on enzyme function are physiological aspects of respiration such as organization and coordination of the electron transport and the use of alternative respiratory enzymes, not well characterized.
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Abstract
Escherichia coli is a versatile facultative anaerobe that can respire on a number of terminal electron acceptors, including oxygen, fumarate, nitrate, and S- and N-oxides. Anaerobic respiration using S- and N-oxides is accomplished by enzymatic reduction of these substrates by dimethyl sulfoxide reductase (DmsABC) and trimethylamine N-oxide reductase (TorCA). Both DmsABC and TorCA are membrane-associated redox enzymes that couple the oxidation of menaquinol to the reduction of S- and N-oxides in the periplasm. DmsABC is membrane bound and is composed of a membrane-extrinsic dimer with a 90.4-kDa catalytic subunit (DmsA) and a 23.1-kDa electron transfer subunit (DmsB). These subunits face the periplasm and are held to the membrane by a 30.8-kDa membrane anchor subunit (DmsC). The enzyme provides the scaffold for an electron transfer relay composed of a quinol binding site, five [4Fe-4S] clusters, and a molybdo-bis(molybdopterin guanine dinucleotide) (present nomenclature: Mo-bis-pyranopterin) (Mo-bisMGD) cofactor. TorCA is composed of a soluble periplasmic subunit (TorA, 92.5 kDa) containing a Mo-bis-MGD. TorA is coupled to the quinone pool via a pentaheme c subunit (TorC, 40.4 kDa) in the membrane. Both DmsABC and TorCA require system-specific chaperones (DmsD or TorD) for assembly, cofactor insertion, and/or targeting to the Tat translocon. In this chapter, we discuss the complex regulation of the dmsABC and torCAD operons, the poorly understood paralogues, and what is known about the assembly and translocation to the periplasmic space by the Tat translocon.
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Bay DC, Chan CS, Turner RJ. NarJ subfamily system specific chaperone diversity and evolution is directed by respiratory enzyme associations. BMC Evol Biol 2015; 15:110. [PMID: 26067063 PMCID: PMC4464133 DOI: 10.1186/s12862-015-0412-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 06/04/2015] [Indexed: 12/04/2022] Open
Abstract
Background Redox enzyme maturation proteins (REMPs) describe a diverse family of prokaryotic chaperones involved in the biogenesis of anaerobic complex iron sulfur molybdoenzyme (CISM) respiratory systems. Many REMP family studies have focused on NarJ subfamily members from Escherichia coli: NarJ, NarW, DmsD, TorD and YcdY. The aim of this bioinformatics study was to expand upon the evolution, distribution and genetic association of these 5 REMP members within 130 genome sequenced taxonomically diverse species representing 324 Prokaryotic sequences. NarJ subfamily member diversity was examined at the phylum-species level and at the amino acid/nucleotide level to determine how close their genetic associations were between their respective CISM systems within phyla. Results This study revealed that NarJ members possessed unique motifs that distinguished Gram-negative from Gram-positive/Archaeal species and identified a strict genetic association with its nitrate reductase complex (narGHI) operon compared to all other members. NarW appears to be found specifically in Gammaproteobacteria. DmsD also showed close associations with the dimethylsulfoxide reductase (dmsABC) operon compared to TorD. Phylogenetic analysis revealed that YcdY has recently evolved from DmsD and that YcdY has likely diverged into 2 subfamilies linked to Zn- dependent alkaline phosphatase (ycdX) operons and a newly identified operon containing part of Zn-metallopeptidase FtsH complex component (hflC) and NADH-quinone dehydrogenase (mdaB). TorD demonstrated the greatest diversity in operon association. TorD was identifed within operons from either trimethylamine-N-oxide reductase (torAC) or formate dehydrogenase (fdhGHI), where each type of TorD had a unique motif. Additionally a subgroup of dmsD and torD members were also linked to operons with biotin sulfoxide (bisC) and polysulfide reductase (nrfD) indicating a potential role in the maturation of diverse CISM. Conclusion Examination of diverse prokaryotic NarJ subfamily members demonstrates that the evolution and genetic association of each member is uniquely biased by its CISM operon association. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0412-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Denice C Bay
- Department of Biological Sciences, University of Calgary, Rm 156 Biological Science Bldg., 2500 University Dr. NW, Calgary, T2N 1 N4, AB, Canada.
| | - Catherine S Chan
- Department of Biological Sciences, University of Calgary, Rm 156 Biological Science Bldg., 2500 University Dr. NW, Calgary, T2N 1 N4, AB, Canada.
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, Rm 156 Biological Science Bldg., 2500 University Dr. NW, Calgary, T2N 1 N4, AB, Canada.
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Yamamoto K, Nakano M, Ishihama A. Regulatory role of transcription factor SutR (YdcN) in sulfur utilization in Escherichia coli. Microbiology (Reading) 2015; 161:99-111. [DOI: 10.1099/mic.0.083550-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kaneyoshi Yamamoto
- Research Institute of Micro-Nano Technology, Hosei University, Koganei, Tokyo 185-8584, Japan
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 185-8584, Japan
| | - Masahiro Nakano
- Research Institute of Micro-Nano Technology, Hosei University, Koganei, Tokyo 185-8584, Japan
| | - Akira Ishihama
- Research Institute of Micro-Nano Technology, Hosei University, Koganei, Tokyo 185-8584, Japan
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 185-8584, Japan
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‘Come into the fold’: A comparative analysis of bacterial redox enzyme maturation protein members of the NarJ subfamily. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2971-2984. [DOI: 10.1016/j.bbamem.2014.08.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/24/2014] [Accepted: 08/15/2014] [Indexed: 11/19/2022]
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Rivardo F, Leach TGH, Chan CS, Winstone TML, Ladner CL, Sarfo KJ, Turner RJ. Unique Photobleaching Phenomena of the Twin-Arginine Translocase Respiratory Enzyme Chaperone DmsD. Open Biochem J 2014; 8:1-11. [PMID: 24497893 PMCID: PMC3912628 DOI: 10.2174/1874091x01408010001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 11/27/2013] [Accepted: 12/01/2013] [Indexed: 11/22/2022] Open
Abstract
DmsD is a chaperone of the redox enzyme maturation protein family specifically required for biogenesis of DMSO reductase in Escherichia coli. It exists in multiple folding forms, all of which are capable of binding its known substrate, the twin-arginine leader sequence of the DmsA catalytic subunit. It is important for maturation of the reductase and targeting to the cytoplasmic membrane for translocation. Here, we demonstrate that DmsD exhibits an irreversible photobleaching phenomenon upon 280 nm excitation irradiation. The phenomenon is due to quenching of the tryptophan residues in DmsD and is dependent on its folding and conformation. We also show that a tryptophan residue involved in DmsA signal peptide binding (W87) is important for photobleaching of DmsD. Mutation of W87, or binding of the DmsA twin-arginine signal peptide to DmsD in the pocket that includes W72, W80, and W91 significantly affects the degree of photobleaching. This study highlights the advantage of a photobleaching phenomenon to study protein folding and conformation changes within a protein that was once considered unusable in fluorescence spectroscopy.
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Affiliation(s)
- Fabrizio Rivardo
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Thorin G H Leach
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Catherine S Chan
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Tara M L Winstone
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Carol L Ladner
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Kwabena J Sarfo
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Raymond J Turner
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
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Aerial exposure to the bacterial volatile compound trimethylamine modifies antibiotic resistance of physically separated bacteria by raising culture medium pH. mBio 2014; 5:e00944-13. [PMID: 24399857 PMCID: PMC3884056 DOI: 10.1128/mbio.00944-13] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED Bacteria release a wide diversity of small bioactive molecules that often correspond to secondary metabolites. Among them, volatile molecules produced under various growth conditions were shown to mediate cross-kingdom interactions with plants, nematodes, and fungi. Although the role of volatile compounds in bacterial biology is not well understood, recent reports indicated that they could play a role in airborne interactions between bacteria and influence antibiotic resistance, biofilm formation, and virulence. In this study, we investigated long-distance effects of 14 previously described Escherichia coli volatile compounds upon the bacteria E. coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Bacillus subtilis. We show that several of these molecules constitute chemical cues influencing growth, adhesion, and motility in exposed bacteria. Moreover, we show that aerial exposure to trimethylamine (TMA), a volatile compound produced in animal intestines and tissues upon biogenic reduction of trimethylamine oxide (TMAO), modifies the antibiotic resistance profiles of all tested Gram-positive and Gram-negative bacteria. We demonstrate that the TMA mode of action is distinct from that previously described for ammonia and results from nonspecific transient alteration of antibiotic uptake due to pH increase in the environment of bacteria aerially exposed to TMA. Our study therefore presents a new way by which volatile compounds can affect community behavior and structure in physically separated bacteria. It further demonstrates that bacterial gases and volatile compounds mediate chemical interactions, triggering functional responses that play an important role in the development of bacterial communities. IMPORTANCE Bacteria release many different volatile compounds during food transformation and fermentation. Here we sought to investigate the role of several bacterial volatile molecules released by Escherichia coli during long-distance airborne interactions with other bacteria. While several tested volatiles affect bacterial motility and surface adhesion, we show that aerial exposure to trimethylamine, a molecule produced by E. coli and many other Gram-negative bacteria in animal intestines and infected tissues, also modulates antibiotic resistance in all tested bacteria. We demonstrate that exposure to trimethylamine increases the pH of the growth medium of exposed bacteria, resulting in modifications in antibiotic uptake and transient alteration of antibiotic resistance. Our study therefore presents a new mechanism by which volatile compounds can affect community behavior and structure in physically separated bacteria, and it illustrates how airborne chemical interactions between bacteria contribute to the development of bacterial communities.
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Identification of the set of genes, including nonannotated morA, under the direct control of ModE in Escherichia coli. J Bacteriol 2013; 195:4496-505. [PMID: 23913318 DOI: 10.1128/jb.00304-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
ModE is the molybdate-sensing transcription regulator that controls the expression of genes related to molybdate homeostasis in Escherichia coli. ModE is activated by binding molybdate and acts as both an activator and a repressor. By genomic systematic evolution of ligands by exponential enrichment (SELEX) screening and promoter reporter assays, we have identified a total of nine operons, including the hitherto identified modA, moaA, dmsA, and napF operons, of which six were activated by ModE and three were repressed. In addition, two promoters were newly identified and direct transcription of novel genes, referred to as morA and morB, located on antisense strands of yghW and torY, respectively. The morA gene encodes a short peptide, MorA, with an unusual initiation codon. Surprisingly, overexpression of the morA 5' untranslated region exhibited an inhibitory influence on colony formation of E. coli K-12.
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Kappler U, Nouwens AS. The molybdoproteome of Starkeya novella – insights into the diversity and functions of molybdenum containing proteins in response to changing growth conditions. Metallomics 2013; 5:325-34. [DOI: 10.1039/c2mt20230a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Shanmugham A, Bakayan A, Völler P, Grosveld J, Lill H, Bollen YJM. The hydrophobic core of twin-arginine signal sequences orchestrates specific binding to Tat-pathway related chaperones. PLoS One 2012; 7:e34159. [PMID: 22479549 PMCID: PMC3316669 DOI: 10.1371/journal.pone.0034159] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 02/27/2012] [Indexed: 11/19/2022] Open
Abstract
Redox enzyme maturation proteins (REMPs) bind pre-proteins destined for translocation across the bacterial cytoplasmic membrane via the twin-arginine translocation system and enable the enzymatic incorporation of complex cofactors. Most REMPs recognize one specific pre-protein. The recognition site usually resides in the N-terminal signal sequence. REMP binding protects signal peptides against degradation by proteases. REMPs are also believed to prevent binding of immature pre-proteins to the translocon. The main aim of this work was to better understand the interaction between REMPs and substrate signal sequences. Two REMPs were investigated: DmsD (specific for dimethylsulfoxide reductase, DmsA) and TorD (specific for trimethylamine N-oxide reductase, TorA). Green fluorescent protein (GFP) was genetically fused behind the signal sequences of TorA and DmsA. This ensures native behavior of the respective signal sequence and excludes any effects mediated by the mature domain of the pre-protein. Surface plasmon resonance analysis revealed that these chimeric pre-proteins specifically bind to the cognate REMP. Furthermore, the region of the signal sequence that is responsible for specific binding to the corresponding REMP was identified by creating region-swapped chimeric signal sequences, containing parts of both the TorA and DmsA signal sequences. Surprisingly, specificity is not encoded in the highly variable positively charged N-terminal region of the signal sequence, but in the more similar hydrophobic C-terminal parts. Interestingly, binding of DmsD to its model substrate reduced membrane binding of the pre-protein. This property could link REMP-signal peptide binding to its reported proofreading function.
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Affiliation(s)
| | | | | | | | | | - Yves J. M. Bollen
- Department of Molecular Cell Biology, VU University Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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Jones SA, Gibson T, Maltby RC, Chowdhury FZ, Stewart V, Cohen PS, Conway T. Anaerobic respiration of Escherichia coli in the mouse intestine. Infect Immun 2011; 79:4218-26. [PMID: 21825069 PMCID: PMC3187261 DOI: 10.1128/iai.05395-11] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 07/26/2011] [Indexed: 12/23/2022] Open
Abstract
The intestine is inhabited by a large microbial community consisting primarily of anaerobes and, to a lesser extent, facultative anaerobes, such as Escherichia coli, which we have shown requires aerobic respiration to compete successfully in the mouse intestine (S. A. Jones et al., Infect. Immun. 75:4891-4899, 2007). If facultative anaerobes efficiently lower oxygen availability in the intestine, then their sustained growth must also depend on anaerobic metabolism. In support of this idea, mutants lacking nitrate reductase or fumarate reductase have extreme colonization defects. Here, we further explore the role of anaerobic respiration in colonization using the streptomycin-treated mouse model. We found that respiratory electron flow is primarily via the naphthoquinones, which pass electrons to cytochrome bd oxidase and the anaerobic terminal reductases. We found that E. coli uses nitrate and fumarate in the intestine, but not nitrite, dimethyl sulfoxide, or trimethylamine N-oxide. Competitive colonizations revealed that cytochrome bd oxidase is more advantageous than nitrate reductase or fumarate reductase. Strains lacking nitrate reductase outcompeted fumarate reductase mutants once the nitrate concentration in cecal mucus reached submillimolar levels, indicating that fumarate is the more important anaerobic electron acceptor in the intestine because nitrate is limiting. Since nitrate is highest in the absence of E. coli, we conclude that E. coli is the only bacterium in the streptomycin-treated mouse large intestine that respires nitrate. Lastly, we demonstrated that a mutant lacking the NarXL regulator (activator of the NarG system), but not a mutant lacking the NarP-NarQ regulator, has a colonization defect, consistent with the advantage provided by NarG. The emerging picture is one in which gene regulation is tuned to balance expression of the terminal reductases that E. coli uses to maximize its competitiveness and achieve the highest possible population in the intestine.
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Affiliation(s)
- Shari A. Jones
- Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019
| | - Terri Gibson
- Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019
| | - Rosalie C. Maltby
- Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019
| | - Fatema Z. Chowdhury
- Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019
| | - Valley Stewart
- Section of Microbiology, University of California, Davis, Davis, California 95616-8665
| | - Paul S. Cohen
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island 02881
| | - Tyrrell Conway
- Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019
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Strader MB, Costantino N, Elkins CA, Chen CY, Patel I, Makusky AJ, Choy JS, Court DL, Markey SP, Kowalak JA. A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12. Mol Cell Proteomics 2010; 10:M110.005199. [PMID: 21169565 DOI: 10.1074/mcp.m110.005199] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
β-methylthiolation is a novel post-translational modification mapping to a universally conserved Asp 88 of the bacterial ribosomal protein S12. This S12 specific modification has been identified on orthologs from multiple bacterial species. The origin and functional significance was investigated with both a proteomic strategy to identify candidate S12 interactors and expression microarrays to search for phenotypes that result from targeted gene knockouts of select candidates. Utilizing an endogenous recombinant E. coli S12 protein with an affinity tag as bait, mass spectrometric analysis identified candidate S12 binding partners including RimO (previously shown to be required for this post-translational modification) and YcaO, a conserved protein of unknown function. Transcriptomic analysis of bacterial strains with deleted genes for RimO and YcaO identified an overlapping transcriptional phenotype suggesting that YcaO and RimO likely share a common function. As a follow up, quantitative mass spectrometry additionally indicated that both proteins dramatically impacted the modification status of S12. Collectively, these results indicate that the YcaO protein is involved in β-methylthiolation of S12 and its absence impairs the ability of RimO to modify S12. Additionally, the proteomic data from this study provides direct evidence that the E. coli specific β-methylthiolation likely occurs when S12 is assembled as part of a ribosomal subunit.
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Affiliation(s)
- Michael Brad Strader
- Laboratory of Neurotoxicology, National Institute of Mental Health, Bethesda, MD 20892, USA.
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Abstract
Proteins that reside partially or completely outside the bacterial cytoplasm require specialized pathways to facilitate their localization. Globular proteins that function in the periplasm must be translocated across the hydrophobic barrier of the inner membrane. While the Sec pathway transports proteins in a predominantly unfolded conformation, the Tat pathway exports folded protein substrates. Protein transport by the Tat machinery is powered solely by the transmembrane proton gradient, and there is no requirement for nucleotide triphosphate hydrolysis. Proteins are targeted to the Tat machinery by N-terminal signal peptides that contain a consensus twin arginine motif. In Escherichia coli and Salmonella there are approximately thirty proteins with twin arginine signal peptides that are transported by the Tat pathway. The majority of these bind complex redox cofactors such as iron sulfur clusters or the molybdopterin cofactor. Here we describe what is known about Tat substrates in E. coli and Salmonella, the function and mechanism of Tat protein export, and how the cofactor insertion step is coordinated to ensure that only correctly assembled substrates are targeted to the Tat machinery.
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28
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Guymer D, Maillard J, Sargent F. A genetic analysis of in vivo selenate reduction by Salmonella enterica serovar Typhimurium LT2 and Escherichia coli K12. Arch Microbiol 2009; 191:519-28. [DOI: 10.1007/s00203-009-0478-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 04/01/2009] [Accepted: 04/06/2009] [Indexed: 11/28/2022]
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Abstract
Induction of the Escherichia coli K-12 ynfEFGHI operon in response to anaerobiosis is repressed by nitrate ions. In this study, we show that the global transcription factor FNR is a class II activator at the ynfEFGHI promoter and that NarL represses activation by binding to a single target that overlaps the promoter -10 element. Electromobility shift assays show that NarL does not prevent RNA polymerase binding and suggest that repression may involve a quaternary NarL-FNR-RNA polymerase-promoter complex.
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Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JLM, Saffarini DA, Serres MH, Spormann AM, Zhulin IB, Tiedje JM. Towards environmental systems biology of Shewanella. Nat Rev Microbiol 2008; 6:592-603. [PMID: 18604222 DOI: 10.1038/nrmicro1947] [Citation(s) in RCA: 629] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Bacteria of the genus Shewanella are known for their versatile electron-accepting capacities, which allow them to couple the decomposition of organic matter to the reduction of the various terminal electron acceptors that they encounter in their stratified environments. Owing to their diverse metabolic capabilities, shewanellae are important for carbon cycling and have considerable potential for the remediation of contaminated environments and use in microbial fuel cells. Systems-level analysis of the model species Shewanella oneidensis MR-1 and other members of this genus has provided new insights into the signal-transduction proteins, regulators, and metabolic and respiratory subsystems that govern the remarkable versatility of the shewanellae.
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Affiliation(s)
- James K Fredrickson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA. ;
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Sargent F. Constructing the wonders of the bacterial world: biosynthesis of complex enzymes. Microbiology (Reading) 2007; 153:633-651. [PMID: 17322183 DOI: 10.1099/mic.0.2006/004762-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The prokaryotic cytoplasmic membrane not only maintains cell integrity and forms a barrier between the cell and its outside environment, but is also the location for essential biochemical processes. Microbial model systems provide excellent bases for the study of fundamental problems in membrane biology including signal transduction, chemotaxis, solute transport and, as will be the topic of this review, energy metabolism. Bacterial respiration requires a diverse array of complex, multi-subunit, cofactor-containing redox enzymes, many of which are embedded within, or located on the extracellular side of, the membrane. The biosynthesis of these enzymes therefore requires carefully controlled expression, assembly, targeting and transport processes. Here, focusing on the molybdenum-containing respiratory enzymes central to anaerobic respiration in Escherichia coli, recent descriptions of a chaperone-mediated 'proofreading' system involved in coordinating assembly and export of complex extracellular enzymes will be discussed. The paradigm proofreading chaperones are members of a large group of proteins known as the TorD family, and recent research in this area highlights common principles that underpin biosynthesis of both exported and non-exported respiratory enzymes.
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Affiliation(s)
- Frank Sargent
- Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Kozmin SG, Schaaper RM. Molybdenum cofactor-dependent resistance to N-hydroxylated base analogs in Escherichia coli is independent of MobA function. Mutat Res 2007; 619:9-15. [PMID: 17349664 PMCID: PMC1934987 DOI: 10.1016/j.mrfmmm.2006.12.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2006] [Revised: 11/09/2006] [Accepted: 12/20/2006] [Indexed: 11/17/2022]
Abstract
Lack of molybdenum cofactor (MoCo) in Escherichia coli and related microorganisms was found to cause hypersensitivity to certain N-hydroxylated base analogs, such as HAP (6-N-hydroxylaminopurine). This observation has lead to a previous proposal that E. coli contains a molybdoenzyme capable of detoxifying such N-hydroxylated analogs. Here, we show that, unexpectedly, deletion of all known or putative molybdoenzymes in E. coli failed to reveal any base-analog sensitivity, suggesting that a novel type of MoCo-dependent activity is involved. Further, we establish that protection against the analogs does not require the common molybdopterin guanine-dinucleotide (MGD) form of the cofactor, but instead the guanosine monophosphate (GMP)-free version of MoCo (MPT) is sufficient.
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Affiliation(s)
- Stanislav G Kozmin
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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Besemann C, Denton A, Carr NJ, Prüβ BM. BISON: Bio-Interface for the Semi-global analysis Of Network patterns. SOURCE CODE FOR BIOLOGY AND MEDICINE 2006; 1:8. [PMID: 17147788 PMCID: PMC1698476 DOI: 10.1186/1751-0473-1-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2006] [Accepted: 11/29/2006] [Indexed: 12/29/2022]
Abstract
Background The large amount of genomics data that have accumulated over the past decade require extensive data mining. However, the global nature of data mining, which includes pattern mining, poses difficulties for users who want to study specific questions in a more local environment. This creates a need for techniques that allow a localized analysis of globally determined patterns. Results We developed a tool that determines and evaluates global patterns based on protein property and network information, while providing all the benefits of a perspective that is targeted at biologist users with specific goals and interests. Our tool uses our own data mining techniques, integrated into current visualization and navigation techniques. The functionality of the tool is discussed in the context of the transcriptional network of regulation in the enteric bacterium Escherichia coli. Two biological questions were asked: (i) Which functional categories of proteins (identified by hidden Markov models) are regulated by a regulator with a specific domain? (ii) Which regulators are involved in the regulation of proteins that contain a common hidden Markov model? Using these examples, we explain the gene-centered and pattern-centered analysis that the tool permits. Conclusion In summary, we have a tool that can be used for a wide variety of applications in biology, medicine, or agriculture. The pattern mining engine is global in the way that patterns are determined across the entire network. The tool still permits a localized analysis for users who want to analyze a subportion of the total network. We have named the tool BISON (Bio-Interface for the Semi-global analysis Of Network patterns).
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Affiliation(s)
- Christopher Besemann
- Department of Computer Sciences, North Dakota State University, Fargo ND 58105, USA
| | - Anne Denton
- Department of Computer Sciences, North Dakota State University, Fargo ND 58105, USA
| | - Nathan J Carr
- Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo ND 58105, USA
| | - Birgit M Prüβ
- Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo ND 58105, USA
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Rollins DK, Zhai D, Joe AL, Guidarelli JW, Murarka A, Gonzalez R. A novel data mining method to identify assay-specific signatures in functional genomic studies. BMC Bioinformatics 2006; 7:377. [PMID: 16907975 PMCID: PMC1599756 DOI: 10.1186/1471-2105-7-377] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2006] [Accepted: 08/14/2006] [Indexed: 11/25/2022] Open
Abstract
Background: The highly dimensional data produced by functional genomic (FG) studies makes it difficult to visualize relationships between gene products and experimental conditions (i.e., assays). Although dimensionality reduction methods such as principal component analysis (PCA) have been very useful, their application to identify assay-specific signatures has been limited by the lack of appropriate methodologies. This article proposes a new and powerful PCA-based method for the identification of assay-specific gene signatures in FG studies. Results: The proposed method (PM) is unique for several reasons. First, it is the only one, to our knowledge, that uses gene contribution, a product of the loading and expression level, to obtain assay signatures. The PM develops and exploits two types of assay-specific contribution plots, which are new to the application of PCA in the FG area. The first type plots the assay-specific gene contribution against the given order of the genes and reveals variations in distribution between assay-specific gene signatures as well as outliers within assay groups indicating the degree of importance of the most dominant genes. The second type plots the contribution of each gene in ascending or descending order against a constantly increasing index. This type of plots reveals assay-specific gene signatures defined by the inflection points in the curve. In addition, sharp regions within the signature define the genes that contribute the most to the signature. We proposed and used the curvature as an appropriate metric to characterize these sharp regions, thus identifying the subset of genes contributing the most to the signature. Finally, the PM uses the full dataset to determine the final gene signature, thus eliminating the chance of gene exclusion by poor screening in earlier steps. The strengths of the PM are demonstrated using a simulation study, and two studies of real DNA microarray data – a study of classification of human tissue samples and a study of E. coli cultures with different medium formulations. Conclusion We have developed a PCA-based method that effectively identifies assay-specific signatures in ranked groups of genes from the full data set in a more efficient and simplistic procedure than current approaches. Although this work demonstrates the ability of the PM to identify assay-specific signatures in DNA microarray experiments, this approach could be useful in areas such as proteomics and metabolomics.
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Affiliation(s)
- Derrick K Rollins
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
- Department of Statistics, Iowa State University, Ames, Iowa 50011, USA
| | - Dongmei Zhai
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
- Department of Statistics, Iowa State University, Ames, Iowa 50011, USA
| | - Alrica L Joe
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
| | - Jack W Guidarelli
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
| | - Abhishek Murarka
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77251-1892, USA
| | - Ramon Gonzalez
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77251-1892, USA
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Chen Z, Schneider TD. Comparative analysis of tandem T7-like promoter containing regions in enterobacterial genomes reveals a novel group of genetic islands. Nucleic Acids Res 2006; 34:1133-47. [PMID: 16493139 PMCID: PMC1380254 DOI: 10.1093/nar/gkj511] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Based on molecular information theory, 10 T7-like promoter models were built for the T7 group of phages and used to scan their host genomes and closely related genomes. 38 genomes were scanned and 12 clusters of tandem promoters were identified in nine enteropathogens. Comparative analysis of these tandem promoter-bearing regions reveals that they are similar to each other, forming prophage-like islands of 4-13 kb. Each island appears to contain two or three tandem T7-like promoters within a stretch of 150-620 bases, but there are no corresponding RNA polymerase (RNAP) genes. The promoters would transcribe two to five putative phage-related proteins, but none of these resemble known phage structural proteins. An integrase belonging to the Int family of site-specific recombinases is encoded upstream of the tandem promoters. A direct repeat of 17-24 bases was found on the ends of all 12 islands. Comparative analysis of the islands shows that these islands appear to have recombined with each other. These results suggest that the islands could encode a group of satellite phages. Activation and function of the islands may depend on transcription by a T7-like RNAP after infection by a T7-like phage or foreign DNA that encodes a T7-like RNAP.
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Affiliation(s)
| | - Thomas D. Schneider
- To whom correspondence should be addressed. Tel: +1 301 846 5581; Fax: +1 301 846 5598;
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Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW. A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth. J Biol Chem 2005; 281:4802-15. [PMID: 16377617 DOI: 10.1074/jbc.m512312200] [Citation(s) in RCA: 207] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The transcription factor FNR, the regulator of fumarate and nitrate reduction, regulates major changes as Escherichia coli adapts from aerobic to anaerobic growth. In an anaerobic glycerol/trimethylamine N-oxide/fumarate medium, the fnr mutant grew as well as the parental strain, E. coli K12 MG1655, enabling us to reveal the response to oxygen, nitrate, and nitrite in the absence of glucose repression or artifacts because of variations in growth rate. Hence, many of the discrepancies between previous microarray studies of the E. coli FNR regulon were resolved. The current microarray data confirmed 31 of the previously characterized FNR-regulated operons. Forty four operons not previously known to be included in the FNR regulon were activated by FNR, and a further 28 operons appeared to be repressed. For each of these operons, a match to the consensus FNR-binding site sequence was identified. The FNR regulon therefore minimally includes at least 103, and possibly as many as 115, operons. Comparison of transcripts in the parental strain and a narXL deletion mutant revealed that transcription of 51 operons is activated, directly or indirectly, by NarL, and a further 41 operons are repressed. The narP gene was also deleted from the narXL mutant to reveal the extent of regulation by phosphorylated NarP. Fourteen promoters were more active in the narP+ strain than in the mutant, and a further 37 were strongly repressed. This is the first report that NarP might function as a global repressor as well as a transcription activator. The data also revealed possible new defense mechanisms against reactive nitrogen species.
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Goh EB, Bledsoe PJ, Chen LL, Gyaneshwar P, Stewart V, Igo MM. Hierarchical control of anaerobic gene expression in Escherichia coli K-12: the nitrate-responsive NarX-NarL regulatory system represses synthesis of the fumarate-responsive DcuS-DcuR regulatory system. J Bacteriol 2005; 187:4890-9. [PMID: 15995204 PMCID: PMC1169511 DOI: 10.1128/jb.187.14.4890-4899.2005] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hierarchical control ensures that facultative bacteria preferentially use the available respiratory electron acceptor with the most positive standard redox potential. Thus, nitrate is used before other electron acceptors such as fumarate for anaerobic respiration. Nitrate regulation is mediated by the NarX-NarL two-component system, which activates the transcription of operons encoding nitrate respiration enzymes and represses the transcription of operons for other anaerobic respiratory enzymes, including enzymes involved in fumarate respiration. These are fumarate reductase (encoded by the frdABCD operon), fumarase B, which generates fumarate from malate, and the DcuB permease for fumarate, malate, and aspartate. The transcription of the corresponding structural genes is activated by the DcuS-DcuR two-component system in response to fumarate or its dicarboxylate precursors. We report results from preliminary transcription microarray experiments that revealed two previously unknown members of the NarL regulon: the aspA gene encoding aspartate-ammonia lyase, which generates fumarate; and the dcuSR operon encoding the dicarboxylate-responsive regulatory system. We measured beta-galactosidase expression from monocopy aspA-lacZ, frdA-lacZ, and dcuS-lacZ operon fusions in response to added nitrate and fumarate and with respect to the dcuR and narL genotypes. Nitrate, acting through the NarX-NarL regulatory system, repressed the transcription of all three operons. Only frdA-lacZ expression, however, was responsive to added fumarate or a dcuR(+) genotype. Phospho-NarL protein protected operator sites in the aspA and dcuS promoter regions from DNase I cleavage in vitro. The overall results are consistent with the hypothesis that nitrate represses frdA operon transcription not only directly, by repressing frdA promoter activity, but also indirectly, by repressing dcuS promoter activity.
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Affiliation(s)
- Ee-Been Goh
- Section of Microbiology, University of California, Davis, 95616-8665, USA
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38
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Kang Y, Weber KD, Qiu Y, Kiley PJ, Blattner FR. Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function. J Bacteriol 2005; 187:1135-60. [PMID: 15659690 PMCID: PMC545700 DOI: 10.1128/jb.187.3.1135-1160.2005] [Citation(s) in RCA: 215] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The major regulator controlling the physiological switch between aerobic and anaerobic growth conditions in Escherichia coli is the DNA binding protein FNR. To identify genes controlled by FNR, we used Affymetrix Antisense GeneChips to compare global gene expression profiles from isogenic MG1655 wild-type and Deltafnr strains grown in glucose minimal media under aerobic or anaerobic conditions. We found that 297 genes contained within 184 operons were regulated by FNR and/or by O2 levels. The expression of many genes known to be involved in anaerobic respiration and fermentation was increased under anaerobic growth conditions, while that of genes involved in aerobic respiration and the tricarboxylic acid cycle were repressed as expected. The expression of nine operons associated with acid resistance was also increased under anaerobic growth conditions, which may reflect the production of acidic fermentation products. Ninety-one genes with no presently defined function were also altered in expression, including seven of the most highly anaerobically induced genes, six of which we found to be directly regulated by FNR. Classification of the 297 genes into eight groups by k-means clustering analysis indicated that genes with common gene expression patterns also had a strong functional relationship, providing clues for studying the function of unknown genes in each group. Six of the eight groups showed regulation by FNR; while some expression groups represent genes that are simply activated or repressed by FNR, others, such as those encoding functions for chemotaxis and motility, showed a more complex pattern of regulation. A computer search for FNR DNA binding sites within predicted promoter regions identified 63 new sites for 54 genes. We suggest that E. coli MG1655 has a larger metabolic potential under anaerobic conditions than has been previously recognized.
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Affiliation(s)
- Yisheng Kang
- Department of Genetics, 425 Henry Mall, University of Wisconsin, Madison, WI 53706, USA
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39
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McCrindle SL, Kappler U, McEwan AG. Microbial Dimethylsulfoxide and Trimethylamine-N-Oxide Respiration. Adv Microb Physiol 2005; 50:147-98. [PMID: 16221580 DOI: 10.1016/s0065-2911(05)50004-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Over the last two decades, the biochemistry and genetics of dimethylsulfoxide (DMSO) and trimethylamine-N-oxide (TMAO) respiration has been characterised, particularly in Escherichia coli marine bacteria of the genus Shewanella and the purple phototrophic bacteria, Rhodobacter sphaeroides and R. capsulatus. All of the enzymes (or catalytic subunits) involved the final step in DMSO and TMAO respiration contain a pterin molybdenum cofactor and are members of the DMSO reductase family of molybdoenzymes. In E. coli, the dimethylsulfoxide reductase (DmsABC) can be purified from membranes as a complex, which exhibits quinol-DMSO oxidoreductase activity. The enzyme is anchored to the membrane via the DmsC subunit and its catalytic subunit DmsA is now considered to face the periplasm. Electron transfer to DmsA involves the DmsB subunit, which is a polyferredoxin related to subunits found in other molybdoenzymes such as nitrate reductase and formate dehydrogenase. A characteristic of the DmsAB-type DMSO reductase is its ability to reduce a variety of S- and N-oxides. E. coli contains a trimethylamine-N-oxide reductase (TorA) that is highly specific for N-oxides. This enzyme is located in the periplasm and is connected to the quinone pool via a membrane-bound penta-haem cytochrome (TorC). DorCA in purple phototrophic bacteria of the genus Rhodobacter is very similar to TorCA with the critical difference that DorA catalyses reduction of both DMSO and TMAO. It is known as a DMSO reductase because the S-oxide is the best substrate. Crystal structures of DorA and TorA have revealed critical differences at the Mo active site that may explain the differences between substrate specificity between the two enzymes. DmsA, TorA and DorA possess a "twin arginine" N-terminal signal sequence consistent with their secretion via the TAT secretory system and not the Sec system. The enzymes are secreted with their bound prosthetic groups: this take place in the cytoplasm and the biogenesis involves a chaperone protein, which is cognate for each enzyme. Expression of the DMSO and TMAO respiratory operons is induced in response to a fall in oxygen tension. dmsABC expression is positively controlled by the oxygen-responsive transcription factor, Fnr and ModE, a transcription factor that binds molybdate. In contrast, torCAD expression is not under Fnr- or ModE-control but is dependent upon a sensor histidine kinase-response regulator pair, TorSR, which activate gene expression under conditions of low oxygen tension in the presence of N- or S-oxide. Regulation of dorCDA expression is similar to that seen for torCAD but it appears that the expression of the sensor histidine kinase-response regulator pair, DorSR is regulated by Fnr and there is an additional tier of regulation involving the ModE-homologue MopB, molybdate and the transcription factor DorX. Analysis of microbial genomes has revealed the presence of dms and tor operons in a wide variety of bacteria and in some archaea and duplicate dms and tor operons have been identified in E. coli. Challenges ahead will include the determination of the significance of the presence of the dms operon in bacterial pathogens and the determination of the significance of DMSO respiration in the global turnover of marine organo-sulfur compounds.
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Affiliation(s)
- Sharon L McCrindle
- School of Molecular and Microbial Sciences, The University of Queensland, Brisbane 4072, Australia
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40
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Patten CL, Kirchhof MG, Schertzberg MR, Morton RA, Schellhorn HE. Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12. Mol Genet Genomics 2004; 272:580-91. [PMID: 15558318 DOI: 10.1007/s00438-004-1089-2] [Citation(s) in RCA: 191] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Accepted: 10/28/2004] [Indexed: 12/01/2022]
Abstract
The alternative sigma factor RpoS controls the expression of many stationary-phase genes in Escherichia coli and other bacteria. Though the RpoS regulon is a large, conserved system that is critical for adaptation to nutrient deprivation and other stresses, it remains incompletely characterized. In this study, we have used oligonucleotide arrays to delineate the transcriptome that is controlled by RpoS during entry into stationary phase of cultures growing in rich medium. The expression of known RpoS-dependent genes was confirmed to be regulated by RpoS, thus validating the use of microarrays for expression analysis. The total number of positively regulated stationary-phase genes was found to be greater than 100. More than 45 new genes were identified as positively controlled by RpoS. Surprisingly, a similar number of genes were found to be negatively regulated by RpoS, and these included almost all genes required for flagellum biosynthesis, genes encoding enzymes of the TCA cycle, and a physically contiguous group of genes located in the Rac prophage region. Negative regulation by RpoS is thus much more extensive than has previously been recognized, and is likely to be an important contributing factor to the competitive growth advantage of rpoS mutants reported in previous studies.
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Affiliation(s)
- C L Patten
- Department of Biology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
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41
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Turner RJ, Papish AL, Sargent F. Sequence analysis of bacterial redox enzyme maturation proteins (REMPs). Can J Microbiol 2004; 50:225-38. [PMID: 15213747 DOI: 10.1139/w03-117] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The twin-arginine protein transport (Tat) system is a remarkable molecular machine dedicated to the translocation of fully folded proteins across energy-transducing membranes. Complex cofactor-containing Tat substrates acquire their cofactors prior to export, and substrate proteins actually require to be folded before transport can proceed. Thus, it is very likely that mechanisms exist to prevent wasteful export of immature Tat substrates or to curb competition between immature and mature substrates for the transporter. Here we assess the primary sequence relationships between the accessory proteins implicated in this process during assembly of key respiratory enzymes in the model prokaryote Escherichia coli. For each respiratory enzyme studied, a redox enzyme maturation protein (REMP) was assigned. The main finding from this review was the hitherto unexpected link between the Tat-linked REMP DmsD and the nitrate reductase biosynthetic protein NarJ. The evolutionary link between Tat transport and cofactor insertion processes is discussed.Key words: Tat translocase, twin-arginine leader, hydrogenase, nitrate reductase, TMAO reductase, DMSO reductase, formate dehydrogenase, Tor, Dms, Hya, Hyb, Fdh, Nap.
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Affiliation(s)
- Raymond J Turner
- Department of Biological Sciences, University of Calgary, Alberta, Canada.
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