1
|
Richter M, Sattler C, Schöne C, Rother M. Pyruvate-dependent growth of Methanosarcina acetivorans. J Bacteriol 2024; 206:e0036323. [PMID: 38305193 PMCID: PMC10882976 DOI: 10.1128/jb.00363-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024] Open
Abstract
Methanogenesis is a key step during anaerobic biomass degradation. Methanogenic archaea (methanogens) are the only organisms coupling methanogenic substrate conversion to energy conservation. The range of substrates utilized by methanogens is limited, with acetate and H2+CO2 being the ecologically most relevant. The only single methanogenic energy substrate containing more carbon-carbon bonds than acetate is pyruvate. Only the aggregate-forming, freshwater methanogen Methanosarcina barkeri Fusaro was shown to grow on this compound. Here, the pyruvate-utilizing capabilities of the single-celled, marine Methanosarcina acetivorans were addressed. Robust pyruvate-dependent, methanogenic, growth could be established by omitting CO2 from the growth medium. Growth rates which were independent of the pyruvate concentration indicated that M. acetivorans actively translocates pyruvate across the cytoplasmic membrane. When 2-bromoethanesulfonate (BES) inhibited methanogenesis to more than 99%, pyruvate-dependent growth was acetogenic and sustained. However, when methanogenesis was completely inhibited M. acetivorans did not grow on pyruvate. Analysis of metabolites showed that acetogenesis is used by BES-inhibited M. acetivorans as a sink for electrons derived from pyruvate oxidation and that other, thus far unidentified, metabolites are produced.IMPORTANCEThe known range of methanogenic growth substrates is very limited and M. acetivorans is only the second methanogenic species for which growth on pyruvate is demonstrated. Besides some commonalities, analysis of M. acetivorans highlights differences in pyruvate metabolism among Methanosarcina species. The observation that M. acetivorans probably imports pyruvate actively indicates that the capabilities for heterotrophic catabolism in methanogens may be underestimated. The mostly acetogenic growth of M. acetivorans on pyruvate with concomitant inhibition of methanogenesis confirms that energy conservation of methanogenic archaea can be independent of methane formation.
Collapse
Affiliation(s)
- Marcus Richter
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
| | | | - Christian Schöne
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
| | - Michael Rother
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
| |
Collapse
|
2
|
Paulini S, Fabiani FD, Weiss AS, Moldoveanu AL, Helaine S, Stecher B, Jung K. The Biological Significance of Pyruvate Sensing and Uptake in Salmonella enterica Serovar Typhimurium. Microorganisms 2022; 10:microorganisms10091751. [PMID: 36144354 PMCID: PMC9504724 DOI: 10.3390/microorganisms10091751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Pyruvate (CH3COCOOH) is the simplest of the alpha-keto acids and is at the interface of several metabolic pathways both in prokaryotes and eukaryotes. In an amino acid-rich environment, fast-growing bacteria excrete pyruvate instead of completely metabolizing it. The role of pyruvate uptake in pathological conditions is still unclear. In this study, we identified two pyruvate-specific transporters, BtsT and CstA, in Salmonella enterica serovar Typhimurium (S. Typhimurium). Expression of btsT is induced by the histidine kinase/response regulator system BtsS/BtsR upon sensing extracellular pyruvate, whereas expression of cstA is maximal in the stationary phase. Both pyruvate transporters were found to be important for the uptake of this compound, but also for chemotaxis to pyruvate, survival under oxidative and nitrosative stress, and persistence of S. Typhimurium in response to gentamicin. Compared with the wild-type cells, the ΔbtsTΔcstA mutant has disadvantages in antibiotic persistence in macrophages, as well as in colonization and systemic infection in gnotobiotic mice. These data demonstrate the surprising complexity of the two pyruvate uptake systems in S. Typhimurium.
Collapse
Affiliation(s)
- Stephanie Paulini
- Department of Microbiology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Florian D. Fabiani
- Department of Microbiology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Anna S. Weiss
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, Ludwig-Maximilians-University Munich, 80336 Munich, Germany
| | - Ana Laura Moldoveanu
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2DD, UK
| | - Sophie Helaine
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2DD, UK
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, Ludwig-Maximilians-University Munich, 80336 Munich, Germany
- German Center for Infection Research (DZIF), Partner Site LMU Munich, 80337 Munich, Germany
| | - Kirsten Jung
- Department of Microbiology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
- Correspondence: ; Tel.: +49-(0)89/2180-74500
| |
Collapse
|
3
|
Ramos AL, Aquino M, García G, Gaspar M, de la Cruz C, Saavedra-Flores A, Brom S, Cervantes-Rivera R, Galindo-Sánchez CE, Hernandez R, Puhar A, Lupas AN, Sepulveda E. RpuS/R Is a Novel Two-Component Signal Transduction System That Regulates the Expression of the Pyruvate Symporter MctP in Sinorhizobium fredii NGR234. Front Microbiol 2022; 13:871077. [PMID: 35572670 PMCID: PMC9100948 DOI: 10.3389/fmicb.2022.871077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/11/2022] [Indexed: 11/16/2022] Open
Abstract
The SLC5/STAC histidine kinases comprise a recently identified family of sensor proteins in two-component signal transduction systems (TCSTS), in which the signaling domain is fused to an SLC5 solute symporter domain through a STAC domain. Only two members of this family have been characterized experimentally, the CrbS/R system that regulates acetate utilization in Vibrio and Pseudomonas, and the CbrA/B system that regulates the utilization of histidine in Pseudomonas and glucose in Azotobacter. In an attempt to expand the characterized members of this family beyond the Gammaproteobacteria, we identified two putative TCSTS in the Alphaproteobacterium Sinorhizobium fredii NGR234 whose sensor histidine kinases belong to the SLC5/STAC family. Using reverse genetics, we were able to identify the first TCSTS as a CrbS/R homolog that is also needed for growth on acetate, while the second TCSTS, RpuS/R, is a novel system required for optimal growth on pyruvate. Using RNAseq and transcriptional fusions, we determined that in S. fredii the RpuS/R system upregulates the expression of an operon coding for the pyruvate symporter MctP when pyruvate is the sole carbon source. In addition, we identified a conserved DNA sequence motif in the putative promoter region of the mctP operon that is essential for the RpuR-mediated transcriptional activation of genes under pyruvate-utilizing conditions. Finally, we show that S. fredii mutants lacking these TCSTS are affected in nodulation, producing fewer nodules than the parent strain and at a slower rate.
Collapse
Affiliation(s)
| | - Maria Aquino
- Facultad de Ciencias, Universidad Autónoma de Baja California, Ensenada, Mexico
| | - Gema García
- Facultad de Biología, Universidad Autónoma de Sinaloa, Culiacan, Mexico
| | - Miriam Gaspar
- Facultad de Ciencias, Universidad Autónoma de Baja California, Ensenada, Mexico
| | - Cristina de la Cruz
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Anaid Saavedra-Flores
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
| | - Susana Brom
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ramón Cervantes-Rivera
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Clara Elizabeth Galindo-Sánchez
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
| | - Rufina Hernandez
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
| | - Andrea Puhar
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Andrei N. Lupas
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Edgardo Sepulveda
- CONACYT-Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
- *Correspondence: Edgardo Sepulveda,
| |
Collapse
|
4
|
Dank A, van Mastrigt O, Boeren S, Lillevang SK, Abee T, Smid EJ. Propionibacterium freudenreichii thrives in microaerobic conditions by complete oxidation of lactate to CO 2. Environ Microbiol 2021; 23:3116-3129. [PMID: 33955639 PMCID: PMC8360058 DOI: 10.1111/1462-2920.15532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 04/13/2021] [Indexed: 11/28/2022]
Abstract
In this study we show increased biomass formation for four species of food-grade propionic acid bacteria (Acidipropionibacterium acidipropionici, Acidipropionibacterium jensenii, Acidipropionibacterium thoenii and Propionibacterium freudenreichii) when exposed to oxygen, implicating functional respiratory systems. Using an optimal microaerobic condition, P. freudenreichii DSM 20271 consumed lactate to produce propionate and acetate initially. When lactate was depleted propionate was oxidized to acetate. We propose to name the switch from propionate production to consumption in microaerobic conditions the 'propionate switch'. When propionate was depleted the 'acetate switch' occurred, resulting in complete consumption of acetate. Both growth rate on lactate (0.100 versus 0.078 h-1 ) and biomass yield (20.5 versus 8.6 g* mol-1 lactate) increased compared to anaerobic conditions. Proteome analysis revealed that the abundance of proteins involved in the aerobic and anaerobic electron transport chains and major metabolic pathways did not significantly differ between anaerobic and microaerobic conditions. This implicates that P. freudenreichii is prepared for utilizing O2 when it comes available in anaerobic conditions. The ecological niche of propionic acid bacteria can conceivably be extended to environments with oxygen gradients from oxic to anoxic, so-called microoxic environments, as found in the rumen, gut and soils, where they can thrive by utilizing low concentrations of oxygen.
Collapse
Affiliation(s)
- Alexander Dank
- Laboratory of Food MicrobiologyWageningen University & Research, P.O. Box 17Wageningen6700AAThe Netherlands
| | - Oscar van Mastrigt
- Laboratory of Food MicrobiologyWageningen University & Research, P.O. Box 17Wageningen6700AAThe Netherlands
| | - Sjef Boeren
- Laboratory of BiochemistryWageningen University & ResearchWageningenThe Netherlands
| | - Søren K. Lillevang
- Arla Innovation Centre, Arla Foods, Agro Food Park 19Aarhus N8200Denmark
| | - Tjakko Abee
- Laboratory of Food MicrobiologyWageningen University & Research, P.O. Box 17Wageningen6700AAThe Netherlands
| | - Eddy J. Smid
- Laboratory of Food MicrobiologyWageningen University & Research, P.O. Box 17Wageningen6700AAThe Netherlands
| |
Collapse
|
5
|
Prokaryotic Solute/Sodium Symporters: Versatile Functions and Mechanisms of a Transporter Family. Int J Mol Sci 2021; 22:ijms22041880. [PMID: 33668649 PMCID: PMC7918813 DOI: 10.3390/ijms22041880] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 11/23/2022] Open
Abstract
The solute/sodium symporter family (SSS family; TC 2.A.21; SLC5) consists of integral membrane proteins that use an existing sodium gradient to drive the uphill transport of various solutes, such as sugars, amino acids, vitamins, or ions across the membrane. This large family has representatives in all three kingdoms of life. The human sodium/iodide symporter (NIS) and the sodium/glucose transporter (SGLT1) are involved in diseases such as iodide transport defect or glucose-galactose malabsorption. Moreover, the bacterial sodium/proline symporter PutP and the sodium/sialic acid symporter SiaT play important roles in bacteria–host interactions. This review focuses on the physiological significance and structural and functional features of prokaryotic members of the SSS family. Special emphasis will be given to the roles and properties of proteins containing an SSS family domain fused to domains typically found in bacterial sensor kinases.
Collapse
|
6
|
Kuprat T, Johnsen U, Ortjohann M, Schönheit P. Acetate Metabolism in Archaea: Characterization of an Acetate Transporter and of Enzymes Involved in Acetate Activation and Gluconeogenesis in Haloferax volcanii. Front Microbiol 2020; 11:604926. [PMID: 33343547 PMCID: PMC7746861 DOI: 10.3389/fmicb.2020.604926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/13/2020] [Indexed: 02/01/2023] Open
Abstract
The haloarchaeon Haloferax volcanii grows on acetate as sole carbon and energy source. The genes and proteins involved in uptake and activation of acetate and in gluconeogenesis were identified and analyzed by characterization of enzymes and by growth experiments with the respective deletion mutants. (i) An acetate transporter of the sodium: solute-symporter family (SSF) was characterized by kinetic analyses of acetate uptake into H. volcanii cells. The functional involvement of the transporter was proven with a Δssf mutant. (ii) Four paralogous AMP-forming acetyl-CoA synthetases that belong to different phylogenetic clades were shown to be functionally involved in acetate activation. (iii) The essential involvement of the glyoxylate cycle as an anaplerotic sequence was concluded from growth experiments with an isocitrate lyase knock-out mutant excluding the operation of the methylaspartate cycle reported for Haloarcula species. (iv) Enzymes involved in phosphoenolpyruvate synthesis from acetate, namely two malic enzymes and a phosphoenolpyruvate synthetase, were identified and characterized. Phylogenetic analyses of haloarchaeal malic enzymes indicate a separate evolutionary line distinct from other archaeal homologs. The exclusive function of phosphoenolpyruvate synthetase in gluconeogenesis was proven by the respective knock-out mutant. Together, this is a comprehensive study of acetate metabolism in archaea.
Collapse
Affiliation(s)
- Tom Kuprat
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
| | - Ulrike Johnsen
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
| | - Marius Ortjohann
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
| | - Peter Schönheit
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
| |
Collapse
|
7
|
Gasperotti A, Göing S, Fajardo-Ruiz E, Forné I, Jung K. Function and Regulation of the Pyruvate Transporter CstA in Escherichia coli. Int J Mol Sci 2020; 21:ijms21239068. [PMID: 33260635 PMCID: PMC7730263 DOI: 10.3390/ijms21239068] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/02/2022] Open
Abstract
Pyruvate is a central metabolite that connects many metabolic pathways in living organisms. To meet the cellular pyruvate requirements, the enterobacterium Escherichia coli has at least three pyruvate uptake systems—the H+/pyruvate symporter BtsT, and two thus far less well-characterized transporters, YhjX and CstA. BtsT and CstA belong to the putative carbon starvation (CstA) family (transporter classification TC# 2.A.114). We have created an E. coli mutant that cannot grow on pyruvate as the sole carbon source and used it to characterize CstA as a pyruvate transporter. Transport studies in intact cells confirmed that CstA is a highly specific pyruvate transporter with moderate affinity and is energized by a proton gradient. When cells of a reporter strain were cultured in complex medium, cstA expression was maximal only in stationary phase. A DNA affinity-capture assay combined with mass spectrometry and an in-vivo reporter assay identified Fis as a repressor of cstA expression, in addition to the known activator cAMP-CRP. The functional characterization and regulation of this second pyruvate uptake system provides valuable information for understanding the complexity of pyruvate sensing and uptake in E. coli.
Collapse
Affiliation(s)
- Ana Gasperotti
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany; (A.G.); (S.G.); (E.F.-R.)
| | - Stephanie Göing
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany; (A.G.); (S.G.); (E.F.-R.)
| | - Elena Fajardo-Ruiz
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany; (A.G.); (S.G.); (E.F.-R.)
| | - Ignasi Forné
- Protein Analysis Unit, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany;
| | - Kirsten Jung
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany; (A.G.); (S.G.); (E.F.-R.)
- Correspondence:
| |
Collapse
|
8
|
Kosaka T, Goda M, Inoue M, Yakushi T, Yamada M. Flagellum-mediated motility in Pelotomaculum thermopropionicum SI. Biosci Biotechnol Biochem 2019; 83:1362-1371. [PMID: 30919743 DOI: 10.1080/09168451.2019.1597618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The basic functions of a propionate-oxidizing bacterium Pelotomaculum thermopropionicum flagellum, such as motility and chemotaxis, have not been studied. To investigate its motility, we compared with that of Syntrophobacter fumaroxidans, an aflagellar propionate-oxidizing bacterium, in soft agar medium. P. thermopropionicum cells spread, while S. fumaroxidans cells moved downward slightly, indicating flagellum-dependent motility in P. thermopropionicum SI. The motility of P. thermopropionicum was inhibited by the addition of carbonyl cyanide m-chlorophenyl hydrazone, a proton uncoupler, which is consistent with the fact that stator protein, MotB of P. thermopropionicum, shared sequence homology with proton-type stators. In addition, 5-N-ethyl-N-isopropyl amiloride, an Na+ channel blocker, showed no inhibitory effect on the motility. Furthermore, motAB of P. thermopropionicum complemented the defective swimming ability of Escherichia coli ∆motAB. These results suggest that the motility of P. thermopropionicum SI depends on the proton-type flagellar motor.
Collapse
Affiliation(s)
- Tomoyuki Kosaka
- a Department of Biological Chemistry, College of Agriculture, Graduate school of Science and Technology for Innovation , Yamaguchi University , Yamaguchi , Japan.,b Research Center for Thermotolerant Microbial Resources , Yamaguchi University , Yamaguchi , Japan
| | - Mutsumi Goda
- a Department of Biological Chemistry, College of Agriculture, Graduate school of Science and Technology for Innovation , Yamaguchi University , Yamaguchi , Japan
| | - Manami Inoue
- a Department of Biological Chemistry, College of Agriculture, Graduate school of Science and Technology for Innovation , Yamaguchi University , Yamaguchi , Japan
| | - Toshiharu Yakushi
- a Department of Biological Chemistry, College of Agriculture, Graduate school of Science and Technology for Innovation , Yamaguchi University , Yamaguchi , Japan.,b Research Center for Thermotolerant Microbial Resources , Yamaguchi University , Yamaguchi , Japan
| | - Mamoru Yamada
- a Department of Biological Chemistry, College of Agriculture, Graduate school of Science and Technology for Innovation , Yamaguchi University , Yamaguchi , Japan.,b Research Center for Thermotolerant Microbial Resources , Yamaguchi University , Yamaguchi , Japan
| |
Collapse
|
9
|
BtsT, a Novel and Specific Pyruvate/H + Symporter in Escherichia coli. J Bacteriol 2017; 200:JB.00599-17. [PMID: 29061664 DOI: 10.1128/jb.00599-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 10/12/2017] [Indexed: 01/11/2023] Open
Abstract
The peptide transporter carbon starvation (CstA) family (transporter classification [TC] 2.A.114) belongs to the second largest superfamily of secondary transporters, the amino acid/polyamine/organocation (APC) superfamily. No representative of the CstA family has previously been characterized either biochemically or structurally, but we have now identified the function of one of its members, the transport protein YjiY of Escherichia coli Expression of the yjiY gene is regulated by the LytS-like histidine kinase BtsS, a sensor of extracellular pyruvate, together with the LytTR-like response regulator BtsR. YjiY consists of 716 amino acids, which form 18 putative transmembrane helices. Transport studies with intact cells provided evidence that YjiY is a specific and high-affinity transporter for pyruvate (Km , 16 μM). Furthermore, reconstitution of the purified YjiY into proteoliposomes revealed that YjiY is a pyruvate/H+ symporter. It has long been assumed that E. coli possesses a transporter(s) for pyruvate, but the present study is the first to definitively identify such a protein. Based on its function, we propose to change the name of the uncharacterized gene yjiY to btsT for Brenztraubensäure (the German word for pyruvate) transporter.IMPORTANCE BtsT (formerly known as YjiY) is found in many commensal and pathogenic representatives of the Enterobacteriaceae This study for the first time characterizes a pyruvate transporter in E. coli, BtsT, as a specific pyruvate/H+ symporter. When nutrients are limiting, BtsT takes up pyruvate from the medium, thus enabling it to be used as a carbon source for the growth and survival of E. coli.
Collapse
|
10
|
Herbold CW, Lehtovirta-Morley LE, Jung MY, Jehmlich N, Hausmann B, Han P, Loy A, Pester M, Sayavedra-Soto LA, Rhee SK, Prosser JI, Nicol GW, Wagner M, Gubry-Rangin C. Ammonia-oxidising archaea living at low pH: Insights from comparative genomics. Environ Microbiol 2017; 19:4939-4952. [PMID: 29098760 PMCID: PMC5767755 DOI: 10.1111/1462-2920.13971] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 10/22/2017] [Indexed: 01/08/2023]
Abstract
Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome‐assembled genome from an acidic fen, and performed comparative genomics of the four Ca. Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca. Nitrosotalea strains represent separate species within the genus. The four Ca. Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia‐oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca. Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca. Nitrosotalea lineage in acidic environments.
Collapse
Affiliation(s)
- Craig W Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Laura E Lehtovirta-Morley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU, UK
| | - Man-Young Jung
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 362-763, South Korea
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, Leipzig 04318, Germany
| | - Bela Hausmann
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Ping Han
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Michael Pester
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Inhoffenstr. 7B, Braunschweig 38124, Germany
| | - Luis A Sayavedra-Soto
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902, USA
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 362-763, South Korea
| | - James I Prosser
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU, UK
| | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, L'Université de Lyon, 36 avenue Guy de Collongue, 69134 Ecully CEDEX, France
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Cécile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU, UK
| |
Collapse
|
11
|
Molecular and Physiological Logics of the Pyruvate-Induced Response of a Novel Transporter in Bacillus subtilis. mBio 2017; 8:mBio.00976-17. [PMID: 28974613 PMCID: PMC5626966 DOI: 10.1128/mbio.00976-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
At the heart of central carbon metabolism, pyruvate is a pivotal metabolite in all living cells. Bacillus subtilis is able to excrete pyruvate as well as to use it as the sole carbon source. We herein reveal that ysbAB (renamed pftAB), the only operon specifically induced in pyruvate-grown B. subtilis cells, encodes a hetero-oligomeric membrane complex which operates as a facilitated transport system specific for pyruvate, thereby defining a novel class of transporter. We demonstrate that the LytST two-component system is responsible for the induction of pftAB in the presence of pyruvate by binding of the LytT response regulator to a palindromic region upstream of pftAB. We show that both glucose and malate, the preferred carbon sources for B. subtilis, trigger the binding of CcpA upstream of pftAB, which results in its catabolite repression. However, an additional CcpA-independent mechanism represses pftAB in the presence of malate. Screening a genome-wide transposon mutant library, we find that an active malic enzyme replenishing the pyruvate pool is required for this repression. We next reveal that the higher the influx of pyruvate, the stronger the CcpA-independent repression of pftAB, which suggests that intracellular pyruvate retroinhibits pftAB induction via LytST. Such a retroinhibition challenges the rational design of novel nature-inspired sensors and synthetic switches but undoubtedly offers new possibilities for the development of integrated sensor/controller circuitry. Overall, we provide evidence for a complete system of sensors, feed-forward and feedback controllers that play a major role in environmental growth of B. subtilis. Pyruvate is a small-molecule metabolite ubiquitous in living cells. Several species also use it as a carbon source as well as excrete it into the environment. The bacterial systems for pyruvate import/export have yet to be discovered. Here, we identified in the model bacterium Bacillus subtilis the first import/export system specific for pyruvate, PftAB, which defines a novel class of transporter. In this bacterium, extracellular pyruvate acts as the signal molecule for the LytST two-component system (TCS), which in turn induces expression of PftAB. However, when the pyruvate influx is high, LytST activity is drastically retroinhibited. Such a retroinhibition challenges the rational design of novel nature-inspired sensors and synthetic switches but undoubtedly offers new possibilities for the development of integrated sensor/controller circuitry.
Collapse
|
12
|
Manzoor S, Bongcam-Rudloff E, Schnürer A, Müller B. Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii. PLoS One 2016; 11:e0166520. [PMID: 27851830 PMCID: PMC5113046 DOI: 10.1371/journal.pone.0166520] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 10/31/2016] [Indexed: 01/29/2023] Open
Abstract
Syntrophaceticus schinkii is a mesophilic, anaerobic bacterium capable of oxidising acetate to CO2 and H2 in intimate association with a methanogenic partner, a syntrophic relationship which operates close to the energetic limits of microbial life. Syntrophaceticus schinkii has been identified as a key organism in engineered methane-producing processes relying on syntrophic acetate oxidation as the main methane-producing pathway. However, due to strict cultivation requirements and difficulties in reconstituting the thermodynamically unfavourable acetate oxidation, the physiology of this functional group is poorly understood. Genome-guided and whole transcriptome analyses performed in the present study provide new insights into habitat adaptation, syntrophic acetate oxidation and energy conservation. The working draft genome of Syntrophaceticus schinkii indicates limited metabolic capacities, with lack of organic nutrient uptake systems, chemotactic machineries, carbon catabolite repression and incomplete biosynthesis pathways. Ech hydrogenase, [FeFe] hydrogenases, [NiFe] hydrogenases, F1F0-ATP synthase and membrane-bound and cytoplasmic formate dehydrogenases were found clearly expressed, whereas Rnf and a predicted oxidoreductase/heterodisulphide reductase complex, both found encoded in the genome, were not expressed under syntrophic growth condition. A transporter sharing similarities to the high-affinity acetate transporters of aceticlastic methanogens was also found expressed, suggesting that Syntrophaceticus schinkii can potentially compete with methanogens for acetate. Acetate oxidation seems to proceed via the Wood-Ljungdahl pathway as all genes involved in this pathway were highly expressed. This study shows that Syntrophaceticus schinkii is a highly specialised, habitat-adapted organism relying on syntrophic acetate oxidation rather than metabolic versatility. By expanding its complement of respiratory complexes, it might overcome limiting bioenergetic barriers, and drive efficient energy conservation from reactions operating close to the thermodynamic equilibrium, which might enable S. schinkii to occupy the same niche as the aceticlastic methanogens. The knowledge gained here will help specify process conditions supporting efficient and robust biogas production and will help identify mechanisms important for the syntrophic lifestyle.
Collapse
Affiliation(s)
- Shahid Manzoor
- Department of Information Technology, University of the Punjab, Lahore, Pakistan
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Science, SLU-Global Bioinformatics Centre, Uppsala, SE 750 07, Sweden
| | - Anna Schnürer
- Department of Microbiology, Swedish University of Agricultural Sciences, BioCenter, Uppsala, SE 750 07, Sweden
| | - Bettina Müller
- Department of Microbiology, Swedish University of Agricultural Sciences, BioCenter, Uppsala, SE 750 07, Sweden
| |
Collapse
|
13
|
Mock J, Zheng Y, Mueller AP, Ly S, Tran L, Segovia S, Nagaraju S, Köpke M, Dürre P, Thauer RK. Energy Conservation Associated with Ethanol Formation from H2 and CO2 in Clostridium autoethanogenum Involving Electron Bifurcation. J Bacteriol 2015; 197:2965-80. [PMID: 26148714 PMCID: PMC4542177 DOI: 10.1128/jb.00399-15] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 06/29/2015] [Indexed: 02/01/2023] Open
Abstract
UNLABELLED Most acetogens can reduce CO2 with H2 to acetic acid via the Wood-Ljungdahl pathway, in which the ATP required for formate activation is regenerated in the acetate kinase reaction. However, a few acetogens, such as Clostridium autoethanogenum, Clostridium ljungdahlii, and Clostridium ragsdalei, also form large amounts of ethanol from CO2 and H2. How these anaerobes with a growth pH optimum near 5 conserve energy has remained elusive. We investigated this question by determining the specific activities and cofactor specificities of all relevant oxidoreductases in cell extracts of H2/CO2-grown C. autoethanogenum. The activity studies were backed up by transcriptional and mutational analyses. Most notably, despite the presence of six hydrogenase systems of various types encoded in the genome, the cells appear to contain only one active hydrogenase. The active [FeFe]-hydrogenase is electron bifurcating, with ferredoxin and NADP as the two electron acceptors. Consistently, most of the other active oxidoreductases rely on either reduced ferredoxin and/or NADPH as the electron donor. An exception is ethanol dehydrogenase, which was found to be NAD specific. Methylenetetrahydrofolate reductase activity could only be demonstrated with artificial electron donors. Key to the understanding of this energy metabolism is the presence of membrane-associated reduced ferredoxin:NAD(+) oxidoreductase (Rnf), of electron-bifurcating and ferredoxin-dependent transhydrogenase (Nfn), and of acetaldehyde:ferredoxin oxidoreductase, which is present with very high specific activities in H2/CO2-grown cells. Based on these findings and on thermodynamic considerations, we propose metabolic schemes that allow, depending on the H2 partial pressure, the chemiosmotic synthesis of 0.14 to 1.5 mol ATP per mol ethanol synthesized from CO2 and H2. IMPORTANCE Ethanol formation from syngas (H2, CO, and CO2) and from H2 and CO2 that is catalyzed by bacteria is presently a much-discussed process for sustainable production of biofuels. Although the process is already in use, its biochemistry is only incompletely understood. The most pertinent question is how the bacteria conserve energy for growth during ethanol formation from H2 and CO2, considering that acetyl coenzyme A (acetyl-CoA), is an intermediate. Can reduction of the activated acetic acid to ethanol with H2 be coupled with the phosphorylation of ADP? Evidence is presented that this is indeed possible, via both substrate-level phosphorylation and electron transport phosphorylation. In the case of substrate-level phosphorylation, acetyl-CoA reduction to ethanol proceeds via free acetic acid involving acetaldehyde:ferredoxin oxidoreductase (carboxylate reductase).
Collapse
Affiliation(s)
- Johanna Mock
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Yanning Zheng
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - San Ly
- LanzaTech Inc., Skokie, Illinois, USA
| | - Loan Tran
- LanzaTech Inc., Skokie, Illinois, USA
| | | | | | | | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| |
Collapse
|
14
|
Oren A. Pyruvate: A key Nutrient in Hypersaline Environments? Microorganisms 2015; 3:407-16. [PMID: 27682096 PMCID: PMC5023246 DOI: 10.3390/microorganisms3030407] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 07/29/2015] [Accepted: 07/31/2015] [Indexed: 11/17/2022] Open
Abstract
Some of the most commonly occurring but difficult to isolate halophilic prokaryotes, Archaea as well as Bacteria, require or prefer pyruvate as carbon and energy source. The most efficient media for the enumeration and isolation of heterotrophic prokaryotes from natural environments, from freshwater to hypersaline, including the widely used R2A agar medium, contain pyruvate as a key ingredient. Examples of pyruvate-loving halophiles are the square, extremely halophilic archaeon Haloquadratum walsbyi and the halophilic gammaproteobacterium Spiribacter salinus. However, surprisingly little is known about the availability of pyruvate in natural environments and about the way it enters the cell. Some halophilic Archaea (Halorubrum saccharovorum, Haloarcula spp.) partially convert sugars and glycerol to pyruvate and other acids (acetate, lactate) which are excreted to the medium. Pyruvate formation from glycerol was also shown during a bloom of halophilic Archaea in the Dead Sea. However, no pyruvate transporters were yet identified in the genomes of halophilic Archaea, and altogether, our understanding of pyruvate transport in the prokaryote world is very limited. Therefore, the preference for pyruvate by fastidious and often elusive halophiles and the empirically proven enhanced colony recovery on agar media containing pyruvate are still poorly understood.
Collapse
Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israel.
| |
Collapse
|
15
|
Müller B, Manzoor S, Niazi A, Bongcam-Rudloff E, Schnürer A. Genome-guided analysis of physiological capacities of Tepidanaerobacter acetatoxydans provides insights into environmental adaptations and syntrophic acetate oxidation. PLoS One 2015; 10:e0121237. [PMID: 25811859 PMCID: PMC4374699 DOI: 10.1371/journal.pone.0121237] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/30/2015] [Indexed: 11/21/2022] Open
Abstract
This paper describes the genome-based analysis of Tepidanaerobacter acetatoxydans strain Re1, a syntrophic acetate-oxidising bacterium (SAOB). Principal issues such as environmental adaptations, metabolic capacities, and energy conserving systems have been investigated and the potential consequences for syntrophic acetate oxidation discussed. Briefly, in pure culture, T. acetatoxydans grows with different organic compounds and produces acetate as the main product. In a syntrophic consortium with a hydrogenotrophic methanogen, it can also reverse its metabolism and instead convert acetate to formate/H2 and CO2. It can only proceed if the product formed is continuously removed. This process generates a very small amount of energy that is scarcely enough for growth, which makes this particular syntrophy of special interest. As a crucial member of the biogas-producing community in ammonium-rich engineered AD processes, genomic features conferring ammonium resistance, bacterial defense, oxygen and temperature tolerance were found, as well as attributes related to biofilm formation and flocculation. It is likely that T. acetatoxydans can form an electrochemical gradient by putative electron-bifurcating Rnf complex and [Fe-Fe] hydrogenases, as observed in other acetogens. However, genomic deficiencies related to acetogenic metabolism and anaerobic respiration were discovered, such as the lack of formate dehydrogenase and F1F0 ATP synthase. This has potential consequences for the metabolic pathways used under SAO and non-SAO conditions. The two complete sets of bacteriophage genomes, which were found to be encoded in the genome, are also worthy of mention.
Collapse
Affiliation(s)
- Bettina Müller
- Department of Microbiology, Swedish University of Agricultural Sciences, BioCenter, Uppsala, Sweden
- * E-mail:
| | - Shahid Manzoor
- Department of Animal Breeding and Genetics Science, Swedish University of Agricultural Science, SLU-Global Bioinformatics Centre, Uppsala, Sweden
- University of the Punjab, Lahore, Pakistan
| | - Adnan Niazi
- Department of Animal Breeding and Genetics Science, Swedish University of Agricultural Science, SLU-Global Bioinformatics Centre, Uppsala, Sweden
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics Science, Swedish University of Agricultural Science, SLU-Global Bioinformatics Centre, Uppsala, Sweden
| | - Anna Schnürer
- Department of Microbiology, Swedish University of Agricultural Sciences, BioCenter, Uppsala, Sweden
| |
Collapse
|
16
|
Trötschel C, Follmann M, Nettekoven JA, Mohrbach T, Forrest LR, Burkovski A, Marin K, Krämer R. Methionine uptake in Corynebacterium glutamicum by MetQNI and by MetPS, a novel methionine and alanine importer of the NSS neurotransmitter transporter family. Biochemistry 2015; 47:12698-709. [PMID: 18991398 DOI: 10.1021/bi801206t] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The soil bacterium Corynebacterium glutamicum is a model organism in amino acid biotechnology. Here we present the identification of two different L-methionine uptake systems including the first characterization of a bacterial secondary methionine carrier. The primary carrier MetQNI is a high affinity ABC-type transporter specific for l-methionine. Its expression is under the control of the transcription factor McbR, the global regulator of sulfur metabolism in C. glutamicum. Besides MetQNI, a novel secondary methionine uptake system of the NSS (neurotransmitter:sodium symporter) family was identified and named MetP. The MetP system is characterized by a lower affinity for methionine and uses Na(+) ions for energetic coupling. It is also the main alanine transporter in C. glutamicum and is expressed constitutively. These observations are consistent with models of methionine, alanine, and leucine bound to MetP, derived from the X-ray crystal structure of the LeuT transporter from Aquifex aeolicus. Complementation studies show that MetP consists of two components, a large subunit with 12 predicted transmembrane segments and, surprisingly, an additional subunit with one predicted transmembrane segment only. Thus, this new member of the NSS transporter family adds a novel feature to this class of carriers, namely, the functional dependence on an additional small subunit.
Collapse
Affiliation(s)
- Christian Trötschel
- Institute of Biochemistry, University of Koln, 50674 Koln, Germany, and Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt, Germany
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Welte C, Kröninger L, Deppenmeier U. Experimental evidence of an acetate transporter protein and characterization of acetate activation in aceticlastic methanogenesis of Methanosarcina mazei. FEMS Microbiol Lett 2014; 359:147-53. [PMID: 25088360 DOI: 10.1111/1574-6968.12550] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 06/12/2014] [Accepted: 07/28/2014] [Indexed: 11/29/2022] Open
Abstract
Aceticlastic methanogens metabolize acetate to methane and carbon dioxide. The central metabolism and the electron transport chains of these organisms have already been investigated. However, no particular attention has been paid to the mechanism by which acetate enters the archaeal cell. In our study we investigated Methanosarcina mazei acetate kinase (Ack) and the acetate uptake reaction. At a concentration of 2 mM acetate, the Ack activity in cell extract of M. mazei was not limiting for the methane formation rate. Instead, the methanogenesis rate was controlled by the substrate concentration and increased 10-fold at 10 mM acetate. Subsequently, we analyzed the involvement of the putative acetate permease MM_0903 using a corresponding deletion mutant. At 2 mM acetate, only 25% of the wild-type methane formation rate was measured in the mutant. This indicated that the supply of acetate to Ack was limiting the rate of methane formation. Moreover, the mutant revealed an increased acetate kinase activity compared with the wild type. These results show for the first time that an acetate transporter is involved in aceticlastic methanogenesis and may be an important factor in the acetate threshold concentration for methanogenesis of Methanosarcina spp.
Collapse
Affiliation(s)
- Cornelia Welte
- Institute for Microbiology & Biotechnology, University of Bonn, Bonn, Germany; Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | | |
Collapse
|
18
|
Abstract
Burkholderia cenocepacia and Burkholderia multivorans are opportunistic drug-resistant pathogens that account for the majority of Burkholderia cepacia complex infections in cystic fibrosis patients and also infect other immunocompromised individuals. While they share similar genetic compositions, B. cenocepacia and B. multivorans exhibit important differences in pathogenesis. We have developed reconciled genome-scale metabolic network reconstructions of B. cenocepacia J2315 and B. multivorans ATCC 17616 in parallel (designated iPY1537 and iJB1411, respectively) to compare metabolic abilities and contextualize genetic differences between species. The reconstructions capture the metabolic functions of the two species and give insight into similarities and differences in their virulence and growth capabilities. The two reconstructions have 1,437 reactions in common, and iPY1537 and iJB1411 have 67 and 36 metabolic reactions unique to each, respectively. After curating the extensive reservoir of metabolic genes in Burkholderia, we identified 6 genes essential to growth that are unique to iPY1513 and 13 genes uniquely essential to iJB1411. The reconstructions were refined and validated by comparing in silico growth predictions to in vitro growth capabilities of B. cenocepacia J2315, B. cenocepacia K56-2, and B. multivorans ATCC 17616 on 104 carbon sources. Overall, we identified functional pathways that indicate B. cenocepacia can produce a wider array of virulence factors compared to B. multivorans, which supports the clinical observation that B. cenocepacia is more virulent than B. multivorans. The reconciled reconstructions provide a framework for generating and testing hypotheses on the metabolic and virulence capabilities of these two related emerging pathogens.
Collapse
|
19
|
Abstract
In the present paper we describe a new carboxylic acid transporter in Escherichia coli encoded by the gene yaaH. In contrast to what had been described for other YaaH family members, the E. coli transporter is highly specific for acetic acid (a monocarboxylate) and for succinic acid (a dicarboxylate), with affinity constants at pH 6.0 of 1.24±0.13 mM for acetic acid and 1.18±0.10 mM for succinic acid. In glucose-grown cells the ΔyaaH mutant is compromised for the uptake of both labelled acetic and succinic acids. YaaH, together with ActP, described previously as an acetate transporter, affect the use of acetic acid as sole carbon and energy source. Both genes have to be deleted simultaneously to abolish acetate transport. The uptake of acetate and succinate was restored when yaaH was expressed in trans in ΔyaaH ΔactP cells. We also demonstrate the critical role of YaaH amino acid residues Leu131 and Ala164 on the enhanced ability to transport lactate. Owing to its functional role in acetate and succinate uptake we propose its assignment as SatP: the Succinate–Acetate Transporter Protein.
Collapse
|
20
|
Kreth J, Lengeler JW, Jahreis K. Characterization of pyruvate uptake in Escherichia coli K-12. PLoS One 2013; 8:e67125. [PMID: 23818977 PMCID: PMC3688616 DOI: 10.1371/journal.pone.0067125] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 05/14/2013] [Indexed: 12/02/2022] Open
Abstract
The monocarboxylate pyruvate is an important metabolite and can serve as sole carbon source for Escherichia coli. Although specific pyruvate transporters have been identified in two bacterial species, pyruvate transport is not well understood in E. coli. In the present study, pyruvate transport was investigated under different growth conditions. The transport of pyruvate shows specific activities depending on the growth substrate used as sole carbon source, suggesting the existence of at least two systems for pyruvate uptake: i) one inducible system and probably highly specific for pyruvate and ii) one system active under non-induced conditions. Using the toxic pyruvate analog 3-fluoropyruvate, a mutant was isolated unable to grow on and transport pyruvate. Further investigation revealed that a revertant selected for growth on pyruvate regained the inducible pyruvate transport activity. Characterization of pyruvate excretion showed that the pyruvate transport negative mutant accumulated pyruvate in the growth medium suggesting an additional transport system for pyruvate excretion. The here presented data give valuable insight into the pyruvate metabolism and transport of E. coli suggesting the presence of at least two uptake systems and one excretion system to balance the intracellular level of pyruvate.
Collapse
Affiliation(s)
- Jens Kreth
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.
| | | | | |
Collapse
|
21
|
Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth. J Bacteriol 2012; 195:990-1004. [PMID: 23264581 DOI: 10.1128/jb.01959-12] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers linked by interspecies electron transfer in syntrophic consortia that may include sulfate-reducing species (e.g., Desulfovibrio). Physiological differences and various gene repertoires implicated in syntrophic metabolism among Desulfovibrio species suggest considerable variation in the biochemical basis of syntrophy. In this study, comparative transcriptional and mutant analyses of Desulfovibrio alaskensis strain G20 and Desulfovibrio vulgaris strain Hildenborough growing syntrophically with Methanococcus maripaludis on lactate were used to develop new and revised models for their alternative electron transfer and energy conservation systems. Lactate oxidation by strain G20 generates a reduced thiol-disulfide redox pair(s) and ferredoxin that are energetically coupled to H(+)/CO(2) reduction by periplasmic formate dehydrogenase and hydrogenase via a flavin-based reverse electron bifurcation process (electron confurcation) and a menaquinone (MQ) redox loop-mediated reverse electron flow involving the membrane-bound Qmo and Qrc complexes. In contrast, strain Hildenborough uses a larger number of cytoplasmic and periplasmic proteins linked in three intertwining pathways to couple H(+) reduction to lactate oxidation. The faster growth of strain G20 in coculture is associated with a kinetic advantage conferred by the Qmo-MQ-Qrc loop as an electron transfer system that permits higher lactate oxidation rates under elevated hydrogen levels (thereby enhancing methanogenic growth) and use of formate as the main electron-exchange mediator (>70% electron flux), as opposed to the primarily hydrogen-based exchange by strain Hildenborough. This study further demonstrates the absence of a conserved gene core in Desulfovibrio that would determine the ability for a syntrophic lifestyle.
Collapse
|
22
|
Su X, Kong KF, Tsang JSH. Transports of acetate and haloacetate in Burkholderia species MBA4 are operated by distinct systems. BMC Microbiol 2012; 12:267. [PMID: 23167477 PMCID: PMC3552994 DOI: 10.1186/1471-2180-12-267] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 11/17/2012] [Indexed: 12/04/2022] Open
Abstract
Background Acetate is a commonly used substrate for biosynthesis while monochloroacetate is a structurally similar compound but toxic and inhibits cell metabolism by blocking the citric acid cycle. In Burkholderia species MBA4 haloacetate was utilized as a carbon and energy source for growth. The degradation of haloacid was mediated by the production of an inducible dehalogenase. Recent studies have identified the presence of a concomitantly induced haloacetate-uptake activity in MBA4. This uptake activity has also been found to transport acetate. Since acetate transporters are commonly found in bacteria it is likely that haloacetate was transported by such a system in MBA4. Results The haloacetate-uptake activity of MBA4 was found to be induced by monochloroacetate (MCA) and monobromoacetate (MBA). While the acetate-uptake activity was also induced by MCA and MBA, other alkanoates: acetate, propionate and 2-monochloropropionate (2MCPA) were also inducers. Competing solute analysis showed that acetate and propionate interrupted the acetate- and MCA- induced acetate-uptake activities. While MCA, MBA, 2MCPA, and butyrate have no effect on acetate uptake they could significantly quenched the MCA-induced MCA-uptake activity. Transmembrane electrochemical potential was shown to be a driving force for both acetate- and MCA- transport systems. Conclusions Here we showed that acetate- and MCA- uptake in Burkholderia species MBA4 are two transport systems that have different induction patterns and substrate specificities. It is envisaged that the shapes and the three dimensional structures of the solutes determine their recognition or exclusion by the two transport systems.
Collapse
Affiliation(s)
- Xianbin Su
- Molecular Microbiology Laboratory, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | | | | |
Collapse
|
23
|
Elías AO, Abarca MJ, Montes RA, Chasteen TG, Pérez-Donoso JM, Vásquez CC. Tellurite enters Escherichia coli mainly through the PitA phosphate transporter. Microbiologyopen 2012. [PMID: 23189244 PMCID: PMC3501828 DOI: 10.1002/mbo3.26] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Several transporters suspected to be involved in tellurite uptake in Escherichia coli were analyzed. Results showed that the PitA phosphate transporter was related to tellurite uptake. Escherichia coli ΔpitA was approximately four-fold more tolerant to tellurite, and cell viability remained almost unchanged during prolonged exposure to the toxicant as compared with wild type or ΔpitB cells. Notably, reduced thiols (toxicant targets) as well as superoxide dismutase, catalase, and fumarase C activities did not change when exposing the ΔpitA strain to tellurite, suggesting that tellurite-triggered oxidative damage is attenuated in the absence of PitA. After toxicant exposure, remaining extracellular tellurite was higher in E. coli ΔpitA than in control cells. Whereas inductively coupled plasma atomic emission spectrometric studies confirmed that E. coli ΔpitA accumulates ∼50% less tellurite than the other strains under study, tellurite strongly inhibited 32Pi uptake suggesting that the PitA transporter is one of the main responsible for tellurite uptake in this bacterium.
Collapse
Affiliation(s)
- Alex O Elías
- Laboratorio de Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile Chile
| | | | | | | | | | | |
Collapse
|
24
|
Mulley G, White JP, Karunakaran R, Prell J, Bourdes A, Bunnewell S, Hill L, Poole PS. Mutation of GOGAT prevents pea bacteroid formation and N2 fixation by globally downregulating transport of organic nitrogen sources. Mol Microbiol 2011; 80:149-67. [PMID: 21276099 DOI: 10.1111/j.1365-2958.2011.07565.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mutation of gltB (encoding glutamate oxoglutarate amidotransferase or GOGAT) in RU2307 increased the intracellular Gln:Glu ratio and inhibited amino acid transport via Aap and Bra. The mechanism probably involves global post-translational inhibition independent of Ntr. Transport was separately restored by increased gene expression of Aap or heterologous transporters. Likewise, second site suppressor mutations in the RNA chaperone Hfq elevated transport by Aap and Bra by increasing mRNA levels. Microarrays showed Hfq regulates 34 ABC transporter genes, including aap, bra and opp. The genes coding for integral membrane proteins and ABC subunits aapQMP braDEFGC were more strongly elevated in the hfq mutants than solute-binding proteins (aapJ braC). aapQMP and braDEFG are immediately downstream of stem-loops, indicating Hfq attenuates downstream translation and stability of mRNA, explaining differential expression of ABC genes. RU2307 nodulated peas and bacteria grew down infection threads, but bacteroid development was arrested and N(2) was not fixed. This probably results from an inability to synthesize or transport amino acids. However, GOGAT and GOGAT/AldA double mutants carrying suppressor mutations that increased amino acid uptake fixed N(2) on pea plants. Thus de novo ammonium assimilation into amino acids is unnecessary in bacteroids demonstrating sufficient amino acids are supplied by plants.
Collapse
Affiliation(s)
- G Mulley
- Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Quinone-dependent D-lactate dehydrogenase Dld (Cg1027) is essential for growth of Corynebacterium glutamicum on D-lactate. BMC Microbiol 2010; 10:321. [PMID: 21159175 PMCID: PMC3022706 DOI: 10.1186/1471-2180-10-321] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 12/15/2010] [Indexed: 02/01/2023] Open
Abstract
Background Corynebacterium glutamicum is able to grow with lactate as sole or combined carbon and energy source. Quinone-dependent L-lactate dehydrogenase LldD is known to be essential for utilization of L-lactate by C. glutamicum. D-lactate also serves as sole carbon source for C. glutamicum ATCC 13032. Results Here, the gene cg1027 was shown to encode the quinone-dependent D-lactate dehydrogenase (Dld) by enzymatic analysis of the protein purified from recombinant E. coli. The absorption spectrum of purified Dld indicated the presence of FAD as bound cofactor. Inactivation of dld resulted in the loss of the ability to grow with D-lactate, which could be restored by plasmid-borne expression of dld. Heterologous expression of dld from C. glutamicum ATCC 13032 in C. efficiens enabled this species to grow with D-lactate as sole carbon source. Homologs of dld of C. glutamicum ATCC 13032 are not encoded in the sequenced genomes of other corynebacteria and mycobacteria. However, the dld locus of C. glutamicum ATCC 13032 shares 2367 bp of 2372 bp identical nucleotides with the dld locus of Propionibacterium freudenreichii subsp. shermanii, a bacterium used in Swiss-type cheese making. Both loci are flanked by insertion sequences of the same family suggesting a possible event of horizontal gene transfer. Conclusions Cg1067 encodes quinone-dependent D-lactate dehydrogenase Dld of Corynebacterium glutamicum. Dld is essential for growth with D-lactate as sole carbon source. The genomic region of dld likely has been acquired by horizontal gene transfer.
Collapse
|
26
|
Abreu C, Sanguinetti M, Amillis S, Ramon A. UreA, the major urea/H+ symporter in Aspergillus nidulans. Fungal Genet Biol 2010; 47:1023-33. [PMID: 20633690 DOI: 10.1016/j.fgb.2010.07.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2010] [Revised: 06/16/2010] [Accepted: 07/08/2010] [Indexed: 10/19/2022]
Abstract
We report here the characterization of UreA, a high-affinity urea/H+ symporter of Aspergillus nidulans. The deletion of the encoding gene abolishes urea transport at low substrate concentrations, suggesting that in these conditions UreA is the sole transport system specific for urea in A. nidulans. The ureA gene is not inducible by urea or its precursors, but responds to nitrogen metabolite repression, necessitating for its expression the AreA GATA factor. In contrast to what was observed for other transporters in A. nidulans, repression by ammonium is also operative during the isotropic growth phase. The activity of UreA is down-regulated post-translationally by ammonium-promoted endocytosis. A number of homologues of UreA have been identified in A. nidulans and other Aspergilli, which cluster in four groups, two of which contain the urea transporters characterized so far in fungi and plants. This phylogeny may have arisen by gene duplication events, giving place to putative transport proteins that could have acquired novel, still unidentified functions.
Collapse
Affiliation(s)
- Cecilia Abreu
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | | | | | | |
Collapse
|
27
|
Bonaldi K, Gherbi H, Franche C, Bastien G, Fardoux J, Barker D, Giraud E, Cartieaux F. The Nod factor-independent symbiotic signaling pathway: development of Agrobacterium rhizogenes-mediated transformation for the legume Aeschynomene indica. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:1537-44. [PMID: 21039272 DOI: 10.1094/mpmi-06-10-0137] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The nitrogen-fixing symbiosis between Aeschynomene indica and photosynthetic bradyrhizobia is the only legume-rhizobium association described to date that does not require lipochito-oligosaccharide Nod factors (NF). To assist in deciphering the molecular basis of this NF-independent interaction, we have developed a protocol for Agrobacterium rhizogenes-mediated transformation of A. indica. The cotransformation frequency (79%), the nodulation efficiency of transgenic roots (90%), and the expression pattern of the 35S Cauliflower mosaic virus promoter in transgenic nodules were all comparable to those obtained for model legumes. We have made use of this tool to monitor the heterologous spatio-temporal expression of the pMtENOD11-β-glucuronidase fusion, a widely used molecular reporter for rhizobial infection and nodulation in both legumes and actinorhizal plants. While MtENOD11 promoter activation was not observed in A. indica roots prior to nodulation, strong reporter-gene expression was observed in the invaded cells of young nodules and in the cell layers bordering the central zone of older nodules. We conclude that pMtENOD11 expression can be used as an infection-related marker in A. indica and that Agrobacterium rhizogenes-mediated root transformation of Aeschynomene spp. will be an invaluable tool for determining the molecular basis of the NF-independent symbiosis.
Collapse
Affiliation(s)
- Katia Bonaldi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, F-34398 Montpellier, France
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Gross J, Bhattacharya D. Uniting sex and eukaryote origins in an emerging oxygenic world. Biol Direct 2010; 5:53. [PMID: 20731852 PMCID: PMC2933680 DOI: 10.1186/1745-6150-5-53] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 08/23/2010] [Indexed: 11/14/2022] Open
Abstract
Background Theories about eukaryote origins (eukaryogenesis) need to provide unified explanations for the emergence of diverse complex features that define this lineage. Models that propose a prokaryote-to-eukaryote transition are gridlocked between the opposing "phagocytosis first" and "mitochondria as seed" paradigms, neither of which fully explain the origins of eukaryote cell complexity. Sex (outcrossing with meiosis) is an example of an elaborate trait not yet satisfactorily addressed in theories about eukaryogenesis. The ancestral nature of meiosis and its dependence on eukaryote cell biology suggest that the emergence of sex and eukaryogenesis were simultaneous and synergic and may be explained by a common selective pressure. Presentation of the hypothesis We propose that a local rise in oxygen levels, due to cyanobacterial photosynthesis in ancient Archean microenvironments, was highly toxic to the surrounding biota. This selective pressure drove the transformation of an archaeal (archaebacterial) lineage into the first eukaryotes. Key is that oxygen might have acted in synergy with environmental stresses such as ultraviolet (UV) radiation and/or desiccation that resulted in the accumulation of reactive oxygen species (ROS). The emergence of eukaryote features such as the endomembrane system and acquisition of the mitochondrion are posited as strategies to cope with a metabolic crisis in the cell plasma membrane and the accumulation of ROS, respectively. Selective pressure for efficient repair of ROS/UV-damaged DNA drove the evolution of sex, which required cell-cell fusions, cytoskeleton-mediated chromosome movement, and emergence of the nuclear envelope. Our model implies that evolution of sex and eukaryogenesis were inseparable processes. Testing the hypothesis Several types of data can be used to test our hypothesis. These include paleontological predictions, simulation of ancient oxygenic microenvironments, and cell biological experiments with Archaea exposed to ROS and UV stresses. Studies of archaeal conjugation, prokaryotic DNA recombination, and the universality of nuclear-mediated meiotic activities might corroborate the hypothesis that sex and the nucleus evolved to support DNA repair. Implications of the hypothesis Oxygen tolerance emerges as an important principle to investigate eukaryogenesis. The evolution of eukaryotic complexity might be best understood as a synergic process between key evolutionary innovations, of which meiosis (sex) played a central role. Reviewers This manuscript was reviewed by Eugene V. Koonin, Anthony M. Poole, and Gáspár Jékely.
Collapse
Affiliation(s)
- Jeferson Gross
- Department of Ecology, Evolution and Natural Resources, Institute of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, 08901, USA
| | | |
Collapse
|
29
|
Karunakaran R, Ramachandran VK, Seaman JC, East AK, Mouhsine B, Mauchline TH, Prell J, Skeffington A, Poole PS. Transcriptomic analysis of Rhizobium leguminosarum biovar viciae in symbiosis with host plants Pisum sativum and Vicia cracca. J Bacteriol 2009; 191:4002-14. [PMID: 19376875 PMCID: PMC2698398 DOI: 10.1128/jb.00165-09] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Accepted: 04/03/2009] [Indexed: 01/20/2023] Open
Abstract
Rhizobium leguminosarum bv. viciae forms nitrogen-fixing nodules on several legumes, including pea (Pisum sativum) and vetch (Vicia cracca), and has been widely used as a model to study nodule biochemistry. To understand the complex biochemical and developmental changes undergone by R. leguminosarum bv. viciae during bacteroid development, microarray experiments were first performed with cultured bacteria grown on a variety of carbon substrates (glucose, pyruvate, succinate, inositol, acetate, and acetoacetate) and then compared to bacteroids. Bacteroid metabolism is essentially that of dicarboxylate-grown cells (i.e., induction of dicarboxylate transport, gluconeogenesis and alanine synthesis, and repression of sugar utilization). The decarboxylating arm of the tricarboxylic acid cycle is highly induced, as is gamma-aminobutyrate metabolism, particularly in bacteroids from early (7-day) nodules. To investigate bacteroid development, gene expression in bacteroids was analyzed at 7, 15, and 21 days postinoculation of peas. This revealed that bacterial rRNA isolated from pea, but not vetch, is extensively processed in mature bacteroids. In early development (7 days), there were large changes in the expression of regulators, exported and cell surface molecules, multidrug exporters, and heat and cold shock proteins. fix genes were induced early but continued to increase in mature bacteroids, while nif genes were induced strongly in older bacteroids. Mutation of 37 genes that were strongly upregulated in mature bacteroids revealed that none were essential for nitrogen fixation. However, screening of 3,072 mini-Tn5 mutants on peas revealed previously uncharacterized genes essential for nitrogen fixation. These encoded a potential magnesium transporter, an AAA domain protein, and proteins involved in cytochrome synthesis.
Collapse
Affiliation(s)
- R Karunakaran
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Identification and characterization of a bacterial transport system for the uptake of pyruvate, propionate, and acetate in Corynebacterium glutamicum. J Bacteriol 2008; 191:940-8. [PMID: 19028892 DOI: 10.1128/jb.01155-08] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The metabolism of monocarboxylic acids is of central importance for bacteria in their natural habitat as well as during biotechnological production. Although biosynthesis and degradation are well understood, the transport of such compounds is still a matter of discussion. Here we present the identification and characterization of a new transport system in Corynebacterium glutamicum with high affinity for acetate and propionate and with lower affinity for pyruvate. Biochemical analysis of this monocarboxylic acid transporter (MctC) revealed for the first time a quantitative discrimination of passive diffusion and active transport of acetate by bacterial cells. MctC is a secondary transporter and belongs to the class of sodium solute symporters, but it is driven by the electrochemical proton potential. The mctC gene is preceded by and cotranscribed with cg0952, a locus encoding a small membrane protein, and the transcription of the cg0952-mctC operon is under the control of the transcriptional regulators RamA and RamB. Both of these proteins directly bind to the promoter region of the operon; RamA is essential for expression and RamB exerts a slightly negative control on expression of the cg0952-mctC operon. mctC expression is induced in the presence of pyruvate and beneficial under substrate-limiting conditions for C. glutamicum.
Collapse
|
31
|
Burow LC, Mabbett AN, McEwan AG, Bond PL, Blackall LL. Bioenergetic models for acetate and phosphate transport in bacteria important in enhanced biological phosphorus removal. Environ Microbiol 2008; 10:87-98. [PMID: 18211269 DOI: 10.1111/j.1462-2920.2007.01432.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most of our understanding of the physiology of microorganisms is the result of investigations in pure culture. However, in order to understand complex environmental processes, there is a need to investigate mixed microbial communities. This is true for enhanced biological phosphorus removal (EBPR), an environmental process that results in the enrichment of the polyphosphate-accumulating organism Accumulibacter spp. and the glycogen non-polyphosphate accumulating organism Defluviicoccus spp. We investigated acetate and inorganic phosphate (P(i)) uptake in enrichments of Accumulibacter spp. and acetate uptake in enrichments of Defluviicoccus spp. For both enrichments, anaerobic acetate uptake assays in the presence of the protonophore, carbonyl cyanide m-chlorophenylhydrazone (CCCP) or the membrane potential (Delta psi) uncoupler valinomycin, indicated that acetate is likely to be taken up by a permease-mediated process driven by the Delta psi. Further investigation with the sodium ionophore monensin suggested that anaerobic acetate uptake by Defluviicoccus spp. may in part be dependent on a sodium potential. Results of this study also suggest that Accumulibacter spp. generate a proton motive force (pmf or Delta p) for anaerobic acetate uptake by efflux of protons in symport with P(i) through an inorganic phosphate transport (Pit) system. In contrast, we suggest that the anaerobic Delta p in Defluviicoccus spp. is generated by an efflux of protons across the cell membrane by the fumarate respiratory system, or by extrusion of sodium ions via decarboxylation of methylmalonyl-CoA. Aerobic P(i) uptake by the Accumulibacter spp. enrichment was strongly inhibited in the presence of an ATPase inhibitor, suggesting that the phosphate-specific transport (Pst) system is important even under relatively high concentrations of P(i). Acetate permease activity in these microorganisms may play an important role in the competition for acetate in the often acetate-limited EBPR process. Activity of a high-velocity Pst system in Accumulibacter spp. may further explain its ability to compete strongly in EBPR.
Collapse
Affiliation(s)
- Luke C Burow
- Advanced Wastewater Management Centre, The University of Queensland, St Lucia, QLD 4072, Australia
| | | | | | | | | |
Collapse
|
32
|
Barr M, East AK, Leonard M, Mauchline TH, Poole PS. In vivo expression technology (IVET) selection of genes of Rhizobium leguminosarum biovar viciae A34 expressed in the rhizosphere. FEMS Microbiol Lett 2008; 282:219-27. [PMID: 18399996 DOI: 10.1111/j.1574-6968.2008.01131.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
IVET was used to identify genes that are specifically expressed in the rhizosphere of the pea-nodulating bacterium Rhizobium leguminosarum A34. A library of R. leguminosarum A34 cloned in the integration vector pIE1, with inserts upstream of a promoter-less purN:gfp:gusA, was conjugated into purN host RU2249 and recombined into the genome. After removal of colonies that expressed the reporter genes of the vector under laboratory conditions, the library was inoculated into a nonsterile pea rhizosphere. The key result is that 29 rhizosphere-induced loci were identified. Sequence analysis of these clones showed that a wide variety of R. leguminosarum A34 genes are expressed specifically in the rhizosphere including those encoding proteins involved in environmental sensing, control of gene expression, metabolic reactions and membrane transport. These genes are likely to be important for survival and colonization of the pea rhizosphere.
Collapse
Affiliation(s)
- Michelle Barr
- School of Biological Sciences, University of Reading, Reading, UK
| | | | | | | | | |
Collapse
|
33
|
Characterization and regulation of PiDur3, a permease involved in the acquisition of urea by the ectomycorrhizal fungus Paxillus involutus. Fungal Genet Biol 2008; 45:912-21. [PMID: 18313954 DOI: 10.1016/j.fgb.2008.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 01/08/2008] [Accepted: 01/13/2008] [Indexed: 11/20/2022]
Abstract
Urea, which is known to be a source of nitrogen for the growth of many organisms, represents an important fertilizer in forest soils. Since most trees form symbiotic associations with ectomycorrhizal fungi, the capacities of these symbionts to take up and assimilate urea would determine the efficiency of urea nitrogen salvaging by plants. We showed that Paxillusinvolutus, an ectomycorrhizal basidiomycete, is capable of using urea as sole nitrogen source. We report the molecular characterization of an active urea transporter (PiDur3) isolated from this fungus. We demonstrated that the import of urea is a minor event on ammonium condition, since the expression of PiDUR3 is repressed by the high intracellular glutamine pool. Interestingly, on urea nutritive condition, the uptake of urea is rather mediated by the intracellular urea pool and particularly by urease efficiency.
Collapse
|
34
|
Borghese R, Marchetti D, Zannoni D. The highly toxic oxyanion tellurite (TeO (3) (2-) ) enters the phototrophic bacterium Rhodobacter capsulatus via an as yet uncharacterized monocarboxylate transport system. Arch Microbiol 2007; 189:93-100. [PMID: 17713758 DOI: 10.1007/s00203-007-0297-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 06/21/2007] [Accepted: 07/26/2007] [Indexed: 11/25/2022]
Abstract
The facultative phototroph Rhodobacter capsulatus takes up the highly toxic oxyanion tellurite when grown under both photosynthetic and respiratory growth conditions. Previous works on Escherichia coli and R. capsulatus suggested that tellurite uptake occurred through a phosphate transporter. Here we present evidences indicating that tellurite enters R. capsulatus cells via a monocarboxylate transport system. Indeed, intracellular accumulation of tellurite was inhibited by the addition of monocarboxylates such as pyruvate, lactate and acetate, but not by dicarboxylates like malate or succinate. Acetate was the strongest tellurite uptake antagonist and this effect was concentration dependent, being already evident at 1 microM acetate. Conversely, tellurite at 100 microM was able to restrict the acetate entry into the cells. Both tellurite and acetate uptakes were energy dependent processes, since they were abolished by the protonophore FCCP and by the respiratory electron transport inhibitor KCN. Interestingly, cells grown on acetate, lactate or pyruvate showed a high level resistance to tellurite, whereas cells grown on malate or succinate proved to be very sensitive to the oxyanion. Taking these data together, we propose that: (a) tellurite enters R. capsulatus cells via an as yet uncharacterized monocarboxylate(s) transporter, (b) competition between acetate and tellurite results in a much higher level of tolerance against the oxyanion and (c) the toxic action of tellurite at the cytosolic level is significantly restricted by preventing tellurite uptake.
Collapse
Affiliation(s)
- Roberto Borghese
- Department of Biology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy.
| | | | | |
Collapse
|
35
|
Yu M, Faan YW, Chung WYK, Tsang JSH. Isolation and characterization of a novel haloacid permease from Burkholderia cepacia MBA4. Appl Environ Microbiol 2007; 73:4874-80. [PMID: 17545323 PMCID: PMC1951043 DOI: 10.1128/aem.00576-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Burkholderia cepacia MBA4 is a bacterium that can utilize 2-haloacids as carbon and energy sources for growth. It has been proposed that dehalogenase-associated permease mediates the uptake of haloacid. In this paper, we report the first cloning and characterization of such a haloacid permease. The structural gene, designated deh4p, was found 353 bases downstream of the dehalogenase gene deh4a. Quantitative analysis of the expression of deh4p showed that it was induced by monochloroacetate (MCA), to a level similar to the MCA-induced level of deh4a. The nucleotide sequence of deh4p was determined, and an open reading frame of 1,656 bp encoding a putative peptide of 552 amino acids was identified. Deh4p has a putative molecular weight of 59,414 and an isoelectric point of 9.88. Deh4p has the signatures of sugar transport proteins and integral membrane proteins of the major facilitator superfamily. Uptake of [(14)C]MCA into the cell was Deh4p dependent. Deh4p has apparent K(m)s of 5.5 and 8.9 muM and V(max)s of 9.1 and 23.1 nmol mg(-1) min(-1) for acetate and MCA, respectively. A mutant with a transposon-inactivated haloacid operon failed to grow on MCA even when deh4a was provided in trans.
Collapse
Affiliation(s)
- Manda Yu
- Molecular Microbiology Laboratory, Department of Botany, The University of Hong Kong, Hong Kong
| | | | | | | |
Collapse
|
36
|
Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BO. Systems approach to refining genome annotation. Proc Natl Acad Sci U S A 2006; 103:17480-4. [PMID: 17088549 PMCID: PMC1859954 DOI: 10.1073/pnas.0603364103] [Citation(s) in RCA: 237] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genome-scale models of Escherichia coli K-12 MG1655 metabolism have been able to predict growth phenotypes in most, but not all, defined growth environments. Here we introduce the use of an optimization-based algorithm that predicts the missing reactions that are required to reconcile computation and experiment when they disagree. The computer-generated hypotheses for missing reactions were verified experimentally in five cases, leading to the functional assignment of eight ORFs (yjjLMN, yeaTU, dctA, idnT, and putP) with two new enzymatic activities and four transport functions. This study thus demonstrates the use of systems analysis to discover metabolic and transport functions and their genetic basis by a combination of experimental and computational approaches.
Collapse
Affiliation(s)
| | | | | | - Andrew R. Joyce
- Departments of *Bioengineering and
- Program in Bioinformatics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412; and
| | | | | | | | | | - Stephen S. Fong
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, P.O. Box 843028, Richmond, VA 23284-3028
| | - Bernhard O. Palsson
- Departments of *Bioengineering and
- To whom correspondence should be addressed at:
Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, Mail Code 0412, La Jolla, CA 92093-0412. E-mail:
| |
Collapse
|
37
|
Fox MA, White JP, Hosie AHF, Lodwig EM, Poole PS. Osmotic upshift transiently inhibits uptake via ABC transporters in gram-negative bacteria. J Bacteriol 2006; 188:5304-7. [PMID: 16816205 PMCID: PMC1539945 DOI: 10.1128/jb.00262-06] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ATP-binding cassette transporters from several rhizobia and Salmonella enterica serovar Typhimurium, but not secondarily coupled systems, were inhibited by high concentrations (100 to 500 mM) of various osmolytes, an effect reversed by the removal of the osmolyte. ABC systems were also inactivated in isolated pea bacteroids, probably due to the obligatory use of high-osmolarity isolation media. Measurement of nutrient cycling in isolated pea bacteroids is impeded by this effect.
Collapse
Affiliation(s)
- M A Fox
- School of Biological Sciences, University of Reading, Whiteknights, P.O. Box 228, Reading RG6 6AJ, United Kingdom.
| | | | | | | | | |
Collapse
|
38
|
Thomas GH, Southworth T, León-Kempis MR, Leech A, Kelly DJ. Novel ligands for the extracellular solute receptors of two bacterial TRAP transporters. MICROBIOLOGY-SGM 2006; 152:187-198. [PMID: 16385129 DOI: 10.1099/mic.0.28334-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Tripartite ATP-independent periplasmic (TRAP) transporters are relatively common prokaryotic secondary transporters which comprise an extracytoplasmic solute receptor (ESR) protein and two dissimilar membrane proteins or domains, yet the substrates and physiological functions of only a few of these systems are so far known. In this study, a biophysical approach was used to identify the ligands for the purified Rhodobacter capsulatus RRC01191 and Escherichia coli YiaO proteins, which are members of two phylogenetically distinct families of TRAP-ESRs found in diverse bacteria. In contrast to previous indirect evidence pointing to RRC01191 orthologues being involved in polyol uptake, it was shown that RRC01191 binds pyruvate, 2-oxobutyrate and a broad range of aliphatic monocarboxylic 2-oxoacid anions with varying affinities (K(d) values 0.08-3 muM), consistent with a predicted role in monocarboxylate transport related to branched-chain amino-acid biosynthesis. The E. coli YiaMNO TRAP transporter has previously been proposed to be an l-xylulose uptake system [Plantinga et al. (2004) Mol Membr Biol 21, 51-57], but purified YiaO did not bind l- or d-xylulose as judged by fluorescence spectroscopy, circular dichroism or mass spectrometry. Instead, these techniques showed that a breakdown product of l-ascorbate, 2,3-diketo-l-gulonate (2,3-DKG), binds by a simple one-step mechanism with sub-micromolar affinity. The data provide the first evidence for the existence of ESR-dependent transporters for 2-oxoacids and 2,3-DKG, homologues of which appear to be widespread amongst prokaryotes. The results also underline the utility of direct ESR ligand-binding studies for TRAP transporter characterization.
Collapse
Affiliation(s)
- Gavin H Thomas
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Thomas Southworth
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Maria Rocio León-Kempis
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Andrew Leech
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - David J Kelly
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| |
Collapse
|
39
|
Nakano S, Fukaya M, Horinouchi S. Putative ABC transporter responsible for acetic acid resistance in Acetobacter aceti. Appl Environ Microbiol 2006; 72:497-505. [PMID: 16391084 PMCID: PMC1352267 DOI: 10.1128/aem.72.1.497-505.2006] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two-dimensional gel electrophoretic analysis of the membrane fraction of Acetobacter aceti revealed the presence of several proteins that were produced in response to acetic acid. A 60-kDa protein, named AatA, which was mostly induced by acetic acid, was prepared; aatA was cloned on the basis of its NH2-terminal amino acid sequence. AatA, consisting of 591 amino acids and containing ATP-binding cassette (ABC) sequences and ABC signature sequences, belonged to the ABC transporter superfamily. The aatA mutation with an insertion of the neomycin resistance gene within the aatA coding region showed reduced resistance to acetic acid, formic acid, propionic acid, and lactic acid, whereas the aatA mutation exerted no effects on resistance to various drugs, growth at low pH (adjusted with HCl), assimilation of acetic acid, or resistance to citric acid. Introduction of plasmid pABC101 containing aatA under the control of the Escherichia coli lac promoter into the aatA mutant restored the defect in acetic acid resistance. In addition, pABC101 conferred acetic acid resistance on E. coli. These findings showed that AatA was a putative ABC transporter conferring acetic acid resistance on the host cell. Southern blot analysis and subsequent nucleotide sequencing predicted the presence of aatA orthologues in a variety of acetic acid bacteria belonging to the genera Acetobacter and Gluconacetobacter. The fermentation with A. aceti containing aatA on a multicopy plasmid resulted in an increase in the final yield of acetic acid.
Collapse
Affiliation(s)
- Shigeru Nakano
- Central Research Institute, Mizkan Group Co., Ltd., Handa-shi, Aichi 475-8585, Japan.
| | | | | |
Collapse
|
40
|
Karunakaran R, Mauchline TH, Hosie AHF, Poole PS. A family of promoter probe vectors incorporating autofluorescent and chromogenic reporter proteins for studying gene expression in Gram-negative bacteria. MICROBIOLOGY-SGM 2005; 151:3249-3256. [PMID: 16207908 DOI: 10.1099/mic.0.28311-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A series of promoter probe vectors for use in Gram-negative bacteria has been made in two broad-host-range vectors, pOT (pBBR replicon) and pJP2 (incP replicon). Reporter fusions can be made to gfpUV, gfpmut3.1, unstable gfpmut3.1 variants (LAA, LVA, AAV and ASV), gfp+, dsRed2, dsRedT.3, dsRedT.4, mRFP1, gusA or lacZ. The two vector families, pOT and pJP2, are compatible with one another and share the same polylinker for facile interchange of promoter regions. Vectors based on pJP2 have the advantage of being ultra-stable in the environment due to the presence of the parABCDE genes. As a confirmation of their usefulness, the dicarboxylic acid transport system promoter (dctA(p)) was cloned into a pOT (pRU1097)- and a pJP2 (pRU1156)-based vector and shown to be expressed by Rhizobium leguminosarum in infection threads of vetch. This indicates the presence of dicarboxylates at the earliest stages of nodule formation.
Collapse
Affiliation(s)
- R Karunakaran
- School of Biological Sciences, University of Reading, Whiteknights, PO Box 228, Reading RG6 6AJ, UK
| | - T H Mauchline
- School of Biological Sciences, University of Reading, Whiteknights, PO Box 228, Reading RG6 6AJ, UK
| | - A H F Hosie
- School of Biological Sciences, University of Reading, Whiteknights, PO Box 228, Reading RG6 6AJ, UK
| | - P S Poole
- School of Biological Sciences, University of Reading, Whiteknights, PO Box 228, Reading RG6 6AJ, UK
| |
Collapse
|
41
|
Gimenez R, Nuñez MF, Badia J, Aguilar J, Baldoma L. The gene yjcG, cotranscribed with the gene acs, encodes an acetate permease in Escherichia coli. J Bacteriol 2003; 185:6448-55. [PMID: 14563880 PMCID: PMC219408 DOI: 10.1128/jb.185.21.6448-6455.2003] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We isolated an Escherichia coli mutant strain that suppresses the glycolate-negative phenotype of a strain deficient in both GlcA and LldP transporters of this compound. This suppressing phenotype was assigned to yjcG, a gene whose function was previously unknown, which was found to encode a membrane protein able to transport glycolate. On the basis of sequence similarity, the yjcG gene product was classified as a member of the sodium:solute symporter family. Northern experiments revealed that yjcG is cotranscribed with its neighbor, acs, encoding acetyl coenzyme A synthetase, which is involved in the scavenging acetate. The fortuitous presence of an IS2 element in acs, which impaired yjcG expression by polarity in our parental strain, allowed us to conclude that the alternative glycolate carrier became active after precise excision of IS2 in the suppressed strain. The finding that yjcG encodes a putative membrane carrier for glycolate and the cotranscription of yjcG with acs suggested that the primary function of the yjcG gene product (proposed gene name, actP) could be acetate transport and allowed us to define an operon involved in acetate metabolism. The time course of [1,2-(14)C]acetate uptake and the results of a concentration kinetics analysis performed with cells expressing ActP or cells deficient in ActP supported the the hypothesis that this carrier is an acetate transporter and suggested that there may be another transport system for this monocarboxylate.
Collapse
Affiliation(s)
- Rosa Gimenez
- Department of Biochemistry, School of Pharmacy, University of Barcelona, E-08028 Barcelona, Spain
| | | | | | | | | |
Collapse
|
42
|
Yost CK, Clark KT, Del Bel KL, Hynes MF. Characterization of the nodulation plasmid encoded chemoreceptor gene mcpG from Rhizobium leguminosarum. BMC Microbiol 2003; 3:1. [PMID: 12553885 PMCID: PMC149452 DOI: 10.1186/1471-2180-3-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2002] [Accepted: 01/28/2003] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In general, chemotaxis in Rhizobium has not been well characterized. Methyl accepting chemotaxis proteins are sensory proteins important in chemotaxis of numerous bacteria, but their involvement in Rhizobium chemotaxis is unclear and merits further investigation. RESULTS A putative methyl accepting chemotaxis protein gene (mcpG) of Rhizobium leguminosarum VF39SM was isolated and characterized. The gene was found to reside on the nodulation plasmid, pRleVF39d. The predicted mcpG ORF displayed motifs common to known methyl-accepting chemotaxis proteins, such as two transmembrane domains and high homology to the conserved methylation and signaling domains of well-characterized MCPs. Phenotypic analysis of mcpG mutants using swarm plates did not identify ligands for this putative receptor. Additionally, gene knockouts of mcpG did not affect a mutant strain's ability to compete for nodulation with the wild type. Notably, mcpG was found to be plasmid-encoded in all strains of R. leguminosarum and R. etli examined, though it was found on the nodulation plasmid only in a minority of strains. CONCLUSIONS Based on sequence homology R. leguminosarum mcpG gene codes for a methyl accepting chemotaxis protein. The gene is plasmid localized in numerous Rhizobium spp. Although localized to the sym plasmid of VF39SM mcpG does not appear to participate in early nodulation events. A ligand for McpG remains to be found. Apparent McpG orthologs appear in a diverse range of proteobacteria. Identification and characterization of mcpG adds to the family of mcp genes already identified in this organism.
Collapse
Affiliation(s)
- Christopher K Yost
- Department of Biological Sciences, University of Calgary, 2500 University Drive SW, Calgary, Alberta, Canada, T2N 1N4
| | - Kirsten T Clark
- Department of Biological Sciences, University of Calgary, 2500 University Drive SW, Calgary, Alberta, Canada, T2N 1N4
| | - Kate L Del Bel
- Department of Biological Sciences, University of Calgary, 2500 University Drive SW, Calgary, Alberta, Canada, T2N 1N4
| | - Michael F Hynes
- Department of Biological Sciences, University of Calgary, 2500 University Drive SW, Calgary, Alberta, Canada, T2N 1N4
| |
Collapse
|