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Gu P, Ma Q, Zhao S, Li Q, Gao J. Alanine dehydrogenases from four different microorganisms: characterization and their application in L-alanine production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:123. [PMID: 37537629 PMCID: PMC10401832 DOI: 10.1186/s13068-023-02373-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Alanine dehydrogenase (AlaDH) belongs to oxidoreductases, and it exists in several different bacteria species and plays a key role in microbial carbon and nitrogen metabolism, spore formation and photosynthesis. In addition, AlaDH can also be applied in biosynthesis of L-alanine from cheap carbon source, such as glucose. RESULTS To achieve a better performance of L-alanine accumulation, system evaluation and comparison of different AlaDH with potential application value are essential. In this study, enzymatic properties of AlaDH from Bacillus subtilis 168 (BsAlaDH), Bacillus cereus (BcAlaDH), Mycobacterium smegmatis MC2 155 (MsAlaDH) and Geobacillus stearothermophilus (GsAlaDH) were firstly carefully investigated. Four different AlaDHs have few similarities in optimum temperature and optimum pH, while they also exhibited significant differences in enzyme activity, substrate affinity and enzymatic reaction rate. The wild E. coli BL21 with these four AlaDHs could produce 7.19 g/L, 7.81 g/L, 6.39 g/L and 6.52 g/L of L-alanine from 20 g/L glucose, respectively. To further increase the L-alanine titer, competitive pathways for L-alanine synthesis were completely blocked in E. coli. The final strain M-6 could produce 80.46 g/L of L-alanine with a yield of 1.02 g/g glucose after 63 h fed-batch fermentation, representing the highest yield for microbial L-alanine production. CONCLUSIONS Enzyme assay, biochemical characterization and structure analysis of BsAlaDH, BcAlaDH, MsAlaDH and GsAlaDH were carried out. In addition, application potential of these four AlaDHs in L-alanine productions were explored. The strategies here can be applied for developing L-alanine producing strains with high titers.
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Affiliation(s)
- Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China.
| | - Qianqian Ma
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Shuo Zhao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Juan Gao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China.
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Ballesteros-Gutiérrez M, Albareda M, Barbas C, López-Gonzálvez Á, Dunn MF, Palacios JM. A host-specific diaminobutyrate aminotransferase contributes to symbiotic performance, homoserine metabolism, and competitiveness in the Rhizobium leguminosarum/ Pisum sativum system. Front Microbiol 2023; 14:1182563. [PMID: 37260681 PMCID: PMC10228743 DOI: 10.3389/fmicb.2023.1182563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/25/2023] [Indexed: 06/02/2023] Open
Abstract
Rhizobium leguminosarum bv. viciae (Rlv) UPM791 effectively nodulates pea and lentil, but bacteroids contain a number of proteins differentially expressed depending on the host. One of these host-dependent proteins (C189) is similar to a diaminobutyrate-2-oxoglutarate aminotransferase (DABA-AT). DABA-AT activity was demonstrated with cell extracts and with purified protein, so C189 was renamed as Dat. The dat gene was strongly induced in the central, active area of pea nodules, but not in lentil. Mutants defective in dat were impaired in symbiotic performance with pea plants, exhibiting reduced shoot dry weight, smaller nodules, and a lower competitiveness for nodulation. In contrast, there were no significant differences between mutant and wild-type in symbiosis with lentil plants. A comparative metabolomic approach using cell-free extracts from bacteroids induced in pea and lentil showed significant differences among the strains in pea bacteroids whereas no significant differences were found in lentil. Targeted metabolomic analysis revealed that the dat mutation abolished the presence of 2,4-diaminobutyrate (DABA) in pea nodules, indicating that DABA-AT reaction is oriented toward the production of DABA from L-aspartate semialdehyde. This analysis also showed the presence of L-homoserine, a likely source of aspartate semialdehyde, in pea bacteroids but not in those induced in lentil. The dat mutant showed impaired growth when cells were grown with L-homoserine as nitrogen source. Inclusion of DABA or L-homoserine as N source suppressed pantothenate auxotropy in Rlv UPM791, suggesting DABA as source of the pantothenate precursor β-alanine. These data indicate that Rlv UPM791 Dat enzyme is part of an adaptation mechanism of this bacterium to a homoserine-rich environment such as pea nodule and rhizosphere.
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Affiliation(s)
- Marta Ballesteros-Gutiérrez
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Consejo Superior de Investigaciones Científicas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
| | - Marta Albareda
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Consejo Superior de Investigaciones Científicas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Coral Barbas
- Facultad de Farmacia, Center for Metabolomics and Bioanalysis (CEMBIO), Universidad San Pablo-CEU, Boadilla del Monte, Spain
| | - Ángeles López-Gonzálvez
- Facultad de Farmacia, Center for Metabolomics and Bioanalysis (CEMBIO), Universidad San Pablo-CEU, Boadilla del Monte, Spain
| | - Michael F. Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - José M. Palacios
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Consejo Superior de Investigaciones Científicas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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3
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Alanine synthesized by alanine dehydrogenase enables ammonium-tolerant nitrogen fixation in Paenibacillus sabinae T27. Proc Natl Acad Sci U S A 2022; 119:e2215855119. [PMID: 36459643 PMCID: PMC9894248 DOI: 10.1073/pnas.2215855119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Most diazotrophs fix nitrogen only under nitrogen-limiting conditions, for example, in the presence of relatively low concentrations of NH4+ (0 to 2 mM). However, Paenibacillus sabinae T27 exhibits an unusual pattern of nitrogen regulation of nitrogen fixation, since although nitrogenase activities are high under nitrogen-limiting conditions (0 to 3 mM NH4+) and are repressed under conditions of nitrogen sufficiency (4 to 30 mM NH4+), nitrogenase activity is reestablished when very high levels of NH4+ (30 to 300 mM) are present in the medium. To further understand this pattern of nitrogen fixation regulation, we carried out transcriptome analyses of P. sabinae T27 in response to increasing ammonium concentrations. As anticipated, the nif genes were highly expressed, either in the absence of fixed nitrogen or in the presence of a high concentration of NH4+ (100 mM), but were subject to negative feedback regulation at an intermediate concentration of NH4+ (10 mM). Among the differentially expressed genes, ald1, encoding alanine dehydrogenase (ADH1), was highly expressed in the presence of a high level of NH4+ (100 mM). Mutation and complementation experiments revealed that ald1 is required for nitrogen fixation at high ammonium concentrations. We demonstrate that alanine, synthesized by ADH1 from pyruvate and NH4+, inhibits GS activity, leading to a low intracellular glutamine concentration that prevents feedback inhibition of GS and mimics nitrogen limitation, enabling activation of nif transcription by the nitrogen-responsive regulator GlnR in the presence of high levels of extracellular ammonium.
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Schulte CCM, Borah K, Wheatley RM, Terpolilli JJ, Saalbach G, Crang N, de Groot DH, Ratcliffe RG, Kruger NJ, Papachristodoulou A, Poole PS. Metabolic control of nitrogen fixation in rhizobium-legume symbioses. SCIENCE ADVANCES 2021; 7:7/31/eabh2433. [PMID: 34330708 PMCID: PMC8324050 DOI: 10.1126/sciadv.abh2433] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/14/2021] [Indexed: 05/16/2023]
Abstract
Rhizobia induce nodule formation on legume roots and differentiate into bacteroids, which catabolize plant-derived dicarboxylates to reduce atmospheric N2 into ammonia. Despite the agricultural importance of this symbiosis, the mechanisms that govern carbon and nitrogen allocation in bacteroids and promote ammonia secretion to the plant are largely unknown. Using a metabolic model derived from genome-scale datasets, we show that carbon polymer synthesis and alanine secretion by bacteroids facilitate redox balance in microaerobic nodules. Catabolism of dicarboxylates induces not only a higher oxygen demand but also a higher NADH/NAD+ ratio than sugars. Modeling and 13C metabolic flux analysis indicate that oxygen limitation restricts the decarboxylating arm of the tricarboxylic acid cycle, which limits ammonia assimilation into glutamate. By tightly controlling oxygen supply and providing dicarboxylates as the energy and electron source donors for N2 fixation, legumes promote ammonia secretion by bacteroids. This is a defining feature of rhizobium-legume symbioses.
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Affiliation(s)
- Carolin C M Schulte
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Khushboo Borah
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | | | | | - Nick Crang
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Daan H de Groot
- Systems Biology Lab, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | | | | | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, UK.
- John Innes Centre, Norwich Research Park, Norwich, UK
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5
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Hu X, Bai Y, Fan TP, Zheng X, Cai Y. A novel type alanine dehydrogenase from Helicobacter aurati: Molecular characterization and application. Int J Biol Macromol 2020; 161:636-642. [PMID: 32534087 DOI: 10.1016/j.ijbiomac.2020.06.067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 01/07/2023]
Abstract
A novel alanine dehydrogenase (ADH; EC.1.4.1.1) with high pyruvate reduced activity was isolated from Helicobacter aurati and expressed in Escherichia coli BL21 (DE3). The optimum pH of the reduction and oxidation reaction were 8.0 and 9.0, respectively, and the optimum temperature was 55 °C. With pyruvate and alanine as substrates, the specific activity of HAADH1 were 268 U·mg-1 and 26 U·mg-1, respectively. HAADH1 had a prominent substrate specificity for alanine (Km = 2.23 mM, kcat/Km = 8.1 s-1·mM-1). In the reduction reaction, HAADH1 showed the highest substrate affinity for pyruvate (Km = 0.56 mM, kcat/Km = 364 s-1·mM-1). Compared to pyruvate, oxaloacetic acid, 2-ketobutyric acid, 3-fluoropyruvate, α-ketoglutaric acids, glyoxylic acid showed a residual activity of 93.30%, 8.93%, 5.62%, 2.57%, 2.51%, respectively. Phylogenetic tree analysis showed that this is a new type of ADH which have a low sequence similarity to available ADH reported in references. 3-Fluoropyruvate was effectively reduced to 3-fluoro-L-alanine by whole-cell catalysis.
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Affiliation(s)
- Xiaoxiang Hu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yajun Bai
- College of Life Sciences, Northwest University, Xi'an, Shanxi 710069, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1T, UK
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, Shanxi 710069, China.
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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Wu Y, Li YH, Shang JY, Wang ET, Chen L, Huo B, Sui XH, Tian CF, Chen WF, Chen WX. Multiple Genes of Symbiotic Plasmid and Chromosome in Type II Peanut Bradyrhizobium Strains Corresponding to the Incompatible Symbiosis With Vigna radiata. Front Microbiol 2020; 11:1175. [PMID: 32655513 PMCID: PMC7324677 DOI: 10.3389/fmicb.2020.01175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/07/2020] [Indexed: 11/19/2022] Open
Abstract
Rhizobia are capable of establishing compatible symbiosis with their hosts of origin and plants in the cross-nodulation group that the hosts of origin belonged to. However, different from the normal peanut Bradyrhizobium (Type I strains), the Type II strains showed incompatible symbiosis with Vigna radiata. Here, we employed transposon mutagenesis to identify the genetic loci related to this incompatibility in Type II strain CCBAU 53363. As results, seven Tn5 transposon insertion mutants resulted in an increase in nodule number on V. radiata. By sequencing analysis of the sequence flanking Tn5 insertion, six mutants were located in the chromosome of CCBAU 53363, respectively encoding acyltransferase (L265) and hypothetical protein (L615)—unique to CCBAU 53363, two hypothetical proteins (L4 and L82), tripartite tricarboxylate transporter substrate binding protein (L373), and sulfur oxidation c-type cytochrome SoxA (L646), while one mutant was in symbiotic plasmid encoding alanine dehydrogenase (L147). Significant differences were observed in L147 gene sequences and the deduced protein 3D structures between the Type II (in symbiotic plasmid) and Type I strains (in chromosome). Conversely, strains in both types shared high homologies in the chromosome genes L373 and L646 and in their protein 3D structures. These data indicated that the symbiotic plasmid gene in Type II strains might have directly affected their symbiosis incompatibility, whereas the chromosome genes might be indirectly involved in this process by regulating the plasmid symbiosis genes. The seven genes may initially explain the complication associated with symbiotic incompatibility.
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Affiliation(s)
- Yue Wu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yong Hua Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiao Ying Shang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - En Tao Wang
- Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Mexico City, Mexico
| | - La Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Bin Huo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xin Hua Sui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chang Fu Tian
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wen Feng Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wen Xin Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
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7
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Van Wieren A, Cook R, Majumdar S. Characterization of Alanine Dehydrogenase and Its Effect on Streptomyces coelicolorA3(2) Development in Liquid Culture. J Mol Microbiol Biotechnol 2019; 29:57-65. [PMID: 31851994 DOI: 10.1159/000504709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/10/2019] [Indexed: 11/19/2022] Open
Abstract
Streptomyces, the most important group of industrial microorganisms, is harvested in liquid cultures for the production of two-thirds of all clinically relevant secondary metabolites. It is demonstrated here that the growth of Streptomyces coelicolor A3(2) is impacted by the deletion of the alanine dehydrogenase (ALD), an essential enzyme that plays a central role in the carbon and nitrogen metabolism. A long lag-phase growth followed by a slow exponential growth of S. coelicolor due to ALD gene deletion was observed in liquid yeast extract mineral salt culture. The slow lag-phase growth was replaced by the normal wild-type like growth by ALD complementation engineering. The ALD enzyme from S. coelicolor was also heterologously cloned and expressed in Escherichia coli for characterization. The optimum enzyme activity for the oxidative deamination reaction was found at 30°C, pH 9.5 with a catalytic efficiency, kcat/KM, of 2.0 ± 0.1 mM-1 s-1. The optimum enzyme activity for the reductive amination reaction was found at 30°C, pH 9.0 with a catalytic efficiency, kcat/KM, of 1.9 ± 0.1 mM-1 s-1.
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Affiliation(s)
- Arie Van Wieren
- Department of Chemistry, Indiana University of Pennsylvania, Indiana, Pennsylvania, USA
| | - Ryan Cook
- Department of Chemistry, Indiana University of Pennsylvania, Indiana, Pennsylvania, USA.,West Virginia University School of Medicine, Morgantown, West Virginia, USA
| | - Sudipta Majumdar
- Department of Chemistry, Indiana University of Pennsylvania, Indiana, Pennsylvania, USA,
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Abstract
Alanine dehydrogenase (AlaDH) (E.C.1.4.1.1) is a microbial enzyme that catalyzes a reversible conversion of L-alanine to pyruvate. Inter-conversion of alanine and pyruvate by AlaDH is central to metabolism in microorganisms. Its oxidative deamination reaction produces pyruvate which plays a pivotal role in the generation of energy through the tricarboxylic acid cycle for sporulation in the microorganisms. Its reductive amination reaction provides a route for the incorporation of ammonia and produces L-alanine which is required for synthesis of the peptidoglycan layer, proteins, and other amino acids. Also, AlaDH helps in redox balancing as its deamination/amination reaction is linked to the reduction/oxidation of NAD+/NADH in microorganisms. AlaDH from a few microorganisms can also reduce glyoxylate into glycine (aminoacetate) in a nonreversible reaction. Both its oxidative and reductive reactions exhibit remarkable applications in the pharmaceutical, environmental, and food industries. The literature addressing the characteristics and applications of AlaDH from a wide range of microorganisms is summarized in the current review.
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Affiliation(s)
| | - Ravi-Kumar Kadeppagari
- b Centre for Incubation, Innovation, Research and Consultancy (CIIRC), Jyothy Institute of Technology Campus , Bengaluru , India
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Thal B, Braun HP, Eubel H. Proteomic analysis dissects the impact of nodulation and biological nitrogen fixation on Vicia faba root nodule physiology. PLANT MOLECULAR BIOLOGY 2018; 97:233-251. [PMID: 29779088 DOI: 10.1007/s11103-018-0736-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 05/08/2018] [Indexed: 05/25/2023]
Abstract
Symbiotic nitrogen fixation in root nodules of legumes is a highly important biological process which is only poorly understood. Root nodule metabolism differs from that of roots. Differences in root and nodule metabolism are expressed by altered protein abundances and amenable to quantitative proteome analyses. Differences in the proteomes may either be tissue specific and related to the presence of temporary endosymbionts (the bacteroids) or related to nitrogen fixation activity. An experimental setup including WT bacterial strains and strains not able to conduct symbiotic nitrogen fixation as well as root controls enables identification of tissue and nitrogen fixation specific proteins. Root nodules are specialized plant organs housing and regulating the mutual symbiosis of legumes with nitrogen fixing rhizobia. As such, these organs fulfill unique functions in plant metabolism. Identifying the proteins required for the metabolic reactions of nitrogen fixation and those merely involved in sustaining the rhizobia:plant symbiosis, is a challenging task and requires an experimental setup which allows to differentiate between these two physiological processes. Here, quantitative proteome analyses of nitrogen fixing and non-nitrogen fixing nodules as well as fertilized and non-fertilized roots were performed using Vicia faba and Rhizobium leguminosarum. Pairwise comparisons revealed altered enzyme abundance between active and inactive nodules. Similarly, general differences between nodules and root tissue were observed. Together, these results allow distinguishing the proteins directly involved in nitrogen fixation from those related to nodulation. Further observations relate to the control of nodulation by hormones and provide supportive evidence for the previously reported correlation of nitrogen and sulfur fixation in these plant organs. Additionally, data on altered protein abundance relating to alanine metabolism imply that this amino acid may be exported from the symbiosomes of V. faba root nodules in addition to ammonia. Data are available via ProteomeXchange with identifier PXD008548.
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Affiliation(s)
- Beate Thal
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hanover, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hanover, Germany
| | - Holger Eubel
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hanover, Germany.
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He G, Xu S, Wang S, Zhang Q, Liu D, Chen Y, Ju J, Zhao B. A conserved residue of l -alanine dehydrogenase from Bacillus pseudofirmus , Lys-73, participates in the catalytic reaction through hydrogen bonding. Enzyme Microb Technol 2018; 110:61-68. [DOI: 10.1016/j.enzmictec.2017.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/25/2017] [Accepted: 10/10/2017] [Indexed: 11/30/2022]
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Jun D, Minic Z, Bhat SV, Vanderlinde EM, Yost CK, Babu M, Dahms TES. Metabolic Adaptation of a C-Terminal Protease A-Deficient Rhizobium leguminosarum in Response to Loss of Nutrient Transport. Front Microbiol 2018; 8:2617. [PMID: 29354107 PMCID: PMC5758756 DOI: 10.3389/fmicb.2017.02617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/15/2017] [Indexed: 11/13/2022] Open
Abstract
Post-translational modification expands the functionality of the proteome beyond genetic encoding, impacting many cellular processes. Cleavage of the carboxyl terminus is one of the many different ways proteins can be modified for functionality. Gel-electrophoresis and mass spectrometric-based techniques were used to identify proteins impacted by deficiency of a C-terminal protease, CtpA, in Rhizobium leguminosarum bv. viciae 3841. Predicted CtpA substrates from 2D silver stained gels were predominantly outer membrane and transport proteins. Proteins with altered abundance in the wild type and ctpA (RL4692) mutant, separated by 2D difference gel electrophoresis, were selected for analysis by mass spectrometry. Of those identified, 9 were the periplasmic solute-binding components of ABC transporters, 5 were amino acid metabolic enzymes, 2 were proteins involved in sulfur metabolism, and 1 each was related to carbon metabolism, protein folding and signal transduction. Alterations to ABC-binding-cassette transporters, nutrient uptake efficiency and to amino acid metabolism indicated an impact on amino acid metabolism and transport for the ctpA mutant, which was validated by measured amino acid levels.
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Affiliation(s)
- Dong Jun
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Zoran Minic
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Supriya V. Bhat
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Elizabeth M. Vanderlinde
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
- Department of Biology, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Chris K. Yost
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Tanya E. S. Dahms
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
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Hood G, Ramachandran V, East AK, Downie JA, Poole PS. Manganese transport is essential for N 2 -fixation by Rhizobium leguminosarum in bacteroids from galegoid but not phaseoloid nodules. Environ Microbiol 2017; 19:2715-2726. [PMID: 28447383 PMCID: PMC5575495 DOI: 10.1111/1462-2920.13773] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 04/19/2017] [Indexed: 12/14/2022]
Abstract
Rhizobium leguminosarum has two high-affinity Mn2+ transport systems encoded by sitABCD and mntH. In symbiosis, sitABCD and mntH were expressed throughout nodules and also strongly induced in Mn2+ -limited cultures of free-living cells. Growth of a sitA mntH double mutant was severely reduced under Mn2+ limitation and sitA and mntH single mutants were more sensitive to oxidative stress. The double sitA mntH mutant of R. leguminosarum was unable to fix nitrogen (Fix- ) with legumes belonging to the galegoid clade (Pisum sativum, Vicia faba and Vicia hirsuta). The presence of infection thread-like structures and sparsely-packed plant cells in nodules suggest that bacteroid development was blocked, either at a late stage of infection thread progression or during bacteroid-release. In contrast, a double sitA mntH mutant was Fix+ on common bean (Phaseoli vulgaris), a member of the phaseoloid clade of legumes, indicating a host-specific symbiotic requirement for Mn2+ transport.
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Affiliation(s)
- Graham Hood
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Vinoy Ramachandran
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Alison K. East
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - J. Allan Downie
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Philip S. Poole
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
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Li YZ, Wang D, Feng XY, Jiao J, Chen WX, Tian CF. Genetic Analysis Reveals the Essential Role of Nitrogen Phosphotransferase System Components in Sinorhizobium fredii CCBAU 45436 Symbioses with Soybean and Pigeonpea Plants. Appl Environ Microbiol 2016; 82:1305-15. [PMID: 26682851 PMCID: PMC4751829 DOI: 10.1128/aem.03454-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/10/2015] [Indexed: 11/20/2022] Open
Abstract
The nitrogen phosphotransferase system (PTS(Ntr)) consists of EI(Ntr), NPr, and EIIA(Ntr). The active phosphate moiety derived from phosphoenolpyruvate is transferred through EI(Ntr) and NPr to EIIA(Ntr). Sinorhizobium fredii can establish a nitrogen-fixing symbiosis with the legume crops soybean (as determinate nodules) and pigeonpea (as indeterminate nodules). In this study, S. fredii strains with mutations in ptsP and ptsO (encoding EI(Ntr) and NPr, respectively) formed ineffective nodules on soybeans, while a strain with a ptsN mutation (encoding EIIA(Ntr)) was not defective in symbiosis with soybeans. Notable reductions in the numbers of bacteroids within each symbiosome and of poly-β-hydroxybutyrate granules in bacteroids were observed in nodules infected by the ptsP or ptsO mutant strains but not in those infected with the ptsN mutant strain. However, these defects of the ptsP and ptsO mutant strains were recovered in ptsP ptsN and ptsO ptsN double-mutant strains, implying a negative role of unphosphorylated EIIA(Ntr) in symbiosis. Moreover, the symbiotic defect of the ptsP mutant was also recovered by expressing EI(Ntr) with or without the GAF domain, indicating that the putative glutamine-sensing domain GAF is dispensable in symbiotic interactions. The critical role of PTS(Ntr) in symbiosis was also observed when related PTS(Ntr) mutant strains of S. fredii were inoculated on pigeonpea plants. Furthermore, nodule occupancy and carbon utilization tests suggested that multiple outputs could be derived from components of PTS(Ntr) in addition to the negative role of unphosphorylated EIIA(Ntr).
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Affiliation(s)
- Yue Zhen Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, and Rhizobium Research Center, China Agricultural University, Beijing, ChinaUniversity of Wisconsin-Madison
| | - Dan Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, and Rhizobium Research Center, China Agricultural University, Beijing, ChinaUniversity of Wisconsin-Madison
| | - Xue Ying Feng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, and Rhizobium Research Center, China Agricultural University, Beijing, ChinaUniversity of Wisconsin-Madison
| | - Jian Jiao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, and Rhizobium Research Center, China Agricultural University, Beijing, ChinaUniversity of Wisconsin-Madison
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, and Rhizobium Research Center, China Agricultural University, Beijing, ChinaUniversity of Wisconsin-Madison
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, and Rhizobium Research Center, China Agricultural University, Beijing, ChinaUniversity of Wisconsin-Madison
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14
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Kazakov AE, Rajeev L, Chen A, Luning EG, Dubchak I, Mukhopadhyay A, Novichkov PS. σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough. BMC Genomics 2015; 16:919. [PMID: 26555820 PMCID: PMC4641369 DOI: 10.1186/s12864-015-2176-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/31/2015] [Indexed: 11/16/2022] Open
Abstract
Background The σ54 subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequenced bacteria. The cellular processes regulated by many of these EBPs remain unknown. Results To characterize the σ54-dependent regulome of D. vulgaris Hildenborough, we identified EBP binding motifs and regulated genes by a combination of computational and experimental techniques. These predictions were supported by our reconstruction of σ54-dependent promoters by comparative genomics. We reassessed and refined the results of earlier studies on regulation in D. vulgaris Hildenborough and consolidated them with our new findings. It allowed us to reconstruct the σ54 regulome in D. vulgaris Hildenborough. This regulome includes 36 regulons that consist of 201 coding genes and 4 non-coding RNAs, and is involved in nitrogen, carbon and energy metabolism, regulation, transmembrane transport and various extracellular functions. To the best of our knowledge, this is the first report of direct regulation of alanine dehydrogenase, pyruvate metabolism genes and type III secretion system by σ54-dependent regulators. Conclusions The σ54-dependent regulome is an important component of transcriptional regulatory network in D. vulgaris Hildenborough and related free-living Deltaproteobacteria. Our study provides a representative collection of σ54-dependent regulons that can be used for regulation prediction in Deltaproteobacteria and other taxa. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2176-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexey E Kazakov
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA.
| | - Lara Rajeev
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA.
| | - Amy Chen
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA.
| | - Eric G Luning
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA.
| | - Inna Dubchak
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA. .,Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
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15
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Abstract
Rhizobia are bacteria in the α-proteobacterial genera Rhizobium, Sinorhizobium, Mesorhizobium, Azorhizobium and Bradyrhizobium that reduce (fix) atmospheric nitrogen in symbiotic association with a compatible host plant. In free-living and/or symbiotically associated rhizobia, amino acids may, in addition to their incorporation into proteins, serve as carbon, nitrogen or sulfur sources, signals of cellular nitrogen status and precursors of important metabolites. Depending on the rhizobia-host plant combination, microsymbiont amino acid metabolism (biosynthesis, transport and/or degradation) is often crucial to the establishment and maintenance of an effective nitrogen-fixing symbiosis and is intimately interconnected with the metabolism of the plant. This review summarizes past findings and current research directions in rhizobial amino acid metabolism and evaluates the genetic, biochemical and genome expression studies from which these are derived. Specific sections deal with the regulation of rhizobial amino acid metabolism, amino acid transport, and finally the symbiotic roles of individual amino acids in different plant-rhizobia combinations.
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16
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Yurgel SN, Rice J, Kahn ML. Transcriptome analysis of the role of GlnD/GlnBK in nitrogen stress adaptation by Sinorhizobium meliloti Rm1021. PLoS One 2013; 8:e58028. [PMID: 23516427 PMCID: PMC3596328 DOI: 10.1371/journal.pone.0058028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 01/30/2013] [Indexed: 11/19/2022] Open
Abstract
Transcriptional changes in the nitrogen stress response (NSR) of wild type S. meliloti Rm1021, and isogenic strains missing both PII proteins, GlnB and GlnK, or carrying a ΔglnD-sm2 mutation were analyzed using whole-genome microarrays. This approach allowed us to identify a number of new genes involved in the NSR and showed that the response of these bacteria to nitrogen stress overlaps with other stress responses, including induction of the fixK2 transcriptional activator and genes that are part of the phosphate stress response. Our data also show that GlnD and GlnBK proteins may regulate many genes that are not part of the NSR. Analysis of transcriptome profiles of the Rm1021 ΔglnD-sm2 strain allowed us to identify several genes that appear to be regulated by GlnD without the participation of the PII proteins.
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Affiliation(s)
- Svetlana N Yurgel
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA.
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17
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Regulatable vectors for environmental gene expression in Alphaproteobacteria. Appl Environ Microbiol 2012; 78:7137-40. [PMID: 22820336 DOI: 10.1128/aem.01188-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two expression vectors utilizing the inducible taurine promoter (tauAp) were developed. Plasmid pLMB51 is a stable low-copy vector enabling expression in the environment and in planta. The higher copy number pLMB509 enables BD restriction-independent cloning, expression, and purification of polyhistidine-tagged proteins.
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18
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AdeR, a PucR-type transcription factor, activates expression of L-alanine dehydrogenase and is required for sporulation of Bacillus subtilis. J Bacteriol 2012; 194:4995-5001. [PMID: 22797752 DOI: 10.1128/jb.00778-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Bacillus subtilis ald gene encodes L-alanine dehydrogenase, which catalyzes the NAD(+)-dependent deamination of L-alanine to pyruvate for the generation of energy and is required for normal sporulation. The transcription of ald is induced by alanine, but the mechanism underlying alanine induction remains unknown. Here we report that a gene (formerly yukF and now designated adeR) located upstream of ald is essential for the basal and alanine-inducible expression of ald. The disruption of the adeR gene caused a sporulation defect, whereas the complementation of an adeR mutation with an intact adeR gene restored the sporulation ability. adeR expression was not subject to autoregulation and alanine induction. Deletion and mutation analyses revealed that an inverted repeat, centered at position -74.5 relative to the transcriptional initiation site of ald, was required for ald expression and also likely served as a ρ-independent transcription terminator. Electrophoretic mobility shift assays showed that purified His-tagged AdeR was a specific DNA-binding protein and that this inverted repeat was required for AdeR binding. AdeR shows no significant amino acid sequence similarity to the known transcriptional activators of ald genes from other bacteria. AdeR appears to be a member of the PucR family of transcriptional regulators. Its orthologs of unknown function are present in some other Bacillus species. Collectively, these findings support the notion that AdeR is a transcriptional activator which mediates ald expression in response to alanine availability and is important for normal sporulation in B. subtilis.
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19
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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.
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Affiliation(s)
- R Karunakaran
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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20
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Williams TJ, Ertan H, Ting L, Cavicchioli R. Carbon and nitrogen substrate utilization in the marine bacterium Sphingopyxis alaskensis strain RB2256. ISME JOURNAL 2009; 3:1036-52. [PMID: 19458655 DOI: 10.1038/ismej.2009.52] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sphingopyxis alaskensis is a marine member of the Alphaproteobacteria that is adapted to heterotrophic growth under nutrient-depleted (oligotrophic) conditions. S. alaskensis strain RB2256 is an ultramicrobacterium (cell volume <0.1 microm(3)), and has a genome size larger than that of the ultramicrobacterium 'Candidatus Pelagibacter ubique' HTCC1062 (SAR11 clade of Alphaproteobacteria): 3.35 versus 1.31 Mbp. In this study, we investigate the carbon and nitrogen metabolism of strain RB2256 using an integrated approach that combines growth and enzyme assays, proteomics and genome analysis. S. alaskensis is able to use specific amino acids and putrescine as a sole carbon and nitrogen source, and higher energy-yielding substrates such as glucose and trehalose as carbon sources. Alanine, in particular, emerges as a very important substrate in S. alaskensis metabolism. In an oligotrophic environment where competition for nutrients is intense, our data support a simplified metabolism for S. alaskensis in which the fate of certain substrates is constrained, especially at the intersections of central carbon and nitrogen metabolism, in order to ensure optimal disposition of scarce resources. This is the first investigation of central metabolism for an oligotrophic ultramicrobacterium that possesses a relatively large genome size. In contrast to the behavior so far observed for SAR11 oligotrophic bacteria, S. alaskensis shows a physiological capacity to exploit increases in ambient nutrient availability and thereby achieve high-population densities.
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Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
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21
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White JP, Prell J, Ramachandran VK, Poole PS. Characterization of a {gamma}-aminobutyric acid transport system of Rhizobium leguminosarum bv. viciae 3841. J Bacteriol 2009; 191:1547-55. [PMID: 19103927 PMCID: PMC2648222 DOI: 10.1128/jb.00926-08] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Accepted: 12/09/2008] [Indexed: 12/29/2022] Open
Abstract
Spontaneous mutants of Rhizobium leguminosarum bv. viciae 3841 were isolated that grow faster than the wild type on gamma-aminobutyric acid (GABA) as the sole carbon and nitrogen source. These strains (RU1736 and RU1816) have frameshift mutations (gtsR101 and gtsR102, respectively) in a GntR-type regulator (GtsR) that result in a high rate of constitutive GABA transport. Tn5 mutagenesis and quantitative reverse transcription-PCR showed that GstR regulates expression of a large operon (pRL100242 to pRL100252) on the Sym plasmid that is required for GABA uptake. An ABC transport system, GtsABCD (for GABA transport system) (pRL100248-51), of the spermidine/putrescine family is part of this operon. GtsA is a periplasmic binding protein, GtsB and GtsC are integral membrane proteins, and GtsD is an ATP-binding subunit. Expression of gtsABCD from a lacZ promoter confirmed that it alone is responsible for high rates of GABA transport, enabling rapid growth of strain 3841 on GABA. Gts transports open-chain compounds with four or five carbon atoms with carboxyl and amino groups at, or close to, opposite termini. However, aromatic compounds with similar spacing between carboxyl and amino groups are excellent inhibitors of GABA uptake so they may also be transported. In addition to the ABC transporter, the operon contains two putative mono-oxygenases, a putative hydrolase, a putative aldehyde dehydrogenase, and a succinate semialdehyde dehydrogenase. This suggests the operon may be involved in the transport and breakdown of a more complex precursor to GABA. Gts is not expressed in pea bacteroids, and gtsB mutants are unaltered in their symbiotic phenotype, suggesting that Bra is the only GABA transport system available for amino acid cycling.
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Affiliation(s)
- J P White
- University of Reading, United Kingdom
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22
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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.
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Affiliation(s)
- Michelle Barr
- School of Biological Sciences, University of Reading, Reading, UK
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23
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Kawashima T, Aramaki H, Oyamada T, Makino K, Yamada M, Okamura H, Yokoyama K, Ishijima SA, Suzuki M. Transcription Regulation by Feast/Famine Regulatory Proteins, FFRPs, in Archaea and Eubacteria. Biol Pharm Bull 2008; 31:173-86. [DOI: 10.1248/bpb.31.173] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Tsuyoshi Kawashima
- National Institute of Advanced Industrial Science and Technology
- Japan Science and Technology Agency, Core Research for Evolutionary Science and Technology
- Yokohama College of Pharmacy, Laboratory of Molecular Biology
| | - Hironori Aramaki
- Department of Molecular Biology, Daiichi College of Pharmaceutical Sciences
| | - Tomoya Oyamada
- Department of Applied Chemistry, National Defense Academy
| | - Kozo Makino
- Department of Applied Chemistry, National Defense Academy
| | - Mitsugu Yamada
- National Institute of Advanced Industrial Science and Technology
- Japan Science and Technology Agency, Core Research for Evolutionary Science and Technology
| | - Hideyasu Okamura
- National Institute of Advanced Industrial Science and Technology
- Japan Science and Technology Agency, Core Research for Evolutionary Science and Technology
| | - Katsushi Yokoyama
- National Institute of Advanced Industrial Science and Technology
- Japan Science and Technology Agency, Core Research for Evolutionary Science and Technology
| | - Sanae Arakawa Ishijima
- National Institute of Advanced Industrial Science and Technology
- Japan Science and Technology Agency, Core Research for Evolutionary Science and Technology
| | - Masashi Suzuki
- National Institute of Advanced Industrial Science and Technology
- Japan Science and Technology Agency, Core Research for Evolutionary Science and Technology
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24
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Yang H, Wang L, Xie Z, Tian Y, Liu G, Tan H. The tyrosine degradation gene hppD is transcriptionally activated by HpdA and repressed by HpdR in Streptomyces coelicolor, while hpdA is negatively autoregulated and repressed by HpdR. Mol Microbiol 2007; 65:1064-77. [PMID: 17640269 DOI: 10.1111/j.1365-2958.2007.05848.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Streptomyces coelicolor produces a brown pigment on nutrient-limited agar medium (Tyr-PM) using l-tyrosine as the sole nitrogen and carbon source. The pigment production is associated with the second step of l-tyrosine catabolism catalysed by 4-hydroxyphenylpyruvate dioxygenase (HppD), which converts 4-hydroxyphenylpyruvate (4HPP) to 2, 5-dihydroxyphenylacetate (homogentisate) to provide the carbon and energy substrates for the growth of S. coelicolor on Tyr-PM. An hppD mutant did not produce brown pigment, and its normal growth was impaired on Tyr-PM. hpdA and hpdR, located close to hppD, were identified as activator and repressor genes for hppD transcription in the presence of tyrosine. hpdA, divergently transcribed from hppD, is negatively autoregulated in the absence of tyrosine, whereas it is repressed by both its own protein and HpdR in the presence of tyrosine. Electrophoretic mobility shift assays and footprinting experiments showed that HpdA and HpdR each bind to an overlapping region spanning the promoters of both hppD and hpdA, and that 4HPP, instead of tyrosine, is the specific ligand modulating the binding patterns and footprints of HpdA and HpdR on the hppD-hpdA promoter region. These results suggested that the transcription of hppD is subject to coarse and fine control by a complex regulatory system.
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Affiliation(s)
- Haihua Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Science, Beijing 100101, China
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25
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Mitsch MJ, Cowie A, Finan TM. Malic enzyme cofactor and domain requirements for symbiotic N2 fixation by Sinorhizobium meliloti. J Bacteriol 2006; 189:160-8. [PMID: 17071765 PMCID: PMC1797227 DOI: 10.1128/jb.01425-06] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The NAD(+)-dependent malic enzyme (DME) and the NADP(+)-dependent malic enzyme (TME) of Sinorhizobium meliloti are representatives of a distinct class of malic enzymes that contain a 440-amino-acid N-terminal region homologous to other malic enzymes and a 330-amino-acid C-terminal region with similarity to phosphotransacetylase enzymes (PTA). We have shown previously that dme mutants of S. meliloti fail to fix N(2) (Fix(-)) in alfalfa root nodules, whereas tme mutants are unimpaired in their N(2)-fixing ability (Fix(+)). Here we report that the amount of DME protein in bacteroids is 10 times greater than that of TME. We therefore investigated whether increased TME activity in nodules would allow TME to function in place of DME. The tme gene was placed under the control of the dme promoter, and despite elevated levels of TME within bacteroids, no symbiotic nitrogen fixation occurred in dme mutant strains. Conversely, expression of dme from the tme promoter resulted in a large reduction in DME activity and symbiotic N(2) fixation. Hence, TME cannot replace the symbiotic requirement for DME. In further experiments we investigated the DME PTA-like domain and showed that it is not required for N(2) fixation. Thus, expression of a DME C-terminal deletion derivative or the Escherichia coli NAD(+)-dependent malic enzyme (sfcA), both of which lack the PTA-like region, restored wild-type N(2) fixation to a dme mutant. Our results have defined the symbiotic requirements for malic enzyme and raise the possibility that a constant high ratio of NADPH + H(+) to NADP in nitrogen-fixing bacteroids prevents TME from functioning in N(2)-fixing bacteroids.
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Affiliation(s)
- Michael J Mitsch
- Center for Environmental Genomics, Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada
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26
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Yokoyama K, Ishijima SA, Clowney L, Koike H, Aramaki H, Tanaka C, Makino K, Suzuki M. Feast/famine regulatory proteins (FFRPs): Escherichia coli Lrp, AsnC and related archaeal transcription factors. FEMS Microbiol Rev 2006; 30:89-108. [PMID: 16438681 DOI: 10.1111/j.1574-6976.2005.00005.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Feast/famine regulatory proteins comprise a diverse family of transcription factors, which have been referred to in various individual identifications, including Escherichia coli leucine-responsive regulatory protein and asparagine synthase C gene product. A full length feast/famine regulatory protein consists of the N-terminal DNA-binding domain and the C-domain, which is involved in dimerization and further assembly, thereby producing, for example, a disc or a chromatin-like cylinder. Various ligands of the size of amino acids bind at the interface between feast/famine regulatory protein dimers, thereby altering their assembly forms. Also, the combination of feast/famine regulatory protein subunits forming the same assembly is altered. In this way, a small number of feast/famine regulatory proteins are able to regulate a large number of genes in response to various environmental changes. Because feast/famine regulatory proteins are shared by archaea and eubacteria, the genome-wide regulation by feast/famine regulatory proteins is traceable back to their common ancestor, being the prototype of highly differentiated transcription regulatory mechanisms found in organisms nowadays.
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Affiliation(s)
- Katsushi Yokoyama
- National Institute of Advanced Industrial Science and Technology, AIST Tsukuba Center, Tsukuba, Japan
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27
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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.
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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
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Majors PD, McLean JS, Pinchuk GE, Fredrickson JK, Gorby YA, Minard KR, Wind RA. NMR methods for in situ biofilm metabolism studies. J Microbiol Methods 2005; 62:337-44. [PMID: 15936835 DOI: 10.1016/j.mimet.2005.04.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Revised: 02/26/2005] [Accepted: 04/06/2005] [Indexed: 11/30/2022]
Abstract
Novel procedures and instrumentation are described for nuclear magnetic resonance (NMR) spectroscopy and imaging studies of live, in situ microbial films. A perfused NMR/optical microscope sample chamber containing a planar biofilm support was integrated into a recirculation/dilution flow loop growth reactor system and used to grow in situ Shewanella oneidensis strain MR-1 biofilms. Localized NMR techniques were developed and used to non-invasively monitor time-resolved metabolite concentrations and to image the biomass volume and distribution. As a first illustration of the feasibility of the methodology an initial 13C-labeled lactate metabolic pathway study was performed, yielding results consistent with existing genomic data for MR-1. These results represent progress toward our ultimate goal of correlating time- and depth-resolved metabolism and mass transport with gene expression in live in situ biofilms using combined NMR/optical microscopy techniques.
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Affiliation(s)
- Paul D Majors
- Pacific Northwest National Laboratory, MSIN: K8-98, Richland, WA 99352, USA
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Kumar S, Bourdès A, Poole P. De novo alanine synthesis by bacteroids of Mesorhizobium loti is not required for nitrogen transfer in the determinate nodules of Lotus corniculatus. J Bacteriol 2005; 187:5493-5. [PMID: 16030244 PMCID: PMC1196047 DOI: 10.1128/jb.187.15.5493-5495.2005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Deletion of both alanine dehydrogenase genes (aldA) in Mesorhizobium loti resulted in the loss of AldA enzyme activity from cultured bacteria and bacteroids but had no effect on the symbiotic performance of Lotus corniculatus plants. Thus, neither indeterminate pea nodules nor determinate L. corniculatus nodules export alanine as the sole nitrogen secretion product.
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Affiliation(s)
- Shalini Kumar
- School of Animal and Microbial Sciences, University of Reading, Whiteknights, P.O. Box 228, Reading RG6 6AJ, United Kingdom
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Jebbar M, Sohn-Bösser L, Bremer E, Bernard T, Blanco C. Ectoine-induced proteins in Sinorhizobium meliloti include an Ectoine ABC-type transporter involved in osmoprotection and ectoine catabolism. J Bacteriol 2005; 187:1293-304. [PMID: 15687193 PMCID: PMC545623 DOI: 10.1128/jb.187.4.1293-1304.2005] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To understand the mechanisms of ectoine-induced osmoprotection in Sinorhizobium meliloti, a proteomic examination of S. meliloti cells grown in minimal medium supplemented with ectoine was undertaken. This revealed the induction of 10 proteins. The protein products of eight genes were identified by using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. Five of these genes, with four other genes whose products were not detected on two-dimensional gels, belong to the same gene cluster, which is localized on the pSymB megaplasmid. Four of the nine genes encode the characteristic components of an ATP-binding cassette transporter that was named ehu, for ectoine/hydroxyectoine uptake. This transporter was encoded by four genes (ehuA, ehuB, ehuC, and ehuD) that formed an operon with another gene cluster that contains five genes, named eutABCDE for ectoine utilization. On the basis of sequence homologies, eutABCDE encode enzymes with putative and hypothetical functions in ectoine catabolism. Analysis of the properties of ehuA and eutA mutants suggests that S. meliloti possesses at least one additional ectoine catabolic pathway as well as a lower-affinity transport system for ectoine and hydroxyectoine. The expression of ehuB, as determined by measurements of UidA activity, was shown to be induced by ectoine and hydroxyectoine but not by glycine betaine or by high osmolality.
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Affiliation(s)
- Mohamed Jebbar
- Université de Rennes I, UMR-CNRS 6026, Département Osmorégulation chez les Bactéries, Campus de Beaulieu, Av. du Général Leclerc, 35042 Rennes, France.
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