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Klein R, Brehm J, Wissig J, Heermann R, Unden G. A signaling complex of adenylate cyclase CyaC of Sinorhizobium meliloti with cAMP and the transcriptional regulators Clr and CycR. BMC Microbiol 2023; 23:236. [PMID: 37633907 PMCID: PMC10463352 DOI: 10.1186/s12866-023-02989-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/21/2023] [Indexed: 08/28/2023] Open
Abstract
BACKGROUND Adenylate cyclases (ACs) generate the second messenger cyclic AMP (cAMP), which is found in all domains of life and is involved in the regulation of various cell physiological and metabolic processes. In the plant symbiotic bacterium Sinorhizobium meliloti, synthesis of cAMP by the membrane-bound AC CyaC responds to the redox state of the respiratory chain and the respiratory quinones. However, nothing is known about the signaling cascade that is initiated by cAMP produced by CyaC. RESULTS Here, the CRP-like transcriptional regulator Clr and the TetR-like regulator CycR (TR01819 protein) were identified to interact with CyaC using the bacterial two-hybrid system (BACTH), co-sedimentation assays, and surface plasmon resonance spectroscopy. Interaction of CycR with Clr, and of CyaC with Clr requires the presence of cAMP and of ATP, respectively, whereas that of CyaC with CycR was independent of the nucleotides. CONCLUSION The data implicate a ternary CyaC×CycR×cAMP-Clr complex, functioning as a specific signaling cascade which is formed after activation of CyaC and synthesis of cAMP. cAMP-Clr is thought to work in complex with CycR to regulate a subset of genes of the cAMP-Clr regulon in S. meliloti.
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Affiliation(s)
- Robin Klein
- Institute of Molecular Physiology (imP), Microbiology and Biotechnology, Johannes Gutenberg University, Biocenter II, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Jannis Brehm
- Institute of Molecular Physiology (imP), Microbiology and Biotechnology, Johannes Gutenberg University, Biocenter II, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Juliane Wissig
- Institute of Molecular Physiology (imP), Microbiology and Biotechnology, Johannes Gutenberg University, Biocenter II, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Ralf Heermann
- Institute of Molecular Physiology (imP), Microbiology and Biotechnology, Johannes Gutenberg University, Biocenter II, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.
| | - Gottfried Unden
- Institute of Molecular Physiology (imP), Microbiology and Biotechnology, Johannes Gutenberg University, Biocenter II, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.
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Franzino T, Boubakri H, Cernava T, Abrouk D, Achouak W, Reverchon S, Nasser W, Haichar FEZ. Implications of carbon catabolite repression for plant-microbe interactions. PLANT COMMUNICATIONS 2022; 3:100272. [PMID: 35529946 PMCID: PMC9073323 DOI: 10.1016/j.xplc.2021.100272] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/17/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Carbon catabolite repression (CCR) plays a key role in many physiological and adaptive responses in a broad range of microorganisms that are commonly associated with eukaryotic hosts. When a mixture of different carbon sources is available, CCR, a global regulatory mechanism, inhibits the expression and activity of cellular processes associated with utilization of secondary carbon sources in the presence of the preferred carbon source. CCR is known to be executed by completely different mechanisms in different bacteria, yeast, and fungi. In addition to regulating catabolic genes, CCR also appears to play a key role in the expression of genes involved in plant-microbe interactions. Here, we present a detailed overview of CCR mechanisms in various bacteria. We highlight the role of CCR in beneficial as well as deleterious plant-microbe interactions based on the available literature. In addition, we explore the global distribution of known regulatory mechanisms within bacterial genomes retrieved from public repositories and within metatranscriptomes obtained from different plant rhizospheres. By integrating the available literature and performing targeted meta-analyses, we argue that CCR-regulated substrate use preferences of microorganisms should be considered an important trait involved in prevailing plant-microbe interactions.
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Affiliation(s)
- Theophile Franzino
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Hasna Boubakri
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz 8010, Austria
| | - Danis Abrouk
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Wafa Achouak
- Aix Marseille Université, CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), 13108 Saint-Paul-Lez-Durance, France
| | - Sylvie Reverchon
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - William Nasser
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Feth el Zahar Haichar
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
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Brito LF, López MG, Straube L, Passaglia LMP, Wendisch VF. Inorganic Phosphate Solubilization by Rhizosphere Bacterium Paenibacillus sonchi: Gene Expression and Physiological Functions. Front Microbiol 2020; 11:588605. [PMID: 33424789 PMCID: PMC7793946 DOI: 10.3389/fmicb.2020.588605] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Due to the importance of phosphorus (P) in agriculture, crop inoculation with phosphate-solubilizing bacteria is a relevant subject of study. Paenibacillus sonchi genomovar Riograndensis SBR5 is a promising candidate for crop inoculation, as it can fix nitrogen and excrete ammonium at a remarkably high rate. However, its trait of phosphate solubilization (PS) has not yet been studied in detail. Here, differential gene expression and functional analyses were performed to characterize PS in this bacterium. SBR5 was cultivated with two distinct P sources: NaH2PO4 as soluble phosphate source (SPi) and hydroxyapatite as insoluble phosphate source (IPi). Total RNA of SBR5 cultivated in those two conditions was isolated and sequenced, and bacterial growth and product formation were monitored. In the IPi medium, the expression of 68 genes was upregulated, whereas 100 genes were downregulated. Among those, genes involved in carbon metabolism, including those coding for subunits of 2-oxoglutarate dehydrogenase, were identified. Quantitation of organic acids showed that the production of tricarboxylic acid cycle-derived organic acids was reduced in IPi condition, whereas acetate and gluconate were overproduced. Increased concentrations of proline, trehalose, and glycine betaine revealed active osmoprotection during growth in IPi. The cultivation with hydroxyapatite also caused the reduction in the motility of SBR5 cells as a response to Pi depletion at the beginning of its growth. SBR5 was able to solubilize hydroxyapatite, which suggests that this organism is a promising phosphate-solubilizing bacterium. Our findings are the initial step in the elucidation of the PS process in P. sonchi SBR5 and will be a valuable groundwork for further studies of this organism as a plant growth-promoting rhizobacterium.
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Affiliation(s)
- Luciana F. Brito
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Marina Gil López
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Lucas Straube
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Volker F. Wendisch
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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Joshi E, Iyer B, Rajkumar S. Glucose and arabinose dependent mineral phosphate solubilization and its succinate-mediated catabolite repression in Rhizobium sp. RM and RS. J Biosci Bioeng 2019; 128:551-557. [PMID: 31147219 DOI: 10.1016/j.jbiosc.2019.04.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 11/27/2022]
Abstract
Rhizobium sp. RM and RS are Vigna radiata root nodule isolates with the ability to solubilize tricalcium phosphate and rock phosphate under 50 mM Tris-Cl buffering conditions. Rhizobium sp. RM and RS were unique as they could produce two different organic acids, gluconic acid and oxalic acid using glucose and arabinose, respectively, which are two of the most prominent sugars present in the rhizospheric soil. However, P solubilization in these isolates was repressed in the presence of succinate resembling the phenomenon of catabolite repression. RM and RS produced 24 mM and 20 mM gluconic acid in presence of glucose which was repressed to 10 mM and 8 mM, respectively, in glucose + succinate conditions. Similarly, RM and RS produced 28 mM and 23 mM oxalic acid in arabinose containing media which was repressed to 9 mM and 8 mM, respectively, in the presence of arabinose + succinate. Results of enzyme activities indicated 66% repression of quinoprotein glucose dehydrogenase in glucose + succinate compared to glucose grown cells and 84% repression of glyoxylate oxidase in arabinose + succinate compared to arabinose grown cells. This is perhaps the first report on mechanism of P solubilization in rhizobia through utilization of two different sugars, glucose and arabinose and its repression by succinate. Succinate-mediated catabolite repression of arabinose is the unique aspect of this study.
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Affiliation(s)
- Ekta Joshi
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat 382481, India
| | - Bhagya Iyer
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat 382481, India
| | - Shalini Rajkumar
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat 382481, India.
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5
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Cai Y, Xia M, Dong H, Qian Y, Zhang T, Zhu B, Wu J, Zhang D. Engineering a vitamin B 12 high-throughput screening system by riboswitch sensor in Sinorhizobium meliloti. BMC Biotechnol 2018; 18:27. [PMID: 29751749 PMCID: PMC5948670 DOI: 10.1186/s12896-018-0441-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 04/30/2018] [Indexed: 12/23/2022] Open
Abstract
Background As a very important coenzyme in the cell metabolism, Vitamin B12 (cobalamin, VB12) has been widely used in food and medicine fields. The complete biosynthesis of VB12 requires approximately 30 genes, but overexpression of these genes did not result in expected increase of VB12 production. High-yield VB12-producing strains are usually obtained by mutagenesis treatments, thus developing an efficient screening approach is urgently needed. Result By the help of engineered strains with varied capacities of VB12 production, a riboswitch library was constructed and screened, and the btuB element from Salmonella typhimurium was identified as the best regulatory device. A flow cytometry high-throughput screening system was developed based on the btuB riboswitch with high efficiency to identify positive mutants. Mutation of Sinorhizobium meliloti (S. meliloti) was optimized using the novel mutation technique of atmospheric and room temperature plasma (ARTP). Finally, the mutant S. meliloti MC5–2 was obtained and considered as a candidate for industrial applications. After 7 d’s cultivation on a rotary shaker at 30 °C, the VB12 titer of S. meliloti MC5–2 reached 156 ± 4.2 mg/L, which was 21.9% higher than that of the wild type strain S. meliloti 320 (128 ± 3.2 mg/L). The genome of S. meliloti MC5–2 was sequenced, and gene mutations were identified and analyzed. Conclusion To our knowledge, it is the first time that a riboswitch element was used in S. meliloti. The flow cytometry high-throughput screening system was successfully developed and a high-yield VB12 producing strain was obtained. The identified and analyzed gene mutations gave useful information for developing high-yield strains by metabolic engineering. Overall, this work provides a useful high-throughput screening method for developing high VB12-yield strains. Electronic supplementary material The online version of this article (10.1186/s12896-018-0441-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yingying Cai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,College of Biotechnology, Tianjin University of Science & Technology, No. 29, thirteenth Avenue Binhai District, Tianjin, 300457, China
| | - Miaomiao Xia
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Yuan Qian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Tongcun Zhang
- College of Biotechnology, Tianjin University of Science & Technology, No. 29, thirteenth Avenue Binhai District, Tianjin, 300457, China
| | - Beiwei Zhu
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian, 116034, People's Republic of China
| | - Jinchuan Wu
- Industrial Biotechnology Division, Institute of Chemical and Engineering Sciences, 1 Pesek Road, Jurong Island, 627833, Singapore
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China. .,School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian, 116034, People's Republic of China.
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6
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A Key Regulator of the Glycolytic and Gluconeogenic Central Metabolic Pathways in Sinorhizobium meliloti. Genetics 2017; 207:961-974. [PMID: 28851745 DOI: 10.1534/genetics.117.300212] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 08/24/2017] [Indexed: 01/22/2023] Open
Abstract
The order Rhizobiales contains numerous agriculturally, biotechnologically, and medically important bacteria, including the rhizobia, and the genera Agrobacterium, Brucella, and Methylobacterium, among others. These organisms tend to be metabolically versatile, but there has been relatively little investigation into the regulation of their central carbon metabolic pathways. Here, RNA-sequencing and promoter fusion data are presented to show that the PckR protein is a key regulator of central carbon metabolism in Sinorhizobium meliloti; during growth with gluconeogenic substrates, PckR represses expression of the complete Entner-Doudoroff glycolytic pathway and induces expression of the pckA and fbaB gluconeogenic genes. Electrophoretic mobility shift assays indicate that PckR binds an imperfect palindromic sequence that overlaps the promoter or transcriptional start site in the negatively regulated promoters, or is present in tandem upstream the promoter motifs in the positively regulated promoters. Genetic and in vitro electrophoretic mobility shift assay experiments suggest that elevated concentrations of a PckR effector ligand results in the dissociation of PckR from its target binding site, and evidence is presented that suggests phosphoenolpyruvate may function as the effector. Characterization of missense pckR alleles identified three conserved residues important for increasing the affinity of PckR for its cognate effector molecule. Bioinformatics analyses illustrates that PckR is limited to a narrow phylogenetic range consisting of the Rhizobiaceae, Phyllobacteriaceae, Brucellaceae, and Bartonellaceae families. These data provide novel insights into the regulation of the core carbon metabolic pathways of this pertinent group of α-proteobacteria.
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Barbier T, Zúñiga-Ripa A, Moussa S, Plovier H, Sternon JF, Lázaro-Antón L, Conde-Álvarez R, De Bolle X, Iriarte M, Moriyón I, Letesson JJ. Brucella central carbon metabolism: an update. Crit Rev Microbiol 2017; 44:182-211. [PMID: 28604247 DOI: 10.1080/1040841x.2017.1332002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The brucellae are facultative intracellular pathogens causing brucellosis, an important zoonosis. Here, we review the nutritional, genetic, proteomic and transcriptomic studies on Brucella carbon uptake and central metabolism, information that is needed for a better understanding of Brucella virulence. There is no uniform picture across species but the studies suggest primary and/or secondary transporters for unknown carbohydrates, lactate, glycerol phosphate, erythritol, xylose, ribose, glucose and glucose/galactose, and routes for their incorporation to central metabolism, including an erythritol pathway feeding the pentose phosphate cycle. Significantly, all brucellae lack phosphoenolpyruvate synthase and phosphofructokinase genes, which confirms previous evidence on glycolysis absence, but carry all Entner-Doudoroff (ED) pathway and Krebs cycle (and glyoxylate pathway) genes. However, glucose catabolism proceeds through the pentose phosphate cycle in the classical species, and the ED pathway operates in some rodent-associated brucellae, suggesting an ancestral character for this pathway in this group. Gluconeogenesis is functional but does not rely exclusively on classical fructose bisphosphatases. Evidence obtained using infection models is fragmentary but suggests the combined or sequential use of hexoses/pentoses, amino acids and gluconeogenic substrates. We also discuss the role of the phosphotransferase system, stringent reponse, quorum sensing, BvrR/S and sRNAs in metabolism control, an essential aspect of the life style of facultative intracellular parasites.
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Affiliation(s)
- T Barbier
- a Unité de Recherche en Biologie des Microorganismes , Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur , Namur , Belgium
| | - A Zúñiga-Ripa
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
| | - S Moussa
- a Unité de Recherche en Biologie des Microorganismes , Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur , Namur , Belgium
| | - H Plovier
- a Unité de Recherche en Biologie des Microorganismes , Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur , Namur , Belgium
| | - J F Sternon
- a Unité de Recherche en Biologie des Microorganismes , Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur , Namur , Belgium
| | - L Lázaro-Antón
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
| | - R Conde-Álvarez
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
| | - X De Bolle
- a Unité de Recherche en Biologie des Microorganismes , Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur , Namur , Belgium
| | - M Iriarte
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
| | - I Moriyón
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
| | - J J Letesson
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
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Krol E, Klaner C, Gnau P, Kaever V, Essen LO, Becker A. Cyclic mononucleotide- and Clr-dependent gene regulation in Sinorhizobium meliloti. MICROBIOLOGY-SGM 2016; 162:1840-1856. [PMID: 27535558 DOI: 10.1099/mic.0.000356] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To identify physiological processes affected by cAMP in the plant-symbiotic nitrogen-fixing α-proteobacterium Sinorhizobium meliloti Rm2011, cAMP levels were artificially increased by overexpression of its cognate adenylate/guanylate cyclase gene cyaJ. This resulted in high accumulation of cAMP in the culture supernatant, decreased swimming motility and increased production of succinoglycan, an exopolysaccharide involved in host invasion. Weaker, similar phenotypic changes were induced by overexpression of cyaB and cyaG1. Effects on swimming motility and succinoglycan production were partially dependent on clr encoding a cyclic AMP receptor-like protein. Transcriptome profiling of an cyaJ-overexpressing strain identified 72 upregulated and 82 downregulated genes. A considerable number of upregulated genes are related to polysaccharide biosynthesis and osmotic stress response. These included succinoglycan biosynthesis genes, genes of the putative polysaccharide synthesis nodP2-exoF3 cluster and feuN, the first gene of the operon encoding the FeuNPQ regulatory system. Downregulated genes were mostly related to respiration, central metabolism and swimming motility. Promoter-probe studies in the presence of externally added cAMP revealed 18 novel Clr-cAMP-regulated genes. Moreover, the addition of cGMP into the growth medium also promoted clr-dependent gene regulation. In vitro binding of Clr-cAMP and Clr-cGMP to the promoter regions of SMc02178, SMb20906,SMc04190, SMc00925, SMc01136 and cyaF2 required the DNA motif (A/C/T)GT(T/C)(T/C/A)C (N4) G(G/A)(T/A)ACA. Furthermore, SMc02178, SMb20906,SMc04190and SMc00653 promoters were activated by Clr-cAMP/cGMP in Escherichia coli as heterologous host. These findings suggest direct activation of these 7 genes by Clr-cAMP/cGMP.
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Affiliation(s)
- Elizaveta Krol
- Faculty of Biology and LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Christina Klaner
- Faculty of Biology and LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Petra Gnau
- Faculty of Chemistry and LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Lars-Oliver Essen
- Faculty of Chemistry and LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Anke Becker
- Faculty of Biology and LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
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9
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Iyer B, Rajput MS, Jog R, Joshi E, Bharwad K, Rajkumar S. Organic acid mediated repression of sugar utilization in rhizobia. Microbiol Res 2016; 192:211-220. [PMID: 27664739 DOI: 10.1016/j.micres.2016.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 07/20/2016] [Accepted: 07/25/2016] [Indexed: 01/17/2023]
Abstract
Rhizobia are a class of symbiotic diazotrophic bacteria which utilize C4 acids in preference to sugars and the sugar utilization is repressed as long as C4 acids are present. This can be manifested as a diauxie when rhizobia are grown in the presence of a sugar and a C4 acid together. Succinate, a C4 acid is known to repress utilization of sugars, sugar alcohols, hydrocarbons, etc by a mechanism termed as Succinate Mediated Catabolite Repression (SMCR). Mechanism of catabolite repression determines the hierarchy of carbon source utilization in bacteria. Though the mechanism of catabolite repression has been well studied in model organisms like E. coli, B. subtilis and Pseudomonas sp., mechanism of SMCR in rhizobia has not been well elucidated. C4 acid uptake is important for effective symbioses while mutation in the sugar transport and utilization genes does not affect symbioses. Deletion of hpr and sma0113 resulted in the partial relief of SMCR of utilization of galactosides like lactose, raffinose and maltose in the presence of succinate. However, no such regulators governing SMCR of glucoside utilization have been identified till date. Though rhizobia can utilize multitude of sugars, high affinity transporters for many sugars are yet to be identified. Identifying high affinity sugar transporters and studying the mechanism of catabolite repression in rhizobia is important to understand the level of regulation of SMCR and the key regulators involved in SMCR.
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Affiliation(s)
- Bhagya Iyer
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
| | | | - Rahul Jog
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India; Environmental Molecular Biology Laboratory, Division of Biosphere, Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ekta Joshi
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
| | - Krishna Bharwad
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
| | - Shalini Rajkumar
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India.
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Zhang Y, Smallbone LA, diCenzo GC, Morton R, Finan TM. Loss of malic enzymes leads to metabolic imbalance and altered levels of trehalose and putrescine in the bacterium Sinorhizobium meliloti. BMC Microbiol 2016; 16:163. [PMID: 27456220 PMCID: PMC4960864 DOI: 10.1186/s12866-016-0780-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 07/15/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malic enzymes decarboxylate the tricarboxylic acid (TCA) cycle intermediate malate to the glycolytic end-product pyruvate and are well positioned to regulate metabolic flux in central carbon metabolism. Despite the wide distribution of these enzymes, their biological roles are unclear in part because the reaction catalyzed by these enzymes can be by-passed by other pathways. The N2-fixing alfalfa symbiont Sinorhizobium meliloti contains both a NAD(P)-malic enzyme (DME) and a separate NADP-malic enzyme (TME) and to help understand the role of these enzymes, we investigated growth, metabolomic, and transcriptional consequences resulting from loss of these enzymes in free-living cells. RESULTS Loss of DME, TME, or both enzymes had no effect on growth with the glycolytic substrate, glucose. In contrast, the dme mutants, but not tme, grew slowly on the gluconeogenic substrate succinate and this slow growth was further reduced upon the addition of glucose. The dme mutant strains incubated with succinate accumulated trehalose and hexose sugar phosphates, secreted malate, and relative to wild-type, these cells had moderately increased transcription of genes involved in gluconeogenesis and pathways that divert metabolites away from the TCA cycle. While tme mutant cells grew at the same rate as wild-type on succinate, they accumulated the compatible solute putrescine. CONCLUSIONS NAD(P)-malic enzyme (DME) of S. meliloti is required for efficient metabolism of succinate via the TCA cycle. In dme mutants utilizing succinate, malate accumulates and is excreted and these cells appear to increase metabolite flow via gluconeogenesis with a resulting increase in the levels of hexose-6-phosphates and trehalose. For cells utilizing succinate, TME activity alone appeared to be insufficient to produce the levels of pyruvate required for efficient TCA cycle metabolism. Putrescine was found to accumulate in tme cells growing with succinate, and whether this is related to altered levels of NADPH requires further investigation.
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Affiliation(s)
- Ye Zhang
- Department of Biology, McMaster University, 1280 Main St. West, Hamilton, ON, L8S 4K1, Canada.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Laura Anne Smallbone
- Department of Biology, McMaster University, 1280 Main St. West, Hamilton, ON, L8S 4K1, Canada
| | - George C diCenzo
- Department of Biology, McMaster University, 1280 Main St. West, Hamilton, ON, L8S 4K1, Canada
| | - Richard Morton
- Department of Biology, McMaster University, 1280 Main St. West, Hamilton, ON, L8S 4K1, Canada
| | - Turlough M Finan
- Department of Biology, McMaster University, 1280 Main St. West, Hamilton, ON, L8S 4K1, Canada.
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11
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Scharf BE, Hynes MF, Alexandre GM. Chemotaxis signaling systems in model beneficial plant-bacteria associations. PLANT MOLECULAR BIOLOGY 2016; 90:549-59. [PMID: 26797793 DOI: 10.1007/s11103-016-0432-4] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 01/04/2016] [Indexed: 05/07/2023]
Abstract
Beneficial plant-microbe associations play critical roles in plant health. Bacterial chemotaxis provides a competitive advantage to motile flagellated bacteria in colonization of plant root surfaces, which is a prerequisite for the establishment of beneficial associations. Chemotaxis signaling enables motile soil bacteria to sense and respond to gradients of chemical compounds released by plant roots. This process allows bacteria to actively swim towards plant roots and is thus critical for competitive root surface colonization. The complete genome sequences of several plant-associated bacterial species indicate the presence of multiple chemotaxis systems and a large number of chemoreceptors. Further, most soil bacteria are motile and capable of chemotaxis, and chemotaxis-encoding genes are enriched in the bacteria found in the rhizosphere compared to the bulk soil. This review compares the architecture and diversity of chemotaxis signaling systems in model beneficial plant-associated bacteria and discusses their relevance to the rhizosphere lifestyle. While it is unclear how controlling chemotaxis via multiple parallel chemotaxis systems provides a competitive advantage to certain bacterial species, the presence of a larger number of chemoreceptors is likely to contribute to the ability of motile bacteria to survive in the soil and to compete for root surface colonization.
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Affiliation(s)
- Birgit E Scharf
- Department of Biological Sciences, Life Sciences I, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Michael F Hynes
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Gladys M Alexandre
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.
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12
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Mostafavi M, Lewis JC, Saini T, Bustamante JA, Gao IT, Tran TT, King SN, Huang Z, Chen JC. Analysis of a taurine-dependent promoter in Sinorhizobium meliloti that offers tight modulation of gene expression. BMC Microbiol 2014; 14:295. [PMID: 25420869 PMCID: PMC4254191 DOI: 10.1186/s12866-014-0295-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/13/2014] [Indexed: 12/20/2022] Open
Abstract
Background Genetic models have been developed in divergent branches of the class Alphaproteobacteria to help answer a wide spectrum of questions regarding bacterial physiology. For example, Sinorhizobium meliloti serves as a useful representative for investigating rhizobia-plant symbiosis and nitrogen fixation, Caulobacter crescentus for studying cell cycle regulation and organelle biogenesis, and Zymomonas mobilis for assessing the potentials of metabolic engineering and biofuel production. A tightly regulated promoter that enables titratable expression of a cloned gene in these different models is highly desirable, as it can facilitate observation of phenotypes that would otherwise be obfuscated by leaky expression. Results We compared the functionality of four promoter regions in S. meliloti (ParaA, PtauA, PrhaR, and PmelA) by constructing strains carrying fusions to the uidA reporter in their genomes and measuring beta-glucuronidase activities when they were induced by arabinose, taurine, rhamnose, or melibiose. PtauA was chosen for further study because it, and, to a lesser extent, PmelA, exhibited characteristics suitable for efficient modulation of gene expression. The levels of expression from PtauA depended on the concentrations of taurine, in both complex and defined media, in S. meliloti as well as C. crescentus and Z. mobilis. Moreover, our analysis indicated that TauR, TauC, and TauY are each necessary for taurine catabolism and substantiated their designated roles as a transcriptional activator, the permease component of an ABC transporter, and a major subunit of the taurine dehydrogenase, respectively. Finally, we demonstrated that PtauA can be used to deplete essential cellular factors in S. meliloti, such as the PleC histidine kinase and TatB, a component of the twin-arginine transport machinery. Conclusions The PtauA promoter of S. meliloti can control gene expression with a relatively inexpensive and permeable inducer, taurine, in diverse alpha-proteobacteria. Regulated expression of the same gene in different hosts can be achieved by placing both tauR and PtauA on appropriate vectors, thus facilitating inspection of conservation of gene function across species. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0295-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mina Mostafavi
- Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA.
| | - Jainee Christa Lewis
- Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA.
| | - Tanisha Saini
- Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA.
| | | | - Ivan Thomas Gao
- Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA.
| | - Tuyet Thi Tran
- Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA.
| | - Sean Nicholas King
- Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA.
| | - Zhenzhong Huang
- Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA.
| | - Joseph C Chen
- Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA.
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Geddes BA, Oresnik IJ. Physiology, genetics, and biochemistry of carbon metabolism in the alphaproteobacterium Sinorhizobium meliloti. Can J Microbiol 2014; 60:491-507. [PMID: 25093748 DOI: 10.1139/cjm-2014-0306] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A large proportion of genes within a genome encode proteins that play a role in metabolism. The Alphaproteobacteria are a ubiquitous group of bacteria that play a major role in a number of environments. For well over 50 years, carbon metabolism in Rhizobium has been studied at biochemical and genetic levels. Here, we review the pre- and post-genomics literature of the metabolism of the alphaproteobacterium Sinorhizobium meliloti. This review provides an overview of carbon metabolism that is useful to readers interested in this organism and to those working on other organisms that do not follow other model system paradigms.
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Affiliation(s)
- Barney A Geddes
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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14
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Biochemical characterization of a nitrogen-type phosphotransferase system reveals that enzyme EI(Ntr) integrates carbon and nitrogen signaling in Sinorhizobium meliloti. J Bacteriol 2014; 196:1901-7. [PMID: 24633875 DOI: 10.1128/jb.01489-14] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In Sinorhizobium meliloti, catabolite repression is influenced by a noncanonical nitrogen-type phosphotransferase system (PTS(Ntr)). In this PTS(Ntr), the protein HPr is phosphorylated on histidine-22 by the enzyme EI(Ntr) and the flux of phosphate through this residue onto downstream proteins leads to an increase in succinate-mediated catabolite repression (SMCR). In order to explore the molecular determinants of HPr phosphorylation by EI(Ntr), both proteins were purified and the activity of EI(Ntr) was measured. Experimentally determined kinetic parameters of EI(Ntr) activity were significantly slower than those determined for the carbohydrate-type EI in Escherichia coli. Enzymatic assays showed that glutamine, a signal of nitrogen availability in many Gram-negative bacteria, strongly inhibits EI(Ntr). Binding experiments using the isolated GAF domain of EI(Ntr) (EIGAF) showed that it is the domain responsible for detection of glutamine. EI(Ntr) activity was not affected by α-ketoglutarate, and no binding between the EIGAF and α-ketoglutarate could be detected. These data suggest that in S. melilloti, EI(Ntr) phosphorylation of HPr is regulated by signals from both carbon metabolism (phosphoenolpyruvate) and nitrogen metabolism (glutamine).
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15
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Repression of oxalic acid-mediated mineral phosphate solubilization in rhizospheric isolates of Klebsiella pneumoniae by succinate. Arch Microbiol 2012; 195:81-8. [PMID: 23124768 DOI: 10.1007/s00203-012-0850-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 10/17/2012] [Accepted: 10/23/2012] [Indexed: 10/27/2022]
Abstract
Two strains of Klebsiella (SM6 and SM11) were isolated from rhizospheric soil that solubilized mineral phosphate by secretion of oxalic acid from glucose. Activities of enzymes for periplasmic glucose oxidation (glucose dehydrogenase) and glyoxylate shunt (isocitrate lyase and glyoxylate oxidase) responsible for oxalic acid production were estimated. In presence of succinate, phosphate solubilization was completely inhibited, and the enzymes glucose dehydrogenase and glyoxylate oxidase were repressed. Significant activity of isocitrate lyase, the key enzyme for carbon flux through glyoxylate shunt and oxalic acid production during growth on glucose suggested that it could be inducible in nature, and its inhibition by succinate appeared to be similar to catabolite repression.
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Garcia PP, Bringhurst RM, Arango Pinedo C, Gage DJ. Characterization of a two-component regulatory system that regulates succinate-mediated catabolite repression in Sinorhizobium meliloti. J Bacteriol 2010; 192:5725-35. [PMID: 20817764 PMCID: PMC2953702 DOI: 10.1128/jb.00629-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 08/25/2010] [Indexed: 01/13/2023] Open
Abstract
When they are available, Sinorhizobium meliloti utilizes C(4)-dicarboxylic acids as preferred carbon sources for growth while suppressing the utilization of some secondary carbon sources such as α- and β-galactosides. The phenomenon of using succinate as the sole carbon source in the presence of secondary carbon sources is termed succinate-mediated catabolite repression (SMCR). Genetic screening identified the gene sma0113 as needed for strong SMCR when S. meliloti was grown in succinate plus lactose, maltose, or raffinose. sma0113 and the gene immediately downstream, sma0114, encode the proteins Sma0113, an HWE histidine kinase with five PAS domains, and Sma0114, a CheY-like response regulator lacking a DNA-binding domain. sma0113 in-frame deletion mutants show a relief of catabolite repression compared to the wild type. sma0114 in-frame deletion mutants overproduce polyhydroxybutyrate (PHB), and this overproduction requires sma0113. Sma0113 may use its five PAS domains for redox level or energy state monitoring and use that information to regulate catabolite repression and related responses.
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Affiliation(s)
- Preston P. Garcia
- University of Connecticut, Department of Molecular and Cell Biology, 91 N. Eagleville Rd., U-3125, Storrs, Connecticut 06269-3125
| | - Ryan M. Bringhurst
- University of Connecticut, Department of Molecular and Cell Biology, 91 N. Eagleville Rd., U-3125, Storrs, Connecticut 06269-3125
| | - Catalina Arango Pinedo
- University of Connecticut, Department of Molecular and Cell Biology, 91 N. Eagleville Rd., U-3125, Storrs, Connecticut 06269-3125
| | - Daniel J. Gage
- University of Connecticut, Department of Molecular and Cell Biology, 91 N. Eagleville Rd., U-3125, Storrs, Connecticut 06269-3125
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17
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Chen AM, Wang YB, Jie S, Yu AY, Luo L, Yu GQ, Zhu JB, Wang YZ. Identification of a TRAP transporter for malonate transport and its expression regulated by GtrA from Sinorhizobium meliloti. Res Microbiol 2010; 161:556-64. [PMID: 20594941 DOI: 10.1016/j.resmic.2010.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Revised: 05/05/2010] [Accepted: 05/06/2010] [Indexed: 10/19/2022]
Abstract
Sinorhizobium meliloti can live as a saprophyte in soil or as a nitrogen-fixing symbiont inside the root nodule cells of alfalfa and related legumes by utilizing different organic compounds as its carbon source. Here we have identified the matPQMAB operon in S. meliloti 1021. Within this operon, matP, matQ and the M region of the fused gene matMA encode an extracytoplasmic solute receptor, a small transmembrane protein and a large transmembrane protein, consisting of three components of the tripartite ATP-independent periplasmic (TRAP) transporter for malonate transport. The A region of the fused gene matMA and matB encode malonate-metabolizing enzymes, malonyl-CoA decarboxylase and malonyl-CoA synthetase. The null mutant of each matPQMAB gene is unable to grow on M9 minimal medium containing malonate as the sole carbon source. However, these mutants can induce the formation of efficient nitrogen-fixing root nodules on alfalfa. The matPQMAB operon is expressed in free-living bacterial cells and symbiotic bacterial cells from infection threads and root nodules. The GntR family transcriptional regulator, GtrA, specifically binds the promoter of the matPQMAB operon, positively regulating its expression. Moreover, the matPQMAB can be transcriptionally induced by malonate. These results suggested that a C(3)-dicarboxylic acid TRAP transporter is responsible for malonate transport in S. meliloti.
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Affiliation(s)
- Ai-Min Chen
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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18
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HPrK regulates succinate-mediated catabolite repression in the gram-negative symbiont Sinorhizobium meliloti. J Bacteriol 2008; 191:298-309. [PMID: 18931135 DOI: 10.1128/jb.01115-08] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The HPrK kinase/phosphatase is a common component of the phosphotransferase system (PTS) of gram-positive bacteria and regulates catabolite repression through phosphorylation/dephosphorylation of its substrate, the PTS protein HPr, at a conserved serine residue. Phosphorylation of HPr by HPrK also affects additional phosphorylation of HPr by the PTS enzyme EI at a conserved histidine residue. Sinorhizobium meliloti can live as symbionts inside legume root nodules or as free-living organisms and is one of the relatively rare gram-negative bacteria known to have a gene encoding HPrK. We have constructed S. meliloti mutants that lack HPrK or that lack key amino acids in HPr that are likely phosphorylated by HPrK and EI. Deletion of hprK in S. meliloti enhanced catabolite repression caused by succinate, as did an S53A substitution in HPr. Introduction of an H22A substitution into HPr alleviated the strong catabolite repression phenotypes of strains carrying Delta hprK or hpr(S53A) mutations, demonstrating that HPr-His22-P is needed for strong catabolite repression. Furthermore, strains with a hpr(H22A) allele exhibited relaxed catabolite repression. These results suggest that HPrK phosphorylates HPr at the serine-53 residue, that HPr-Ser53-P inhibits phosphorylation at the histidine-22 residue, and that HPr-His22-P enhances catabolite repression in the presence of succinate. Additional experiments show that Delta hprK mutants overproduce exopolysaccharides and form nodules that do not fix nitrogen.
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19
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Construction and expression of sugar kinase transcriptional gene fusions by using the Sinorhizobium meliloti ORFeome. Appl Environ Microbiol 2008; 74:6756-65. [PMID: 18791020 DOI: 10.1128/aem.01468-08] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Sinorhizobium meliloti ORFeome project cloned 6,314 open reading frames (ORFs) into a modified Gateway entry vector system from which the ORFs could be transferred to destination vectors in vivo via bacterial conjugation. In this work, a reporter gene destination vector, pMK2030, was constructed and used to generate ORF-specific transcriptional fusions to beta-glucuronidase (gusA) and green fluorescent protein (gfp) reporter genes. A total of 6,290 ORFs were successfully transferred from the entry vector library into pMK2030. To demonstrate the utility of this system, reporter plasmids corresponding to 30 annotated sugar kinase genes were integrated into the S. meliloti SM1021 and/or SM8530 genome. Expression of these genes was measured using a high-throughput beta-glucuronidase assay to track expression on nine different carbon sources. Six ORFs integrated into SM1021 and SM8530 had different basal levels of expression in the two strains. The annotated activities of three other sugar kinases were also confirmed.
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20
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Pinedo CA, Bringhurst RM, Gage DJ. Sinorhizobium meliloti mutants lacking phosphotransferase system enzyme HPr or EIIA are altered in diverse processes, including carbon metabolism, cobalt requirements, and succinoglycan production. J Bacteriol 2008; 190:2947-56. [PMID: 18281401 PMCID: PMC2293241 DOI: 10.1128/jb.01917-07] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Accepted: 02/06/2008] [Indexed: 11/20/2022] Open
Abstract
Sinorhizobium meliloti is a member of the Alphaproteobacteria that fixes nitrogen when it is in a symbiotic relationship. Genes for an incomplete phosphotransferase system (PTS) have been found in the genome of S. meliloti. The genes present code for Hpr and ManX (an EIIA(Man)-type enzyme). HPr and EIIA regulate carbon utilization in other bacteria. hpr and manX in-frame deletion mutants exhibited altered carbon metabolism and other phenotypes. Loss of HPr resulted in partial relief of succinate-mediated catabolite repression, extreme sensitivity to cobalt limitation, rapid die-off during stationary phase, and altered succinoglycan production. Loss of ManX decreased expression of melA-agp and lac, the operons needed for utilization of alpha- and beta-galactosides, slowed growth on diverse carbon sources, and enhanced accumulation of high-molecular-weight succinoglycan. A strain with both hpr and manX deletions exhibited phenotypes similar to those of the strain with a single hpr deletion. Despite these strong phenotypes, deletion mutants exhibited wild-type nodulation and nitrogen fixation when they were inoculated onto Medicago sativa. The results show that HPr and ManX (EIIA(Man)) are involved in more than carbon regulation in S. meliloti and suggest that the phenotypes observed occur due to activity of HPr or one of its phosphorylated forms.
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Affiliation(s)
- Catalina Arango Pinedo
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd., U-3125, Storrs, CT 06269-3125, USA
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21
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Poysti NJ, Loewen EDM, Wang Z, Oresnik IJ. Sinorhizobium meliloti pSymB carries genes necessary for arabinose transport and catabolism. Microbiology (Reading) 2007; 153:727-736. [PMID: 17322193 DOI: 10.1099/mic.0.29148-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arabinose is a known component of plant cell walls and is found in the rhizosphere. In this work, a previously undeleted region of the megaplasmid pSymB was identified as encoding genes necessary for arabinose catabolism, by Tn5-B20 random mutagenesis and subsequent complementation. Transcription of this region was measured by beta-galactosidase assays of Tn5-B20 fusions, and shown to be strongly inducible by arabinose, and moderately so by galactose and seed exudate. Accumulation of [(3)H]arabinose in mutants and wild-type was measured, and the results suggested that this operon is necessary for arabinose transport. Although catabolite repression of the arabinose genes by succinate or glucose was not detected at the level of transcription, both glucose and galactose were found to inhibit accumulation of arabinose when present in excess. To determine if glucose was also taken up by the arabinose transport proteins, [(14)C]glucose uptake rates were measured in wild-type and arabinose mutant strains. No differences in glucose uptake rates were detected between wild-type and arabinose catabolism mutant strains, indicating that excess glucose did not compete with arabinose for transport by the same system. Arabinose mutants were tested for the ability to form nitrogen-fixing nodules on alfalfa, and to compete with the wild-type for nodule occupancy. Strains unable to utilize arabinose did not display any symbiotic defects, and were not found to be less competitive than wild-type for nodule occupancy in co-inoculation experiments. Moreover, the results suggest that other loci are required for arabinose catabolism, including a gene encoding arabinose dehydrogenase.
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Affiliation(s)
- Nathan J Poysti
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Erin D M Loewen
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Zexi Wang
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ivan J Oresnik
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Deutscher J, Francke C, Postma PW. How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev 2007; 70:939-1031. [PMID: 17158705 PMCID: PMC1698508 DOI: 10.1128/mmbr.00024-06] [Citation(s) in RCA: 985] [Impact Index Per Article: 57.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The phosphoenolpyruvate(PEP):carbohydrate phosphotransferase system (PTS) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. To carry out its catalytic function in sugar transport and phosphorylation, the PTS uses PEP as an energy source and phosphoryl donor. The phosphoryl group of PEP is usually transferred via four distinct proteins (domains) to the transported sugar bound to the respective membrane component(s) (EIIC and EIID) of the PTS. The organization of the PTS as a four-step phosphoryl transfer system, in which all P derivatives exhibit similar energy (phosphorylation occurs at histidyl or cysteyl residues), is surprising, as a single protein (or domain) coupling energy transfer and sugar phosphorylation would be sufficient for PTS function. A possible explanation for the complexity of the PTS was provided by the discovery that the PTS also carries out numerous regulatory functions. Depending on their phosphorylation state, the four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB) can phosphorylate or interact with numerous non-PTS proteins and thereby regulate their activity. In addition, in certain bacteria, one of the PTS components (HPr) is phosphorylated by ATP at a seryl residue, which increases the complexity of PTS-mediated regulation. In this review, we try to summarize the known protein phosphorylation-related regulatory functions of the PTS. As we shall see, the PTS regulation network not only controls carbohydrate uptake and metabolism but also interferes with the utilization of nitrogen and phosphorus and the virulence of certain pathogens.
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Affiliation(s)
- Josef Deutscher
- Microbiologie et Génétique Moléculaire, INRA-CNRS-INA PG UMR 2585, Thiverval-Grignon, France.
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Cardon ZG, Gage DJ. Resource Exchange in the Rhizosphere: Molecular Tools and the Microbial Perspective. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2006. [DOI: 10.1146/annurev.ecolsys.37.091305.110207] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zoe G. Cardon
- Department of Ecology and Evolutionary Biology and Center for Integrative Geosciences, University of Connecticut, Storrs, Connecticut 06269;
| | - Daniel J. Gage
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269;
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Yurgel SN, Kahn ML. Dicarboxylate transport by rhizobia. FEMS Microbiol Rev 2004; 28:489-501. [PMID: 15374663 DOI: 10.1016/j.femsre.2004.04.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2003] [Revised: 01/03/2004] [Accepted: 04/04/2004] [Indexed: 11/27/2022] Open
Abstract
Soil bacteria collectively known as rhizobia are able to convert atmospheric dinitrogen to ammonia while participating in a symbiotic association with legume plants. This capability has made the bacteria an attractive research subject at many levels of investigation, especially since physiological and metabolic specialization are central to this ecological niche. Dicarboxylate transport plays an important role in the operation of an effective, nitrogen-fixing symbiosis and considerable evidence suggests that dicarboxylates are a major energy and carbon source for the nitrogen-fixing rhizobia. The dicarboxylate transport (Dct) system responsible for importing these compounds generally consists of a dicarboxylate carrier protein, DctA, and a two component kinase regulatory system, DctB/DctD. DctA and DctB/D differ in the substrates that they recognize and a model for substrate recognition by DctA and DctB is discussed. In some rhizobia, DctA expression can be induced during symbiosis in the absence of DctB/DctD by an alternative, uncharacterized, mechanism. The DctA protein belongs to a subgroup of the glutamate transporter family now thought to have an unusual structure that combines aspects of permeases and ion channels. While the structure of C(4)-dicarboxylate transporters has not been analyzed in detail, mutagenesis of S. meliloti DctA has produced results consistent with the alignment of the rhizobial protein with the more characterized bacterial and eukaryotic glutamate transporters in this family.
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Affiliation(s)
- Svetlana N Yurgel
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA.
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Yost CK, Del Bel KL, Quandt J, Hynes MF. Rhizobium leguminosarum methyl-accepting chemotaxis protein genes are down-regulated in the pea nodule. Arch Microbiol 2004; 182:505-13. [PMID: 15502966 DOI: 10.1007/s00203-004-0736-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2004] [Revised: 09/22/2004] [Accepted: 09/24/2004] [Indexed: 11/26/2022]
Abstract
Regulation of methyl-accepting chemotaxis protein (MCP) genes of Rhizobium leguminosarum was studied under symbiotic conditions. Transcriptional fusions using both beta-galactosidase and beta-glucuronidase genes within two different mcp genes demonstrated that mcp expression decreased significantly during nodulation. Immunoblots using an anti-MCP antibody detected MCPs in free-living cells but not in bacteroids. Down-regulation during nodulation was not dependent upon known regulatory proteins involved in induction of expression of genes involved in nitrogen fixation. Environmental conditions found in the bacteroid that may trigger down-regulation were investigated by growing free-living cultures under a variety of growth conditions. Growth under low oxygen concentration or using succinate as a sole carbon source did not lower expression of the mcp gene fusions.
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Affiliation(s)
- Christopher K Yost
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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