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Sequential uptake of aldoses over fructose and enhanced phosphate solubilization in Rhizobium sp. RM. Appl Microbiol Biotechnol 2022; 106:4251-4268. [DOI: 10.1007/s00253-022-11997-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/19/2022] [Accepted: 05/22/2022] [Indexed: 11/02/2022]
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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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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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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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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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Bringhurst RM, Gage DJ. Control of inducer accumulation plays a key role in succinate-mediated catabolite repression in Sinorhizobium meliloti. J Bacteriol 2002; 184:5385-92. [PMID: 12218025 PMCID: PMC135350 DOI: 10.1128/jb.184.19.5385-5392.2002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2002] [Accepted: 06/24/2002] [Indexed: 11/20/2022] Open
Abstract
The symbiotic, nitrogen-fixing bacterium Sinorhizobium meliloti favors succinate and related dicarboxylic acids as carbon sources. As a preferred carbon source, succinate can exert catabolite repression upon genes needed for the utilization of many secondary carbon sources, including the alpha-galactosides raffinose and stachyose. We isolated lacR mutants in a genetic screen designed to find S. meliloti mutants that had abnormal succinate-mediated catabolite repression of the melA-agp genes, which are required for the utilization of raffinose and other alpha-galactosides. The loss of catabolite repression in lacR mutants was seen in cells grown in minimal medium containing succinate and raffinose and grown in succinate and lactose. For succinate and lactose, the loss of catabolite repression could be attributed to the constitutive expression of beta-galactoside utilization genes in lacR mutants. However, the inactivation of lacR did not cause the constitutive expression of alpha-galactoside utilization genes but caused the aberrant expression of these genes only when succinate was present. To explain the loss of diauxie in succinate and raffinose, we propose a model in which lacR mutants overproduce beta-galactoside transporters, thereby overwhelming the inducer exclusion mechanisms of succinate-mediated catabolite repression. Thus, some raffinose could be transported by the overproduced beta-galactoside transporters and cause the induction of alpha-galactoside utilization genes in the presence of both succinate and raffinose. This model is supported by the restoration of diauxie in a lacF lacR double mutant (lacF encodes a beta-galactoside transport protein) grown in medium containing succinate and raffinose. Biochemical support for the idea that succinate-mediated repression operates by preventing inducer accumulation also comes from uptake assays, which showed that cells grown in raffinose and exposed to succinate have a decreased rate of raffinose transport compared to control cells not exposed to succinate.
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Affiliation(s)
- Ryan M Bringhurst
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
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Abstract
Infection of legume roots or stems with soil bacteria of the Rhizobiaceae results in the formation of nodules that become symbiotic nitrogen-fixing organs. Within the infected cells of these nodules, bacteria are enveloped in a membrane of plant origin, called the peribacteroid membrane (PBM), and divide and differentiate to form nitrogen-fixing bacteroids. The organelle-like structure comprised of PBM and bacteroids is termed the symbiosome, and is the basic nitrogen-fixing unit of the nodule. The major exchange of nutrients between the symbiotic partners is reduced carbon from the plant, to fuel nitrogenase activity in the bacteroid, and fixed nitrogen from the bacteroid, which is assimilated in the plant cytoplasm. However, many other metabolites are also exchanged. The metabolic interaction between the plant and the bacteroids is regulated by a series of transporters and channels on the PBM and the bacteroid membrane, and these form the focus of this review.
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Affiliation(s)
- Michael K. Udvardi
- Division of Biochemistry and Molecular Biology, Faculty of Science, Australian National University, Canberra ACT, 0200, Australia
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Streeter JG. Integration of Plant and Bacterial Metabolism in Nitrogen Fixing Systems. ACTA ACUST UNITED AC 1995. [DOI: 10.1007/978-94-011-0379-4_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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