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Lipa P, Janczarek M. Phosphorylation systems in symbiotic nitrogen-fixing bacteria and their role in bacterial adaptation to various environmental stresses. PeerJ 2020; 8:e8466. [PMID: 32095335 PMCID: PMC7020829 DOI: 10.7717/peerj.8466] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/27/2019] [Indexed: 12/23/2022] Open
Abstract
Symbiotic bacteria, commonly called rhizobia, lead a saprophytic lifestyle in the soil and form nitrogen-fixing nodules on legume roots. During their lifecycle, rhizobia have to adapt to different conditions prevailing in the soils and within host plants. To survive under these conditions, rhizobia fine-tune the regulatory machinery to respond rapidly and adequately to environmental changes. Symbiotic bacteria play an essential role in the soil environment from both ecological and economical point of view, since these bacteria provide Fabaceae plants (legumes) with large amounts of accessible nitrogen as a result of symbiotic interactions (i.e., rhizobia present within the nodule reduce atmospheric dinitrogen (N2) to ammonia, which can be utilized by plants). Because of its restricted availability in the soil, nitrogen is one of the most limiting factors for plant growth. In spite of its high content in the atmosphere, plants are not able to assimilate it directly in the N2 form. During symbiosis, rhizobia infect host root and trigger the development of specific plant organ, the nodule. The aim of root nodule formation is to ensure a microaerobic environment, which is essential for proper activity of nitrogenase, i.e., a key enzyme facilitating N2 fixation. To adapt to various lifestyles and environmental stresses, rhizobia have developed several regulatory mechanisms, e.g., reversible phosphorylation. This key mechanism regulates many processes in both prokaryotic and eukaryotic cells. In microorganisms, signal transduction includes two-component systems (TCSs), which involve membrane sensor histidine kinases (HKs) and cognate DNA-binding response regulators (RRs). Furthermore, regulatory mechanisms based on phosphoenolopyruvate-dependent phosphotranspherase systems (PTSs), as well as alternative regulatory pathways controlled by Hanks-type serine/threonine kinases (STKs) and serine/threonine phosphatases (STPs) play an important role in regulation of many cellular processes in both free-living bacteria and during symbiosis with the host plant (e.g., growth and cell division, envelope biogenesis, biofilm formation, response to stress conditions, and regulation of metabolism). In this review, we summarize the current knowledge of phosphorylation systems in symbiotic nitrogen-fixing bacteria, and their role in the physiology of rhizobial cells and adaptation to various environmental conditions.
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Affiliation(s)
- Paulina Lipa
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Sklodowska University Lublin, Lublin, Poland
| | - Monika Janczarek
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Sklodowska University Lublin, Lublin, Poland
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Patron K, Gilot P, Rong V, Hiron A, Mereghetti L, Camiade E. Inductors and regulatory properties of the genomic island-associatedfru2metabolic operon ofStreptococcus agalactiae. Mol Microbiol 2016; 103:678-697. [DOI: 10.1111/mmi.13581] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Kévin Patron
- Bactéries et Risque Materno-Foetal, UMR1282 Infectiologie et Santé Publique, Université François Rabelais, INRA; Tours F-37032 France
| | - Philippe Gilot
- Bactéries et Risque Materno-Foetal, UMR1282 Infectiologie et Santé Publique, Université François Rabelais, INRA; Tours F-37032 France
| | - Vanessa Rong
- Bactéries et Risque Materno-Foetal, UMR1282 Infectiologie et Santé Publique, Université François Rabelais, INRA; Tours F-37032 France
| | - Aurélia Hiron
- Bactéries et Risque Materno-Foetal, UMR1282 Infectiologie et Santé Publique, Université François Rabelais, INRA; Tours F-37032 France
| | - Laurent Mereghetti
- Bactéries et Risque Materno-Foetal, UMR1282 Infectiologie et Santé Publique, Université François Rabelais, INRA; Tours F-37032 France
- Service de Bactériologie-Virologie-Hygiène; Centre Hospitalier Universitaire de Tours; Tours F-37044 France
| | - Emilie Camiade
- Bactéries et Risque Materno-Foetal, UMR1282 Infectiologie et Santé Publique, Université François Rabelais, INRA; Tours F-37032 France
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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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The bacterial phosphoenolpyruvate:carbohydrate phosphotransferase system: regulation by protein phosphorylation and phosphorylation-dependent protein-protein interactions. Microbiol Mol Biol Rev 2015; 78:231-56. [PMID: 24847021 DOI: 10.1128/mmbr.00001-14] [Citation(s) in RCA: 277] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The bacterial phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) carries out both catalytic and regulatory functions. It catalyzes the transport and phosphorylation of a variety of sugars and sugar derivatives but also carries out numerous regulatory functions related to carbon, nitrogen, and phosphate metabolism, to chemotaxis, to potassium transport, and to the virulence of certain pathogens. For these different regulatory processes, the signal is provided by the phosphorylation state of the PTS components, which varies according to the availability of PTS substrates and the metabolic state of the cell. PEP acts as phosphoryl donor for enzyme I (EI), which, together with HPr and one of several EIIA and EIIB pairs, forms a phosphorylation cascade which allows phosphorylation of the cognate carbohydrate bound to the membrane-spanning EIIC. HPr of firmicutes and numerous proteobacteria is also phosphorylated in an ATP-dependent reaction catalyzed by the bifunctional HPr kinase/phosphorylase. PTS-mediated regulatory mechanisms are based either on direct phosphorylation of the target protein or on phosphorylation-dependent interactions. For regulation by PTS-mediated phosphorylation, the target proteins either acquired a PTS domain by fusing it to their N or C termini or integrated a specific, conserved PTS regulation domain (PRD) or, alternatively, developed their own specific sites for PTS-mediated phosphorylation. Protein-protein interactions can occur with either phosphorylated or unphosphorylated PTS components and can either stimulate or inhibit the function of the target proteins. This large variety of signal transduction mechanisms allows the PTS to regulate numerous proteins and to form a vast regulatory network responding to the phosphorylation state of various PTS components.
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Lee J, Park YH, Kim YR, Seok YJ, Lee CR. Dephosphorylated NPr is involved in an envelope stress response of Escherichia coli. MICROBIOLOGY-SGM 2015; 161:1113-1123. [PMID: 25701731 PMCID: PMC4635465 DOI: 10.1099/mic.0.000056] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/10/2015] [Indexed: 01/20/2023]
Abstract
Besides the canonical phosphoenolpyruvate-dependent phosphotransferase system (PTS) for carbohydrate transport, most Proteobacteria possess the so-called nitrogen PTS (PTSNtr) that transfers a phosphate group from phosphoenolpyruvate (PEP) over enzyme INtr (EINtr) and NPr to enzyme IIANtr (EIIANtr). The PTSNtr lacks membrane-bound components and functions exclusively in a regulatory capacity. While EIIANtr has been implicated in a variety of cellular processes such as potassium homeostasis, phosphate starvation, nitrogen metabolism, carbon metabolism, regulation of ABC transporters and poly-β-hydroxybutyrate accumulation in many Proteobacteria, the only identified role of NPr is the regulation of biosynthesis of the lipopolysaccharide (LPS) layer by direct interaction with LpxD in Escherichia coli. In this study, we provide another phenotype related to NPr. Several lines of evidence demonstrate that E. coli strains with increased levels of dephosphorylated NPr are sensitive to envelope stresses, such as osmotic, ethanol and SDS stresses, and these phenotypes are independent of LpxD. The C-terminal region of NPr plays an important role in sensitivity to envelope stresses. Thus, our data suggest that the dephospho-form of NPr affects adaptation to envelope stresses through a C-terminus-dependent mechanism.
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Affiliation(s)
- Jaeseop Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido 449-728, Republic of Korea
| | - Young-Ha Park
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Yeon-Ran Kim
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Yeong-Jae Seok
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 151-742, Republic of Korea.,Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido 449-728, Republic of Korea
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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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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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Untiet V, Karunakaran R, Krämer M, Poole P, Priefer U, Prell J. ABC transport is inactivated by the PTS(Ntr) under potassium limitation in Rhizobium leguminosarum 3841. PLoS One 2013; 8:e64682. [PMID: 23724079 PMCID: PMC3665714 DOI: 10.1371/journal.pone.0064682] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 04/17/2013] [Indexed: 11/29/2022] Open
Abstract
PTSNtr is a regulatory phosphotransferase system in many bacteria. Mutation of the PTSNtr enzymes causes pleiotropic growth phenotypes, dry colony morphology and a posttranslational inactivation of ABC transporters in Rhizobium leguminosarum 3841. The PTSNtr proteins EINtr and 2 copies of EIIANtr have been described previously. Here we identify the intermediate phosphocarrier protein NPr and show its phosphorylation by EINtrin vitro. Furthermore we demonstrate that phosphorylation of EINtr and NPr is required for ABC transport activation and that the N-terminal GAF domain of EINtr is not required for autophosphorylation. Previous studies have shown that non-phosphorylated EIIANtr is able to modulate the transcriptional activation of the high affinity potassium transporter KdpABC. In R. leguminosarum 3841 kdpABC expression strictly depends on EIIANtr. Here we demonstrate that under strong potassium limitation ABC transport is inactivated, presumably by non-phosphorylated EIIANtr. This is to our knowledge the first report where PTSNtr dictates an essential cellular function. This is achieved by the inverse regulation of two important ATP dependent transporter classes.
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Affiliation(s)
| | | | | | - Philip Poole
- Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Jürgen Prell
- Soil Ecology, RWTH Aachen, Aachen, Germany
- * E-mail:
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Erni B. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS): an interface between energy and signal transduction. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2012. [DOI: 10.1007/s13738-012-0185-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Prell J, Mulley G, Haufe F, White JP, Williams A, Karunakaran R, Downie JA, Poole PS. The PTS(Ntr) system globally regulates ATP-dependent transporters in Rhizobium leguminosarum. Mol Microbiol 2012; 84:117-29. [PMID: 22340847 DOI: 10.1111/j.1365-2958.2012.08014.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mutation of ptsP encoding EI(Ntr) of the PTS(Ntr) system in Rhizobium leguminosarum strain Rlv3841 caused a pleiotropic phenotype as observed with many bacteria. The mutant formed dry colonies and grew poorly on organic nitrogen or dicarboxylates. Most strikingly the ptsP mutant had low activity of a broad range of ATP-dependent ABC transporters. This lack of activation, which occurred post-translationally, may explain many of the pleiotropic effects. In contrast proton-coupled transport systems were not inhibited in a ptsP mutant. Regulation by PtsP also involves two copies of ptsN that code for EIIA(Ntr) , resulting in a phosphorylation cascade. As in Escherichia coli, the Rlv3841 PTS(Ntr) system also regulates K(+) homeostasis by transcriptional activation of the high-affinity ATP-dependent K(+) transporter KdpABC. This involves direct interaction of a two-component sensor regulator pair KdpDE with unphosphorylated EIIA(Ntr) . Critically, ptsP mutants, which cannot phosphorylate PtsN1 or PtsN2, had a fully activated KdpABC transporter. This is the opposite pattern from that observed with ABC transporters which apparently require phosphorylation of PtsN. These results suggest that ATP-dependent transport might be regulated via PTS(Ntr) responding to the cellular energy charge. ABC transport may be inactivated at low energy charge, conserving ATP for essential processes including K(+) homeostasis.
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Affiliation(s)
- J Prell
- Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Mulley G, White JP, Karunakaran R, Prell J, Bourdes A, Bunnewell S, Hill L, Poole PS. Mutation of GOGAT prevents pea bacteroid formation and N2 fixation by globally downregulating transport of organic nitrogen sources. Mol Microbiol 2011; 80:149-67. [PMID: 21276099 DOI: 10.1111/j.1365-2958.2011.07565.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mutation of gltB (encoding glutamate oxoglutarate amidotransferase or GOGAT) in RU2307 increased the intracellular Gln:Glu ratio and inhibited amino acid transport via Aap and Bra. The mechanism probably involves global post-translational inhibition independent of Ntr. Transport was separately restored by increased gene expression of Aap or heterologous transporters. Likewise, second site suppressor mutations in the RNA chaperone Hfq elevated transport by Aap and Bra by increasing mRNA levels. Microarrays showed Hfq regulates 34 ABC transporter genes, including aap, bra and opp. The genes coding for integral membrane proteins and ABC subunits aapQMP braDEFGC were more strongly elevated in the hfq mutants than solute-binding proteins (aapJ braC). aapQMP and braDEFG are immediately downstream of stem-loops, indicating Hfq attenuates downstream translation and stability of mRNA, explaining differential expression of ABC genes. RU2307 nodulated peas and bacteria grew down infection threads, but bacteroid development was arrested and N(2) was not fixed. This probably results from an inability to synthesize or transport amino acids. However, GOGAT and GOGAT/AldA double mutants carrying suppressor mutations that increased amino acid uptake fixed N(2) on pea plants. Thus de novo ammonium assimilation into amino acids is unnecessary in bacteroids demonstrating sufficient amino acids are supplied by plants.
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Affiliation(s)
- G Mulley
- Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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The interplay of the EIIA(Ntr) component of the nitrogen-related phosphotransferase system (PTS(Ntr)) of Pseudomonas putida with pyruvate dehydrogenase. Biochim Biophys Acta Gen Subj 2011; 1810:995-1005. [PMID: 21236318 DOI: 10.1016/j.bbagen.2011.01.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Revised: 01/05/2011] [Accepted: 01/06/2011] [Indexed: 11/20/2022]
Abstract
BACKGROUND Pseudomonas putida KT2440 is endowed with a variant of the phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS(Ntr)), which is not related to sugar transport but believed to rule the metabolic balance of carbon vs. nitrogen. The metabolic targets of such a system are largely unknown. METHODS Dielectric breakdown of P. putida cells grown in rich medium revealed the presence of forms of the EIIA(Ntr) (PtsN) component of PTS(Ntr), which were strongly associated to other cytoplasmic proteins. To investigate such intracellular partners of EIIA(Ntr), a soluble protein extract of bacteria bearing an E epitope tagged version of PtsN was immunoprecipitated with a monoclonal anti-E antibody and the pulled-down proteins identified by mass spectrometry. RESULTS The E1 subunit of the pyruvate dehydrogenase (PDH) complex, the product of the aceE gene, was identified as a major interaction partner of EIIA(Ntr). To examine the effect of EIIA(Ntr) on PDH, the enzyme activity was measured in extracts of isogenic ptsN(+)/ptsN(-)P. putida strains and the role of phosphorylation was determined. Expression of PtsN and AceE proteins fused to different fluorescent moieties and confocal laser microscopy indicated a significant co-localization of the two proteins in the bacterial cytoplasm. CONCLUSION EIIA(Ntr) down-regulates PDH activity. Both genetic and biochemical evidence revealed that the non-phosphorylated form of PtsN is the protein species that inhibits PDH. GENERAL SIGNIFICANCE EIIA(Ntr) takes part in the node of C metabolism that checks the flux of carbon from carbohydrates into the Krebs cycle by means of direct protein-protein interactions with AceE. This type of control might connect metabolism to many other cellular functions. This article is part of a Special Issue entitled: Systems Biology of Microorganisms.
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Regulatory roles of the bacterial nitrogen-related phosphotransferase system. Trends Microbiol 2010; 18:205-14. [DOI: 10.1016/j.tim.2010.02.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 01/27/2010] [Accepted: 02/08/2010] [Indexed: 11/20/2022]
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The phosphoenolpyruvate phosphotransferase system regulates Vibrio cholerae biofilm formation through multiple independent pathways. J Bacteriol 2010; 192:3055-67. [PMID: 20400550 DOI: 10.1128/jb.00213-10] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The bacterial phosphoenolpyruvate phosphotransferase system (PTS) is a highly conserved phosphotransfer cascade that participates in the transport and phosphorylation of selected carbohydrates and modulates many cellular functions in response to carbohydrate availability. It plays a role in the virulence of many bacterial pathogens. Components of the carbohydrate-specific PTS include the general cytoplasmic components enzyme I (EI) and histidine protein (HPr), the sugar-specific cytoplasmic components enzymes IIA (EIIA) and IIB (EIIB), and the sugar-specific membrane-associated multisubunit components enzymes IIC (EIIC) and IID (EIID). Many bacterial genomes also encode a parallel PTS pathway that includes the EI homolog EI(Ntr), the HPr homolog NPr, and the EIIA homolog EIIA(Ntr). This pathway is thought to be nitrogen specific because of the proximity of the genes encoding this pathway to the genes encoding the nitrogen-specific sigma factor sigma(54). We previously reported that phosphorylation of HPr and FPr by EI represses Vibrio cholerae biofilm formation in minimal medium supplemented with glucose or pyruvate. Here we report two additional PTS-based biofilm regulatory pathways that are active in LB broth but not in minimal medium. These pathways involve the glucose-specific enzyme EIIA (EIIA(Glc)) and two nitrogen-specific EIIA homologs, EIIA(Ntr1) and EIIA(Ntr2). The presence of multiple, independent biofilm regulatory circuits in the PTS supports the hypothesis that the PTS and PTS-dependent substrates have a central role in sensing environments suitable for a surface-associated existence.
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Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways. Microbiol Mol Biol Rev 2010; 73:594-651. [PMID: 19946135 DOI: 10.1128/mmbr.00024-09] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aspartokinase (Ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. Lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ASK network or from alternative pathways. Ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. Two subhomology divisions, ASK(alpha) and ASK(beta), have been recognized. The ASK(alpha) subhomology division is the most ancient, being widely distributed throughout the Archaea and Eukarya and in some Bacteria. Within an indel region of about 75 amino acids near the N terminus, ASK(beta) sequences differ from ASK(alpha) sequences by the possession of a proposed ancient deletion. ASK(beta) sequences are present in most Bacteria and usually exhibit an in-frame internal translational start site that can generate a small Ask subunit that is identical to the C-terminal portion of the larger subunit of a heterodimeric unit. Particularly novel are ask genes embedded in gene contexts that imply specialization for ectoine (osmotic agent) or aromatic amino acids. The cohesion group approach is well suited for the easy recognition of relatively recent lateral gene transfer (LGT) events, and many examples of these are described. Given the current density of genome representation for Proteobacteria, it is possible to reconstruct more ancient landmark LGT events. Thus, a plausible scenario in which the three well-studied and iconic Ask homologs of Escherichia coli are not within the vertical genealogy of Gammaproteobacteria, but rather originated via LGT from a Bacteroidetes donor, is supported.
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Cases I, Velázquez F, de Lorenzo V. The ancestral role of the phosphoenolpyruvate–carbohydrate phosphotransferase system (PTS) as exposed by comparative genomics. Res Microbiol 2007; 158:666-70. [PMID: 17913467 DOI: 10.1016/j.resmic.2007.08.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Revised: 08/01/2007] [Accepted: 08/02/2007] [Indexed: 11/19/2022]
Abstract
The normal role of the phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS) is phosphorylation and subsequent uptake of specific sugars. However, analysis of the distribution of PTS proteins in 206 genomes covering major bacterial groups indicates that the conventional function of PTS proteins as devices for carbohydrate phosphorylation and transport is an exception found in Enterobacteriacea, Vibrionales and Firmicutes, rather than a rule for all bacteria. Instead, available evidence suggests that a core set of C-responsive phosphotransferases have been evolutionarily drafted towards diversity of regulatory functions in response inter alia to the global economy of the C and N pools.
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Affiliation(s)
- Ildefonso Cases
- Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid 28049, Spain.
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Velázquez F, Pflüger K, Cases I, De Eugenio LI, de Lorenzo V. The phosphotransferase system formed by PtsP, PtsO, and PtsN proteins controls production of polyhydroxyalkanoates in Pseudomonas putida. J Bacteriol 2007; 189:4529-33. [PMID: 17416664 PMCID: PMC1913348 DOI: 10.1128/jb.00033-07] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome of Pseudomonas putida KT2440 encodes five proteins of the phosphoenolpyruvate-carbohydrate phosphotransferase system. Two of these (FruA and FruB) form a dedicated system for fructose intake, while enzyme I(Ntr) (EI(Ntr); encoded by ptsP), NPr (ptsO), and EII(Ntr) (ptsN) act in concert to control the intracellular accumulation of polyhydroxyalkanoates, a typical product of carbon overflow.
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Affiliation(s)
- Francisco Velázquez
- Centro Nacional de Biotecnología-CSIC, Campus UAM-Cantoblanco, Madrid 28049, Spain
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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: 989] [Impact Index Per Article: 58.2] [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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Affiliation(s)
- Alan Peterkofsky
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, Bethesda, MD 20892-8017, USA.
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Mavrodi OV, Mavrodi DV, Weller DM, Thomashow LS. Role of ptsP, orfT, and sss recombinase genes in root colonization by Pseudomonas fluorescens Q8r1-96. Appl Environ Microbiol 2006; 72:7111-22. [PMID: 16936061 PMCID: PMC1636191 DOI: 10.1128/aem.01215-06] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas fluorescens Q8r1-96 produces 2,4-diacetylphloroglucinol (2,4-DAPG), a polyketide antibiotic that suppresses a wide variety of soilborne fungal pathogens, including Gaeumannomyces graminis var. tritici, which causes take-all disease of wheat. Strain Q8r1-96 is representative of the D-genotype of 2,4-DAPG producers, which are exceptional because of their ability to aggressively colonize and maintain large populations on the roots of host plants, including wheat, pea, and sugar beet. In this study, three genes, an sss recombinase gene, ptsP, and orfT, which are important in the interaction of Pseudomonas spp. with various hosts, were investigated to determine their contributions to the unusual colonization properties of strain Q8r1-96. The sss recombinase and ptsP genes influence global processes, including phenotypic plasticity and organic nitrogen utilization, respectively. The orfT gene contributes to the pathogenicity of Pseudomonas aeruginosa in plants and animals and is conserved among saprophytic rhizosphere pseudomonads, but its function is unknown. Clones containing these genes were identified in a Q8r1-96 genomic library, sequenced, and used to construct gene replacement mutants of Q8r1-96. Mutants were characterized to determine their 2,4-DAPG production, motility, fluorescence, colony morphology, exoprotease and hydrogen cyanide (HCN) production, carbon and nitrogen utilization, and ability to colonize the rhizosphere of wheat grown in natural soil. The ptsP mutant was impaired in wheat root colonization, whereas mutants with mutations in the sss recombinase gene and orfT were not. However, all three mutants were less competitive than wild-type P. fluorescens Q8r1-96 in the wheat rhizosphere when they were introduced into the soil by paired inoculation with the parental strain.
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Affiliation(s)
- Olga V Mavrodi
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
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Xu H, Lin W, Xia H, Xu S, Li Y, Yao H, Bai F, Zhang X, Bai Y, Saris P, Qiao M. Influence of ptsP gene on pyocyanin production in Pseudomonas aeruginosa. FEMS Microbiol Lett 2006; 253:103-9. [PMID: 16239083 DOI: 10.1016/j.femsle.2005.09.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2005] [Revised: 06/01/2005] [Accepted: 09/15/2005] [Indexed: 11/25/2022] Open
Abstract
A pyocyanin overproducer with insertional inactivation of ptsP gene was isolated from a mini-Mu insertion library in Pseudomonas aeruginosa PA68. The mutation was complemented by a functional ptsP gene in trans. The pyocyanin-overproducing phenotype was also found in a ptsP mutant constructed by gene replacement in the P. aeruginosa PAO1 strain. Reporter plasmids with P(qscR)-lacZ, P(lasI)-lacZ and P(rhlI)-lacZ were constructed and the beta-galactosidase activity in the ptsP mutant/wild-type background was measured. The results showed that lack of Enzyme I(Ntr) (EI(Ntr), encoded by ptsP) decreased transcription from the P(qscR) promoter and increased the activity of the P(lasI) and P(rhlI) promoters. Normally, QscR represses the quorum-sensing LasR-LasI and RhlR-RhlI systems involved in pyocyanin regulation. Our results showed that the ptsP gene has an important role in the regulation of pyocyanin production and that two quorum-sensing systems and their repressor QscR are involved in this regulation.
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Affiliation(s)
- Haijin Xu
- Tianjin Key Laboratory of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
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Barabote RD, Saier MH. Comparative genomic analyses of the bacterial phosphotransferase system. Microbiol Mol Biol Rev 2005; 69:608-34. [PMID: 16339738 PMCID: PMC1306802 DOI: 10.1128/mmbr.69.4.608-634.2005] [Citation(s) in RCA: 205] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (PTS). These included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. Homologues of PTS proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding PTS proteins has not occurred between the three domains of life. Of the 174 bacterial genomes (136 bacterial species) analyzed, 30 diverse species have no PTS homologues, and 29 species have cytoplasmic PTS phosphoryl transfer protein homologues but lack recognizable PTS permeases. These soluble homologues presumably function in regulation. The remaining 77 species possess all PTS proteins required for the transport and phosphorylation of at least one sugar via the PTS. Up to 3.2% of the genes in a bacterium encode PTS proteins. These homologues were analyzed for family association, range of protein types, domain organization, and organismal distribution. Different strains of a single bacterial species often possess strikingly different complements of PTS proteins. Types of PTS protein domain fusions were analyzed, showing that certain types of domain fusions are common, while others are rare or prohibited. Select PTS proteins were analyzed from different phylogenetic standpoints, showing that PTS protein phylogeny often differs from organismal phylogeny. The results document the frequent gain and loss of PTS protein-encoding genes and suggest that the lateral transfer of these genes within the bacterial domain has played an important role in bacterial evolution. Our studies provide insight into the development of complex multicomponent enzyme systems and lead to predictions regarding the types of protein-protein interactions that promote efficient PTS-mediated phosphoryl transfer.
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Affiliation(s)
- Ravi D Barabote
- Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116, USA
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Abstract
Nitrogen limitation in Escherichia coli controls the expression of about 100 genes of the nitrogen regulated (Ntr) response, including the ammonia-assimilating glutamine synthetase. Low intracellular glutamine controls the Ntr response through several regulators, whose activities are modulated by a variety of metabolites. Ntr proteins assimilate ammonia, scavenge nitrogen-containing compounds, and appear to integrate ammonia assimilation with other aspects of metabolism, such as polyamine metabolism and glutamate synthesis. The leucine-responsive regulatory protein (Lrp) controls the synthesis of glutamate synthase, which controls the Ntr response, presumably through its effect on intracellular glutamine. Some Ntr proteins inhibit the expression of some Lrp-activated genes. Guanosine tetraphosphate appears to control Lrp synthesis. In summary, a network of interacting global regulators that senses different aspects of metabolism integrates nitrogen assimilation with other metabolic processes.
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Affiliation(s)
- Larry Reitzer
- Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75080-0688, USA.
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O'Brian MR, Thöny-Meyer L. Biochemistry, regulation and genomics of haem biosynthesis in prokaryotes. Adv Microb Physiol 2002; 46:257-318. [PMID: 12073655 DOI: 10.1016/s0065-2911(02)46006-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Haems are involved in many cellular processes in prokaryotes and eukaryotes. The biosynthetic pathway leading to haem formation is, with few exceptions, well-conserved, and is controlled in accordance with cellular function. Here, we review the biosynthesis of haem and its regulation in prokaryotes. In addition, we focus on a modification of haem for cytochrome c biogenesis, a complex process that entails both transport between cellular compartments and a specific thioether linkage between the haem moiety and the apoprotein. Finally, a whole genome analysis from 63 prokaryotes indicates intriguing exceptions to the universality of the haem biosynthetic pathway and helps define new frontiers for future study.
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Affiliation(s)
- Mark R O'Brian
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14214, USA
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