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Gellatly SL, Bains M, Breidenstein EBM, Strehmel J, Reffuveille F, Taylor PK, Yeung ATY, Overhage J, Hancock REW. Novel roles for two-component regulatory systems in cytotoxicity and virulence-related properties in Pseudomonas aeruginosa. AIMS Microbiol 2018; 4:173-191. [PMID: 31294209 PMCID: PMC6605022 DOI: 10.3934/microbiol.2018.1.173] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/26/2018] [Indexed: 11/18/2022] Open
Abstract
The rapid adaptation of the opportunistic bacterial pathogen Pseudomonas aeruginosa to various growth modes and environmental conditions is controlled in part through diverse two-component regulatory systems. Some of these systems are well studied, but the majority are poorly characterized, even though it is likely that several of these systems contribute to virulence. Here, we screened all available strain PA14 mutants in 50 sensor kinases, 50 response regulators and 5 hybrid sensor/regulators, for contributions to cytotoxicity against cultured human bronchial epithelial cells, as assessed by the release of cytosolic lactate dehydrogenase. This enabled the identification of 8 response regulators and 3 sensor kinases that caused substantial decreases in cytotoxicity, and 5 response regulators and 8 sensor kinases that significantly increased cytotoxicity by 15-58% or more. These regulators were additionally involved in motility, adherence, type 3 secretion, production of cytotoxins, and the development of biofilms. Here we investigated in more detail the roles of FleSR, PilSR and WspR. Not all cognate pairs contributed to cytotoxicity (e.g. PhoPQ, PilSR) in the same way and some differences could be detected between the same mutants in PAO1 and PA14 strain backgrounds (e.g. FleSR, PhoPQ). This study highlights the potential importance of these regulators and their downstream targets on pathogenesis and demonstrates that cytotoxicity can be regulated by several systems and that their contributions are partly dependent on strain background.
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Affiliation(s)
- Shaan L Gellatly
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Manjeet Bains
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Elena B M Breidenstein
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Janine Strehmel
- Microbiology of Natural and Technical Interfaces Department, Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Fany Reffuveille
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Patrick K Taylor
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Amy T Y Yeung
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Joerg Overhage
- Microbiology of Natural and Technical Interfaces Department, Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Robert E W Hancock
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
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Geddes BA, Oresnik IJ. The Mechanism of Symbiotic Nitrogen Fixation. ADVANCES IN ENVIRONMENTAL MICROBIOLOGY 2016. [DOI: 10.1007/978-3-319-28068-4_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Tatke G, Kumari H, Silva-Herzog E, Ramirez L, Mathee K. Pseudomonas aeruginosa MifS-MifR Two-Component System Is Specific for α-Ketoglutarate Utilization. PLoS One 2015; 10:e0129629. [PMID: 26114434 PMCID: PMC4482717 DOI: 10.1371/journal.pone.0129629] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/10/2015] [Indexed: 12/31/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative, metabolically versatile opportunistic pathogen that elaborates a multitude of virulence factors, and is extraordinarily resistant to a gamut of clinically significant antibiotics. This ability, in part, is mediated by two-component regulatory systems (TCS) that play a crucial role in modulating virulence mechanisms and metabolism. MifS (PA5512) and MifR (PA5511) form one such TCS implicated in biofilm formation. MifS is a sensor kinase whereas MifR belongs to the NtrC superfamily of transcriptional regulators that interact with RpoN (σ54). In this study we demonstrate that the mifS and mifR genes form a two-gene operon. The close proximity of mifSR operon to poxB (PA5514) encoding a ß-lactamase hinted at the role of MifSR TCS in regulating antibiotic resistance. To better understand this TCS, clean in-frame deletions were made in P. aeruginosa PAO1 creating PAO∆mifS, PAO∆mifR and PAO∆mifSR. The loss of mifSR had no effect on the antibiotic resistance profile. Phenotypic microarray (BioLOG) analyses of PAO∆mifS and PAO∆mifR revealed that these mutants were unable to utilize C5-dicarboxylate α-ketoglutarate (α-KG), a key tricarboxylic acid cycle intermediate. This finding was confirmed using growth analyses, and the defect can be rescued by mifR or mifSR expressed in trans. These mifSR mutants were able to utilize all the other TCA cycle intermediates (citrate, succinate, fumarate, oxaloacetate or malate) and sugars (glucose or sucrose) except α-KG as the sole carbon source. We confirmed that the mifSR mutants have functional dehydrogenase complex suggesting a possible defect in α-KG transport. The inability of the mutants to utilize α-KG was rescued by expressing PA5530, encoding C5-dicarboxylate transporter, under a regulatable promoter. In addition, we demonstrate that besides MifSR and PA5530, α-KG utilization requires functional RpoN. These data clearly suggests that P. aeruginosa MifSR TCS is involved in sensing α-KG and regulating its transport and subsequent metabolism.
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Affiliation(s)
- Gorakh Tatke
- Department of Biological Sciences, College of Arts & Sciences, Florida International University, Miami, Florida, United States of America
- Department of Molecular Microbiology and Infectious Diseases, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
| | - Hansi Kumari
- Department of Molecular Microbiology and Infectious Diseases, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
| | - Eugenia Silva-Herzog
- Department of Molecular Microbiology and Infectious Diseases, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
| | - Lourdes Ramirez
- Department of Biological Sciences, College of Arts & Sciences, Florida International University, Miami, Florida, United States of America
| | - Kalai Mathee
- Department of Molecular Microbiology and Infectious Diseases, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
- * E-mail:
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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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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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Gautam US, Jajoo A, Singh A, Chakrabartty PK, Das SK. Characterization of an rpoN mutant of Mesorhizobium ciceri. J Appl Microbiol 2008; 103:1798-807. [PMID: 17953590 DOI: 10.1111/j.1365-2672.2007.03432.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To study the genetic basis of C(4)-dicarboxylate transport (Dct) in relation to symbiotic nitrogen fixation in Mesorhizobium ciceri. METHODS AND RESULTS A Tn5-induced mutant strain (TL16) of M. ciceri, unable to grow on C(4)-dicarboxylates, was isolated from the wild-type strain TAL 620. The mutant lacked activities of the enzymes, which use C(4)-dicarboxylates as substrate. The sequencing of the 3.2kb EcoRI fragment, which was the site of Tn5 insertion, revealed three complete and two partial open reading frames. In the mutant, Tn5 interrupted the rpoN gene, of which only one copy was there. Complementation and biochemical studies suggest that the M. ciceri rpoN activity is required for C(4)-Dct, maturation of bacteroids and symbiotic nitrogen fixation. The fine structure of the ineffective nodules produced by TL16 on Cicer arietinum L changed in comparison with those produced by the wild type. CONCLUSIONS The mutant strain TL16 suffered a disruption in the rpoN gene. Only one copy of rpoN gene is present in M. ciceri. The mutation abolishes Dct activity. It additionally abolishes the symbiotic nitrogen fixation activity of the bacteroids in the nodules. SIGNIFICANCE AND IMPACT OF THE STUDY This first document in M. ciceri shows that a functional rpoN gene is essential for the transport of dicarboxylic acids and symbiotic nitrogen fixation.
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Affiliation(s)
- U S Gautam
- National Research Center on Plant Biotechnology, Indian Agricultural Research Institute, Pusa, New Delhi, India
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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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Park S, Zhang H, Jones AD, Nixon BT. Biochemical evidence for multiple dimeric states of the Sinorhizobium meliloti DctD receiver domain. Biochemistry 2002; 41:10934-41. [PMID: 12206664 DOI: 10.1021/bi0260031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
X-ray crystal structures suggest very different dimeric states for the inactive and active forms of the two-component receiver domain of Sinorhizobium meliloti DctD, a sigma(54)-dependent AAA+ ATPase. Moreover, the receiver domain in crystals grown from unphosphorylated protein is refractory to phosphorylation whereas solution protein is fully phosphorylatable, and equilibrium analytical ultracentrifugation data are consistent with solution dimers for both phosphorylated and unphosphorylated forms of the protein. Here we report biochemical data consistent with the presence of multiple dimeric conformations in the inactive and active states, and evidence for significant change in the dimeric state upon activation by phosphorylation or binding of Mg(2+) and BeF(3)(-).
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Affiliation(s)
- Sungdae Park
- Department of Biochemistry and Molecular Biology and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Kanner BI, Borre L. The dual-function glutamate transporters: structure and molecular characterisation of the substrate-binding sites. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1555:92-5. [PMID: 12206897 DOI: 10.1016/s0005-2728(02)00260-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Glutamate transporters are essential for terminating synaptic excitation and for maintaining extracellular glutamate concentrations below neurotoxic levels. These transporters also mediate a thermodynamically uncoupled chloride flux, activated by two of the molecules they transport, sodium and glutamate. Five eukaryotic glutamate transporters have been cloned and identified. They exhibit approximately 50% identity and this homology is even greater at the carboxyl terminal half, which is predicted to have an unusual topology. Determination of the topology shows that the carboxyl terminal part contains several transmembrane domains separated by two reentrant loops that are in close proximity to each other. We have identified several conserved amino acid residues in the carboxyl terminal half that play crucial roles in the interaction of the transporter with its substrates: sodium, potassium and glutamate. The conformation of the transporter gating the anion conductance is different from that during substrate translocation. However, there exists a dynamic equilibrium between these conformations.
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Affiliation(s)
- B I Kanner
- Department of Biochemistry, Hadassah Medical School, The Hebrew University, Jerusalem, Israel.
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Dombrecht B, Marchal K, Vanderleyden J, Michiels J. Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales. Genome Biol 2002; 3:RESEARCH0076. [PMID: 12537565 PMCID: PMC151178 DOI: 10.1186/gb-2002-3-12-research0076] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2002] [Revised: 09/16/2002] [Accepted: 10/18/2002] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND In the rhizobia, a group of symbiotic Gram-negative soil bacteria, RpoN (sigma54, sigmaN, NtrA) is best known as the sigma factor enabling transcription of the nitrogen fixation genes. Recent reports, however, demonstrate the involvement of RpoN in other symbiotic functions, although no large-scale effort has yet been undertaken to unravel the RpoN-regulon in rhizobia. We screened two complete rhizobial genomes (Mesorhizobium loti, Sinorhizobium meliloti) and four symbiotic regions (Rhizobium etli, Rhizobium sp. NGR234, Bradyrhizobium japonicum, M. loti) for the presence of the highly conserved RpoN-binding sites. A comparison was also made with two closely related non-symbiotic members of the Rhizobiales (Agrobacterium tumefaciens, Brucella melitensis). RESULTS A highly specific weight-matrix-based screening method was applied to predict members of the RpoN-regulon, which were stored in a highly annotated and manually curated dataset. Possible enhancer-binding proteins (EBPs) controlling the expression of RpoN-dependent genes were predicted with a profile hidden Markov model. CONCLUSIONS The methodology used to predict RpoN-binding sites proved highly effective as nearly all known RpoN-controlled genes were identified. In addition, many new RpoN-dependent functions were found. The dependency of several of these diverse functions on RpoN seems species-specific. Around 30% of the identified genes are hypothetical. Rhizobia appear to have recruited RpoN for symbiotic processes, whereas the role of RpoN in A. tumefaciens and B. melitensis remains largely to be elucidated. All species screened possess at least one uncharacterized EBP as well as the usual ones. Lastly, RpoN could significantly broaden its working range by direct interfering with the binding of regulatory proteins to the promoter DNA.
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Affiliation(s)
- Bruno Dombrecht
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium
| | - Kathleen Marchal
- ESAT-SCD, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium
| | - Jos Vanderleyden
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium
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Phalip V, Li JH, Zhang CC. HstK, a cyanobacterial protein with both a serine/threonine kinase domain and a histidine kinase domain: implication for the mechanism of signal transduction. Biochem J 2001; 360:639-44. [PMID: 11736654 PMCID: PMC1222267 DOI: 10.1042/0264-6021:3600639] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Two distinct families of protein kinases are involved in signal transduction: Ser, Thr and Tyr kinases, which are predominantly found among eukaryotes, and His kinases, as part of bacterial two-component signalling systems. Genetic studies in Arabidopsis and Saccharomyces have demonstrated that bacterial-type two-component systems may act upstream of Ser/Thr kinases in the same signalling pathway, but how this coupling is accomplished remains unclear. In the present study, we report the characterization of a protein kinase, HstK, from the N(2)-fixing cyanobacterium Anabaena sp. PCC 7120, that possesses both a Ser/Thr kinase domain and a His kinase domain. Proteins with a structural architecture similar to that of HstK can be found in the eukaryote, Schizosaccharomyces pombe, and the bacterium, Rhodococcus sp. M5. HstK was present in cells grown with NH(4)(+) or N(2) as the nitrogen source, but was absent in cells grown with NO(3)(-). The hstK gene was inactivated and the mutant phenotype was characterized. The catalytic domain of the Ser/Thr kinase of HstK functionally replaced that of Hog1p, a well-characterized protein kinase required for the response to high osmolarity in the S. cerevisiae heterologous system. The unusual multidomain structure of HstK suggests that a two-component system could be directly coupled to Ser/Thr kinases in the same signal transduction pathway.
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Affiliation(s)
- V Phalip
- Unité d'Immunotechnologie et Microbiologie Moléculaire, Ecole Superieure de Biotechnologie de Strasbourg, Université Louis Pasteur de Strasbourg, Boulevard Sebastien Brandt, F-67400 Illkirch, France
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Nishijyo T, Haas D, Itoh Y. The CbrA-CbrB two-component regulatory system controls the utilization of multiple carbon and nitrogen sources in Pseudomonas aeruginosa. Mol Microbiol 2001; 40:917-31. [PMID: 11401699 DOI: 10.1046/j.1365-2958.2001.02435.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A novel two-component system, CbrA-CbrB, was discovered in Pseudomonas aeruginosa; cbrA and cbrB mutants of strain PAO were found to be unable to use several amino acids (such as arginine, histidine and proline), polyamines and agmatine as sole carbon and nitrogen sources. These mutants were also unable to use, or used poorly, many other carbon sources, including mannitol, glucose, pyruvate and citrate. A 7 kb EcoRI fragment carrying the cbrA and cbrB genes was cloned and sequenced. The cbrA and cbrB genes encode a sensor/histidine kinase (Mr 108 379, 983 residues) and a cognate response regulator (Mr 52 254, 478 residues) respectively. The amino-terminal half (490 residues) of CbrA appears to be a sensor membrane domain, as predicted by 12 possible transmembrane helices, whereas the carboxy-terminal part shares homology with the histidine kinases of the NtrB family. The CbrB response regulator shows similarity to the NtrC family members. Complementation and primer extension experiments indicated that cbrA and cbrB are transcribed from separate promoters. In cbrA or cbrB mutants, as well as in the allelic argR9901 and argR9902 mutants, the aot-argR operon was not induced by arginine, indicating an essential role for this two-component system in the expression of the ArgR-dependent catabolic pathways, including the aruCFGDB operon specifying the major aerobic arginine catabolic pathway. The histidine catabolic enzyme histidase was not expressed in cbrAB mutants, even in the presence of histidine. In contrast, proline dehydrogenase, responsible for proline utilization (Pru), was expressed in a cbrB mutant at a level comparable with that of the wild-type strain. When succinate or other C4-dicarboxylates were added to proline medium at 1 mM, the cbrB mutant was restored to a Pru+ phenotype. Such a succinate-dependent Pru+ property was almost abolished by 20 mM ammonia. In conclusion, the CbrA-CbrB system controls the expression of several catabolic pathways and, perhaps together with the NtrB-NtrC system, appears to ensure the intracellular carbon: nitrogen balance in P. aeruginosa.
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Affiliation(s)
- T Nishijyo
- Division of Applied Microbiology, National Food Research Institute, Ministry of Agriculture, Forestry and Fisheries, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8642, Japan
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Abstract
One of the paradigms of symbiotic nitrogen fixation has been that bacteroids reduce N2 to ammonium and secrete it without assimilation into amino acids. This has recently been challenged by work with soybeans showing that only alanine is excreted in 15N2 labelling experiments. Work with peas shows that the bacteroid nitrogen secretion products during in vitro experiments depend on the experimental conditions. There is a mixed secretion of both ammonium and alanine depending critically on the concentration of bacteroids and ammonium concentration. The pathway of alanine synthesis has been shown to be via alanine dehydrogenase, and mutation of this enzyme indicates that in planta there is likely to be mixed secretion of ammonium and alanine. Alanine synthesis directly links carbon catabolism and nitrogen assimilation in the bacteroid. There is now overwhelming evidence that the principal carbon sources of bacteroids are the C4-dicarboxylic acids. This is based on labelling and bacteroid respiration data, and mutation of both the dicarboxylic acid transport system (dct) and malic enzyme. L-malate is at a key bifurcation point in bacteroid metabolism, being oxidized to oxaloacetate and oxidatively decarboxylated to pyruvate. Pyruvate can be aminated to alanine or converted to acetyl-CoA where it either enters the TCA cycle by condensation with oxaloacetate or forms polyhydroxybutyrate (PHB). Thus regulation of carbon and nitrogen metabolism are strongly connected. Efficient catabolism of C4-dicarboxylates requires the balanced input and removal of intermediates from the TCA cycle. The TCA cycle in bacteroids may be limited by the redox state of NADH/NAD+ at the 2-ketoglutarate dehydrogenase complex, and a number of pathways may be involved in bypassing this block. These pathways include PHB synthesis, glutamate synthesis, glycogen synthesis, GABA shunt and glutamine cycling. Their operation may be critical in maintaining the optimum redox poise and carbon balance of the TCA cycle. They can also be considered to be overflow pathways since they act to remove or add electrons and carbon into the TCA cycle. Optimum operation of the TCA cycle has a major impact on nitrogen fixation.
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Affiliation(s)
- P Poole
- Division of Microbiology, School of Animal and Microbial Sciences, University of Reading, UK
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Wei Z, Kim JF, Beer SV. Regulation of hrp genes and type III protein secretion in Erwinia amylovora by HrpX/HrpY, a novel two-component system, and HrpS. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2000; 13:1251-62. [PMID: 11059492 DOI: 10.1094/mpmi.2000.13.11.1251] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Two novel regulatory components, hrpX and hrpY, of the hrp system of Erwinia amylovora were identified. The hrpXY operon is expressed in rich media, but its transcription is increased threefold by low pH, nutrient, and temperature levels--conditions that mimic the plant apoplast. hrpXY is autoregulated and directs the expression of hrpL; hrpL, in turn, activates transcription of other loci in the hrp gene cluster (Z.-M. Wei and S. V. Beer, J. Bacteriol. 177:6201-6210, 1995). The deduced amino -acid sequences of hrpX and hrpY are similar to bacterial two-component regulators including VsrA/VsrD of Pseudomonas (Ralstonia) solanacearum, DegS/DegU of Bacillus subtilis, and UhpB/UhpA and NarX/NarP, NarL of Escherichia coli. The N-terminal signal-input domain of HrpX contains PAS domain repeats. hrpS, located downstream of hrpXY, encodes a protein with homology to WtsA (HrpS) of Erwinia (Pantoea) stewartii, HrpR and HrpS of Pseudomonas syringae, and other delta54-dependent, enhancer-binding proteins. Transcription of hrpS also is induced under conditions that mimic the plant apoplast. However, hrpS is not autoregulated, and its expression is not affected by hrpXY. When hrpS or hrpL were provided on multicopy plasmids, both hrpX and hrpY mutants recovered the ability to elicit the hypersensitive reaction in tobacco. This confirms that hrpS and hrpL are not epistatic to hrpXY. A model of the regulatory cascades leading to the induction of the E. amylovora type III system is proposed.
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Affiliation(s)
- Z Wei
- Department of Plant Pathology, Cornell University, Ithaca, NY 14853, USA
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Barrios H, Valderrama B, Morett E. Compilation and analysis of sigma(54)-dependent promoter sequences. Nucleic Acids Res 1999; 27:4305-13. [PMID: 10536136 PMCID: PMC148710 DOI: 10.1093/nar/27.22.4305] [Citation(s) in RCA: 294] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Promoters recognized by the RNA-polymerase with the alternative sigma factor sigma(54) (Esigma54) are unique in having conserved positions around -24 and -12 nucleotides upstream from the transcriptional start site, instead of the typical -35 and -10 boxes. Here we compile 186 -24/-12 promoter sequences reported in the literature and generate an updated and extended consensus sequence. The use of the extended consensus increases the probability of identifying genuine -24/-12 promoters. The effect of several reported mutations at the -24/-12 elements on RNA-polymerase binding and promoter strength is discussed in the light of the updated consensus.
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Affiliation(s)
- H Barrios
- Departamento de Reconocimiento Molecular y Bioestructura, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62271, México
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16
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Sojda J, Gu B, Lee J, Hoover TR, Nixon BT. A rhizobial homolog of IHF stimulates transcription of dctA in Rhizobium leguminosarum but not in Sinorhizobium meliloti. Gene 1999; 238:489-500. [PMID: 10570977 DOI: 10.1016/s0378-1119(99)00366-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Sequence inspection identified several potential IHF binding sites adjacent to the Rhizobium leguminosarum dctA promoter. IHF protected the -30 to -76 region from DNase I digestion, but systematic error in quantitative assays suggested that this protein DNA interaction is complex. IHF stimulated DctD-mediated transcriptional activation from the R. leguminosarum dctA promoter both in vivo and in vitro. In contrast to R. leguminosarum dctA, the Sinorhizobium meliloti dctA promoter region was found to have a much weaker match to the consensus IHF binding site and a low affinity for IHF. Moreover, IHF had no effect on transcriptional activation from the S. meliloti dctA promoter in vitro. A base substitution was introduced into the IHF binding site of R. leguminosarum dtA that reduced the affinity of the promoter regulatory region for IHF by approximately 30-fold and resulted in an eight-fold decrease in transcriptional activation in both R. leguminosarum and S. meliloti. These data suggest that both rhizobial species have an IHF homolog that stimulates DctD-mediated transcriptional activation from the R. leguminosarum dctA promoter. Consistent with this hypothesis, a 12.5 kDa protein was identified from R. leguminosarum as a putative homolog of IHF subunit beta by immunoblotting and N-terminal sequence analysis.
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Affiliation(s)
- J Sojda
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park 16802, USA
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17
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Suominen L, Paulin L, Saano A, Saren AM, Tas E, Lindström K. Identification of nodulation promoter (nod-box) regions of Rhizobium galegae. FEMS Microbiol Lett 1999; 177:217-23. [PMID: 10474187 DOI: 10.1111/j.1574-6968.1999.tb13735.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
A hybridisation analysis of a genomic clone library of Rhizobium galegae HAMBI 1174 located four EcoRI fragments homologous to the nod-box promoter sequence of Sinorhizobium meliloti in two separate gene regions. Two of the five nod-boxes detected in the R. galegae genome were carried on a single cosmid clone, pRg30, upstream from the nodABCIJ and nodF genes, whereas the other three nod-boxes were carried on a different cosmid clone, pRg10. Hybridisations with various nod gene probes from S. meliloti and Rhizobium leguminosarum species detected a nodD homolog in pRg10. The sequence data obtained from regions adjacent to each nod-box in pRg10 confirmed the presence of a second nodD in the R. galegae genome and, in addition, revealed the presence of nodN, nodU, dctA nifH and nifQ-like genes in pRg10. Thus, by using a promoter-specific nod-box probe we could identify a new region carrying genes involved in nitrogen fixation and host specificity functions.
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Affiliation(s)
- L Suominen
- Department of Applied Chemistry and Microbiology, Helsinki University, Finland.
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18
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Kaspar S, Perozzo R, Reinelt S, Meyer M, Pfister K, Scapozza L, Bott M. The periplasmic domain of the histidine autokinase CitA functions as a highly specific citrate receptor. Mol Microbiol 1999; 33:858-72. [PMID: 10447894 DOI: 10.1046/j.1365-2958.1999.01536.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The two-component regulatory system CitA/CitB is essential for induction of the citrate fermentation genes in Klebsiella pneumoniae. CitA represents a membrane-bound sensor kinase consisting of a periplasmic domain flanked by two transmembrane helices, a linker domain and the conserved kinase or transmitter domain. A fusion protein (MalE-CitAC) composed of the maltose-binding protein and the CitA kinase domain (amino acids 327-547) showed constitutive autokinase activity and transferred the gamma-phosphate group of ATP to its cognate response regulator CitB. The autokinase activity of CitA was abolished by an H350L exchange, and phosphorylation of CitB was inhibited by a D56N exchange, indicating that H-350 and D-56 represent the phosphorylation sites of CitA and CitB respectively. In the presence of ATP, CitB-D56N formed a stable complex with MalE-CitAC. To analyse the sensory properties of CitA, the periplasmic domain (amino acids 45-176) was overproduced as a soluble, cytoplasmic protein with a C-terminally attached histidine tag (CitAPHis). Purified CitAPHis bound citrate, but none of the other tri- and dicarboxylates tested, with high affinity (KD approximately 5 microM at pH 7) in a 1:1 stoichiometry. As shown by isothermal titration calorimetry, the binding reaction was driven by the enthalpy change (DeltaH = -76.3 kJ mol-1), whereas the entropy change was opposed (-TDeltaS = + 46.3 kJ mol-1). The pH dependency of the binding reaction indicated that the dianionic form H-citrate2- is the citrate species recognized by CitAPHis. In the presence of Mg2+ ions, the dissociation constant increased significantly, suggesting that the Mg-citrate complex is not bound by CitAPHis. This work defines the periplasmic domain of CitA as a highly specific citrate receptor and elucidates the binding characteristics of CitAPHis.
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Affiliation(s)
- S Kaspar
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, Schmelzbergstrasse 7, CH-8092 Zürich, Switzerland
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19
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Abstract
PAS domains are newly recognized signaling domains that are widely distributed in proteins from members of the Archaea and Bacteria and from fungi, plants, insects, and vertebrates. They function as input modules in proteins that sense oxygen, redox potential, light, and some other stimuli. Specificity in sensing arises, in part, from different cofactors that may be associated with the PAS fold. Transduction of redox signals may be a common mechanistic theme in many different PAS domains. PAS proteins are always located intracellularly but may monitor the external as well as the internal environment. One way in which prokaryotic PAS proteins sense the environment is by detecting changes in the electron transport system. This serves as an early warning system for any reduction in cellular energy levels. Human PAS proteins include hypoxia-inducible factors and voltage-sensitive ion channels; other PAS proteins are integral components of circadian clocks. Although PAS domains were only recently identified, the signaling functions with which they are associated have long been recognized as fundamental properties of living cells.
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Affiliation(s)
- B L Taylor
- Department of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA.
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20
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Golby P, Davies S, Kelly DJ, Guest JR, Andrews SC. Identification and characterization of a two-component sensor-kinase and response-regulator system (DcuS-DcuR) controlling gene expression in response to C4-dicarboxylates in Escherichia coli. J Bacteriol 1999; 181:1238-48. [PMID: 9973351 PMCID: PMC93502 DOI: 10.1128/jb.181.4.1238-1248.1999] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/1998] [Accepted: 12/08/1998] [Indexed: 11/20/2022] Open
Abstract
The dcuB gene of Escherichia coli encodes an anaerobic C4-dicarboxylate transporter that is induced anaerobically by FNR, activated by the cyclic AMP receptor protein, and repressed in the presence of nitrate by NarL. In addition, dcuB expression is strongly induced by C4-dicarboxylates, suggesting the presence of a novel C4-dicarboxylate-responsive regulator in E. coli. This paper describes the isolation of a Tn10 mutant in which the 160-fold induction of dcuB expression by C4-dicarboxylates is absent. The corresponding Tn10 mutation resides in the yjdH gene, which is adjacent to the yjdG gene and close to the dcuB gene at approximately 93.5 min in the E. coli chromosome. The yjdHG genes (redesignated dcuSR) appear to constitute an operon encoding a two-component sensor-regulator system (DcuS-DcuR). A plasmid carrying the dcuSR operon restored the C4-dicarboxylate inducibility of dcuB expression in the dcuS mutant to levels exceeding those of the dcuS+ strain by approximately 1.8-fold. The dcuS mutation affected the expression of other genes with roles in C4-dicarboxylate transport or metabolism. Expression of the fumarate reductase (frdABCD) operon and the aerobic C4-dicarboxylate transporter (dctA) gene were induced 22- and 4-fold, respectively, by the DcuS-DcuR system in the presence of C4-dicarboxylates. Surprisingly, anaerobic fumarate respiratory growth of the dcuS mutant was normal. However, under aerobic conditions with C4-dicarboxylates as sole carbon sources, the mutant exhibited a growth defect resembling that of a dctA mutant. Studies employing a dcuA dcuB dcuC triple mutant unable to transport C4-dicarboxylates anaerobically revealed that C4-dicarboxylate transport is not required for C4-dicarboxylate-responsive gene regulation. This suggests that the DcuS-DcuR system responds to external substrates. Accordingly, topology studies using 14 DcuS-BlaM fusions showed that DcuS contains two putative transmembrane helices flanking a approximately 140-residue N-terminal domain apparently located in the periplasm. This topology strongly suggests that the periplasmic loop of DcuS serves as a C4-dicarboxylate sensor. The cytosolic region of DcuS (residues 203 to 543) contains two domains: a central PAS domain possibly acting as a second sensory domain and a C-terminal transmitter domain. Database searches showed that DcuS and DcuR are closely related to a subgroup of two-component sensor-regulators that includes the citrate-responsive CitA-CitB system of Klebsiella pneumoniae. DcuS is not closely related to the C4-dicarboxylate-sensing DctS or DctB protein of Rhodobacter capsulatus or rhizobial species, respectively. Although all three proteins have similar topologies and functions, and all are members of the two-component sensor-kinase family, their periplasmic domains appear to have evolved independently.
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Affiliation(s)
- P Golby
- The School of Animal and Microbial Sciences, University of Reading, Whiteknights, Reading RG6 6AJ, United Kingdom
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21
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Klose KE, Novik V, Mekalanos JJ. Identification of multiple sigma54-dependent transcriptional activators in Vibrio cholerae. J Bacteriol 1998; 180:5256-9. [PMID: 9748465 PMCID: PMC107568 DOI: 10.1128/jb.180.19.5256-5259.1998] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/1998] [Accepted: 07/29/1998] [Indexed: 11/20/2022] Open
Abstract
In the pathogenic bacterium Vibrio cholerae, the alternate sigma factor sigma54 is required for expression of multiple sets of genes, including an unidentified gene(s) necessary for enhanced colonization within the host. To identify sigma54-dependent transcriptional activators involved in colonization, PCR was performed with V. cholerae chromosomal DNA and degenerate primers, revealing six novel and distinct coding sequences with homology to sigma54-dependent activators. One sequence had high homology to the luxO gene of V. harveyi, which in that organism is involved in quorum sensing. Phenotypes of V. cholerae strains containing mutations in each of the six putative sigma54-dependent activator genes identified one as a probable ntrC homologue. None of the mutant strains exhibited a defect in the ability to colonize infant mice, suggesting the presence of additional sigma54-dependent activators not identified by this technique.
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Affiliation(s)
- K E Klose
- Department of Microbiology, University of Texas Health Science Center, San Antonio, Texas 78284-7758, USA
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22
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Palacín M, Estévez R, Bertran J, Zorzano A. Molecular biology of mammalian plasma membrane amino acid transporters. Physiol Rev 1998; 78:969-1054. [PMID: 9790568 DOI: 10.1152/physrev.1998.78.4.969] [Citation(s) in RCA: 587] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Molecular biology entered the field of mammalian amino acid transporters in 1990-1991 with the cloning of the first GABA and cationic amino acid transporters. Since then, cDNA have been isolated for more than 20 mammalian amino acid transporters. All of them belong to four protein families. Here we describe the tissue expression, transport characteristics, structure-function relationship, and the putative physiological roles of these transporters. Wherever possible, the ascription of these transporters to known amino acid transport systems is suggested. Significant contributions have been made to the molecular biology of amino acid transport in mammals in the last 3 years, such as the construction of knockouts for the CAT-1 cationic amino acid transporter and the EAAT2 and EAAT3 glutamate transporters, as well as a growing number of studies aimed to elucidate the structure-function relationship of the amino acid transporter. In addition, the first gene (rBAT) responsible for an inherited disease of amino acid transport (cystinuria) has been identified. Identifying the molecular structure of amino acid transport systems of high physiological relevance (e.g., system A, L, N, and x(c)- and of the genes responsible for other aminoacidurias as well as revealing the key molecular mechanisms of the amino acid transporters are the main challenges of the future in this field.
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Affiliation(s)
- M Palacín
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Spain
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23
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Reid CJ, Poole PS. Roles of DctA and DctB in signal detection by the dicarboxylic acid transport system of Rhizobium leguminosarum. J Bacteriol 1998; 180:2660-9. [PMID: 9573150 PMCID: PMC107217 DOI: 10.1128/jb.180.10.2660-2669.1998] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The dctA gene, coding for the dicarboxylate transport protein, has an inducible promoter dependent on activation by the two-component sensor-regulator pair DctB and DctD. LacZ fusion analysis indicates that there is a single promoter for dctB and dctD. The dctA promoter is also induced by nitrogen limitation, an effect that requires DctB-DctD and NtrC. DctB alone is able to detect dicarboxylates in the absence of DctA and initiate transcription via DctD. However, DctA modifies signal detection by DctB such that in the absence of DctA, the ligand specificity of DctB is broader. dctAp also responds to heterologous induction by osmotic stress in the absence of DctA. This effect requires both DctB and DctD. A transposon insertion in the dctA-dctB intergenic region (dctA101) which locks transcription of dctA at a constitutive level independent of DctB-DctD results in improper signalling by DctB-DctD. Strain RU150, which carries this insertion, is defective in nitrogen fixation (Fix-) and grows very poorly on ammonia as a nitrogen source whenever the DctB-DctD signalling circuit is activated by the presence of a dicarboxylate ligand. Mutation of dctB or dctD in strain RU150 reinstates normal growth on dicarboxylates. This suggests that DctD-P improperly regulates a heterologous nitrogen-sensing operon. Increased expression of DctA, either via a plasmid or by chromosomal duplication, restores control of DctB-DctD and allows strain RU150 to grow on ammonia in the presence of a dicarboxylate. Thus, while DctB is a sensor for dicarboxylates in its own right, it is regulated by DctA. The absence of DctA allows DctB and DctD to become promiscuous with regard to signal detection and cross talk with other operons. This indicates that DctA contributes significantly to the signalling specificity of DctB-DctD and attenuates cross talk with other operons.
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Affiliation(s)
- C J Reid
- School of Animal and Microbial Sciences, University of Reading, Reading RG6 6AJ, United Kingdom
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24
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Gao Y, Wang YK, Hoover TR. Mutational analysis of the phosphate-binding loop of Rhizobium meliloti DctD, a sigma54-dependent activator. J Bacteriol 1998; 180:2792-5. [PMID: 9573172 PMCID: PMC107239 DOI: 10.1128/jb.180.10.2792-2795.1998] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The phosphate-binding loop of sigma54-dependent activators is thought to participate in ATP binding and/or hydrolysis. Alanine substitutions at positions 3, 4, 6, 7, and 8 of this motif in Rhizobium meliloti DctD disrupted transcriptional activation and ATP hydrolysis. Interestingly, substitution of alanine at position 7 also affected DNA binding.
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Affiliation(s)
- Y Gao
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
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25
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Wang YK, Hoover TR. Alterations within the activation domain of the sigma 54-dependent activator DctD that prevent transcriptional activation. J Bacteriol 1997; 179:5812-9. [PMID: 9294439 PMCID: PMC179471 DOI: 10.1128/jb.179.18.5812-5819.1997] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Rhizobium meliloti DctD (C4-dicarboxylate transport protein D) is a transcriptional activator that catalyzes the ATP-dependent isomerization of closed complexes between sigma 54-RNA polymerase holoenzyme and the dctA promoter to open complexes. Following random mutagenesis of dctD, 55 independent mutant forms of DctD that failed to activate transcription from a dctA'-'lacZ reporter gene in Escherichia coli were selected, and the amino acid substitutions were determined for these mutant proteins. Amino acid substitutions were distributed throughout the central domain of the protein, the domain responsible for transcription activation, but most of the substitutions occurred within three highly conserved regions of the protein. Selected mutant proteins were purified, and their activities were studied in vitro. All of the purified mutant proteins appeared to have normal DNA-binding activity and interacted with sigma 54 and core RNA polymerase, as determined from protein crosslinking assays. Proteins with amino acid substitutions in a region spanning amino acid positions 222 to 225 retained their ATPase activities, whereas proteins with substitutions in other regions had little or no ATPase activity. Taken together, these data suggest that the region that encompasses amino acid residues 222 through 225 probably functions in coupling the energy released from ATP hydrolysis to open complex formation rather than as a major determinant for binding to RNA polymerase.
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Affiliation(s)
- Y K Wang
- Department of Microbiology, University of Georgia, Athens 30602, USA
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26
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Genetic approach to the intensification of Rhizobium leguminosarum bv. viciae symbiotic nitrogen fixation. Process Biochem 1997. [DOI: 10.1016/s0032-9592(96)00038-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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Scholl D, Nixon BT. Cooperative binding of DctD to the dctA upstream activation sequence of Rhizobium meliloti is enhanced in a constitutively active truncated mutant. J Biol Chem 1996; 271:26435-42. [PMID: 8824302 DOI: 10.1074/jbc.271.42.26435] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
DctD, a sigma54-dependent, two-component regulator, binds to promoter distal (A) and promoter proximal (B) sites in an activation sequence located upstream of the dctA promoter. We report gel filtration and quantitative DNase I footprint experiments supporting a model in which DctD2 binds to these sites cooperatively. The global analysis of upstream activation sequences containing sites A and B, A and B one-half helical turn out of phase, and only B yielded values for the intrinsic and cooperative binding free energies of DeltaG0A = -9.5 +/- 0.3, DeltaG0B = -11.2 +/- 0.2, and DeltaG0AB = -2.5 +/- 0.5. A separate analysis of data from upstream activation sequences containing site A and a point mutant of site B, and site A and mutant site B one-half helical turn out of phase confirmed the estimate of cooperativity, yielding free energy values of DeltaG0A = -9.4 +/- 0.2, DeltaG0B(G-->C) = -10.0 +/- 0.2, and DeltaG0AB(G-->C) = -2.2 +/- 0.4. We previously showed that removing the two-component receiver domain from DctD, making DctDDelta(1-142), yields a constitutively active truncated protein. Global analysis of binding data for DctDDelta(1-142) showed that this constitutively active mutant has intrinsic binding energies equal to that of the inactive DctD protein, but that it displays significantly higher cooperativity (DeltaG0A = -9.4 +/- 0.6, DeltaG0B = -11.1 +/- 0.3, and DeltaG0AB = -3.8 +/- 0.6.).
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Affiliation(s)
- D Scholl
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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28
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Kaufman RI, Nixon BT. Use of PCR to isolate genes encoding sigma54-dependent activators from diverse bacteria. J Bacteriol 1996; 178:3967-70. [PMID: 8682806 PMCID: PMC232662 DOI: 10.1128/jb.178.13.3967-3970.1996] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Degenerate PCR probes were used to amplify gene fragments encoding the catalytic domain of sigma54-dependent transcription activators. The procedure should be widely applicable, as it recovered both known and novel gene fragments: 5 from Rhizobium meliloti, 13 from Myxococcus xanthus, and 3 from Bacillus subtilis. No fragments were obtained from Synechococcus sp. strain PCC 7002 or Saccharomyces cerevisiae.
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Affiliation(s)
- R I Kaufman
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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29
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Abstract
To investigate the modular structure of the Rhizobium meliloti dicarboxylic acid sensor protein, DctB, three truncated DctB proteins (DctB4, DctB5 and DctB4G) were constructed, overproduced in Escherichia coli and purified. The DctB4G protein was composed of 446 amino acids of the DctB C-terminus and displayed strong autophosphorylation activity in vitro. This activity was sustained when a further 120 amino acids at the N-terminus of the polypeptide were deleted (DctB5). This protein which has an intact transmitter domain exhibits specific but inefficient phospho-transfer capabilities. Removal of 58 amino acids from the DctB4G C-terminus which included blocks F and G2 of the transmitter domain, rendered the resultant protein (DctB4) incompetent in autophosphorylation. Phosphorylation activity was restored to DctB4 through intramolecular complementation with DctB. Therefore, it would appear that the R. meliloti DctB protein is active as a dimer (or higher order oligomer). Furthermore, the intramolecular complementation experiments indicate that the amino acids 171-291, a predicted periplasmic stretch, play an important role in the dimerization process.
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Affiliation(s)
- L Giblin
- Microbiology Department, University College, Cork, Ireland
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30
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Regulation of dct genes in the Rhizobium meliloti-alfalfa interaction. World J Microbiol Biotechnol 1996; 12:151-6. [DOI: 10.1007/bf00364679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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31
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Isaac RE, MacGregor D, Coates D. Metabolism and inactivation of neurotransmitters in nematodes. Parasitology 1996; 113 Suppl:S157-73. [PMID: 9051933 DOI: 10.1017/s0031182000077957] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The nematode nervous system employs many of the same neurotransmitters as are found in higher animals. The inactivation of neurotransmitters is absolutely essential for the correct functioning of the nervous system. In this article we discuss the various mechanisms used generally in animal nervous systems for synaptic inactivation of neurotransmitters and review the evidence for similar mechanisms operating in parasitic and free-living nematodes. The sequencing of the entire Caenorhabditis elegans genome means that the sequence of nematode genes can be accessed from the C. elegans database (ACeDB) and this wealth of information together with the increasing knowledge of the genetics of this free-living nematode will have great impact on all aspects of nematode neurobiology. The review will provide an insight into how this information may be exploited to identify and characterize target proteins for the development of novel anti-nematode drugs.
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Affiliation(s)
- R E Isaac
- Department of Biology, University of Leeds, UK
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32
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Lee JH, Hoover TR. Protein crosslinking studies suggest that Rhizobium meliloti C4-dicarboxylic acid transport protein D, a sigma 54-dependent transcriptional activator, interacts with sigma 54 and the beta subunit of RNA polymerase. Proc Natl Acad Sci U S A 1995; 92:9702-6. [PMID: 7568201 PMCID: PMC40870 DOI: 10.1073/pnas.92.21.9702] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Rhizobium meliloti C4-dicarboxylic acid transport protein D (DCTD) activates transcription by a form of RNA polymerase holoenzyme that has sigma 54 as its sigma factor (referred to as E sigma 54). DCTD catalyzes the ATP-dependent isomerization of closed complexes between E sigma 54 and the dctA promoter to transcriptionally productive open complexes. Transcriptional activation probably involves specific protein-protein interactions between DCTD and E sigma 54. Interactions between sigma 54-dependent activators and E sigma 54 are transient, and there has been no report of a biochemical assay for contact between E sigma 54 and any activator to date. Heterobifunctional crosslinking reagents were used to examine protein-protein interactions between the various subunits of E sigma 54 and DCTD. DCTD was crosslinked to Salmonella typhimurium sigma 54 with the crosslinking reagents succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate and N-hydroxysulfosuccinimidyl-4-azidobenzoate. Cys-307 of sigma 54 was identified by site-directed mutagenesis as the residue that was crosslinked to DCTD. DCTD was also crosslinked to the beta subunit of Escherichia coli core RNA polymerase with succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate, but not with N-hydroxysulfosuccinimidyl-4-azidobenzoate. These data suggest that interactions of DCTD with sigma 54 and the beta subunit may be important for transcriptional activation and offer evidence for interactions between a sigma 54-dependent activator and sigma 54, as well as the beta subunit of RNA polymerase.
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Affiliation(s)
- J H Lee
- Department of Microbiology, University of Georgia, Athens 30602, USA
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33
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van der Ploeg J, Janssen DB. Sequence analysis of the upstream region of dhlB, the gene encoding haloalkanoic acid dehalogenase of Xanthobacter autotrophicus GJ10. Biodegradation 1995; 6:257-63. [PMID: 7580000 DOI: 10.1007/bf00700465] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The DNA sequence upstream of the dhlB gene encoding the haloalkanoic acid dehalogenase of Xanthobacter autotrophicus GJ10 was determined and contained an open reading frame, designated dhlC, which encoded a protein with a significant similarity with the family of Na(+)-dependent symport proteins. The dhlC gene was subcloned under control of a T7 promoter, and found to encode a polypeptide of 45 kDa on SDS-PAGE. Upstream of dhlC, a -24/-12 promoter sequence was found. Further upstream, in the opposite direction of transcription, another open reading frame, designated dhlR, with homology with the family of sigma 54-dependent transcriptional activator proteins was detected. The dhlR gene was cloned and expressed under the control of a T7 promoter and encoded a polypeptide of 51 kDa on SDS-PAGE. The genetic organization of the dhlB region suggested that the expression of dhlC and dhlB was controlled by the product of dhlR and sigma 54 which may explain the observed overexpression of the haloalkanoic acid dehalogenase under starvation conditions.
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Affiliation(s)
- J van der Ploeg
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology The Netherlands
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34
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Pines G, Zhang Y, Kanner BI. Glutamate 404 is involved in the substrate discrimination of GLT-1, a (Na+ + K+)-coupled glutamate transporter from rat brain. J Biol Chem 1995; 270:17093-7. [PMID: 7615503 DOI: 10.1074/jbc.270.29.17093] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Sodium-coupled glutamate transporters, located in the plasma membrane of nerve terminals and glial processes, serve to keep its extracellular glutamate concentration below extracellular levels. Moreover, they help in conjunction with diffusion to terminate the transmitter's action in synaptic transmission. We have investigated the role of negatively charged amino acid residues of GLT-1, a cloned (Na+ + K+)-coupled glutamate transporter from rat brain. Using site-directed mutagenesis we modified these negative residues, which are located in hydrophobic surroundings and are highly conserved within the glutamate transporter family. Out of five residues meeting these criteria, three, aspartate 398, glutamate 404, and aspartate 470, are critical for heterologously expressed glutamate transport. This defective transport cannot be attributed to the mere requirement of a negative charge at these positions. After prelabeling of the proteins with [35S]methionine, immunoprecipitation of all mutant transporters indicates that their expression levels are similar to that of wild type. No cryptic activity was revealed by reconstitution experiments aimed to monitor the activity of transporter molecules not located in the plasma membrane. Significantly, whereas all of the mutants at the glutamate 404 position exhibit impaired transport of glutamate, they possess considerable transport of D- and L-aspartate, up to 80% of wild type values. Binding of glutamate is not impaired in these mutants. Our observations indicate that the glutamate 404 residue may be located in the vicinity of the glutamate-aspartate permeation pathway.
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Affiliation(s)
- G Pines
- Department of Biochemistry, Hadassah Medical School, Hebrew University, Jerusalem, Israel
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35
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Grunewald M, Kanner B. Conformational changes monitored on the glutamate transporter GLT-1 indicate the existence of two neurotransmitter-bound states. J Biol Chem 1995; 270:17017-24. [PMID: 7622523 DOI: 10.1074/jbc.270.28.17017] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Membrane vesicles from rat brain have been subjected to trypsin treatment in the absence and presence of substrates of the (Na+ + K+)-coupled L-glutamate transporter GLT-1. The fragments of this transporter have been detected upon immunoblotting employing several antibodies raised against sequences from this transporter. At the amino terminus, initially a fragment of an apparent molecular mass of 30 kDa is generated. This fragment is subsequently cleaved to one of 16 kDa. The generation of these bands is greatly inhibited in the presence of lithium. Moreover, lithium abolishes the positive cooperative activation of the transporter by sodium. The generation of the 30- and 16-kDa fragments is accelerated in the presence of L-glutamate and other transportable analogues, provided sodium is present as well. The 30-kDa fragment also contains an epitope from the loop connecting the putative membrane-spanning alpha-helices 3 and 4. This epitope, in contrast with the amino-terminal one, is destroyed with time. The carboxyl-terminal epitope is predominantly located on a 43-kDa fragment which is slowly converted to one of 35 kDa. This conversion is not inhibited by lithium. It is, however, stimulated by L-glutamate and other transportable analogues, but only in sodium-containing media. Potassium also stimulates this conversion regardless of the presence of L-glutamate. The stimulation of generation of amino- and carboxyl-terminal fragments by L-glutamate is not mimicked by the nontransportable analogue dihydrokainate. However, the analogue blocks the stimulation exerted by L-glutamate. In addition to new experimental information on the transporters topology, our observations provide novel information on the function of the GLT-1 transporter. Although lithium by itself does not sustain transport, it may occupy one of the sodium sites and be transported. Furthermore, the transporter-glutamate complex appears to exist in at least two states. After the initial binding (suggested to be important for the decay of synaptic glutamate), it undergoes a conformational change which represents, or is tightly associated with, the transport step.
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Affiliation(s)
- M Grunewald
- Department of Biochemistry, Hadassah Medical School, Hebrew University, Jerusalem, Israel
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36
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Urban JE, Gerren R, Zoelle J. Effects of microgravity on the binding of acetylsalicylic acid by Rhizobium leguminosarum bv. trifolii. ACTA ASTRONAUTICA 1995; 36:129-133. [PMID: 11540747 DOI: 10.1016/0094-5765(95)00047-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Bacteroids can be induced in vitro by treating growing Rhizobium leguminosarum bv. trifolii with succinic acid or succinic acid structural analogs like acetysalicylic acid. Quantitating bacteroid induction by measuring acetylsalicylic binding under normal (1 g) conditions showed two forms of binding to occur. In one form of binding cells immediately bound comparatively high levels of acetylsalicylic acid, but the binding was quickly reversed. The second form of binding increased with time by first order kinetics and reached saturation in 40 s. Similar experiments performed in the microgravity environment aboard the NASA 930 aircraft showed only one form of binding and total acetylsalicyclic acid bound was 32% higher than at 1 g.
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Affiliation(s)
- J E Urban
- BioServe Space Technologies, Kansas State University, Manhattan 66506-4901, USA
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37
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Tolner B, Ubbink-Kok T, Poolman B, Konings WN. Characterization of the proton/glutamate symport protein of Bacillus subtilis and its functional expression in Escherichia coli. J Bacteriol 1995; 177:2863-9. [PMID: 7751298 PMCID: PMC176960 DOI: 10.1128/jb.177.10.2863-2869.1995] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Transport of acidic amino acids in Bacillus subtilis is an electrogenic process in which L-glutamate or L-aspartate is symported with at least two protons. This is shown by studies of transport in membrane vesicles in which a proton motive force is generated by oxidation of ascorbate-phenazine methosulfate or by artificial ion gradients. An inwards-directed sodium gradient had no (stimulatory) effect on proton motive force-driven L-glutamate uptake. The transporter is specific for L-glutamate and L-aspartate. L-Glutamate transport is inhibited by beta-hydroxyaspartate and cysteic acid but not by alpha-methyl-glutamate. The gene encoding the L-glutamate transport protein of B. subtilis (gltPBsu) was cloned by complementation of Escherichia coli JC5412 for growth on glutamate as the sole source of carbon, energy, and nitrogen, and its nucleotide sequence was determined. Putative promoter, terminator, and ribosome binding site sequences were found in the flanking regions. UUG is most likely the start codon. gltPBsu encodes a polypeptide of 414 amino acid residues and is homologous to several proteins that transport glutamate and/or structurally related compounds such as aspartate, fumarate, malate, and succinate. Both sodium- and proton-coupled transporters belong to this family of dicarboxylate transporters. Hydropathy profiling and multiple alignment of the family of carboxylate transporters suggest that each of the proteins spans the cytoplasmic membrane 12 times with both the amino and carboxy termini on the inside.
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Affiliation(s)
- B Tolner
- Department of Microbiology, University of Groningen, Haren, The Netherlands
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38
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Borowsky B, Hoffman BJ. Neurotransmitter transporters: molecular biology, function, and regulation. INTERNATIONAL REVIEW OF NEUROBIOLOGY 1995; 38:139-99. [PMID: 8537200 DOI: 10.1016/s0074-7742(08)60526-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- B Borowsky
- Unit on Molecular Pharmacology, National Institute of Mental Health, Bethesda, Maryland 20892-4090, USA
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39
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Michiels J, Vanderleyden J. Molecular basis of the establishment and functioning of a N2-fixing root nodule. World J Microbiol Biotechnol 1994; 10:612-30. [DOI: 10.1007/bf00327946] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/27/1994] [Accepted: 08/03/1994] [Indexed: 12/01/2022]
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40
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Bosworth AH, Williams MK, Albrecht KA, Kwiatkowski R, Beynon J, Hankinson TR, Ronson CW, Cannon F, Wacek TJ, Triplett EW. Alfalfa yield response to inoculation with recombinant strains of Rhizobium meliloti with an extra copy of dctABD and/or modified nifA expression. Appl Environ Microbiol 1994; 60:3815-32. [PMID: 7986051 PMCID: PMC201891 DOI: 10.1128/aem.60.10.3815-3832.1994] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The construction of rhizobial strains which increase plant biomass under controlled conditions has been previously reported. However, there is no evidence that these newly constructed strains increase legume yield under agricultural conditions. This work tested the hypothesis that carefully manipulating expression of additional copies of nifA and dctABD in strains of Rhizobium meliloti would increase alfalfa yield in the field. The rationale for this hypothesis is based on the positive regulatory role that nifA plays in the expression of the nif regulon and the fact that a supply of dicarboxylic acids from the plant is required as a carbon and energy source for nitrogen fixation by the Rhizobium bacteroids in the nodule. These recombinant strains, as well as the wild-type strains from which they were derived, are ideal tools to examine the effects of modifying or increasing the expression of these genes on alfalfa biomass. The experimental design comprised seven recombinant strains, two wild-type strains, and an uninoculated control. Each treatment was replicated eight times and was conducted at four field sites in Wisconsin. Recombinant strain RMBPC-2, which has an additional copy of both nifA and dctABD, increased alfalfa biomass by 12.9% compared with the yield with the wild-type strain RMBPC and 17.9% over that in the uninoculated control plot at the site where soil nitrogen and organic matter content was lowest. These increases were statistically significant at the 5% confidence interval for each of the three harvests made during the growing season. Strain RMBPC-2 did increase alfalfa biomass at the Hancock site; however, no other significant increases or decreases in alfalfa biomass were observed with the seven other recombinant strains at that site. At three sites where this experiment was conducted, either native rhizobial populations or soil nitrogen concentrations were high. At these sites, none of the recombinant strains affected yield. We conclude that RMBPC -2 can increase alfalfa yields under field conditions of nitrogen limitation, low endogenous rhizobial competitors, and sufficient moisture.
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Affiliation(s)
- A H Bosworth
- Department of Agronomy, University of Wisconsin-Madison 53706
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41
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The C4-dicarboxylate transport system ofRhizobium meliloti and its role in nitrogen fixation during symbiosis with alfalfa (Medicago sativa). ACTA ACUST UNITED AC 1994. [DOI: 10.1007/bf01923473] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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42
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Abstract
This review presents a comparison between the complex genetic regulatory networks that control nitrogen fixation in three representative rhizobial species, Rhizobium meliloti, Bradyrhizobium japonicum, and Azorhizobium caulinodans. Transcription of nitrogen fixation genes (nif and fix genes) in these bacteria is induced primarily by low-oxygen conditions. Low-oxygen sensing and transmission of this signal to the level of nif and fix gene expression involve at least five regulatory proteins, FixL, FixJ, FixK, NifA, and RpoN (sigma 54). The characteristic features of these proteins and their functions within species-specific regulatory pathways are described. Oxygen interferes with the activities of two transcriptional activators, FixJ and NifA. FixJ activity is modulated via phosphorylation-dephosphorylation by the cognate sensor hemoprotein FixL. In addition to the oxygen responsiveness of the NifA protein, synthesis of NifA is oxygen regulated at the level of transcription. This type of control includes FixLJ in R. meliloti and FixLJ-FixK in A. caulinodans or is brought about by autoregulation in B. japonicum. NifA, in concert with sigma 54 RNA polymerase, activates transcription from -24/-12-type promoters associated with nif and fix genes and additional genes that are not directly involved in nitrogen fixation. The FixK proteins constitute a subgroup of the Crp-Fnr family of bacterial regulators. Although the involvement of FixLJ and FixK in nifA regulation is remarkably different in the three rhizobial species discussed here, they constitute a regulatory cascade that uniformly controls the expression of genes (fixNOQP) encoding a distinct cytochrome oxidase complex probably required for bacterial respiration under low-oxygen conditions. In B. japonicum, the FixLJ-FixK cascade also controls genes for nitrate respiration and for one of two sigma 54 proteins.
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Affiliation(s)
- H M Fischer
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland
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43
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Constitutive ATP hydrolysis and transcription activation by a stable, truncated form of Rhizobium meliloti DCTD, a sigma 54-dependent transcriptional activator. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)32006-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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44
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Lenz O, Schwartz E, Dernedde J, Eitinger M, Friedrich B. The Alcaligenes eutrophus H16 hoxX gene participates in hydrogenase regulation. J Bacteriol 1994; 176:4385-93. [PMID: 8021224 PMCID: PMC205652 DOI: 10.1128/jb.176.14.4385-4393.1994] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Nucleotide sequence analysis revealed a 1,791-bp open reading frame in the hox gene cluster of the gram-negative chemolithotroph Alcaligenes eutrophus H16. In order to investigate the biological role of this open reading frame, we generated an in-frame deletion allele via a gene replacement strategy. The resulting mutant grew significantly more slowly than the wild type under lithoautotrophic conditions (6.1 versus 4.2 h doubling time). A reduction in the level of the soluble NAD-reducing hydrogenase (60% of the wild-type activity) was shown to be the cause of the slow lithoautotrophic growth. We used plasmid-borne gene fusions to monitor the expression of the operons encoding the soluble and membrane-bound hydrogenases. The expression of both operons was lower in the mutant than in the wild-type strain. These results suggest that the newly identified gene, designated hoxX, encodes a regulatory component which, in conjunction with the transcriptional activator HoxA, controls hydrogenase synthesis.
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Affiliation(s)
- O Lenz
- Institut für Pflanzenphysiologie und Mikrobiologie, Freien Universität Berlin, Germany
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45
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Gu B, Lee JH, Hoover TR, Scholl D, Nixon BT. Rhizobium meliloti DctD, a sigma 54-dependent transcriptional activator, may be negatively controlled by a subdomain in the C-terminal end of its two-component receiver module. Mol Microbiol 1994; 13:51-66. [PMID: 7984094 DOI: 10.1111/j.1365-2958.1994.tb00401.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Rhizobium meliloti DctD is believed to have three functional domains: an N-terminal, two-component receiver domain; and like other sigma 54-dependent activators, C-terminal and central domains for DNA binding and transcription activation. We have characterized a progressive series of N-terminal deletions of R. meliloti DctD. The N-terminal domain was not needed for binding the dctA upstream activation sequence. Only 25% of the C-terminal end of the receive domain was needed to significantly inhibit the central domain, and proteins lacking up to 60% of the N-terminal end of the receiver domain were 'inducible' in R. meliloti cells. We hypothesize that the N-terminal two-thirds of the DctD receiver domain augments and controls an adjacent subdomain for inhibiting the central domain.
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Affiliation(s)
- B Gu
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park 16802
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46
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Reizer J, Reizer A, Saier MH. A functional superfamily of sodium/solute symporters. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1197:133-66. [PMID: 8031825 DOI: 10.1016/0304-4157(94)90003-5] [Citation(s) in RCA: 164] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Eleven families of sodium/solute symporters are defined based on their degrees of sequence similarities, and the protein members of these families are characterized in terms of their solute and cation specificities, their sizes, their topological features, their evolutionary relationships, and their relative degrees and regions of sequence conservation. In some cases, particularly where site-specific mutagenesis analyses have provided functional information about specific proteins, multiple alignments of members of the relevant families are presented, and the degrees of conservation of the mutated residues are evaluated. Signature sequences for several of the eleven families are presented to facilitate identification of new members of these families as they become sequenced. Phylogenetic tree construction reveals the evolutionary relationships between members of each family. One of these families is shown to belong to the previously defined major facilitator superfamily. The other ten families do not show sufficient sequence similarity with each other or with other identified transport protein families to establish homology between them. This study serves to clarify structural, functional and evolutionary relationships among eleven distinct families of functionally related transport proteins.
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Affiliation(s)
- J Reizer
- Department of Biology, University of California at San Diego, La Jolla 92093-0116
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47
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Jording D, Pühler A. The membrane topology of the Rhizobium meliloti C4-dicarboxylate permease (DctA) as derived from protein fusions with Escherichia coli K12 alkaline phosphatase (PhoA) and beta-galactosidase (LacZ). MOLECULAR & GENERAL GENETICS : MGG 1993; 241:106-14. [PMID: 8232193 DOI: 10.1007/bf00280207] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The Rhizobium meliloti dctA gene encodes the C4-dicarboxylate permease which mediates uptake of C4-dicarboxylates, both in free-living and symbiotic cells. Based on the hydrophobicity of the DctA protein, 12 putative membrane spanning regions were predicted. The membrane topology was further analysed by isolating in vivo fusions of DctA to Escherichia coli alkaline phosphatase (PhoA) and E. coli beta-galactosidase (LacZ). Of 10 different fusions 7 indicated a periplasmic and 3 a cytoplasmic location of the corresponding region of the DctA protein. From these data a two-dimensional model of DctA was constructed which comprised twelve transmembrane alpha-helices with the amino-terminus and the carboxy-terminus located in the cytoplasm. In addition, four conserved amino acid motifs present in many eukaryotic and prokaryotic transport proteins were observed.
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Affiliation(s)
- D Jording
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Germany
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48
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Frederick RD, Majerczak DR, Coplin DL. Erwinia stewartii WtsA, a positive regulator of pathogenicity gene expression, is similar to Pseudomonas syringae pv. phaseolicola HrpS. Mol Microbiol 1993; 9:477-85. [PMID: 8412697 DOI: 10.1111/j.1365-2958.1993.tb01709.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Erwinia stewartii contains a large cluster of wts genes that are required by this bacterium for pathogenicity on corn plants. Three complementation groups within the right half of this cluster, wtsA, wtsC, and wtsB, were previously identified. In this study, WtsA was found to be a positive activator of wtsB::lacZ expression. The wtsA locus was sequenced and a single open reading frame is present within the wtsA locus, which has the capacity to encode a 323 amino acid polypeptide. A corresponding 38 kDa protein was observed in Escherichia coli minicells containing the cloned wtsA gene. The predicted WtsA polypeptide has significant similarity to HrpS from Pseudomonas syringae pv. phaseolicola, as well as other members of the NtrC class of prokaryotic regulatory proteins. Similar to other genes activated by NtrC regulators, wtsB::lacZ expression in E. coli was dependent upon rpoN.
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Affiliation(s)
- R D Frederick
- Department of Plant Pathology, Ohio State University, Columbus 43210-1087
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49
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North AK, Klose KE, Stedman KM, Kustu S. Prokaryotic enhancer-binding proteins reflect eukaryote-like modularity: the puzzle of nitrogen regulatory protein C. J Bacteriol 1993; 175:4267-73. [PMID: 8331061 PMCID: PMC204865 DOI: 10.1128/jb.175.14.4267-4273.1993] [Citation(s) in RCA: 141] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- A K North
- Department of Plant Pathology, University of California, Berkeley 94720
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50
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Abstract
The removal of neurotransmitters by their transporters in presynaptic nerve terminals and glial cells plays an important role in the termination of synaptic transmission. Many neurotransmitter transporters, which are sodium- and chloride-coupled, have been cloned and shown to constitute a large superfamily. Glutamate is the major excitatory neurotransmitter in the central nervous system. If not efficiently removed, it causes death of neuronal cells. Its transporter couples the flow of glutamate to that of sodium and potassium. Recently three different but related glutamate transporters have been cloned, which have no significant homology to the members of the superfamily.
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Affiliation(s)
- B I Kanner
- Department of Biochemistry, Hadassah Medical School, Hebrew University, Jerusalem, Israel
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