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Chen WF, Meng XF, Jiao YS, Tian CF, Sui XH, Jiao J, Wang ET, Ma SJ. Bacteroid Development, Transcriptome, and Symbiotic Nitrogen-Fixing Comparison of Bradyrhizobium arachidis in Nodules of Peanut (Arachis hypogaea) and Medicinal Legume Sophora flavescens. Microbiol Spectr 2023; 11:e0107922. [PMID: 36656008 PMCID: PMC9927569 DOI: 10.1128/spectrum.01079-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/29/2022] [Indexed: 01/20/2023] Open
Abstract
Bradyrhizobium arachidis strain CCBAU 051107 could differentiate into swollen and nonswollen bacteroids in determinate root nodules of peanut (Arachis hypogaea) and indeterminate nodules of Sophora flavescens, respectively, with different N2 fixation efficiencies. To reveal the mechanism of bacteroid differentiation and symbiosis efficiency in association with different hosts, morphologies, transcriptomes, and nitrogen fixation efficiencies of the root nodules induced by strain CCBAU 051107 on these two plants were compared. Our results indicated that the nitrogenase activity of peanut nodules was 3 times higher than that of S. flavescens nodules, demonstrating the effects of rhizobium-host interaction on symbiotic effectiveness. With transcriptome comparisons, genes involved in biological nitrogen fixation (BNF) and energy metabolism were upregulated, while those involved in DNA replication, bacterial chemotaxis, and flagellar assembly were significantly downregulated in both types of bacteroids compared with those in free-living cells. However, expression levels of genes involved in BNF, the tricarboxylic acid (TCA) cycle, the pentose phosphate pathway, hydrogenase synthesis, poly-β-hydroxybutyrate (PHB) degradation, and peptidoglycan biosynthesis were significantly greater in the swollen bacteroids of peanut than those in the nonswollen bacteroids of S. flavescens, while contrasting situations were found in expression of genes involved in urea degradation, PHB synthesis, and nitrogen assimilation. Especially higher expression of ureABEF and aspB genes in bacteroids of S. flavescens might imply that the BNF product and nitrogen transport pathway were different from those in peanut. Our study revealed the first differences in bacteroid differentiation and metabolism of these two hosts and will be helpful for us to explore higher-efficiency symbiosis between rhizobia and legumes. IMPORTANCE Rhizobial differentiation into bacteroids in leguminous nodules attracts scientists to investigate its different aspects. The development of bacteroids in the nodule of the important oil crop peanut was first investigated and compared to the status in the nodule of the extremely promiscuous medicinal legume Sophora flavescens by using just a single rhizobial strain of Bradyrhizobium arachidis, CCBAU 051107. This strain differentiates into swollen bacteroids in peanut nodules and nonswollen bacteroids in S. flavescens nodules. The N2-fixing efficiency of the peanut nodules is three times higher than that of S. flavescens. By comparing the transcriptomes of their bacteroids, we found that they have similar gene expression spectra, such as nitrogen fixation and motivity, but different spectra in terms of urease activity and peptidoglycan biosynthesis. Those altered levels of gene expression might be related to their functions and differentiation in respective nodules. Our studies provided novel insight into the rhizobial differentiation and metabolic alteration in different hosts.
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Affiliation(s)
- Wen Feng Chen
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - Xiang Fei Meng
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - Yin Shan Jiao
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - Xin Hua Sui
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - Jian Jiao
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, México
| | - Sheng Jun Ma
- College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi, Xinjiang Uygur Autonomous Region, People’s Republic of China
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Lipa P, Janczarek M. Phosphorylation systems in symbiotic nitrogen-fixing bacteria and their role in bacterial adaptation to various environmental stresses. PeerJ 2020; 8:e8466. [PMID: 32095335 PMCID: PMC7020829 DOI: 10.7717/peerj.8466] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/27/2019] [Indexed: 12/23/2022] Open
Abstract
Symbiotic bacteria, commonly called rhizobia, lead a saprophytic lifestyle in the soil and form nitrogen-fixing nodules on legume roots. During their lifecycle, rhizobia have to adapt to different conditions prevailing in the soils and within host plants. To survive under these conditions, rhizobia fine-tune the regulatory machinery to respond rapidly and adequately to environmental changes. Symbiotic bacteria play an essential role in the soil environment from both ecological and economical point of view, since these bacteria provide Fabaceae plants (legumes) with large amounts of accessible nitrogen as a result of symbiotic interactions (i.e., rhizobia present within the nodule reduce atmospheric dinitrogen (N2) to ammonia, which can be utilized by plants). Because of its restricted availability in the soil, nitrogen is one of the most limiting factors for plant growth. In spite of its high content in the atmosphere, plants are not able to assimilate it directly in the N2 form. During symbiosis, rhizobia infect host root and trigger the development of specific plant organ, the nodule. The aim of root nodule formation is to ensure a microaerobic environment, which is essential for proper activity of nitrogenase, i.e., a key enzyme facilitating N2 fixation. To adapt to various lifestyles and environmental stresses, rhizobia have developed several regulatory mechanisms, e.g., reversible phosphorylation. This key mechanism regulates many processes in both prokaryotic and eukaryotic cells. In microorganisms, signal transduction includes two-component systems (TCSs), which involve membrane sensor histidine kinases (HKs) and cognate DNA-binding response regulators (RRs). Furthermore, regulatory mechanisms based on phosphoenolopyruvate-dependent phosphotranspherase systems (PTSs), as well as alternative regulatory pathways controlled by Hanks-type serine/threonine kinases (STKs) and serine/threonine phosphatases (STPs) play an important role in regulation of many cellular processes in both free-living bacteria and during symbiosis with the host plant (e.g., growth and cell division, envelope biogenesis, biofilm formation, response to stress conditions, and regulation of metabolism). In this review, we summarize the current knowledge of phosphorylation systems in symbiotic nitrogen-fixing bacteria, and their role in the physiology of rhizobial cells and adaptation to various environmental conditions.
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Affiliation(s)
- Paulina Lipa
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Sklodowska University Lublin, Lublin, Poland
| | - Monika Janczarek
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Sklodowska University Lublin, Lublin, Poland
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3
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Hagberg KL, Yurgel SN, Mulder M, Kahn ML. Interaction between Nitrogen and Phosphate Stress Responses in Sinorhizobium meliloti. Front Microbiol 2016; 7:1928. [PMID: 27965651 PMCID: PMC5127829 DOI: 10.3389/fmicb.2016.01928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/16/2016] [Indexed: 11/13/2022] Open
Abstract
Bacteria have developed various stress response pathways to improve their assimilation and allocation of limited nutrients, such as nitrogen and phosphate. While both the nitrogen stress response (NSR) and phosphate stress response (PSR) have been studied individually, there are few experiments reported that characterize effects of multiple stresses on one or more pathways in Sinorhizobium meliloti, a facultatively symbiotic, nitrogen-fixing bacteria. The PII proteins, GlnB and GlnK, regulate the NSR activity, but analysis of global transcription changes in a PII deficient mutant suggest that the S. meliloti PII proteins may also regulate the PSR. PII double deletion mutants grow very slowly and pseudoreversion of the slow growth phenotype is common. To understand this phenomenon better, transposon mutants were isolated that had a faster growing phenotype. One mutation was in phoB, the response regulator for a two component regulatory system that is important in the PSR. phoB::Tn5 mutants had different phenotypes in the wild type compared to a PII deficient background. This led to the hypothesis that phosphate stress affects the NSR and conversely, that nitrogen stress affects the PSR. Our results show that phosphate availability affects glutamine synthetase activity and expression, which are often used as indicators of NSR activity, but that nitrogen availability did not affect alkaline phosphatase activity and expression, which are indicators of PSR activity. We conclude that the NSR is co-regulated by nitrogen and phosphate, whereas the PSR does not appear to be co-regulated by nitrogen in addition to its known phosphate regulation.
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Affiliation(s)
- Kelly L Hagberg
- School of Molecular Biosciences, Washington State University, PullmanWA, USA; Institute of Biological Chemistry, Washington State University, PullmanWA, USA
| | - Svetlana N Yurgel
- Institute of Biological Chemistry, Washington State University, Pullman WA, USA
| | - Monika Mulder
- Institute of Biological Chemistry, Washington State University, Pullman WA, USA
| | - Michael L Kahn
- School of Molecular Biosciences, Washington State University, PullmanWA, USA; Institute of Biological Chemistry, Washington State University, PullmanWA, USA
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Sallet E, Roux B, Sauviac L, Jardinaud MF, Carrère S, Faraut T, de Carvalho-Niebel F, Gouzy J, Gamas P, Capela D, Bruand C, Schiex T. Next-generation annotation of prokaryotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011. DNA Res 2013; 20:339-54. [PMID: 23599422 PMCID: PMC3738161 DOI: 10.1093/dnares/dst014] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The availability of next-generation sequences of transcripts from prokaryotic organisms offers the opportunity to design a new generation of automated genome annotation tools not yet available for prokaryotes. In this work, we designed EuGene-P, the first integrative prokaryotic gene finder tool which combines a variety of high-throughput data, including oriented RNA-Seq data, directly into the prediction process. This enables the automated prediction of coding sequences (CDSs), untranslated regions, transcription start sites (TSSs) and non-coding RNA (ncRNA, sense and antisense) genes. EuGene-P was used to comprehensively and accurately annotate the genome of the nitrogen-fixing bacterium Sinorhizobium meliloti strain 2011, leading to the prediction of 6308 CDSs as well as 1876 ncRNAs. Among them, 1280 appeared as antisense to a CDS, which supports recent findings that antisense transcription activity is widespread in bacteria. Moreover, 4077 TSSs upstream of protein-coding or non-coding genes were precisely mapped providing valuable data for the study of promoter regions. By looking for RpoE2-binding sites upstream of annotated TSSs, we were able to extend the S. meliloti RpoE2 regulon by ∼3-fold. Altogether, these observations demonstrate the power of EuGene-P to produce a reliable and high-resolution automatic annotation of prokaryotic genomes.
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Affiliation(s)
- Erika Sallet
- INRA, Laboratoire des Interactions Plantes-Microorganismes-LIPM, UMR 441, Castanet-Tolosan F-31326, France
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5
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Yurgel SN, Rice J, Mulder M, Kahn ML. GlnB/GlnK PII proteins and regulation of the Sinorhizobium meliloti Rm1021 nitrogen stress response and symbiotic function. J Bacteriol 2010; 192:2473-81. [PMID: 20304991 PMCID: PMC2863565 DOI: 10.1128/jb.01657-09] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 03/10/2010] [Indexed: 11/20/2022] Open
Abstract
The Sinorhizobium meliloti Rm1021 Delta glnD-sm2 mutant, which is predicted to make a GlnD nitrogen sensor protein truncated at its amino terminus, fixes nitrogen in symbiosis with alfalfa, but the plants cannot use this nitrogen for growth (S. N. Yurgel and M. L. Kahn, Proc. Natl. Acad. Sci. U. S. A. 105:18958-18963, 2008). The mutant also has a generalized nitrogen stress response (NSR) defect. These results suggest a connection between GlnD, symbiotic metabolism, and the NSR, but the nature of this connection is unknown. In many bacteria, GlnD modifies the PII proteins, GlnB and GlnK, as it transduces a measurement of bacterial nitrogen status to a cellular response. We have now constructed and analyzed Rm1021 mutants missing GlnB, GlnK, or both proteins. Rm1021 Delta glnK Delta glnB was much more defective in its NSR than either single mutant, suggesting that GlnB and GlnK overlap in regulating the NSR in free-living Rm1021. The single mutants and the double mutant all formed an effective symbiosis, indicating that symbiotic nitrogen exchange could occur without the need for either GlnB or GlnK. N-terminal truncation of the GlnD protein interfered with PII protein modification in vitro, suggesting either that unmodified PII proteins were responsible for the glnD mutant's ineffective phenotype or that connecting GlnD and appropriate symbiotic behavior does not require the PII proteins.
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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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6
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A mutant GlnD nitrogen sensor protein leads to a nitrogen-fixing but ineffective Sinorhizobium meliloti symbiosis with alfalfa. Proc Natl Acad Sci U S A 2008; 105:18958-63. [PMID: 19020095 DOI: 10.1073/pnas.0808048105] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nitrogen-fixing symbiosis between rhizobia and legume plants is a model of coevolved nutritional complementation. The plants reduce atmospheric CO(2) by photosynthesis and provide carbon compounds to symbiotically associated bacteria; the rhizobia use these compounds to reduce (fix) atmospheric N(2) to ammonia, a form of nitrogen the plants can use. A key feature of symbiotic N(2) fixation is that N(2) fixation is uncoupled from bacterial nitrogen stress metabolism so that the rhizobia generate "excess" ammonia and release this ammonia to the plant. In the symbiosis between Sinorhizobium meliloti and alfalfa, mutations in GlnD, the major bacterial nitrogen stress response sensor protein, led to a symbiosis in which nitrogen was fixed (Fix(+)) but was not effective (Eff(-)) in substantially increasing plant growth. Fixed (15)N(2) was transported to the shoots, but most fixed (15)N was not present in the plant after 24 h. Analysis of free-living S. meliloti strains with mutations in genes related to nitrogen stress response regulation (glnD, glnB, ntrC, and ntrA) showed that catabolism of various nitrogen-containing compounds depended on the NtrC and GlnD components of the nitrogen stress response cascade. However, only mutants of GlnD with an amino terminal deletion had the unusual Fix(+)Eff(-) symbiotic phenotype, and the data suggest that these glnD mutants export fixed nitrogen in a form that the plants cannot use. These results indicate that bacterial nitrogen stress regulation is important to symbiotic productivity and suggest that GlnD may act in a novel way to influence symbiotic behavior.
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Finan TM, Weidner S, Wong K, Buhrmester J, Chain P, Vorhölter FJ, Hernandez-Lucas I, Becker A, Cowie A, Gouzy J, Golding B, Pühler A. The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti. Proc Natl Acad Sci U S A 2001; 98:9889-94. [PMID: 11481431 PMCID: PMC55548 DOI: 10.1073/pnas.161294698] [Citation(s) in RCA: 249] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Analysis of the 1,683,333-nt sequence of the pSymB megaplasmid from the symbiotic N(2)-fixing bacterium Sinorhizobium meliloti revealed that the replicon has a high gene density with a total of 1,570 protein-coding regions, with few insertion elements and regions duplicated elsewhere in the genome. The only copies of an essential arg-tRNA gene and the minCDE genes are located on pSymB. Almost 20% of the pSymB sequence carries genes encoding solute uptake systems, most of which were of the ATP-binding cassette family. Many previously unsuspected genes involved in polysaccharide biosynthesis were identified and these, together with the two known distinct exopolysaccharide synthesis gene clusters, show that 14% of the pSymB sequence is dedicated to polysaccharide synthesis. Other recognizable gene clusters include many involved in catabolic activities such as protocatechuate utilization and phosphonate degradation. The functions of these genes are consistent with the notion that pSymB plays a major role in the saprophytic competence of the bacteria in the soil environment.
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Affiliation(s)
- T M Finan
- Department of Biology, McMaster University, Hamilton, ON, Canada.
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Tatè R, Mandrich L, Spinosa MR, Riccio A, Lamberti A, Iaccarino M, Patriarca EJ. The Rhizobium GstI protein reduces the NH4+ assimilation capacity of Rhizobium leguminosarum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2001; 14:823-831. [PMID: 11437255 DOI: 10.1094/mpmi.2001.14.7.823] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We show that the protein encoded by the glutamine synthetase translational inhibitor (gstI) gene reduces the NH4+ assimilation capacity of Rhizobium leguminosarum. In this organism, gstI expression is regulated by the ntr system, including the PII protein, as a function of the nitrogen (N) status of the cells. The GstI protein, when expressed from an inducible promoter, inhibits glutamine synthetase II (glnII) expression under all N conditions tested. The induction of gstI affects the growth of a glutamine synthetase I (glnA-) strain and a single amino acid substitution (W48D) results in the complete loss of GstI function. During symbiosis, gstI is expressed in young differentiating symbiosomes (SBs) but not in differentiated N2-fixing SBs. In young SBs, the PII protein modulates the transcription of NtrC-regulated genes such as gstI and glnII. The evidence presented herein strengthens the idea that the endocytosis of bacteria inside the cytoplasm of the host cells is a key step in the regulation of NH4+ metabolism.
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Affiliation(s)
- R Tatè
- International Institute of Genetics and Biophysics, CNR, Naples, Italy
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Schlüter A, Nöhlen M, Krämer M, Defez R, Priefer UB. The Rhizobium leguminosarum bv. viciae glnD gene, encoding a uridylyltransferase/uridylyl-removing enzyme, is expressed in the root nodule but is not essential for nitrogen fixation. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 11):2987-2996. [PMID: 11065377 DOI: 10.1099/00221287-146-11-2987] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A Rhizobium leguminosarum bv. viciae VF39 gene (glnD) encoding the uridylyltransferase/uridylyl-removing enzyme, which constitutes the sensory component of the nitrogen regulation (ntr) system, was identified, cloned and characterized. The deduced amino acid sequence contains the conserved active site motif of the nucleotidyltransferase superfamily and is highly homologous to the glnD gene products of other bacterial species. Downstream of the VF39 glnD resides an open reading frame with similarity to the Salmonella typhimurium virulence factor gene mviN. Mutation of the glnD gene abolished the ability to use nitrate as a sole nitrogen source but not glutamine. In addition, neither uridylylation of P(II) nor induction of the ntr-regulated glnII gene (encoding glutamine synthetase II) under ammonium deficiency could be observed in mutant strains. This strongly suggests that glnD mutants harbour a permanently deuridylylated P(II) protein and as a consequence are unable to activate transcription from NtrC-dependent promoters. The glnD gene itself is expressed constitutively, irrespective of the nitrogen content of the medium. A functional GlnD protein is not essential for nitrogen fixation in R. leguminosarum bv. viciae, but in situ detection of glnD expression in the symbiotic and infection zone of the root nodule and quantitative measurements suggest that at least part of the ntr system functions in symbiosis. The results also indicate that the N-terminal part of GlnD is essential for the cell, as deletions in the 5'-region of the gene appear to be lethal and mutations possibly affecting the expression of the first half of the protein have a significant effect on the vitality of the mutant strain.
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Affiliation(s)
- Andreas Schlüter
- Ökologie des Bodens, Botanisches Institut, RWTH Aachen, Worringerweg 1, 52056 Aachen, Germany1
| | - Michael Nöhlen
- Ökologie des Bodens, Botanisches Institut, RWTH Aachen, Worringerweg 1, 52056 Aachen, Germany1
| | - Maria Krämer
- Ökologie des Bodens, Botanisches Institut, RWTH Aachen, Worringerweg 1, 52056 Aachen, Germany1
| | - Roberto Defez
- International Institute of Genetics and Biophysics - CNR, Via Marconi 12, 80125 Napoli, Italy2
| | - Ursula B Priefer
- Ökologie des Bodens, Botanisches Institut, RWTH Aachen, Worringerweg 1, 52056 Aachen, Germany1
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Spinosa M, Riccio A, Mandrich L, Manco G, Lamberti A, Iaccarino M, Merrick M, Patriarca EJ. Inhibition of glutamine synthetase II expression by the product of the gstI gene. Mol Microbiol 2000; 37:443-52. [PMID: 10931338 DOI: 10.1046/j.1365-2958.2000.02018.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the identification of a previously unrecognized gene that is involved in the regulation of the Rhizobium leguminosarum glnII (glutamine synthetase II) gene. This gene, which is situated immediately upstream of glnII, was identified by means of a deletion/complementation analysis performed in the heterologous background of Klebsiella pneumoniae. It has been designated gstI (glutamine synthetase translational Inhibitor) because, when a complete version of gstI is present, it is possible to detect glnII-specific mRNA, but neither GSII activity nor GSII protein. The gstI gene encodes a small (63 amino acids) protein, which acts in cis or in trans with respect to glnII and is transcribed divergently with respect to glnII from a promoter that was found to be strongly repressed by the nitrogen transcriptional regulator NtrC. A mutated version of GstI lacking the last 14 amino acids completely lost its capacity to repress glnII expression. Our results indicate that gstI mediates the translation inhibition of glnII mRNA and, based on in silico analyses, a mechanism for GstI action is proposed.
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Affiliation(s)
- M Spinosa
- International Institute of Genetics and Biophysics, CNR, Via G. Marconi 10, 80125 Naples, Italy
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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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12
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Kersten MA, Baars JJ, Op den Camp HJ, Van Griensven LJ, van der Drift C. Regulation of glutamine synthetase from the white button mushroom Agaricus bisporus. Arch Biochem Biophys 1999; 364:228-34. [PMID: 10190978 DOI: 10.1006/abbi.1999.1119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The regulation of glutamine synthetase (GS) from Agaricus bisporus was studied at the posttranscriptional level using a specific antibody fraction directed against purified GS. The cross-reactivity of the antiserum against various Agaricus species and other fungi was tested and low reactivity with the Ascomycetes was found. GS protein and activity levels were measured in cell-free extracts of mycelium grown on different N sources. In mycelium grown on glutamine or ammonium as N source, the biosynthetic GS activity is higher than the transferase activity. Moreover, the results show a correlation between GS biosynthetic activity, GS protein, and previously reported mRNA levels. Also, after addition of ammonium or glutamine to glutamate-utilizing cultures, transferase activity decreased more rapidly than biosynthetic activity and GS protein level. This suggests a conformational modification which only affects transferase activity.
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Affiliation(s)
- M A Kersten
- Department of Microbiology and Evolutionary Biology, Faculty of Science, University of Nijmegen, Toernooiveld 1, Nijmegen, NL-6525 ED, The Netherlands.
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Mendoza A, Valderrama B, Leija A, Mora J. NifA-dependent expression of glutamate dehydrogenase in Rhizobium etli modifies nitrogen partitioning during symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 1998; 11:83-90. [PMID: 9450332 DOI: 10.1094/mpmi.1998.11.2.83] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Constitutive expression of foreign glutamate dehydrogenase in Rhizobium etli inhibits bean plant nodulation (A. Mendoza, A. Leija, E. Martínez-Romero, G. Hernández, and J. Mora. Mol. Plant-Microbe Interact. 8:584-592, 1995). Here we report that this inhibition is overcome when controlling gdhA expression by NifA, thus delaying the GDH activity onset after nodule establishment. Expression of gdhA modifies the nitrogen partitioning inside the bacteroid, where newly synthesized ammonia is preferentially incorporated into the amino acid pool instead of being exported to the infected cells. As a consequence, the fixed nitrogen transport to the leaves, measured as the ureides content in xylem sap, is significantly reduced. Nitrogenase activity, although not nifHDK expression, is significantly reduced in bacteroids expressing gdhA, probably due to the utilization of energy and reducing power for nitrogen assimilation. Here we show that ammonia assimilation inside R. etli bacteroids is active, albeit at low levels, and when enhanced is deleterious to the symbiotic performance. This leads us to believe that further reduction of the basal nitrogen metabolism in the bacteroid might stimulate the nitrogenase activity and increase the nitrogen supply to the plant.
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Affiliation(s)
- A Mendoza
- Departamento de Ecología Molecular, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
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Abstract
Infection of legume roots or stems with soil bacteria of the Rhizobiaceae results in the formation of nodules that become symbiotic nitrogen-fixing organs. Within the infected cells of these nodules, bacteria are enveloped in a membrane of plant origin, called the peribacteroid membrane (PBM), and divide and differentiate to form nitrogen-fixing bacteroids. The organelle-like structure comprised of PBM and bacteroids is termed the symbiosome, and is the basic nitrogen-fixing unit of the nodule. The major exchange of nutrients between the symbiotic partners is reduced carbon from the plant, to fuel nitrogenase activity in the bacteroid, and fixed nitrogen from the bacteroid, which is assimilated in the plant cytoplasm. However, many other metabolites are also exchanged. The metabolic interaction between the plant and the bacteroids is regulated by a series of transporters and channels on the PBM and the bacteroid membrane, and these form the focus of this review.
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Affiliation(s)
- Michael K. Udvardi
- Division of Biochemistry and Molecular Biology, Faculty of Science, Australian National University, Canberra ACT, 0200, Australia
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15
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Abstract
Nitrogen metabolism in prokaryotes involves the coordinated expression of a large number of enzymes concerned with both utilization of extracellular nitrogen sources and intracellular biosynthesis of nitrogen-containing compounds. The control of this expression is determined by the availability of fixed nitrogen to the cell and is effected by complex regulatory networks involving regulation at both the transcriptional and posttranslational levels. While the most detailed studies to date have been carried out with enteric bacteria, there is a considerable body of evidence to show that the nitrogen regulation (ntr) systems described in the enterics extend to many other genera. Furthermore, as the range of bacteria in which the phenomenon of nitrogen control is examined is being extended, new regulatory mechanisms are also being discovered. In this review, we have attempted to summarize recent research in prokaryotic nitrogen control; to show the ubiquity of the ntr system, at least in gram-negative organisms; and to identify those areas and groups of organisms about which there is much still to learn.
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Affiliation(s)
- M J Merrick
- Nitrogen Fixation Laboratory, John Innes Centre, Norwich, United Kingdom
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16
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Osterås M, Stanley J, Finan TM. Identification of Rhizobium-specific intergenic mosaic elements within an essential two-component regulatory system of Rhizobium species. J Bacteriol 1995; 177:5485-94. [PMID: 7559334 PMCID: PMC177356 DOI: 10.1128/jb.177.19.5485-5494.1995] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Analysis of the DNA regions upstream of the phosphoenolpyruvate carboxykinase gene (pckA) in Rhizobium meliloti and Rhizobium sp. strain NGR234 identified an open reading frame which was highly homologous to the Agrobacterium tumefaciens chromosomal virulence gene product ChvI. A second gene product, 500 bp downstream of the chvI-like gene in R. meliloti, was homologous to the A. tumefaciens ChvG protein. The homology between the R. meliloti and A. tumefaciens genes was confirmed, because the R. meliloti chvI and chvG genes complemented A. tumefaciens chvI and chvG mutants for growth on complex media. We were unable to construct chvI or chvG insertion mutants of R. meliloti, whereas mutants carrying insertions outside of these genes were readily obtained. A 108-bp repeat element characterized by two large palindromes was identified in the chvI and chvG intergenic regions of both Rhizobium species. This element was duplicated in Rhizobium sp. strain NGR234. Another structurally similar element with a size of 109 bp was present in R. meliloti but not in Rhizobium sp. strain NGR234. These elements were named rhizobium-specific intergenic mosaic elements (RIMEs), because their distribution seems to be limited to members of the family Rhizobiaceae. A homology search in GenBank detected six more copies of the first element (RIME1), all in Rhizobium species, and three extra copies of the second element (RIME2), only in R. meliloti. Southern blot analysis with a probe specific to RIME1 showed the presence of several copies of the element in the genome of R. meliloti, Rhizobium sp. strain NGR234, Rhizobium leguminosarum, and Agrobacterium rhizogenes, but none was present in A. tumefaciens and Bradyrhizobium japonicum.
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Affiliation(s)
- M Osterås
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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17
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Powell BS, Court DL, Inada T, Nakamura Y, Michotey V, Cui X, Reizer A, Saier MH, Reizer J. Novel proteins of the phosphotransferase system encoded within the rpoN operon of Escherichia coli. Enzyme IIANtr affects growth on organic nitrogen and the conditional lethality of an erats mutant. J Biol Chem 1995; 270:4822-39. [PMID: 7876255 DOI: 10.1074/jbc.270.9.4822] [Citation(s) in RCA: 177] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Two rpoN-linked delta Tn10-kan insertions suppress the conditionally lethal erats allele. One truncates rpoN while the second disrupts another gene (ptsN) in the rpoN operon and does not affect classical nitrogen regulation. Neither alter expression of era indicating that suppression is post-translational. Plasmid clones of ptsN prevent suppression by either disruption mutation indicating that this gene is important for lethality caused by erats. rpoN and six neighboring genes were sequenced and compared with sequences in the database. Two of these genes encode proteins homologous to Enzyme IIAFru and HPr of the phosphoenolpyruvate:sugar phosphotransferase system. We designate these proteins IIANtr (ptsN) and NPr (npr). Purified IIANtr and NPr exchange phosphate appropriately with Enzyme I, HPr, and Enzyme IIA proteins of the phosphoenolpyruvate: sugar phosphotransferase system. Several sugars and tricarboxylic acid cycle intermediates inhibited growth of the ptsN disruption mutant on medium containing an amino acid or nucleoside base as a combined source of nitrogen, carbon, and energy. This growth inhibition was relieved by supplying the ptsN gene or ammonium salts but was not aleviated by altering levels of exogenously supplied cAMP. These results support our previous proposal of a novel mechanism linking carbon and nitrogen assimilation and relates IIANtr to the unknown process regulated by the essential GTPase Era.
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Affiliation(s)
- B S Powell
- Laboratory of Chromosome Biology, NCI-Frederick Cancer Research and Development Center, Maryland 21702-1201
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18
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Abstract
The control of glutamine synthetase (GS), the first enzyme in the main pathway used by Rhizobium meliloti to assimilate ammonia, is central to cellular nitrogen metabolism. R. meliloti is unusual in having three distinct types of GS, including a unique GS, GSIII, that differs considerably from both GSI, which resembles other bacterial GS proteins and GSII, which resembles the GS found in eukaryotes. We show here that GSIII can be post-translationally modified in vivo by ADP-ribosylation at an arginine residue. 32PO4 attached to GSIII during bacterial growth as part of the modifying group could be removed by treatment with snake venom phosphodiesterase or by turkey erythrocyte ADP-ribosylarginine hydrolase. Treatment of modified GSIII with hydroxylamine at neutral pH releases a chromophore that has the retention time of ADP-ribose when analyzed by reversed-phase high performance liquid chromatography. ADP-ribosylation inhibits GSIII activity.
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Affiliation(s)
- Y Liu
- Department of Microbiology, Washington State University, Pullman 99164-6340
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19
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Botsford JL, Alvarez M, Hernandez R, Nichols R. Accumulation of glutamate by Salmonella typhimurium in response to osmotic stress. Appl Environ Microbiol 1994; 60:2568-74. [PMID: 7915510 PMCID: PMC201685 DOI: 10.1128/aem.60.7.2568-2574.1994] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Salmonella typhimurium accumulates glutamate in response to osmotic stress. Cells in aerobic exponential growth have an intracellular pool of approximately 125 nmol of glutamate mg of protein-1. When cells were grown in minimal medium with 500 mM NaCl, KCl, or sucrose, 290 to 430 nmol of glutamate was found to accumulate. Values were lower when cells were harvested in stationary phase. Cells were grown in conventional medium, harvested, washed, resuspended in the control medium or in medium with osmolytes, and aerated for 1 h. With aeration, glutamate was found to accumulate at levels comparable to those observed in exponential cultures. Antibiotics inhibiting protein synthesis did not affect glutamate accumulation when cells were aerated. Strains with mutations in glutamate synthase (glt) or in glutamate dehydrogenase (gdh) accumulated nearly normal levels of glutamate under these conditions. A double (gdh glt) mutant accumulated much less glutamate (63.9 nmol mg of protein-1), but a 1.9-fold excess accumulated when cells were aerated with osmotic stress. Methionine sulfone, an inhibitor of glutamate synthase, did not prevent accumulation of glutamate in cells aerated with osmotic stress. Glutamate dehydrogenase is thought to have minimum activity when ammonium is limiting. Resuspending cells with limiting ammonium reduced glutamate production but did not eliminate accumulation of excess glutamate when cells were osmotically stressed. Amino oxyacetic acid, an inhibitor of transamination reactions, did not prevent accumulation of excess glutamate.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- J L Botsford
- Department of Biology, New Mexico State University, Las Cruces 88003
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20
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Cullen PJ, Foster-Hartnett D, Gabbert KK, Kranz RG. Structure and expression of the alternative sigma factor, RpoN, in Rhodobacter capsulatus; physiological relevance of an autoactivated nifU2-rpoN superoperon. Mol Microbiol 1994; 11:51-65. [PMID: 8145646 DOI: 10.1111/j.1365-2958.1994.tb00289.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The alternative sigma factor, RpoN (sigma 54) is responsible for recruiting core RNA polymerase to the promoters of genes required for diverse physiological functions in a variety of eubacterial species. The RpoN protein in Rhodobacter capsulatus is a putative sigma factor specific for nitrogen fixation (nif) genes. Insertional mutagenesis was used to define regions important for the function of the R. capsulatus RpoN protein. Insertions of four amino acids in the predicted helixturn-helix or in the highly conserved C-terminal eight amino acid residues (previously termed the RpoN box), and an in-frame deletion of the glutamine-rich N-terminus completely inactivated the R. capsulatus RpoN protein. Two separate insertions in the second hydrophobic heptad repeat, a putative leucine zipper, resulted in a partially functional RpoN protein. Eight other linkers in the rpoN open reading frame (ORF) resulted in a completely or partially functional RpoN protein. The rpoN gene in R. capsulatus is downstream from the nifHDKU2 genes, in a nifU2-rpoN operon. Results of genetic experiments on the nifU2-rpoN locus show that the rpoN gene is organized in a nifU2-rpoN superoperon. A primary promoter directly upstream of the rpoN ORF is responsible for the initial expression of rpoN. Deletion analysis and insertional mutagenesis were used to define the primary promoter to 50 bp, between 37 and 87 nucleotides upstream of the predicted rpoN translational start site. This primary promoter is expressed constitutively with respect to nitrogen, and it is necessary and sufficient for growth under nitrogen-limiting conditions typically used in the laboratory. A secondary promoter upstream of nifU2 is autoactivated by RpoN and NifA to increase the expression of rpoN, which ultimately results in higher expression of RpoN-dependent genes. Moreover, rpoN expression from this secondary promoter is physiologically beneficial under certain stressful conditions, such as nitrogen-limiting environments that contain high salt (> 50 mM NaCl) or low iron (< 400 nM FeSO4).
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Affiliation(s)
- P J Cullen
- Department of Biology, Washington University, St. Louis, Missouri 63130
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21
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Espín G, Moreno S, Guzman J. Molecular genetics of the glutamine synthetases in Rhizobium species. Crit Rev Microbiol 1994; 20:117-23. [PMID: 7915906 DOI: 10.3109/10408419409113551] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Soil bacteria of the genus Rhizobium and Bradyrhizobium establish symbiotic interactions with leguminous plants that result in the formation of specialized structures, the nodules, in which the bacteria differentiate into bacteroids and fix nitrogen. Rhizobial glutamine synthetase (GS) activity is very low in the nodule. The ammonia produced by the bacteroids is exported to the plant cell, where it is assimilated by the GS from the plant, whereas in the free-living state, Rhizobium and Bradyrhizobium species assimilate ammonia for growth. Another characteristic of these species is that they possess two glutamine synthetase isozymes, known as GSI and GSII. A third glutamine synthetase isozyme, called GSIII, has been found in R. meliloti and R. etli.
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Affiliation(s)
- G Espín
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos
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22
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Cohen-Kupiec R, Gurevitz M, Zilberstein A. Expression of glnA in the cyanobacterium Synechococcus sp. strain PCC 7942 is initiated from a single nif-like promoter under various nitrogen conditions. J Bacteriol 1993; 175:7727-31. [PMID: 7902350 PMCID: PMC206936 DOI: 10.1128/jb.175.23.7727-7731.1993] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The glnA mRNA, encoding glutamine synthetase, is differentially accumulated in the cyanobacterium Synechococcus sp. strain PCC 7942 in media containing different nitrogen sources. With the different nitrogen compounds, transcription of glnA initiated at a single site located -146 nucleotides upstream of the translation start site of the gene. A similarity of the nif-like promoter of the glnA gene of Anabaena sp. strain PCC 7120 and a binding-site sequence for the Synechococcus sp. strain PCC 7942 transcription regulator, NtcA, were found upstream of the transcription initiation site.
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Affiliation(s)
- R Cohen-Kupiec
- Department of Botany, Tel Aviv University, Ramat-Aviv, Israel
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23
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Abstract
Frankia strains are N2-fixing actinomycetes whose isolation and cultivation were first reported in 1978. They induce N2-fixing root nodules on diverse nonleguminous (actinorhizal) plants that are important in ecological successions and in land reclamation and remediation. The genus Frankia encompasses a diverse group of soil actinomycetes that have in common the formation of multilocular sporangia, filamentous growth, and nitrogenase-containing vesicles enveloped in multilaminated lipid envelopes. The relatively constant morphology of vesicles in culture is modified by plant interactions in symbiosis to give a diverse array of vesicles shapes. Recent studies of the genetics and molecular genetics of these organisms have begun to provide new insights into higher-plant-bacterium interactions that lead to productive N2-fixing symbioses. Sufficient information about the relationship of Frankia strains to other bacteria, and to each other, is now available to warrant the creation of some species based on phenotypic and genetic criteria.
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Affiliation(s)
- D R Benson
- Department of Molecular and Cell Biology, University of Connecticut, Storrs 06269-3044
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24
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Labes M, Rastogi V, Watson R, Finan TM. Symbiotic nitrogen fixation by a nifA deletion mutant of Rhizobium meliloti: the role of an unusual ntrC allele. J Bacteriol 1993; 175:2662-73. [PMID: 8478331 PMCID: PMC204569 DOI: 10.1128/jb.175.9.2662-2673.1993] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
In the N2-fixing alfalfa symbiont Rhizobium meliloti, the three sigma 54 (NTRA)-dependent positively acting regulatory proteins NIFA, NTRC, and DCTD are required for activation of promoters involved in N2 fixation (pnifHDKE and pfixABCX), nitrogen assimilation (pglnII), and C4-dicarboxylate transport (pdctA), respectively. Here, we describe an allele of ntrC which results in the constitutive activation of the above NTRC-, NIFA-, and DCTD-regulated promoters. The expression and activation of wild-type NTRC occur in response to nitrogen availability, whereas in cells carrying the ntrC283 allele, the NTRC283 protein appears constitutively active and is constitutively expressed. The ntrC283 allele was shown to carry a single mutation resulting in the replacement of an Asp by a Tyr residue in the helix-turn-helix motif of ntrC283. Introduction of the ntrC283 allele into a nifA deletion mutant restores the N2-fixation ability to 70 to 80% of the wild-type level. Thus, the nifA gene is dispensable for symbiotic N2 fixation.
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Affiliation(s)
- M Labes
- McMaster University, Department of Biology, Hamilton, Ontario, Canada
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25
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Shatters R, Liu Y, Kahn M. Isolation and characterization of a novel glutamine synthetase from Rhizobium meliloti. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)54175-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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26
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Patriarca EJ, Chiurazzi M, Manco G, Riccio A, Lamberti A, De Paolis A, Rossi M, Defez R, Iaccarino M. Activation of the Rhizobium leguminosarum glnII gene by NtrC is dependent on upstream DNA sequences. ACTA ACUST UNITED AC 1992; 234:337-45. [PMID: 1357539 DOI: 10.1007/bf00538692] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The cloning and sequence determination is reported of the DNA region of Rhizobium leguminosarum coding for glutamine synthetase II (GSII). An open reading frame (ORF) encoding 326 amino acids was defined as the glnII gene on the basis of its similarity to other glnII genes and the ability of a DNA fragment carrying this ORF to complement the glutamine auxotrophy of a Klebsiella pneumoniae glnA mutant. We find that the glnII gene in R. leguminosarum is transcribed as a monocistronic unit from a single promoter, which shows structural features characteristic of rpoN (ntrA)-dependent promoters. In K. pneumoniae, such promoters require the ntrC and rpoN (ntrA) gene products for transcription. The intracellular level of glnII mRNA changes when R. leguminosarum is grown on different nitrogen sources, as expected for regulation by the nitrogen regulatory system. Promoter deletion analysis has shown that an extensive upstream DNA sequence (316 bp) is essential for in vivo activation of the glnII promoter in different biovars of R. leguminosarum. This DNA region requires a wild-type ntrC gene for activity and includes two conserved putative NtrC-binding site sequences. The results conclusively show that transcription from the R. leguminosarum glnII promoter is fully dependent on positive control by NtrC protein and on an upstream activator sequence (UAS).
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Affiliation(s)
- E J Patriarca
- International Institute of Genetics and Biophysics, CNR, Naples, Italy
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27
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Lundquist PO, Huss-Danell K. Immunological studies of glutamine synthetase inFrankia-Alnus incanasymbioses. FEMS Microbiol Lett 1992. [DOI: 10.1111/j.1574-6968.1992.tb05199.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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28
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Slooten JC, Stanley J. Molecular analysis of an essential gene upstream of rpoNin RhizobiumNGR234. FEMS Microbiol Lett 1991. [DOI: 10.1111/j.1574-6968.1991.tb04864.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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29
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Coppard JR, Merrick MJ. Cassette mutagenesis implicates a helix-turn-helix motif in promoter recognition by the novel RNA polymerase sigma factor sigma 54. Mol Microbiol 1991; 5:1309-17. [PMID: 1787787 DOI: 10.1111/j.1365-2958.1991.tb00777.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cassette mutagenesis has been used to study the role of a helix-turn-helix (HTH) motif in the novel RNA polymerase sigma factor sigma 54 of Klebsiella pneumoniae. Of the four residues which are predicted to be solvent-exposed in the second helix, the first (Glu-378) tolerated all substitutions, and some mutations of this residue increased expression from sigma 54-dependent promoters. Certain substitutions in the third exposed residue (Ser-382) produced a promoter-specific phenotype and all substitutions in the fourth residue (Arg-383) inactivated the protein, identifying this residue as being likely to be involved in base-specific interactions with the promoter. In vivo footprinting indicated that the inactive HTH mutants of sigma 54 were defective in interaction with both the -24 and -12 regions of the glnAp2 promoter.
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Affiliation(s)
- J R Coppard
- AFRC Nitrogen Fixation Laboratory, University of Sussex, Brighton, UK
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30
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Chiurazzi M, Iaccarino M. Transcriptional analysis of the glnB-glnA region of Rhizobium leguminosarum biovar viciae. Mol Microbiol 1990; 4:1727-35. [PMID: 2077357 DOI: 10.1111/j.1365-2958.1990.tb00550.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We report that the glnB and glnA genes of Rhizobium leguminosarum biovar viciae are preceded by promoters located upstream of each gene. We find the presence of a glnB-glnA and a glnA mRNA whose intracellular concentration changes two- to three-fold when R. leguminosarum is grown on different nitrogen sources. Primer extension analysis shows unique transcriptional initiation sites upstream of glnB and glnA. The glnB promoter is rpoN(ntrA)-dependent, while the glnA promoter does not contain a typical consensus sequence for previously described promoters. In Klebsiella pneumoniae the glnB promoter requires active ntrC and ntrA genes and a DNA fragment containing 53 nucleotides upstream of the transcription initiation site shows full promoter activity, thus indicating that no NtrC binding sites are necessary for this activation in the glnB upstream region.
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Affiliation(s)
- M Chiurazzi
- Istituto Internazionale di Genetica e Biofisica, CNR, Napoli, Italy
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31
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Abstract
Streptomyces hygroscopicus, which produces the glutamine synthetase inhibitor phosphinothricin, possesses at least two genes (glnA and glnB) encoding distinct glutamine synthetase isoforms (GSI and GSII). The glnB gene was cloned from S. hygroscopicus DNA by complementation in an Escherichia coli glutamine auxotrophic mutant (glnA). glnB was subcloned in Streptomyces plasmids by insertion into pIJ486 (pMSG3) and pIJ702 (pMSG5). Both constructions conferred resistance to the tripeptide form of phosphinothricin (bialaphos) and were able to complement a glutamine auxotrophic marker in S. coelicolor. Sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis of S. lividans(pMSG5) revealed a highly overexpressed 40-kilodalton protein. When GS was purified from this strain, it was indistinguishable in apparent molecular mass from the 40-kilodalton protein. The nucleic acid sequence of the cloned region contained an open reading frame which encoded a protein whose size, amino acid composition, and N-terminal sequence corresponded to those of the purified GS. glnB had a high G + C content and codon usage typical of streptomycete genes. A comparison of its predicted amino acid sequence with the protein data bases revealed that it encoded a GSII-type enzyme which had previously been found only in various eucaryotes (47 to 50% identity) and nodulating bacteria such as Bradyrhizobium spp. (42% identity). glnB had only 13 to 18% identity with eubacterial GSI enzymes. Southern blot hybridization experiments showed that sequences similar to glnB were present in all of the five other Streptomyces species tested, as well as Frankia species. These results do not support the previous suggestion that GSII-type enzymes found in members of the family Rhizobiaceae represent a unique example of interkingdom gene transfer associated with symbiosis in the nodule. Instead they imply that the presence of more than one gene encoding GS may be more common among soil microorganisms than previously appreciated.
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32
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New nucleotide sequence data on the EMBL File Server. Nucleic Acids Res 1989; 17:9511-24. [PMID: 2587282 PMCID: PMC335188 DOI: 10.1093/nar/17.22.9511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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33
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Somerville JE, Shatters RG, Kahn ML. Isolation, characterization, and complementation of Rhizobium meliloti 104A14 mutants that lack glutamine synthetase II activity. J Bacteriol 1989; 171:5079-86. [PMID: 2570058 PMCID: PMC210320 DOI: 10.1128/jb.171.9.5079-5086.1989] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The glutamine synthetase (GS)-glutamate synthase pathway is the primary route used by members of the family Rhizobiaceae to assimilate ammonia. Two forms of glutamine synthetase, GSI and GSII, are found in Rhizobium and Bradyrhizobium species. These are encoded by the glnA and glnII genes, respectively. Starting with a Rhizobium meliloti glnA mutant as the parent strain, we isolated mutants unable to grow on minimal medium with ammonia as the sole nitrogen source. For two auxotrophs that lacked any detectable GS activity, R. meliloti DNA of the mutated region was cloned and partially characterized. Lack of cross-hybridization indicated that the cloned regions were not closely linked to each other or to glnA; they therefore contain two independent genes needed for GSII synthesis or activity. One of the cloned regions was identified as glnII. An R. meliloti glnII mutant and an R. meliloti glnA glnII double mutant were constructed. Both formed effective nodules on alfalfa. This is unlike the B. japonicum-soybean symbiosis, in which at least one of these GS enzymes must be present for nitrogen-fixing nodules to develop. However, the R. meliloti double mutant was not a strict glutamine auxotroph, since it could grow on media that contained glutamate and ammonia, an observation that suggests that a third GS may be active in this species.
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Affiliation(s)
- J E Somerville
- Department of Microbiology, Washington State University, Pullman 99164-6340
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