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Tighilt L, Boulila F, De Sousa BFS, Giraud E, Ruiz-Argüeso T, Palacios JM, Imperial J, Rey L. The Bradyrhizobium Sp. LmicA16 Type VI Secretion System Is Required for Efficient Nodulation of Lupinus Spp. Microb Ecol 2022; 84:844-855. [PMID: 34697646 DOI: 10.1007/s00248-021-01892-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/30/2021] [Indexed: 05/06/2023]
Abstract
Many bacteria of the genus Bradyrhizobium are capable of inducing nodules in legumes. In this work, the importance of a type VI secretion system (T6SS) in a symbiotic strain of the genus Bradyrhizobium is described. T6SS of Bradyrhizobium sp. LmicA16 (A16) is necessary for efficient nodulation with Lupinus micranthus and Lupinus angustifolius. A mutant in the gene vgrG, coding for a component of the T6SS nanostructure, induced less nodules and smaller plants than the wild-type (wt) strain and was less competitive when co-inoculated with the wt strain. A16 T6SS genes are organized in a 26-kb DNA region in two divergent gene clusters of nine genes each. One of these genes codes for a protein (Tsb1) of unknown function but containing a methyltransferase domain. A tsb1 mutant showed an intermediate symbiotic phenotype regarding vgrG mutant and higher mucoidity than the wt strain in free-living conditions. T6SS promoter fusions to the lacZ reporter indicate expression in nodules but not in free-living cells grown in different media and conditions. The analysis of nodule structure revealed that the level of nodule colonization was significantly reduced in the mutants with respect to the wt strain.
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Affiliation(s)
- L Tighilt
- Laboratoire d'Ecologie Microbienne, Faculté Des Sciences de La Nature Et de La Vie, Université de Bejaia, 06000, Bejaia, Algeria
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
| | - F Boulila
- Laboratoire d'Ecologie Microbienne, Faculté Des Sciences de La Nature Et de La Vie, Université de Bejaia, 06000, Bejaia, Algeria
| | - B F S De Sousa
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
- Departamento de Biotecnología Y Biología Vegetal, ETSI Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - E Giraud
- IRD, Laboratoire Des Symbioses Tropicales Et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/Université de Montpellier/CIRAD, TA-A82/J-Campus International de Baillarguet, 34398Cedex 5, Montpellier, France
| | - T Ruiz-Argüeso
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
- Departamento de Biotecnología Y Biología Vegetal, ETSI Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - J M Palacios
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
- Departamento de Biotecnología Y Biología Vegetal, ETSI Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - J Imperial
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
- Instituto de Ciencias Agrarias, CSIC, 28006, Madrid, Spain
| | - L Rey
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain.
- Departamento de Biotecnología Y Biología Vegetal, ETSI Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain.
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Keller J, Imperial J, Ruiz-Argüeso T, Privet K, Lima O, Michon-Coudouel S, Biget M, Salmon A, Aïnouche A, Cabello-Hurtado F. RNA sequencing and analysis of three Lupinus nodulomes provide new insights into specific host-symbiont relationships with compatible and incompatible Bradyrhizobium strains. Plant Sci 2018; 266:102-116. [PMID: 29241560 DOI: 10.1016/j.plantsci.2017.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/11/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
Nitrogen fixation in the legume root-nodule symbiosis has a critical importance in natural and agricultural ecosystems and depends on the proper choice of the symbiotic partners. However, the genetic determinism of symbiotic specificity remains unclear. To study this process, we inoculated three Lupinus species (L. albus, L. luteus, L. mariae-josephae), belonging to the under-investigated tribe of Genistoids, with two Bradyrhizobium strains (B. japonicum, B. valentinum) presenting contrasted degrees of symbiotic specificity depending on the host. We produced the first transcriptomes (RNA-Seq) from lupine nodules in a context of symbiotic specificity. For each lupine species, we compared gene expression between functional and non-functional interactions and determined differentially expressed (DE) genes. This revealed that L. luteus and L. mariae-josephae (nodulated by only one of the Bradyrhizobium strains) specific nodulomes were richest in DE genes than L. albus (nodulation with both microsymbionts, but non-functional with B. valentinum) and share a higher number of these genes between them than with L. albus. In addition, a functional analysis of DE genes highlighted the central role of the genetic pathways controlling infection and nodule organogenesis, hormones, secondary, carbon and nitrogen metabolisms, as well as the implication of plant defence in response to compatible or incompatible Bradyrhizobium strains.
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Affiliation(s)
- J Keller
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - J Imperial
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Pozuelo de Alarcón, Madrid, Spain; Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - T Ruiz-Argüeso
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Pozuelo de Alarcón, Madrid, Spain
| | - K Privet
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - O Lima
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - S Michon-Coudouel
- Environmental and Human Genomics Platform, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - M Biget
- Environmental and Human Genomics Platform, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - A Salmon
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - A Aïnouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - F Cabello-Hurtado
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France.
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Palacios JM, Manyani H, Martínez M, Ureta AC, Brito B, Báscones E, Rey L, Imperial J, Ruiz-Argüeso T. Genetics and biotechnology of the H(2)-uptake [NiFe] hydrogenase from Rhizobium leguminosarum bv. viciae, a legume endosymbiotic bacterium. Biochem Soc Trans 2005; 33:94-6. [PMID: 15667275 DOI: 10.1042/bst0330094] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A limited number of strains belonging to several genera of Rhizobiaceae are capable of expressing a hydrogenase system that allows partial or full recycling of hydrogen evolved by nitrogenase, thus increasing the energy efficiency of the nitrogen fixation process. This review is focused on the genetics and biotechnology of the hydrogenase system from Rhizobium leguminosarum bv. viciae, a frequent inhabitant of European soils capable of establishing symbiotic association with peas, lentils, vetches and other legumes.
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Affiliation(s)
- J M Palacios
- Laboratorio de Microbiología, Department of Biotechnology, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain.
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Brito B, Baginsky C, Palacios JM, Cabrera E, Ruiz-Argüeso T, Imperial J. Biodiversity of uptake hydrogenase systems from legume endosymbiotic bacteria. Biochem Soc Trans 2005; 33:33-5. [PMID: 15667257 DOI: 10.1042/bst0330033] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Uptake hydrogenases in legume endosymbiotic bacteria recycle hydrogen produced during the nitrogen fixation process in legume nodules. Despite the described beneficial effect on plant productivity, the hydrogen oxidation capability is not widespread in the Rhizobiaceae family. Characterization of hydrogenase gene clusters in strains belonging to Rhizobium, Bradyrhizobium and Azorhizobium reveals a similar overall genetic organization along with important differences in gene regulation. In addition, phylogenetic analysis of hup genes indicates distinct evolutionary origins for hydrogenase genes in Rhizobia.
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Affiliation(s)
- B Brito
- Laboratorio de Microbiología, E.T.S. Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
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Brito B, Palacios JM, Imperial J, Ruiz-Argüeso T. Engineering the Rhizobium leguminosarum bv. viciae hydrogenase system for expression in free-living microaerobic cells and increased symbiotic hydrogenase activity. Appl Environ Microbiol 2002; 68:2461-7. [PMID: 11976122 PMCID: PMC127565 DOI: 10.1128/aem.68.5.2461-2467.2002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhizobium leguminosarum bv. viciae UPM791 induces hydrogenase activity in pea (Pisum sativum L.) bacteroids but not in free-living cells. The symbiotic induction of hydrogenase structural genes (hupSL) is mediated by NifA, the general regulator of the nitrogen fixation process. So far, no culture conditions have been found to induce NifA-dependent promoters in vegetative cells of this bacterium. This hampers the study of the R. leguminosarum hydrogenase system. We have replaced the native NifA-dependent hupSL promoter with the FnrN-dependent fixN promoter, generating strain SPF25, which expresses the hup system in microaerobic free-living cells. SPF25 reaches levels of hydrogenase activity in microaerobiosis similar to those induced in UPM791 bacteroids. A sixfold increase in hydrogenase activity was detected in merodiploid strain SPF25(pALPF1). A time course induction of hydrogenase activity in microaerobic free-living cells of SPF25(pALPF1) shows that hydrogenase activity is detected after 3 h of microaerobic incubation. Maximal hydrogen uptake activity was observed after 10 h of microaerobiosis. Immunoblot analysis of microaerobically induced SPF25(pALPF1) cell fractions indicated that the HupL active form is located in the membrane, whereas the unprocessed protein remains in the soluble fraction. Symbiotic hydrogenase activity of strain SPF25 was not impaired by the promoter replacement. Moreover, bacteroids from pea plants grown in low-nickel concentrations induced higher levels of hydrogenase activity than the wild-type strain and were able to recycle all hydrogen evolved by nodules. This constitutes a new strategy to improve hydrogenase activity in symbiosis.
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Affiliation(s)
- B Brito
- Laboratorio de Microbiología, E. T. S. Ingenieros Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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Báscones E, Imperial J, Ruiz-Argüeso T, Palacios JM. Generation of new hydrogen-recycling Rhizobiaceae strains by introduction of a novel hup minitransposon. Appl Environ Microbiol 2000; 66:4292-9. [PMID: 11010872 PMCID: PMC92298 DOI: 10.1128/aem.66.10.4292-4299.2000] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hydrogen evolution by nitrogenase is a source of inefficiency for the nitrogen fixation process by the Rhizobium-legume symbiosis. To develop a strategy to generate rhizobial strains with H(2)-recycling ability, we have constructed a Tn5 derivative minitransposon (TnHB100) that contains the ca. 18-kb H(2) uptake (hup) gene cluster from Rhizobium leguminosarum bv. viciae UPM791. Bacteroids from TnHB100-containing strains of R. leguminosarum bv. viciae PRE, Bradyrhizobium japonicum, R. etli, and Mesorhizobium loti expressed high levels of hydrogenase activity that resulted in full recycling of the hydrogen evolved by nitrogenase in nodules. Efficient processing of the hydrogenase large subunit (HupL) in these strains was shown by immunoblot analysis of bacteroid extracts. In contrast, Sinorhizobium meliloti, M. ciceri, and R. leguminosarum bv. viciae UML2 strains showed poor expression of the hup system that resulted in H(2)-evolving nodules. For the latter group of strains, no immunoreactive material was detected in bacteroid extracts using anti-HupL antiserum, suggesting a low level of transcription of hup genes or HupL instability. A general procedure for the characterization of the minitransposon insertion site and removal of antibiotic resistance gene included in TnHB100 has been developed and used to generate engineered strains suitable for field release.
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Affiliation(s)
- E Báscones
- Laboratorio de Microbiología, Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
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Colombo MV, Gutiérrez D, Palacios JM, Imperial J, Ruiz-Argüeso T. A novel autoregulation mechanism of fnrN expression in Rhizobium leguminosarum bv viciae. Mol Microbiol 2000; 36:477-86. [PMID: 10792733 DOI: 10.1046/j.1365-2958.2000.01867.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The fnrN gene from Rhizobium leguminosarum UPM791 controls microaerobic expression of both nitrogen fixation and hydrogenase activities in symbiotic cells. Two copies of fnrN are present in this strain, one chromosomal (fnrN1) and the other located in the symbiotic plasmid (fnrN2). Their expression was studied by cloning the regulatory regions in lacZ promoter-probe vectors. The fnrN genes were found to be autoregulated: they are expressed only at basal levels under aerobic conditions; they are highly expressed under microaerobic conditions; and they are expressed at basal levels in the double mutant DG2 (fnrN1 fnrN2) under any condition. The promoters of both genes contain two FnrN-binding sequences (anaeroboxes), centred at positions -12.5 (proximal anaerobox) and -44.5 (distal anaerobox). Expression analysis and gel retardation experiments with fnrN1-derivative promoter mutants altered in key bases of the anaerobox sequences demonstrated that binding of FnrN1 to the distal anaerobox is necessary for microaerobic activation of transcription, and that binding of FnrN1 to the proximal anaerobox results in transcriptional repression. The apparent affinity of FnrN1 for the proximal anaerobox was fivefold lower than for the distal anaerobox, resulting in repression of transcription of fnrN1 only at high-FnrN1 concentrations. This positive and negative autoregulation mechanism ensures an equilibrated expression of fnrN in response to microaerobic conditions.
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Affiliation(s)
- M V Colombo
- Laboratorio de Microbiología, E.T.S. Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria, s/n, 28040 Madrid, Spain
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Brito B, Monza J, Imperial J, Ruiz-Argüeso T, Palacios JM. Nickel availability and hupSL activation by heterologous regulators limit symbiotic expression of the Rhizobium leguminosarum bv. viciae hydrogenase system in Hup(-) rhizobia. Appl Environ Microbiol 2000; 66:937-42. [PMID: 10698755 PMCID: PMC91926 DOI: 10.1128/aem.66.3.937-942.2000] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A limited number of Rhizobium and Bradyrhizobium strains possess a hydrogen uptake (Hup) system that recycles the hydrogen released from the nitrogen fixation process in legume nodules. To extend this ability to rhizobia that nodulate agronomically important crops, we investigated factors that affect the expression of a cosmid-borne Hup system from Rhizobium leguminosarum bv. viciae UPM791 in R. leguminosarum bv. viciae, Rhizobium etli, Mesorhizobium loti, and Sinorhizobium meliloti Hup(-) strains. After cosmid pAL618 carrying the entire hup system of strain UPM791 was introduced, all recipient strains acquired the ability to oxidize H(2) in symbioses with their hosts, although the levels of hydrogenase activity were found to be strain and species dependent. The levels of hydrogenase activity were correlated with the levels of nickel-dependent processing of the hydrogenase structural polypeptides and with transcription of structural genes. Expression of the NifA-dependent hupSL promoter varied depending on the genetic background, while the hyp operon, which is controlled by the FnrN transcriptional regulator, was expressed at similar levels in all recipient strains. With the exception of the R. etli-bean symbiosis, the availability of nickel to bacteroids strongly affected hydrogenase processing and activity in the systems tested. Our results indicate that efficient transcriptional activation by heterologous regulators and processing of the hydrogenase as a function of the availability of nickel to the bacteroid are relevant factors that affect hydrogenase expression in heterologous rhizobia.
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Affiliation(s)
- B Brito
- Laboratorio de Microbiología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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Van Soom C, Lerouge I, Vanderleyden J, Ruiz-Argüeso T, Palacios JM. Identification and characterization of hupT, a gene involved in negative regulation of hydrogen oxidation in Bradyrhizobium japonicum. J Bacteriol 1999; 181:5085-9. [PMID: 10438783 PMCID: PMC94000 DOI: 10.1128/jb.181.16.5085-5089.1999] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Bradyrhizobium japonicum hupT gene was sequenced, and its gene product was found to be homologous to NtrB-like histidine kinases. A hupT mutant expresses higher levels of hydrogenase activity than the wild-type strain under hydrogenase-inducing conditions (i.e., microaerobiosis plus hydrogen, or symbiosis), whereas in noninduced hupT cells, hupSL expression is derepressed but does not lead to hydrogenase activity. We conclude that HupT is involved in the repression of HupSL synthesis at the transcriptional level but that enzymatic activation requires inducing conditions.
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Affiliation(s)
- C Van Soom
- F. A. Janssens Laboratory of Genetics, Katholieke Universiteit Leuven, B-3001 Heverlee, Belgium
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Hernando Y, Palacios J, Imperial J, Ruiz-Argüeso T. Rhizobium leguminosarum bv. viciae hypA gene is specifically expressed in pea (Pisum sativum) bacteroids and required for hydrogenase activity and processing. FEMS Microbiol Lett 1998; 169:295-302. [PMID: 9868773 DOI: 10.1111/j.1574-6968.1998.tb13332.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Rhizobium leguminosarum bv. viciae strain UPM791 induces in symbiosis with peas the synthesis of a nickel-containing hydrogenase which recycles the hydrogen evolved by nitrogenase. The genes required for synthesis of this hydrogenase, hupSLCDEFGHIJKhypABFCDEX, are clustered in the symbiotic plasmid. Analysis of a hypA-deficient mutant showed that HypA is essential for symbiotic hydrogenase activity and required for correct processing of the hydrogenase large subunit. Unlike other microoxically induced hyp genes, the hypA gene was only expressed in pea bacteroids from its own promoter. The hypA mRNA 5' end was mapped 109 bp upstream of the translational start codon. This distinct pattern of expression suggests a different role for HypA and the remaining Hyp proteins in hydrogenase synthesis.
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Affiliation(s)
- Y Hernando
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Spain
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Gutiérrez D, Hernando Y, Palacios JM, Imperial J, Ruiz-Argüeso T. FnrN controls symbiotic nitrogen fixation and hydrogenase activities in Rhizobium leguminosarum biovar viciae UPM791. J Bacteriol 1997; 179:5264-70. [PMID: 9286975 PMCID: PMC179391 DOI: 10.1128/jb.179.17.5264-5270.1997] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Rhizobium leguminosarum bv. viciae UPM791 contains a second copy of the fnrN gene, which encodes a redox-sensitive transcriptional activator functionally homologous to Escherichia coli Fnr. This second copy (fnrN2) is located in the symbiotic plasmid, while fnrN1 is in the chromosome. Isolation and sequencing of the fnrN2 gene revealed that the deduced amino acid sequence of FnrN2 is 87.5% identical to the sequence of FnrN1, including a conserved cysteine-rich motif characteristic of Fnr-like proteins. Individual R. leguminosarum fnrN1 and fnrN2 mutants exhibited a Fix+ phenotype and near wild-type levels of nitrogenase and hydrogenase activities in pea (Pisum sativum L.) nodules. In contrast, an fnrN1 fnrN2 double mutant formed ineffective nodules lacking both nitrogenase and hydrogenase activities. Unlike the wild-type strain and single fnrN1 or fnrN2 mutants, the fnrN1 fnrN2 double mutant was unable to induce micro-oxic or bacteroid activation of the hypBFCDEX operon, which encodes proteins essential for hydrogenase synthesis. In the search for symbiotic genes that could be controlled by FnrN, a fixNOQP operon, putatively encoding a micro-oxically induced, bacteroid-specific cbb3-type terminal cytochrome oxidase, was isolated from strain UPM791 and partially sequenced. The fixNOQP operon was present in a single copy located in the symbiotic plasmid, and an anaerobox was identified in the fixN promoter region. Consistent with this, a fixNOQP'-lacZ fusion was shown to be highly induced in micro-oxic cells of the wild-type strain. A high level of micro-oxic induction was also observed in single fnrN1 and fnrN2 mutants, but no detectable induction was observed in the fnrN1 fnrN2 double mutant. The lack of expression of fixNOQP in the fnrN1 fnrN2 double mutant is likely to cause the observed Fix- phenotype. These data demonstrate that, contrary to the situation in other rhizobia, FnrN controls both hydrogenase and nitrogenase activities of R. leguminosarum bv. viciae UPM791 in the nodule and suggest that this strain lacks a functional fixK gene.
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Affiliation(s)
- D Gutiérrez
- Laboratorio de Microbiología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Spain
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Brito B, Martínez M, Fernández D, Rey L, Cabrera E, Palacios JM, Imperial J, Ruiz-Argüeso T. Hydrogenase genes from Rhizobium leguminosarum bv. viciae are controlled by the nitrogen fixation regulatory protein nifA. Proc Natl Acad Sci U S A 1997; 94:6019-24. [PMID: 9177161 PMCID: PMC20993 DOI: 10.1073/pnas.94.12.6019] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/1996] [Accepted: 04/07/1997] [Indexed: 02/04/2023] Open
Abstract
Rhizobium leguminosarum bv. viciae expresses an uptake hydrogenase in symbiosis with peas (Pisum sativum) but, unlike all other characterized hydrogen-oxidizing bacteria, cannot express it in free-living conditions. The hydrogenase-specific transcriptional activator gene hoxA described in other species was shown to have been inactivated in R. leguminosarum by accumulation of frameshift and deletion mutations. Symbiotic transcription of hydrogenase structural genes hupSL originates from a -24/-12 type promoter (hupSp). A regulatory region located in the -173 to -88 region was essential for promoter activity in R. leguminosarum. Activation of hupSp was observed in Klebsiella pneumoniae and Escherichia coli cells expressing the K. pneumoniae nitrogen fixation regulator NifA, and in E. coli cells expressing R. meliloti NifA. This activation required direct interaction of NifA with the essential -173 to -88 regulatory region. However, no sequences resembling known NifA-binding sites were found in or around this region. NifA-dependent activation was also observed in R. etli bean bacteroids. NifA-dependent hupSp activity in heterologous hosts was also absolutely dependent on the RpoN sigma-factor and on integration host factor. Proteins immunologically related to integration host factor were identified in R. leguminosarum. The data suggest that hupSp is structurally and functionally similar to nitrogen fixation promoters. The requirement to coordinate nitrogenase-dependent H2 production and H2 oxidation in nodules might be the reason for the loss of HoxA in R. leguminosarum and the concomitant NifA control of hup gene expression. This evolutionary acquired control would ensure regulated synthesis of uptake hydrogenase in the most common H2-rich environment for rhizobia, the legume nodule.
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Affiliation(s)
- B Brito
- Laboratorio de Microbiología, Escuela Técnica Superior Ingenieros Agrónomos, Universidad Politécnica de Madrid, Spain
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Rey L, Fernández D, Brito B, Hernando Y, Palacios JM, Imperial J, Ruiz-Argüeso T. The hydrogenase gene cluster of Rhizobium leguminosarum bv. viciae contains an additional gene (hypX), which encodes a protein with sequence similarity to the N10-formyltetrahydrofolate-dependent enzyme family and is required for nickel-dependent hydrogenase processing and activity. Mol Gen Genet 1996; 252:237-48. [PMID: 8842143 DOI: 10.1007/bf02173769] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Plasmid pAL618 contains the genetic determinants for H2 uptake (hup) from Rhizobium leguminosarum bv. viciae, including a cluster of 17 genes named hupSLCDEFGHIJK-hypABFCDE. A 1.7-kb segment of insert DNA located downstream of hypE has now been sequenced, thus completing the sequence of the 20441-bp insert DNA in plasmid pAL618. An open reading frame (designated hypX) encoding a protein with a calculated M(r) of 62300 that exhibits extensive sequence similarity with HoxX from Alcaligenes eutrophus (52% identity) and Bradyrhizobium japonicum (57% identity) was identified 10 bp downstream of hypE. Nodule bacteroids produced by hypX mutants in pea (Pisum sativum L.) plants grown at optimal nickel concentrations (100 microM) for hydrogenase expression, exhibited less than 5% of the wild-type levels of hydrogenase activity. These bacteroids contained wild-type levels of mRNA from hydrogenase structural genes (hupSL) but accumulated large amounts of the immature form of HupL protein. The Hup-deficient mutants were complemented for normal hydrogenase activity and nickel-dependent maturation of HupL by a hypX gene provided in trans. From expression analysis of hypX-lacZ fusion genes, it appears that hypX gene is transcribed from the FnrN-dependent hyp promoter, thus placing hypX in the hyp operon (hypBFCDEX). Comparisons of the HypX/HoxX sequences with those in databases provided unexpected insights into their function in hydrogenase synthesis. Similarities were restricted to two distinct regions in the HypX/HoxX sequences. Region I, corresponding to a sequence conserved in N10-formyltetrahydrofolate-dependent enzymes involved in transferring one-carbon units (C1), was located in the N-terminal half of the protein, whereas region II, corresponding to a sequence conserved in enzymes of the enoyl-CoA hydratase/isomerase family, was located in the C-terminal half. These similarities strongly suggest that HypX/HoxX have dual functions: binding of the C1 donor N10-formyltetrahydrofolate and transfer of the C1 to an unknown substrate, and catalysis of a reaction involving polarization of the C = O bond of an X-CO-SCoA substrate. These results also suggest the involvement of a small organic molecule, possibly synthesized with the participation of an X-CO-SCoA precursor and of formyl groups, in the synthesis of the metal-containing active centre of hydrogenase.
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Affiliation(s)
- L Rey
- Laboratorio de Microbiologia, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Spain
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Brito B, Palacios JM, Ruiz-Argüeso T, Imperial J. Identification of a gene for a chemoreceptor of the methyl-accepting type in the symbiotic plasmid of Rhizobium leguminosarum bv. viciae UPM791. Biochim Biophys Acta 1996; 1308:7-11. [PMID: 8765742 DOI: 10.1016/0167-4781(96)00083-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The 4 kb DNA region located immediately upstream of the Rhizobium leguminosarum bv. viciae UPM791 hydrogen structural genes was sequenced and found to encode a chemoreceptor of the methyl-accepting type, the first to be described in a rhizobial symbiotic plasmid. Two additional open reading frames were found. Their protein products showed sequence homology to dehydrogenases and isomerases involved in the metabolism of aromatic compounds. Mutant analysis showed that this region is not required for hydrogenase activity.
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Affiliation(s)
- B Brito
- Laboratorio de Microbiología. Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Spain
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Hernando Y, Palacios JM, Imperial J, Ruiz-Argüeso T. The hypBFCDE operon from Rhizobium leguminosarum biovar viciae is expressed from an Fnr-type promoter that escapes mutagenesis of the fnrN gene. J Bacteriol 1995; 177:5661-9. [PMID: 7559356 PMCID: PMC177378 DOI: 10.1128/jb.177.19.5661-5669.1995] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Pea (Pisum sativum L.) bacteroids produced by Rhizobium leguminosarum bv. viciae UPM791 synthesize a membrane-bound (NiFe) hydrogenase which oxidizes H2 arising from the nitrogen fixation process in root nodules. Synthesis of the active enzyme requires the products of the structural genes hupSL and an array of accessory proteins from at least 15 additional genes, including the gene cluster hypABFCDE, likely involved in nickel metabolism. Unlike the hupSL genes, which are expressed only in symbiosis, the hypBFCDE operon was also activated in vegetative cells in response to low pO2 in the culture medium. In microaerobic cells and in bacteroids, transcription of the hypBFCDE operon occurred from a promoter, P5b, with a transcription initiation site located 190 bp upstream of the ATG start codon of hypB, within the coding sequence of hypA. Transcription start site 5b was preceded by an Fnr box (anaerobox), 5'-TTGAgccatgTCAA-3', centered at position -39.5. Expression of the P5b promoter in the heterologous Rhizobium meliloti bacterial host was dependent on the presence of an active fixK gene. A 2.6-kb EcoRI fragment was isolated from an R. leguminosarum bv. viciae UPM791 gene bank by complementing an R. meliloti FixK- mutant. Sequencing of this DNA fragment identified an fnrN gene, and cassette insertion mutagenesis demonstrated that R. leguminosarum bv. viciae fnrN is able to replace the R. meliloti fixK gene for activation of both the R. leguminosarum bv. viciae hypBFCDE operon and the R. meliloti fix genes. However, bacteroids from a genomic FnrN- mutant of R. leguminosarum bv. viciae exhibited wild-type levels of hydrogenase activity. Microaerobic expression of P(5b) was reduced to ca. 50% of the wild-type level in the FnrN(-) mutant. These results indicate that hyp gene expression escapes mutagenesis of the fnrN gene and suggest the existence of a second fnr-like gene in R. leguminosarum by. viciae. Southern blot analysis with an fnrN internal probe revealed the presence of a second genomic region with homology to fnrN.
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Affiliation(s)
- Y Hernando
- Laboratorio de Microbiología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Spain
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Rey L, Imperial J, Palacios JM, Ruiz-Argüeso T. Purification of Rhizobium leguminosarum HypB, a nickel-binding protein required for hydrogenase synthesis. J Bacteriol 1994; 176:6066-73. [PMID: 7928968 PMCID: PMC196826 DOI: 10.1128/jb.176.19.6066-6073.1994] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The products of the Rhizobium leguminosarum hyp gene cluster are necessary for synthesis of a functional uptake [NiFe] hydrogenase system in symbiosis with pea plants, and at least for HypB and HypF, a role in hydrogenase-specific nickel metabolism has been postulated (L. Rey, J. Murillo, Y. Hernando, E. Hidalgo, E. Cabrera, J. Imperial, and T. Ruiz-Argüeso, Mol. Microbiol. 8:471-481, 1993). The R. leguminosarum hypB gene product has been overexpressed in Escherichia coli and purified by immobilized nickel chelate affinity chromatography in a single step. The purified recombinant HypB protein was able to bind 3.9 +/- 0.1 Ni2+ ions per HypB monomer in solution. Co2+, Cu2+, and Zn2+ ions competed with Ni2+ with increasing efficiency. Monospecific HypB antibodies were raised and used to show that HypB is synthesized in R. leguminosarum microaerobic vegetative cells and pea bacteroids but not in R. leguminosarum aerobic cells. HypB protein synthesized by R. leguminosarum microaerobic vegetative cells could also be isolated by immobilized nickel chelate affinity chromatography. A histidine-rich region at the amino terminus of the protein (23-HGHHHH DGHHDHDHDHDHHRGDHEHDDHHH-54) is proposed to play a role in nickel binding, both in solution and in chelated form.
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Affiliation(s)
- L Rey
- Laboratorio de Microbiología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Spain
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Brito B, Palacios JM, Hidalgo E, Imperial J, Ruiz-Argüeso T. Nickel availability to pea (Pisum sativum L.) plants limits hydrogenase activity of Rhizobium leguminosarum bv. viciae bacteroids by affecting the processing of the hydrogenase structural subunits. J Bacteriol 1994; 176:5297-303. [PMID: 8071205 PMCID: PMC196714 DOI: 10.1128/jb.176.17.5297-5303.1994] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Rhizobium leguminosarum bv. viciae UPM791 induces the synthesis of an [NiFe] hydrogenase in pea (Pisum sativum L.) bacteroids which oxidizes the H2 generated by the nitrogenase complex inside the root nodules. The synthesis of this hydrogenase requires the genes for the small and large hydrogenase subunits (hupS and hupL, respectively) and 15 accessory genes clustered in a complex locus in the symbiotic plasmid. We show here that the bacteroid hydrogenase activity is limited by the availability of nickel to pea plants. Addition of Ni2+ to plant nutrient solutions (up to 10 mg/liter) resulted in sharp increases (up to 15-fold) in hydrogenase activity. This effect was not detected when other divalent cations (Zn2+, Co2+, Fe2+, and Mn2+) were added at the same concentrations. Determinations of the steady-state levels of hupSL-specific mRNA indicated that this increase in hydrogenase activity was not due to stimulation of transcription of structural genes. Immunoblot analysis with antibodies raised against the large and small subunits of the hydrogenase enzyme demonstrated that in the low-nickel situation, both subunits are mainly present in slow-migrating, unprocessed forms. Supplementation of the plant nutrient solution with increasing nickel concentrations caused the conversion of the slow-migrating forms of both subunits into fast-moving, mature forms. This nickel-dependent maturation process of the hydrogenase subunits is mediated by accessory gene products, since bacteroids from H2 uptake-deficient mutants carrying Tn5 insertions in hupG and hupK and in hypB and hypE accumulated the immature forms of both hydrogenase subunits even in the presence of high nickel levels.
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Affiliation(s)
- B Brito
- Laboratorio de Microbiología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Spain
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18
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Imperial J, Rey L, Palacios JM, Ruiz-Argüeso T. HupK, a hydrogenase-ancillary protein from Rhizobium leguminosarum, shares structural motifs with the large subunit of NiFe hydrogenases and could be a scaffolding protein for hydrogenase metal cofactor assembly. Mol Microbiol 1993; 9:1305-6. [PMID: 7934943 DOI: 10.1111/j.1365-2958.1993.tb01260.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Rey L, Murillo J, Hernando Y, Hidalgo E, Cabrera E, Imperial J, Ruiz-Argüeso T. Molecular analysis of a microaerobically induced operon required for hydrogenase synthesis in Rhizobium leguminosarum biovar viciae. Mol Microbiol 1993; 8:471-81. [PMID: 8326860 DOI: 10.1111/j.1365-2958.1993.tb01591.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The nucleotide sequence (6138 bp) of a microaerobically inducible region (hupV/VI) from the Rhizobium leguminosarum bv. viciae hydrogenase gene cluster has been determined. Six genes, arranged as a single operon, were identified, and designated hypA, B, F, C, D and E based on the sequence similarities of all of them, except hypF, to genes from the hydrogenase pleiotropic operon (hyp) from Escherichia coli. The gene products from hypBFCDE were identified by in vivo expression analysis in E. coli, and their molecular sizes were consistent with those predicted from the nucleotide sequence. Transposon Tn5 insertions into hypB, hypF, hypD and hypE resulted in R. leguminosarum mutants that lacked any hydrogenase activity in symbiosis with peas, but still were able to synthesize the polypeptide for the hydrogenase large subunit. The gene products HypA, HypB, HypF and HypD contained CX2C motifs characteristic of metal-binding proteins. In addition, HypB bore a long histidine-rich stretch of amino acids near the N-terminus, suggesting a possible role in nickel binding for this protein. The gene product HypF, which was translationally coupled to HypB, presented two cysteine motifs (CX2CX18CX2C) with a capacity to form zinc finger-like structures in the N-terminal third of the protein. A role in nickel metabolism in relation to hydrogenase synthesis is postulated for proteins HypB and HypF.
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Affiliation(s)
- L Rey
- Departamento de Microbiología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica, Madrid, Spain
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Rey L, Hidalgo E, Palacios J, Ruiz-Argüeso T. Nucleotide sequence and organization of an H2-uptake gene cluster from Rhizobium leguminosarum bv. viciae containing a rubredoxin-like gene and four additional open reading frames. J Mol Biol 1992; 228:998-1002. [PMID: 1469733 DOI: 10.1016/0022-2836(92)90886-o] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The nucleotide sequence of a 3.2 kb region following the hydrogenase structural operon (hupSLCDEF) in the H2-uptake gene cluster from Rhizobium leguminosarum by viciae strain 128C53 has been determined. Five closely linked genes encoding products of 16.3 (HupG), 30.5 (HupH), 8.0 (HupI), 18.4 (HupJ) and 38.7 (HupK) kDa were identified 166 bp downstream from hupF. Transposon insertions into hupG, hupH, hupJ and hupK suppress the H2-oxidizing capability of the wild-type strain. The amino acid sequence deduced from hupI contains two Cys-X-X-Cys motifs, characteristic of rubredoxins, separated by 29 amino acid residues showing strong sequence homology with other bacterial rubredoxins. The amino acid-derived sequence from hupG and hupH showed homology to products from genes hyaE and hyaF of the operon encoding hydrogenase 1 from Escherichia coli, and hupJ and hupK were related to open reading frames identified in Rhodobacter capsulatus and Azotobacter vinelandii hydrogenase gene clusters. An involvement of the hupGHIJK gene cluster in redox reactions related to hydrogenase synthesis or activity is predicted on the basis of the function as electron carrier attributed to rubredoxin.
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Affiliation(s)
- L Rey
- Departamento de Microbiología, ETS de Ingenieros Agrónomos-UPM, Madrid, Spain
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21
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Hidalgo E, Palacios JM, Murillo J, Ruiz-Argüeso T. Nucleotide sequence and characterization of four additional genes of the hydrogenase structural operon from Rhizobium leguminosarum bv. viciae. J Bacteriol 1992; 174:4130-9. [PMID: 1597428 PMCID: PMC206125 DOI: 10.1128/jb.174.12.4130-4139.1992] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The nucleotide sequence of a 2.5-kbp region following the hydrogenase structural genes (hupSL) in the H2 uptake gene cluster from Rhizobium leguminosarum bv. viciae UPM791 was determined. Four closely linked genes encoding peptides of 27.9 (hupC), 22.1 (hupD), 19.0 (hupE), and 10.4 (hupF) kDa were identified immediately downstream of hupL. Proteins with comparable apparent molecular weights were detected by heterologous expression of these genes in Escherichia coli. The six genes, hupS to hupF, are arranged as an operon, and by mutant complementation analysis, it was shown that genes hupSLCD are cotranscribed. A transcription start site preceded by the -12 to -24 consensus sequence characteristic of NtrA-dependent promoters was identified upstream of hupS. On the basis of the lack of oxygen-dependent H2 uptake activity of a hupC::Tn5 mutant and on structural characteristics of the protein, we postulate that HupC is a b-type cytochrome involved in electron transfer from hydrogenase to oxygen. The product from hupE, which is needed for full hydrogenase activity, exhibited characteristics typical of a membrane protein. The features of HupC and HupE suggest that they form, together with the hydrogenase itself, a membrane-bound protein complex involved in hydrogen oxidation.
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Affiliation(s)
- E Hidalgo
- Departamento de Microbiología, Escuela Técnica Superior de Ingenieros Agrónomos, Madrid, Spain
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Palacios JM, Murillo J, Leyva A, Ditta G, Ruiz-Argüeso T. Differential expression of hydrogen uptake (hup) genes in vegetative and symbiotic cells of Rhizobium leguminosarum. Mol Gen Genet 1990; 221:363-70. [PMID: 2166228 DOI: 10.1007/bf00259401] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The genetic determinants responsible for H2-uptake (hup genes) in Rhizobium leguminosarum are organized in six transcriptional units, designated regions hupI to hupVI, with region hupI coding for the hydrogenase structural genes (Leyva et al. 1990). Regulation of the expression of hup genes from R. leguminosarum was examined by using hup-lacZ fusions and mRNA dot-blot analysis. None of the six hup regions is transcribed in vegetative cells grown under normal aerobic conditions, whereas all six regions are transcribed in pea bacteroids. Additionally, exposure of cell cultures to low oxygen tensions specifically induces the expression of regions hupV and hupVI. By studying the expression of hupV- and hupVI-lacZ fusions in R. meliloti mutants it was determined that the microaerobic induction of these two regions is dependent on the regulatory fixLJ system, and that this control is exerted through fixK. Such expression was also shown to be nifA and ntrA independent. The functions of the hupV and hupVI gene products are unknown. The possibility that they play a regulatory role in hup gene expression is unlikely, since pea bacteroids from R. leguminosarum Hup- mutants carrying Tn5 insertions in regions hupV and hupVI contained normal levels of mRNA transcripts corresponding to the remaining hup regions.
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Affiliation(s)
- J M Palacios
- Laboratorio de Microbiología, Escuela Técnica Superior de Ingenieros Agrónomos, Madrid, Spain
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Mozo T, Cabrera E, Ruiz-Argüeso T. Isolation of the replication DNA region from a Rhizobium plasmid and examination of its potential as a replicon for Rhizobiaceae cloning vectors. Plasmid 1990; 23:201-15. [PMID: 2217572 DOI: 10.1016/0147-619x(90)90052-e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The DNA region essential for replication and stability of a native plasmid (pTM5) from Rhizobium sp. (Hedysarum) has been identified and isolated within a 5.4-kb PstI restriction fragment. The isolation of this region was accomplished by cloning endonuclease-restricted pTM5 DNA into a ColE1-type replicon and selecting the recombinant plasmids containing the pTM5 replicator (pTM5 derivative plasmids) by their ability to replicate in Rhizobium. DNA homology studies revealed that pTM5-like replicons are present in cryptic plasmids from some Rhizobium sp. (Hedysarum) strains but not in plasmids from strains of other Rhizobium species or Agrobacterium tumefaciens. The pTM5 derivative plasmids were able to replicate in Escherichia coli and A. tumefaciens and in a wide range of Rhizobium species. On the basis of stability assays in the absence of antibiotic selective pressure, the pTM5 derivative plasmids were shown to be highly stable in both free-living and symbiotic cells of Rhizobium sp. (Hedysarum). The stability of these plasmids in other species of Rhizobium and in A. tumefaciens varied depending on the host and on the plasmid. Most pTM5 derivative plasmids tested showed significantly higher symbiotic stability than RK2 derivative plasmids pRK290 and pAL618 in Rhizobium sp. (Hedysarum), R. meliloti, and R. leguminosarum by. phaseoli. Consequently, we consider that the constructed pTM5 derivative plasmids are potentially useful as cloning vectors for Rhizobiaceae.
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Affiliation(s)
- T Mozo
- Laboratorio de Microbiología, ETS Ingenieros Agrónomos, Universidad Politécnica, Madrid, Spain
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Murillo J, Villa A, Chamber M, Ruiz-Argüeso T. Occurrence of H(2)-Uptake Hydrogenases in Bradyrhizobium sp. (Lupinus) and Their Expression in Nodules of Lupinus spp. and Ornithopus compressus. Plant Physiol 1989; 89:78-85. [PMID: 16666550 PMCID: PMC1055800 DOI: 10.1104/pp.89.1.78] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Fifty-four strains of Bradyrhizobium sp. (Lupinus) from worldwide collections were screened by a colony hybridization method for the presence of DNA sequences homologous to the structural genes of the Bradyrhizobium japonicum hydrogenase. Twelve strains exhibited strong colony hybridization signals, and subsequent Southern blot hybridization experiments showed that they fell into two different groups on the basis of the pattern of EcoRI fragments containing the homology to the hup probe. All strains in the first group (UPM860, UPM861, and 750) expressed uptake hydrogenase activity in symbiosis with Lupinus albus, Lupinus angustifolius, Lupinus luteus, and Ornithopus compressus, but both the rate of H(2) uptake by bacteroids and the relative efficiency of N(2) fixation (RE = 1 - [H(2) evolved in air/acetylene reduced]) by nodules were markedly affected by the legume host. L. angustifolius was the less permissive host for hydrogenase expression in symbiosis with the three strains (average RE = 0.76), and O. compressus was the more permissive (average RE = 1.0). None of the strains in the second group expressed hydrogenase activity in lupine nodules, and only one exhibited low H(2)-uptake activity in symbiosis with O. compressus. The inability of these putative Hup(+) strains to induce hydrogenase activity in lupine nodules is discussed on the basis of the legume host effect. Among the 42 strains showing no homology to the B. japonicum hup-specific probe in the colony hybridization assay, 10 were examined in symbiosis with L. angustifolius. The average RE for these strains was 0.51. However, one strain, IM43B, exhibited high RE values (higher than 0.80) and high levels of hydrogenase activity in symbiosis with L. angustifolius, L. albus, and L. luteus. In Southern blot hybridization experiments, no homology was detected between the B. japonicum hup-specific DNA probe and total DNA from vegetative cells or bacteroids from strain IM43B even under low stringency hybridization conditions. We conclude from these results that strain IM43B contains hup DNA sequences different from those in B. japonicum and in other lupine rhizobia strains.
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Affiliation(s)
- J Murillo
- Departamento de Microbiologia, E.T.S. Ingenieros Agrónomos, Universidad Politécnica, 28040 Madrid, Spain
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Mozo T, Cabrera E, Ruiz-Argüeso T. Diversity of Plasmid Profiles and Conservation of Symbiotic Nitrogen Fixation Genes in Newly Isolated
Rhizobium
Strains Nodulating Sulla (
Hedysarum coronarium
L.). Appl Environ Microbiol 1988; 54:1262-7. [PMID: 16347636 PMCID: PMC202637 DOI: 10.1128/aem.54.5.1262-1267.1988] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Forty-five
Rhizobium
strains nodulating sulla (
Hedysarum coronarium
L.), isolated from plants grown in different sites in Menorca Island and southern Spain, were examined for plasmid content and the location and organization of
nif
(nitrogen fixation) and
nod
(nodulation) sequences. A great diversity in both number and size of the plasmids was observed in this native population of strains, which could be distributed among 19 different groups according to their plasmid profiles. No correlation was found between plasmid profile and geographical origin of the strains. In each strain a single plasmid ranging from 187 to 349 megadaltons hybridized to
Rhizobium meliloti nifHD
and
nodD
DNA, and in three strains the spontaneous loss of this plasmid resulted in the loss of the nodulation capacity. In addition to the symbiotic plasmid, 18 different cryptic plasmids were identified. A characteristic cryptic plasmid of >1,000 megadaltons was present in all strains. Total DNA hybridization experiments, with
nifHD
and portions of
nodC
and
nodD
genes (coding for common nodulation functions) from
R. meliloti
as probes, demonstrated that both the sequence and organization of
nif
and common
nod
genes were highly conserved within rhizobia nodulating sulla. Evidence for reiteration of
nodD
sequences and for linkage of
nodC
to at least one copy of
nodD
was obtained for all the strains examined. From these results we conclude that
Rhizobium
strains nodulating sulla are a homogeneous group of symbiotic bacteria that are closely related to the classical fast-growing group of rhizobia.
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Affiliation(s)
- T Mozo
- Departamento de Microbiología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica, 28040 Madrid, Spain
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26
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Barate M, Reyes P, Munilla R, Fernández VM, Ballesteros A, Ruiz-Argüeso T. Effect of pH on tritium exchange and hydrogen production and uptake in free-living cells and in bacteroids of Bradyrhizobium japonicum. Arch Biochem Biophys 1987; 259:639-44. [PMID: 3322198 DOI: 10.1016/0003-9861(87)90530-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Soybean nodule bacteroids and Bradyrhizobium japonicum free-living cells induced for H2-uptake hydrogenase, actively catalyze the evolution of H2 in a reaction highly dependent on the pH. The optimal pHs for the evolution and uptake reactions were 4.0 and 7.5-8.0, respectively. No differences were found between free-living cells and bacteroids with respect to hydrogen acceptor specificity, although absolute rates of H2 uptake were higher for free-living cells. Both types of cells were able to evolve hydrogen from reduced methyl viologen at low pH. These intact cells also catalyzed the exchange reaction between tritium and water in the absence of oxygen. The pH profile of the exchange activity showed two peaks at values near the optimal pHs for the evolution and uptake reactions.
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Affiliation(s)
- M Barate
- Instituto de Catálisis, CSIC, Madrid, Spain
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27
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Abstract
A gene library of genomic DNA from the hydrogen uptake (Hup)-positive strain 128C53 of Rhizobium leguminosarum was constructed by using the broad-host-range mobilizable cosmid vector pLAFR1. The resulting recombinant cosmids contained insert DNA averaging 21 kilobase pairs (kb) in length. Two clones from the above gene library were identified by colony hybridization with DNA sequences from plasmid pHU1 containing hup genes of Bradyhizobium japonicum. The corresponding recombinant cosmids, pAL618 and pAL704, were isolated, and a region of about 28 kb containing the sequences homologous to B. japonicum hup-specific DNA was physically mapped. Further hybridization analysis with three fragments from pHU1 (5.9-kb HindIII, 2.9-kb EcoRI, and 5.0-kb EcoRI) showed that the overall arrangement of the R. leguminosarum hup-specific region closely parallels that of B. japonicum. The presence of functional hup genes within the isolated cosmid DNA was demonstrated by site-directed Tn5 mutagenesis of the 128C53 genome and analysis of the Hup phenotype of the Tn5 insertion strains in symbiosis with peas. Transposon Tn5 insertions at six different sites spanning 11 kb of pAL618 completely suppressed the hydrogenase activity of the pea bacteroids.
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Affiliation(s)
- A Leyva
- Departamento de Microbiología, Universidad Politécnica, Madrid, Spain
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28
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Leyva A, Palacios JM, Ruiz-Argüeso T. Conserved Plasmid Hydrogen-Uptake (
hup
)-Specific Sequences within Hup
+
Rhizobium leguminosarum
Strains. Appl Environ Microbiol 1987; 53:2539-43. [PMID: 16347471 PMCID: PMC204142 DOI: 10.1128/aem.53.10.2539-2543.1987] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thirteen
Rhizobium leguminosarum
strains previously reported as H
2
-uptake hydrogenase positive (Hup
+
) or negative (Hup
−
) were analyzed for the presence and conservation of DNA sequences homologous to cloned
Bradyrhizobium japonicum hup
-specific DNA from cosmid pHU1 (M. A. Cantrell, R. A. Haugland, and H. J. Evans, Proc. Natl. Acad. Sci. USA 80:181-185, 1983). The Hup phenotype of these strains was reexamined by determining hydrogenase activity induced in bacteroids from pea nodules. Five strains, including H
2
oxidation-ATP synthesis-coupled and -uncoupled strains, induced significant rates of H
2
-uptake hydrogenase activity and contained DNA sequences homologous to three probe DNA fragments (5.9-kilobase [kb]
Hin
dIII, 2.9-kb
Eco
RI, and 5.0-kb
Eco
RI) from pHU1. The pattern of genomic DNA
Hin
dIII and
Eco
RI fragments with significant homology to each of the three probes was identical in all five strains regardless of the H
2
-dependent ATP generation trait. The restriction fragments containing the homology totalled about 22 kb of DNA common to the five strains. In all instances the putative
hup
sequences were located on a plasmid that also contained
nif
genes. The molecular sizes of the identified
hup-sym
plasmids ranged between 184 and 212 megadaltons. No common DNA sequences homologous to
B. japonicum hup
DNA were found in genomic DNA from any of the eight remaining strains showing no significant hydrogenase activity in pea bacteroids. These results suggest that the identified DNA region contains genes essential for hydrogenase activity in
R. leguminosarum
and that its organization is highly conserved within Hup
+
strains in this symbiotic species.
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Affiliation(s)
- A Leyva
- Departamento de Microbiología, Escuela Tecnica Superior de Ingenieros Agrónomos, Universidad Politécnica, 28040-Madrid, Spain
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29
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López M, Carbonero V, Cabrera E, Ruiz-Argüeso T. Effects of host on the expression of the H2-uptake hydrogenase of Rhizobium in legume nodules. ACTA ACUST UNITED AC 1983. [DOI: 10.1016/0304-4211(83)90143-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Ruiz-Argüeso T, Cabrera E, de Bertalmio MB. Selection of symbiotically energy efficient strains of Rhizobium japonicum by their ability to induce a H2-uptake hydrogenase in the free-living state. Arch Microbiol 1981. [DOI: 10.1007/bf00422529] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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31
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Emerich DW, Ruiz-Argüeso T, Russell SA, Evans HJ. Investigation of the H(2) Oxidation System in Rhizobium japonicum 122 DES Nodule Bacteroids. Plant Physiol 1980; 66:1061-6. [PMID: 16661577 PMCID: PMC440790 DOI: 10.1104/pp.66.6.1061] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The H(2)-oxidizing complex in Rhizobium japonicum 122 DES bacteroids failed to catalyze, at a measurable rate, (2)H(1)H exchange from a mixture of (2)H(2) and (1)H(2) in presence of (2)H(2)O and (1)H(2)O, providing no evidence for reversibility of the hydrogenase reaction in vivo. In the H(2) oxidation reaction, there was no significant discrimination between (2)H(2) and (1)H(2), indicating that the initial H(2)-activation step in the over-all H(2) oxidation reaction is not rate-limiting. By use of improved methods, an apparent K(m) for H(2) of 0.05 micromolar was determined. The H(2) oxidation reaction in bacteroids was strongly inhibited by cyanide (88% at 0.05 millimolar), theonyltrifluoroacetone, and other metal-complexing agents. Carbonyl cyanide m-chlorophenylhydrazone at 0.005 millimolar and 2,4-dinitrophenol at 0.5 millimolar inhibited H(2) oxidation and stimulated O(2) uptake. This and other evidence suggest the involvement of cytochromes and nonheme iron proteins in the pathway of electron transport from H(2) to O(2). Partial pressures of H(2) at 0.03 atmosphere and below had a pronounced inhibitory effect on endogenous respiration by bacteroid suspensions. The inhibition of CO(2) evolution by low partial pressures of H(2) suggests that H(2) utilization may result in conservation of oxidizable substrates and benefits the symbiosis under physiological conditions. Succinate, acetate, and formate at concentrations of 50 millimolar inhibited rates of H(2) uptake by 8, 29, and 25%, respectively. The inhibition by succinate was noncompetitive and that by acetate and formate was uncompetitive. A concentration of 11.6 millimolar CO(2) (initial concentration) in solution inhibited H(2) uptake by bacteroid suspensions by 18%. Further research is necessary to establish the significance of the inhibition of H(2) uptake by succinate, acetate, formate, and CO(2) in the metabolism of the H(2)-uptake-positive strains of Rhizobium.
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Affiliation(s)
- D W Emerich
- Laboratory for Nitrogen Fixation Research, Oregon State University, Corvallis, Oregon 97331
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Ruiz-Argüeso T, Maier RJ, Evans HJ. Hydrogen Evolution from Alfalfa and Clover Nodules and Hydrogen Uptake by Free-Living
Rhizobium meliloti. Appl Environ Microbiol 1979; 37:582-7. [PMID: 16345361 PMCID: PMC243258 DOI: 10.1128/aem.37.3.582-587.1979] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A series of
Rhizobium meliloti
and
Rhizobium trifolii
strains were used as inocula for alfalfa and clover, respectively, grown under bacteriologically controlled conditions. Replicate samples of nodules formed by each strain were assayed for rates of H
2
evolution in air, rates of H
2
evolution under Ar and O
2
, and rates of C
2
H
2
reduction. Nodules formed by all strains of
R. meliloti
and
R. trifolii
on their respective hosts lost at least 17% of the electron flow through nitrogenase as evolved H
2
. The mean loss from alfalfa nodules formed by 19
R. meliloti
strains was 25%, and the mean loss from clover nodules formed by seven
R. trifolii
strains was 35%.
R. meliloti
and
R. trifolii
strains also were cultured under conditions that were previously established for derepression of hydrogenase synthesis. Only strains 102F65 and 102F51 of
R. meliloti
showed measurable activity under free-living conditions. Bacteroids from nodules formed by the two strains showing hydrogenase activity under free-living conditions also oxidized H
2
at low rates. The specific activity of hydrogenase in bacteroids formed by either strain 102F65 or strain 102F51 of
R. meliloti
was less than 0.1% of the specific activity of the hydrogenase system in bacteroids formed by H
2
uptake-positive
Rhizobium japonicum
USDA 110, which has been investigated previously.
R. meliloti
and
R. trifolii
strains tested possessed insufficient hydrogenase to recycle a substantial proportion of the H
2
evolved from the nitrogenase reaction in nodules of their hosts. Additional research is needed, therefore, to develop strains of
R. meliloti
and
R. trifolii
that possess an adequate H
2
-recycling system.
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Affiliation(s)
- T Ruiz-Argüeso
- Laboratory for Nitrogen Fixation Research, Oregon State University, Corvallis, Oregon 97331
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33
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Ruiz-Argüeso T, Emerich DW, Evans HJ. Hydrogenase system in legume nodules: a mechanism of providing nitrogenase with energy and protection from oxygen damage. Biochem Biophys Res Commun 1979; 86:259-64. [PMID: 426786 DOI: 10.1016/0006-291x(79)90860-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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34
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Emerich DW, Ruiz-Argüeso T, Ching TM, Evans HJ. Hydrogen-dependent nitrogenase activity and ATP formation in Rhizobium japonicum bacteroids. J Bacteriol 1979; 137:153-60. [PMID: 762010 PMCID: PMC218429 DOI: 10.1128/jb.137.1.153-160.1979] [Citation(s) in RCA: 151] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Rhizobium japonicum 122 DES bacteroids from soybean nodules possess an active H(2)-oxidizing system that recycles all of the H(2) lost through nitrogenase-dependent H(2) evolution. The addition of 72 muM H(2) to suspensions of bacteroids increased O(2) uptake 300% and the rate of C(2)H(2) reduction 300 to 500%. The optimal partial pressure of O(2) was increased, and the partial pressure of O(2) range for C(2)H(2) reduction was extended by adding H(2). A supply of succinate to bacteroids resulted in effects similar to those obtained by adding H(2). Both H(2) and succinate provided respiratory protection for the N(2)-fixing system in bacteroids. The oxidation of H(2) by bacteroids increased the steady-state pool of ATP by 20 to 40%. In the presence of 50 mM iodoacetate, which caused much greater inhibition of endogenous respiration than of H(2) oxidation, the addition of H(2) increased the steady-state pool of ATP in bacteroids by 500%. Inhibitor evidence and an absolute requirement for O(2) indicated that the H(2)-stimulated ATP synthesis occurred through oxidative phosphorylation. In the presence of 50 mM iodoacetate, H(2)-dependent ATP synthesis occurred at a rate sufficient to support nitrogenase activity. The addition of H(2) to H(2) uptake-negative strains of R. japonicum had no effect on ATP formation or C(2)H(2) reduction. It is concluded that the H(2)-oxidizing system in H(2) uptake-positive bacteroids benefits the N(2)-fixing process by providing respiratory protection of the O(2)-labile nitrogenase proteins and generating ATP to support maximal rates of C(2)H(2) reduction by oxidation of the H(2) produced from the nitrogenase system.
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35
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36
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Abstract
A wide range of tolerance to Li+ has been found among 12 different yeasts. Concentrations that do not allow long-term growth of an actively growing culture within 2-5 hr. At the same concentrations protein and RNA synthesis are inhibited with little or no lag period (less than 50 min) but respiration is not affected at these concentrations. Lower concentrations that do not inhibit growth, may impair sporulation. For given extracellular conditions, intracellular Li+ concentrations are lower in the more tolerant yeast strains.
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37
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