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Martin Del Campo JS, Rigsbee J, Bueno Batista M, Mus F, Rubio LM, Einsle O, Peters JW, Dixon R, Dean DR, Dos Santos PC. Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in Azotobacter vinelandii. Crit Rev Biochem Mol Biol 2023; 57:492-538. [PMID: 36877487 DOI: 10.1080/10409238.2023.2181309] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Understanding how Nature accomplishes the reduction of inert nitrogen gas to form metabolically tractable ammonia at ambient temperature and pressure has challenged scientists for more than a century. Such an understanding is a key aspect toward accomplishing the transfer of the genetic determinants of biological nitrogen fixation to crop plants as well as for the development of improved synthetic catalysts based on the biological mechanism. Over the past 30 years, the free-living nitrogen-fixing bacterium Azotobacter vinelandii emerged as a preferred model organism for mechanistic, structural, genetic, and physiological studies aimed at understanding biological nitrogen fixation. This review provides a contemporary overview of these studies and places them within the context of their historical development.
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Affiliation(s)
| | - Jack Rigsbee
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| | | | - Florence Mus
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
| | - Oliver Einsle
- Department of Biochemistry, University of Freiburg, Freiburg, Germany
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
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2
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Abstract
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Nitrogenase harbors three distinct
metal prosthetic groups that
are required for its activity. The simplest one is a [4Fe-4S] cluster
located at the Fe protein nitrogenase component. The MoFe protein
component carries an [8Fe-7S] group called P-cluster and a [7Fe-9S-C-Mo-R-homocitrate] group called FeMo-co. Formation of nitrogenase
metalloclusters requires the participation of the structural nitrogenase
components and many accessory proteins, and occurs both in
situ, for the P-cluster, and in external assembly sites for
FeMo-co. The biosynthesis of FeMo-co is performed stepwise and involves
molecular scaffolds, metallochaperones, radical chemistry, and novel
and unique biosynthetic intermediates. This review provides a critical
overview of discoveries on nitrogenase cofactor structure, function,
and activity over the last four decades.
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Affiliation(s)
- Stefan Burén
- Centro de Biotecnologı́a y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Emilio Jiménez-Vicente
- Department of Biochemistry, Virginia Polytechnic Institute, Blacksburg, Virginia 24061, United States
| | - Carlos Echavarri-Erasun
- Centro de Biotecnologı́a y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Luis M Rubio
- Centro de Biotecnologı́a y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
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3
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Bai Y, Chen T, Happe T, Lu Y, Sawyer A. Iron-sulphur cluster biogenesis via the SUF pathway. Metallomics 2019; 10:1038-1052. [PMID: 30019043 DOI: 10.1039/c8mt00150b] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Iron-sulphur (Fe-S) clusters are versatile cofactors, which are essential for key metabolic processes in cells, such as respiration and photosynthesis, and which may have also played a crucial role in establishing life on Earth. They can be found in almost all living organisms, from unicellular prokaryotes and archaea to multicellular animals and plants, and exist in diverse forms. This review focuses on the most ancient Fe-S cluster assembly system, the sulphur utilization factor (SUF) mechanism, which is crucial in bacteria for cell survival under stress conditions such as oxidation and iron starvation, and which is also present in the chloroplasts of green microalgae and plants, where it is responsible for plastidial Fe-S protein maturation. We explain the SUF Fe-S cluster assembly process, the proteins involved, their regulation and provide evolutionary insights. We specifically focus on examples from Fe-S cluster synthesis in the model organisms Escherichia coli and Arabidopsis thaliana and discuss in an in vivo context the assembly of the [FeFe]-hydrogenase H-cluster from Chlamydomonas reinhardtii.
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Affiliation(s)
- Y Bai
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
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4
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Li XX, Liu Q, Liu XM, Shi HW, Chen SF. Using synthetic biology to increase nitrogenase activity. Microb Cell Fact 2016; 15:43. [PMID: 26897628 PMCID: PMC4761190 DOI: 10.1186/s12934-016-0442-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/08/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nitrogen fixation has been established in protokaryotic model Escherichia coli by transferring a minimal nif gene cluster composed of 9 genes (nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV) from Paenibacillus sp. WLY78. However, the nitrogenase activity in the recombinant E. coli 78-7 is only 10 % of that observed in wild-type Paenibacillus. Thus, it is necessary to increase nitrogenase activity through synthetic biology. RESULTS In order to increase nitrogenase activity in heterologous host, a total of 28 selected genes from Paenibacillus sp. WLY78 and Klebsiella oxytoca were placed under the control of Paenibacillus nif promoter in two different vectors and then they are separately or combinationally transferred to the recombinant E. coli 78-7. Our results demonstrate that Paenibacillus suf operon (Fe-S cluster assembly) and the potential electron transport genes pfoAB, fldA and fer can increase nitrogenase activity. Also, K. oxytoca nifSU (Fe-S cluster assembly) and nifFJ (electron transport specific for nitrogenase) can increase nitrogenase activity. Especially, the combined assembly of the potential Paenibacillus electron transporter genes (pfoABfldA) with K. oxytoca nifSU recovers 50.1 % of wild-type (Paenibacillus) activity. However, K. oxytoca nifWZM and nifQ can not increase activity. CONCLUSION The combined assembly of the potential Paenibacillus electron transporter genes (pfoABfldA) with K. oxytoca nifSU recovers 50.1 % of wild-type (Paenibacillus) activity in the recombinant E. coli 78-7. Our results will provide valuable insights for the enhancement of nitrogenase activity in heterogeneous host and will provide guidance for engineering cereal plants with minimal nif genes.
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Affiliation(s)
- Xin-Xin Li
- Key Laboratory for Agrobiotechnology and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China.
| | - Qi Liu
- Key Laboratory for Agrobiotechnology and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China.
| | - Xiao-Meng Liu
- Key Laboratory for Agrobiotechnology and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China.
| | - Hao-Wen Shi
- Key Laboratory for Agrobiotechnology and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China.
| | - San-Feng Chen
- Key Laboratory for Agrobiotechnology and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China.
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5
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Mevarech M, Rice D, Haselkorn R. Nucleotide sequence of a cyanobacterial nifH gene coding for nitrogenase reductase. Proc Natl Acad Sci U S A 2010; 77:6476-80. [PMID: 16592916 PMCID: PMC350308 DOI: 10.1073/pnas.77.11.6476] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nucleotide sequence of nifH, the structural gene for nitrogenase reductase (component II or Fe protein of nitrogenase) from the cyanobacterium Anabaena 7120 has been determined. Also reported are 194 bases of the 5'-flanking sequence and 170 bases of the 3'-flanking sequence. The predicted amino acid sequence was compared with that determined for the complete nitrogenase reductase of Clostridium pasteurianum and the cysteine-containing peptides of the protein from Azotobacter vinelandii. Amino acid sequences around five cysteines, located in the NH(2)-terminal two-thirds of the protein, are highly conserved in all three species. Codon usage in the first gene from a cyanobacterium to be sequenced shows striking asymmetries for eight amino acids.
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Affiliation(s)
- M Mevarech
- Department of Biophysics and Theoretical Biology, The University of Chicago, Chicago, Illinois 60637
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6
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Quinto C, De La Vega H, Flores M, Leemans J, Cevallos MA, Pardo MA, Azpiroz R, De Lourdes Girard M, Calva E, Palacios R. Nitrogenase reductase: A functional multigene family in Rhizobium phaseoli. Proc Natl Acad Sci U S A 2010; 82:1170-4. [PMID: 16593543 PMCID: PMC397216 DOI: 10.1073/pnas.82.4.1170] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The complete coding sequence of the nitrogenase reductase gene (nifH) is present in three different regions of a Rhizobium phaseoli symbiotic plasmid. Homology between two of the regions containing nifH coding sequences extends over 5 kilobases. These in turn share 1.3 kilobases of homology with the third region. The nucleotide sequences of the three nitrogenase reductase genes were found to be identical. Site-directed insertion mutagenesis indicated that none of the three genes is indispensable for nitrogen fixation during symbiosis with Phaseolus vulgaris. This implies that at least two of the reiterated genes can be functionally expressed.
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Affiliation(s)
- C Quinto
- Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apartado postal 565-A, Cuernavaca, Morelos, Mexico
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7
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Mazur BJ, Rice D, Haselkorn R. Identification of blue-green algal nitrogen fixation genes by using heterologous DNA hybridization probes. Proc Natl Acad Sci U S A 2010; 77:186-90. [PMID: 16592748 PMCID: PMC348233 DOI: 10.1073/pnas.77.1.186] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the filamentous blue-green alga Anabaena 7120, aerobic nitrogen fixation is linked to the differentiation of specialized cells called heterocysts. In order to study control of heterocyst development and nitrogen fixation in Anabaena, we have used cloned fragments of the Klebsiella pneumoniae nitrogen fixation (nif) genes as probes in DNA.DNA hybridizations with restriction endonuclease fragments of Anabaena DNA. Using this technique, we were able to identify and clone Anabaena nif genes, demonstrating the feasibility of using heterologous probes to identify genes for which no traditional genetic selection exists. From the patterns of hybridization observed, we deduced that although DNA sequence homology has been retained between some of the nif genes of these divergent organisms, the nif gene order has been rearranged.
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Affiliation(s)
- B J Mazur
- Department of Biophysics and Theoretical Biology, The University of Chicago, Chicago, Illinois 60637
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8
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Ligon JM, Nakas JP. Isolation and Characterization of Frankia sp. Strain FaC1 Genes Involved in Nitrogen Fixation. Appl Environ Microbiol 2010; 53:2321-7. [PMID: 16347453 PMCID: PMC204107 DOI: 10.1128/aem.53.10.2321-2327.1987] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genomic DNA was isolated from Frankia sp. strain FaC1, an Alnus root nodule endophyte, and used to construct a genomic library in the cosmid vector pHC79. The genomic library was screened by in situ colony hybridization to identify clones of Frankia nitrogenase (nif) genes based on DNA sequence homology to structural nitrogenase genes from Klebsiella pneumoniae. Several Frankia nif clones were isolated, and hybridization with individual structural nitrogenase gene fragments (nifH, nifD, and nifK) from K. pneumoniae revealed that they all contain the nifD and nifK genes, but lack the nifH gene. Restriction endonuclease mapping of the nifD and nifK hybridizing region from one clone revealed that the nifD and nifK genes in Frankia sp. are contiguous, while the nifH gene is absent from a large region of DNA on either side of the nifDK gene cluster. Additional hybridizations with gene fragments derived from K. pneumoniae as probes and containing other genes involved in nitrogen fixation demonstrated that the Frankia nifE and nifN genes, which play a role in the biosynthesis of the iron-molybdenum cofactor, are located adjacent to the nifDK gene cluster.
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Affiliation(s)
- J M Ligon
- College of Environmental Science and Forestry, State University of New York, Syracuse, New York 13210
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9
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Abstract
The iron-molybdenum cofactor (FeMo-co), located at the active site of the molybdenum nitrogenase, is one of the most complex metal cofactors known to date. During the past several years, an intensive effort has been made to purify the proteins involved in FeMo-co synthesis and incorporation into nitrogenase. This effort is starting to provide insights into the structures of the FeMo-co biosynthetic intermediates and into the biochemical details of FeMo-co synthesis.
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Affiliation(s)
- Luis M Rubio
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.
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10
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Zhao D, Curatti L, Rubio LM. Evidence for nifU and nifS participation in the biosynthesis of the iron-molybdenum cofactor of nitrogenase. J Biol Chem 2007; 282:37016-25. [PMID: 17959596 DOI: 10.1074/jbc.m708097200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nifU and nifS genes encode the components of a cellular machinery dedicated to the assembly of [2Fe-2S] and [4Fe-4S] clusters required for growth under nitrogen-fixing conditions. The NifU and NifS proteins are involved in the production of active forms of the nitrogenase component proteins, NifH and NifDK. Although NifH contains a [4Fe-4S] cluster, the NifDK component carries two complex metalloclusters, the iron-molybdenum cofactor (FeMo-co) and the [8Fe-7S] P-cluster. FeMo-co, located at the active site of NifDK, is composed of 7 iron, 9 sulfur, 1 molybdenum, 1 homocitrate, and 1 unidentified light atom. To investigate whether NifUS are required for FeMo-co biosynthesis and to understand at what level(s) they might participate in this process, we analyzed the effect of nifU and nifS mutations on the formation of active NifB protein and on the accumulation of NifB-co, an isolatable intermediate of the FeMo-co biosynthetic pathway synthesized by the product of the nifB gene. The nifU and nifS genes were required to accumulate NifB-co in a nifN mutant background. This result clearly demonstrates the participation of NifUS in NifB-co synthesis and suggests a specific role of NifUS as the major provider of [Fe-S] clusters that serve as metabolic substrates for the biosynthesis of FeMo-co. Surprisingly, although nifB expression was attenuated in nifUS mutants, the assembly of the [Fe-S] clusters of NifB was compensated by other non-nif machinery for the assembly of [Fe-S] clusters, indicating that NifUS are not essential to synthesize active NifB.
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Affiliation(s)
- Dehua Zhao
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
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11
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Curatti L, Ludden PW, Rubio LM. NifB-dependent in vitro synthesis of the iron-molybdenum cofactor of nitrogenase. Proc Natl Acad Sci U S A 2006; 103:5297-301. [PMID: 16567617 PMCID: PMC1414635 DOI: 10.1073/pnas.0601115103] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biological nitrogen fixation, an essential process of the biogeochemical nitrogen cycle that supports life on Earth, is catalyzed by the nitrogenase enzyme. The nitrogenase active site contains an iron and molybdenum cofactor (FeMo-co) composed of 7Fe-9S-Mo-homocitrate and one not-yet-identified atom, which probably is the most complex [Fe-S] cluster in nature. Here, we show the in vitro synthesis of FeMo-co from its simple constituents, Fe, S, Mo, and homocitrate. The in vitro FeMo-co synthesis requires purified NifB and depends on S-adenosylmethionine, indicating that radical chemistry is required during FeMo-co assembly.
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Affiliation(s)
- Leonardo Curatti
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Paul W. Ludden
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Luis M. Rubio
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- *To whom correspondence should be addressed. E-mail:
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12
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Scott JD, Ludwig RA. Azorhizobium caulinodans electron-transferring flavoprotein N electrochemically couples pyruvate dehydrogenase complex activity to N2 fixation. MICROBIOLOGY-SGM 2004; 150:117-126. [PMID: 14702404 DOI: 10.1099/mic.0.26603-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Azorhizobium caulinodans thermolabile point mutants unable to fix N2 at 42 degrees C were isolated and mapped to three, unlinked loci; from complementation tests, several mutants were assigned to the fixABCX locus. Of these, two independent fixB mutants carried missense substitutions in the product electron-transferring flavoprotein N (ETFN) alpha-subunit. Both thermolabile missense variants Y238H and D229G mapped to the ETFNalpha interdomain linker. Unlinked thermostable suppressors of these two fixB missense mutants were identified and mapped to the lpdA gene, encoding dihydrolipoamide dehydrogenase (LpDH), immediately distal to the pdhABC genes, which collectively encode the pyruvate dehydrogenase (PDH) complex. These two suppressor alleles encoded LpDH NAD-binding domain missense mutants G187S and E210G. Crude cell extracts of these fixB lpdA double mutants showed 60-70% of the wild-type PDH activity; neither fixB lpdA double mutant strain exhibited any growth phenotype at the restrictive or the permissive temperature. The genetic interaction between two combinations of lpdA and fixB missense alleles implies a physical interaction of their respective products, LpDH and ETFN. Presumably, this interaction electrochemically couples LpDH as the electron donor to ETFN as the electron acceptor, allowing PDH complex activity (pyruvate oxidation) to drive soluble electron transport via ETFN to N2, which acts as the terminal electron acceptor. If so, then, the A. caulinodans PDH complex activity sustains N2 fixation both as the driving force for oxidative phosphorylation and as the metabolic electron donor.
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Affiliation(s)
- John D Scott
- Department of Molecular, Cellular and Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA
| | - Robert A Ludwig
- Department of Molecular, Cellular and Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA
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Halbleib CM, Zhang Y, Roberts GP, Ludden PW. Effects of perturbations of the nitrogenase electron transfer chain on reversible ADP-ribosylation of nitrogenase Fe protein in Klebsiella pneumoniae strains bearing the Rhodospirillum rubrum dra operon. J Bacteriol 2000; 182:3681-7. [PMID: 10850982 PMCID: PMC94538 DOI: 10.1128/jb.182.13.3681-3687.2000] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The redox state of nitrogenase Fe protein is shown to affect regulation of ADP-ribosylation in Klebsiella pneumoniae strains transformed by plasmids carrying dra genes from Rhodospirillum rubrum. The dra operon encodes dinitrogenase reductase ADP-ribosyltransferase and dinitrogenase reductase-activating glycohydrolase, enzymes responsible for the reversible inactivation, via ADP-ribosylation, of nitrogenase Fe protein in R. rubrum. In bacteria containing the dra operon in their chromosomes, inactivation occurs in response to energy limitation or nitrogen sufficiency. The dra gene products, expressed at a low level in K. pneumoniae, enable transformants to reversibly ADP-ribosylate nitrogenase Fe protein in response to the presence of fixed nitrogen. The activities of both regulatory enzymes are regulated in vivo as described in R. rubrum. Genetic perturbations of the nitrogenase electron transport chain were found to affect the rate of inactivation of Fe protein. Strains lacking the electron donors to Fe protein (NifF or NifJ) were found to inactivate Fe protein more quickly than a strain with wild-type background. Deletion of nifD, which encodes a subunit of nitrogenase MoFe protein, was found to result in a slower inactivation response. No variation was found in the reactivation responses of these strains. It is concluded that the redox state of the Fe protein contributes to the regulation of the ADP-ribosylation of Fe protein.
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Affiliation(s)
- C M Halbleib
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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14
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Zou L, Baguinon MC, Guo X, Guo SY, Yu Y, Davis LC. Interaction with magnesium and ADP stabilizes both components of nitrogenase from Klebsiella pneumoniae against urea denaturation. Protein Sci 2000; 9:121-8. [PMID: 10739254 PMCID: PMC2144431 DOI: 10.1110/ps.9.1.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The nitrogenase enzyme of Klebsiella pneumoniae consists of two separable proteins, each with multiple subunits and one or more oxygen sensitive metallocenters. The wild-type nitrogenase proteins are stable to electrophoresis in high concentrations of urea under anaerobic conditions. Addition of Mg+2 and ADP greatly increases the stability of the smaller Fe protein (from <4 to >6 M for full unfolding), an effect directly analogous to stabilization in p21ras induced by Mg+2 and GDP. Stabilization by Mg+2 is slight for the holo MoFe protein (from approximately 1.5 to approximately 2.4 M) but more dramatic for the apo protein form of the MoFe protein accumulated by certain Fe protein (nifH gene) mutants. The potent product inhibitor of nitrogenase function, MgADP, increases stability of the MoFe protein more than Mg+2 alone, to approximately 3.6 M, showing that nucleotides interact with the MoFe protein. Mutations of the nifM gene result in slower accumulation of less stable Fe protein, indicating that NifM is involved in correct folding of the Fe protein. Mutationally altered proteins are often difficult to purify for study because of their inherent instability, low expression level, or oxygen lability. Crude extracts of 11 different mutants of Fe protein (nifH gene) were examined by transverse urea gradient gels to rapidly screen for stabilizing interactions in the presence or absence of substrate or inhibitor analogs. Amino acid alterations D44N and R188C, at the interface of the dimer, in the vicinity of the nucleotide binding site(s), have significantly lower stability than the wild-type enzyme in the absence of Mg+2 but comparable stability in its presence, showing the importance of Mg+2 in the subunit interactions. Mutations N163S and E266K, in which residues normally involved in hydrogen bonding far from the active site were altered, are more labile than the wild-type even with Mg+2 added. Seven other mutants, though nonfunctional, did not appear altered in stability compared to the wild-type.
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Affiliation(s)
- L Zou
- Department of Biochemistry, Kansas State University, Manhattan 66506, USA
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15
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Rangaraj P, Ryle MJ, Lanzilotta WN, Goodwin PJ, Dean DR, Shah VK, Ludden PW. Inhibition of iron-molybdenum cofactor biosynthesis by L127Delta NifH and evidence for a complex formation between L127Delta NifH and NifNE. J Biol Chem 1999; 274:29413-9. [PMID: 10506203 DOI: 10.1074/jbc.274.41.29413] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Besides serving as the obligate electron donor to dinitrogenase during nitrogenase turnover, dinitrogenase reductase (NifH) is required for the biosynthesis of the iron-molybdenum cofactor (FeMo-co) and for the maturation of alpha(2)beta(2) apo-dinitrogenase (apo-dinitrogenase maturation). In an attempt to understand the role of NifH in FeMo-co biosynthesis, a site-specific altered form of NifH in which leucine at position 127 has been deleted, L127Delta, was employed in in vitro FeMo-co synthesis assays. This altered form of NifH has been shown to inhibit substrate reduction by the wild-type nitrogenase complex, forming a tight protein complex with dinitrogenase. The L127Delta NifH was found to inhibit in vitro FeMo-co synthesis by wild-type NifH as detected by the gamma gel shift assay. Increasing the concentration of NifNE and NifB-cofactor (NifB-co) relieved the inhibition of FeMo-co synthesis by L127Delta NifH. The formation of a complex of L127Delta NifH with NifNE was investigated by gel filtration chromatography. We herein report the formation of a complex between L127Delta NifH and NifNE in the presence of NifB-co. This work presents evidence for one of the possible roles for NifH in FeMo-co biosynthesis, i.e. the interaction of NifH with a NifNE.NifB-co complex.
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Affiliation(s)
- P Rangaraj
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, Wisconsin 53706, USA
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16
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Rüttimann-Johnson C, Staples CR, Rangaraj P, Shah VK, Ludden PW. A vanadium and iron cluster accumulates on VnfX during iron-vanadium-cofactor synthesis for the vanadium nitrogenase in Azotobacter vinelandii. J Biol Chem 1999; 274:18087-92. [PMID: 10364262 DOI: 10.1074/jbc.274.25.18087] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The vnf-encoded nitrogenase from Azotobacter vinelandii contains an iron-vanadium cofactor (FeV-co) in its active site. Little is known about the synthesis pathway of FeV-co, other than that some of the gene products required are also involved in the synthesis of the iron-molybdenum cofactor (FeMo-co) of the widely studied molybdenum-dinitrogenase. We have found that VnfX, the gene product of one of the genes contained in the vnf-regulon, accumulates iron and vanadium in a novel V-Fe cluster during synthesis of FeV-co. The electron paramagnetic resonance (EPR) and metal analyses of the V-Fe cluster accumulated on VnfX are consistent with a VFe7-8Sx precursor of FeV-co. The EPR spectrum of VnfX with the V-Fe cluster bound strongly resembles that of isolated FeV-co and a model VFe3S4 compound. The V-Fe cluster accumulating on VnfX does not contain homocitrate. No accumulation of V-Fe cluster on VnfX was observed in strains with deletions in genes known to be involved in the early steps of FeV-co synthesis, suggesting that it corresponds to a precursor of FeV-co. VnfX purified from a nifB strain incapable of FeV-co synthesis has a different electrophoretic mobility in native anoxic gels than does VnfX, which has the V-Fe cluster bound. NifB-co, the Fe and S precursor of FeMo-co (and presumably FeV-co), binds to VnfX purified from the nifB strain, producing a shift in its electrophoretic mobility on anoxic native gels. The data suggest that a precursor of FeV-co that contains vanadium and iron accumulates on VnfX, and thus, VnfX is involved in the synthesis of FeV-co.
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Affiliation(s)
- C Rüttimann-Johnson
- Department of Biochemistry, College of Agriculture and Life Sciences, University of Wisconsin, Madison, Wisconsin 53706, USA
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17
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Simon HM, Gosink MM, Roberts GP. Importance of cis determinants and nitrogenase activity in regulated stability of the Klebsiella pneumoniae nitrogenase structural gene mRNA. J Bacteriol 1999; 181:3751-60. [PMID: 10368150 PMCID: PMC93853 DOI: 10.1128/jb.181.12.3751-3760.1999] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Klebsiella pneumoniae nitrogen fixation (nif) mRNAs are unusually stable, with half-lives of 20 to 30 min under conditions favorable to nitrogen fixation (limiting nitrogen, anaerobiosis, temperatures of 30 degrees C). Addition of O2 or fixed nitrogen or temperature increases to 37 degrees C or more result in the dramatic destabilization of the nif mRNAs, decreasing the half-lives by a factor of 3 to 5. A plasmid expression system, independent of nif transcriptional regulation, was used to define cis determinants required for the regulated stability of the 5.2-kb nifHDKTY mRNA and to test the model suggested by earlier work that NifA is required in trans to stabilize nif mRNA under nif-derepressing conditions. O2 regulation of nifHDKTY mRNA stability is impaired in a plasmid containing a deletion of a 499-bp region of nifH, indicating that a site(s) required for the O2-regulated stability of the mRNA is located within this region. The simple model suggested from earlier work that NifA is required for stabilizing nif mRNA under conditions favorable for nitrogen fixation was disproved, and in its place, a more complicated model involving the sensing of nitrogenase activity as a component of the system regulating mRNA stability is proposed. Analysis of nifY mutants and overexpression suggests a possible involvement of the protein in this sensing process.
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Affiliation(s)
- H M Simon
- Department of Bacteriology and the Center for the Study of Nitrogen Fixation, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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18
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Shah VK, Rangaraj P, Chatterjee R, Allen RM, Roll JT, Roberts GP, Ludden PW. Requirement of NifX and other nif proteins for in vitro biosynthesis of the iron-molybdenum cofactor of nitrogenase. J Bacteriol 1999; 181:2797-801. [PMID: 10217770 PMCID: PMC93721 DOI: 10.1128/jb.181.9.2797-2801.1999] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The iron-molybdenum cofactor (FeMo-co) of nitrogenase contains molybdenum, iron, sulfur, and homocitrate in a ratio of 1:7:9:1. In vitro synthesis of FeMo-co has been established, and the reaction requires an ATP-regenerating system, dithionite, molybdate, homocitrate, and at least NifB-co (the metabolic product of NifB), NifNE, and dinitrogenase reductase (NifH). The typical in vitro FeMo-co synthesis reaction involves mixing extracts from two different mutant strains of Azotobacter vinelandii defective in the biosynthesis of cofactor or an extract of a mutant strain complemented with the purified missing component. Surprisingly, the in vitro synthesis of FeMo-co with only purified components failed to generate significant FeMo-co, suggesting the requirement for one or more other components. Complementation of these assays with extracts of various mutant strains demonstrated that NifX has a role in synthesis of FeMo-co. In vitro synthesis of FeMo-co with purified components is stimulated approximately threefold by purified NifX. Complementation of these assays with extracts of A. vinelandii DJ42. 48 (DeltanifENX DeltavnfE) results in a 12- to 15-fold stimulation of in vitro FeMo-co synthesis activity. These data also demonstrate that apart from the NifX some other component(s) is required for the cofactor synthesis. The in vitro synthesis of FeMo-co with purified components has allowed the detection, purification, and identification of an additional component(s) required for the synthesis of cofactor.
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Affiliation(s)
- V K Shah
- Departments of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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19
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Nakai Y, Yoshihara Y, Hayashi H, Kagamiyama H. cDNA cloning and characterization of mouse nifS-like protein, m-Nfs1: mitochondrial localization of eukaryotic NifS-like proteins. FEBS Lett 1998; 433:143-8. [PMID: 9738949 DOI: 10.1016/s0014-5793(98)00897-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have isolated a mouse cDNA which shows significant sequence similarity to the yeast nifS-like gene (y-NFS1), and termed it m-Nfs1. The deduced protein sequence (459 amino acids long) has several characteristic features common to those of bacterial NifS proteins, but distinct from them by its amino-terminal extension which contains a typical mitochondrial targeting presequence. m-Nfs1 was found to be a soluble 47-kDa protein in the matrix fraction of mouse liver mitochondria. The m-Nfs1 gene was ubiquitously expressed in most tissues, suggesting its housekeeping function in vivo. We also found that the gamma-NFS1 protein was localized in the mitochondrial matrix in yeast cells. These results suggest that both eukaryotic NifS-like proteins may play some roles in mitochondrial functions.
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Affiliation(s)
- Y Nakai
- Department of Biochemistry, Osaka Medical College, Japan
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20
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Govantes F, Andújar E, Santero E. Mechanism of translational coupling in the nifLA operon of Klebsiella pneumoniae. EMBO J 1998; 17:2368-77. [PMID: 9545248 PMCID: PMC1170580 DOI: 10.1093/emboj/17.8.2368] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The nifLA operon of Klebsiella pneumoniae encodes the sensor-activator pair involved in the regulation of other nif genes. Balanced synthesis of both proteins, which is required for correct regulation, is achieved by coupling translation of nifA to that of nifL. The mechanism of translational coupling at the nifLA operon was analysed using a specialized ribosome system, and the effect of substituting the natural Shine-Dalgarno of nifL or nifA for specialized Shine-Dalgarno sequences was determined. Our results indicate that translational coupling occurs in this operon by a reinitiation mechanism. Additionally, reinitiation at the nifA can happen even in the absence of good Shine-Dalgarno recognition by the reinitiating ribosome, although its efficiency is lower. The effect of a putative translational enhancer sequence (downstream box) on translational coupling efficiency was also determined. Mutations that reduce the homology of the putative downstream box to the consensus had only a minor effect on nifA translation by wild-type ribosomes. However, they had a significant effect on nifA translation by specialized ribosomes, suggesting that recognition of the downstream box may compensate inefficient ribosomal interactions with the Shine-Dalgarno sequence.
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Affiliation(s)
- F Govantes
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Ap. 1095, 41080-Sevilla, Spain
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21
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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] [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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22
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Govantes F, Molina-López JA, Santero E. Mechanism of coordinated synthesis of the antagonistic regulatory proteins NifL and NifA of Klebsiella pneumoniae. J Bacteriol 1996; 178:6817-23. [PMID: 8955302 PMCID: PMC178581 DOI: 10.1128/jb.178.23.6817-6823.1996] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The nifLA operon of Klebsiella pneumoniae codes for the two antagonistic regulatory proteins which control expression of all other nitrogen fixation genes. NifA is a transcriptional activator, and NifL inhibits NifA. The importance of a correct NifL-NifA stoichiometry for efficient regulation of nitrogen fixation genes has been investigated by constructing a strain with an altered nifL-nifA gene dosage ratio, resulting from the integration of an extra copy of nifA. Results showed that a balanced synthesis of both gene products is essential for correct regulation. Effects of mutations provoking translation termination of nifL upstream or downstream of its natural stop codon, combined with overproduction of both proteins when the genes are transcribed and translated from signals of the phi10 gene of the phage T7, showed that, in addition to the previously reported transcriptional polarity, there is translational coupling between nifL and nifA. In spite of the apparently efficient ribosome binding site of nifA, its rate of independent translation is very low. This is due to a secondary structure masking the Shine-Dalgarno sequence of nifA, which could be melted by ribosomes translating nifL. Mutational analysis confirmed the functional significance of the secondary structure in preventing independent translation of nifA. Translational coupling between the two cistrons is proposed as an efficient mechanism to prevent production of an excess of NifA, which would affect the normal regulation of nitrogen fixation genes.
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Affiliation(s)
- F Govantes
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Spain
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23
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Simon HM, Homer MJ, Roberts GP. Perturbation of nifT expression in Klebsiella pneumoniae has limited effect on nitrogen fixation. J Bacteriol 1996; 178:2975-7. [PMID: 8631690 PMCID: PMC178037 DOI: 10.1128/jb.178.10.2975-2977.1996] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In the nitrogenase system of Klebsiella pneumoniae, nifT is located between nifDK, the structural genes for dinitrogenase, and nifY, whose product is involved in nitrogenase maturation. It is, therefore, a reasonable hypothesis that the NifT protein might also have a role in the maturation of nitrogenase. However, the phenotypic characterization of nifT and nifT-overexpressing strains for effects on the regulation, maturation, and activity of nitrogenase identified no properties that were distinct from those of the wild type. We conclude that the K. pneumoniae NifT protein is not essential for nitrogen fixation under the conditions examined.
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Affiliation(s)
- H M Simon
- Department of Bacteriology, University of Wisconsin-Madison 53706, USA
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24
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Govantes F, Santero E. Transcription termination within the regulatory nifLA operon of Klebsiella pneumoniae. MOLECULAR & GENERAL GENETICS : MGG 1996; 250:447-54. [PMID: 8602162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The effect of premature stop codons in the nifL gene on the expression of nifA-lacZ operon and protein fusions in Klebsiella pneumoniae was analysed in detail. Our results revealed transcriptional polarity in this operon. By dissecting the operon, intragenic regions containing Rho-dependent transcription terminators have been identified. As shown for other Rho-dependent terminators, their cytosine content is much higher than the incidence of guanines. However, other regions of the operon that have this feature did not show termination activity, suggesting that, contrary to previous reports, a correlation between these parameters cannot readily be established. Some of our results alos suggested that, in addition to polarity, other mechanisms may prevent expression of nifA when translation of nifL is altered. Their importance for efficient regulation of nitrogen fixation genes is discussed.
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Affiliation(s)
- F Govantes
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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25
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Allen RM, Chatterjee R, Ludden PW, Shah VK. Incorporation of iron and sulfur from NifB cofactor into the iron-molybdenum cofactor of dinitrogenase. J Biol Chem 1995; 270:26890-6. [PMID: 7592933 DOI: 10.1074/jbc.270.45.26890] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
NifB-co is an iron- and sulfur-containing precursor to the iron-molybdenum cofactor (FeMo-co) of dinitrogenase. The synthesis of NifB-co requires at least the product of the nifB gene. Incorporation of 55Fe and 35S from NifB-co into FeMo-co was observed only when all components of the in vitro FeMo-co synthesis system were present. Incorporation of iron and sulfur from NifB-co into dinitrogenase was not observed in control experiments in which the apodinitrogenase (lacking FeMo-co) was initially activated with purified, unlabeled FeMo-co or in assays where NifB-co was oxygen-inactivated prior to addition to the synthesis system. These data clearly demonstrate that iron and sulfur from active NifB-co are specifically incorporated into FeMo-co of dinitrogenase and provide direct biochemical identification of an iron-sulfur precursor of FeMo-co. Under different in vitro FeMo-co synthesis conditions, iron and sulfur from NifB-co were associated with at least two other proteins (NIFNE and gamma) that are involved in the formation of active dinitrogenase. The results presented here suggest that multiple FeMo-co processing steps might occur on NIFNE and that FeMo-co synthesis is most likely completed prior to the association of FeMo-co with gamma.
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Affiliation(s)
- R M Allen
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison 53706, USA
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26
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Homer MJ, Dean DR, Roberts GP. Characterization of the gamma protein and its involvement in the metallocluster assembly and maturation of dinitrogenase from Azotobacter vinelandii. J Biol Chem 1995; 270:24745-52. [PMID: 7559591 DOI: 10.1074/jbc.270.42.24745] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Dinitrogenase, the enzyme capable of catalyzing the reduction of N2, is a heterotetramer (alpha 2 beta 2) and contains the iron-molybdenum cofactor (FeMo-co) at the active site of the enzyme. Mutant strains unable to synthesize FeMo-co accumulate an apo form of dinitrogenase, which is enzymatically inactive but can be activated in vitro by the addition of purified FeMo-co. Apodinitrogenase from certain mutant strains of Azotobacter vinelandii has a subunit composition of alpha 2 beta 2 gamma 2. The gamma subunit has been implicated as necessary for the efficient activation of apodinitrogenase in vitro. Characterization of gamma protein in crude extracts and partially pure fractions has suggested that it is a chaperone-insertase required by apodinitrogenase for the insertion of FeMo-co. These are three major forms of gamma protein detectable by Western analysis of native gels. An apodinitrogenase-associated form is found in extracts of nifB or nifNE strains and dissociates from the apocomplex upon addition of purified FeMo-co. A second form of gamma protein is unassociated with other proteins and exists as a homodimer. Both of these forms of gamma protein can be converted to a third form by the addition of purified FeMo-co. This conversion requires the addition of active FeMo-co and correlates with the incorporation of iron into gamma protein. Crude extracts that contain this form of gamma protein are capable of donating FeMo-co to apodinitrogenase, thereby activating the apodinitrogenase. These data support a model in which gamma protein is able to interact with both FeMo-co and apodinitrogenase, facilitate FeMo-co insertion into apodinitrogenase, and then dissociate from the activated dinitrogenase complex.
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Affiliation(s)
- M J Homer
- Department of Bacteriology, University of Wisconsin, Madison 53706, USA
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27
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Roll JT, Shah VK, Dean DR, Roberts GP. Characteristics of NIFNE in Azotobacter vinelandii strains. Implications for the synthesis of the iron-molybdenum cofactor of dinitrogenase. J Biol Chem 1995; 270:4432-7. [PMID: 7876209 DOI: 10.1074/jbc.270.9.4432] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The products of the nifN and nifE genes of Azotobacter vinelandii function as a 200-kDa alpha 2 beta 2 tetramer (NIFNE) in the synthesis of the iron-molybdenum cofactor (FeMo-co) of nitrogenase, the enzyme system required for biological nitrogen fixation. NIFNE was purified using a modification of the published protocol. Immunoblot analysis of anoxic native gels indicated that distinct forms of NIFNE accumulate in strains deficient in either NIFB (delta nifB::kan delta nifDK) or NIFH (delta nifHDK). During the purification of NIFNE from the delta nifHDK mutant, its mobility in these gels changed, becoming similar to that of NIFNE from the delta nifB::kan delta nifDK mutant. While NIFB activity initially co-purified with the NIFNE activity from the delta nifHDK mutant, further purification of NIFNE activity resulted in the loss of the co-purifying NIFB activity; this loss correlated with the change in NIFNE mobility on native gels. These results suggest that the form of NIFNE accumulated in the delta nifHDK mutant is associated with NIFB activity in crude extract but loses this association during NIFNE purification. Addition of the purified metabolic product of NIFB, termed NifB-co, to either NIFNE purified from the delta nifHDK strain or to the NIFNE in crude extract of the delta nifB::kan delta nifDK strain caused a change in the mobility of NIFNE on anoxic native gels to that of the form accumulated in a delta nifHDK mutant. These results support a model where both NifB-co and dinitrogenase reductase participate in FeMo-co synthesis through NIFNE, which serves as a scaffold for this process.
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Affiliation(s)
- J T Roll
- Department of Bacteriology, College of Agricultural and Life Sciences, University of Wisconsin-Madison 53706
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28
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In vitro synthesis of the iron-molybdenum cofactor of nitrogenase. Purification and characterization of NifB cofactor, the product of NIFB protein. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)42235-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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29
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Stumpf F, Halda L, Klingmüller W. pMH2, a small plasmid bearing the nif gene cluster of Enterobacter agglomerans 333 as an excisable cassette. MOLECULAR & GENERAL GENETICS : MGG 1993; 241:236-40. [PMID: 8232207 DOI: 10.1007/bf00280221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A small plasmid containing the entire nif gene cluster of Enterobacter agglomerans 333 as an excisable cassette has been constructed, using pACYC177 as a vector. Two cosmid clones taken from a gene library of E. agglomerans plasmid pEA3 were used as a source of nif genes. A SmaI fragment of peaMS2-2, containing the H,D,K,Y,E,N,X,U,S,V,W,Z,M,L,A and B genes and an ApaI fragment of peaMS2-16 containing nif A,B,Q,F and J were selected to construct pMH2. The resulting plasmid of 33 kb carries the complete nif gene cluster as a nif cassette on a single XbaI fragment. The nif construct pMH2 in Escherichia coli strains has significant nitrogenase activity compared to wild-type E. agglomerans 333. The nif gene cluster construct was found to be very stable.
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Affiliation(s)
- F Stumpf
- Lehrstuhl für Genetik, Universität Bayreuth, Germany
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30
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Drummond M, Huff S, Green A. Roulette mutagenesis of the FMN-binding site of Klebsiella pneumoniae flavodoxin. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 217:395-400. [PMID: 8223578 DOI: 10.1111/j.1432-1033.1993.tb18258.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A method of randomising specific regions of coding sequences has been devised which utilises the Lac phenotype to identify mutants. Intact genes can be mutagenised, making it unnecessary to reclone the mutations before examining mutant phenotypes. The method has been applied to three residues around the N-terminus of the first alpha helix of the Klebsiella pneumoniae nitrogenase flavodoxin, which are predicted to form part of the phosphate-binding subsite. Surprisingly, most substitutions at Gly12, a highly conserved residue in the chain reversal preceding the alpha helix, appeared to be fairly stable in vivo and were found to retain some function. Substitutions at Lys13, a surface residue which contributes to a patch of positive charge characteristic of the nitrogenase flavodoxins, had no major effect on stability or function. However, most substitutions at Thr14, which is predicted to hydrogen bond to the phosphate of the prosthetic group FMN, were much more destabilising and grossly reduced function. The exceptions were Ala, Cys, Ser and Val, which suggests that the bulk of the residue at this position is critical.
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Affiliation(s)
- M Drummond
- AFRC IPSR Nitrogen Fixation Laboratory, University of Sussex, Brighton, England
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31
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Homer MJ, Paustian TD, Shah VK, Roberts GP. The nifY product of Klebsiella pneumoniae is associated with apodinitrogenase and dissociates upon activation with the iron-molybdenum cofactor. J Bacteriol 1993; 175:4907-10. [PMID: 8335644 PMCID: PMC204945 DOI: 10.1128/jb.175.15.4907-4910.1993] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Apodinitrogenase, which lacks the iron-molybdenum cofactor at its active site, is an oligomer that contains an additional protein not found in the active dinitrogenase tetramer. This associated protein in Klebsiella pneumoniae is shown to be the product of the nifY gene. When apodinitrogenase is activated by the addition of the iron-molybdenum cofactor, NifY dissociates from the apodinitrogenase complex. The conditions for this dissociation are described. Finally, there are aspects of the dissociation and insertion process in K. pneumoniae that are different from that in Azotobacter vinelandii.
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Affiliation(s)
- M J Homer
- Department of Bacteriology, University of Wisconsin, Madison 53706
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32
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Rodríguez-Quiñones F, Bosch R, Imperial J. Expression of the nifBfdxNnifOQ region of Azotobacter vinelandii and its role in nitrogenase activity. J Bacteriol 1993; 175:2926-35. [PMID: 8491713 PMCID: PMC204610 DOI: 10.1128/jb.175.10.2926-2935.1993] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The nifBQ transcriptional unit of Azotobacter vinelandii has been previously shown to be required for activity of the three nitrogenase systems, Mo nitrogenase, V nitrogenase, and Fe nitrogenase, present in this organism. We studied regulation of expression and the role of the nifBQ region by means of translational beta-galactosidase fusions to each of the five open reading frames: nifB, orf2 (fdxN), orf3 (nifO), nifQ, and orf5. Expression of the first three open reading frames was observed under all three diazotrophic conditions; expression of orf5 was never observed. Genes nifB and fdxN were expressed at similar levels. With Mo, expression of nifO and nifQ was approximately 20- and approximately 400-fold lower than that of fdxN, respectively. Without Mo, expression of nifB dropped three- to fourfold and that of nifQ dropped to the detection limit. However, expression of nifO increased threefold. The products of nifB, fdxN, nifO, and nifQ have been visualized in A. vinelandii as beta-galactosidase fusion proteins with the expected molecular masses. The NifB- fusion lacked activity for any of the three nitrogenase systems and showed an iron-molybdenum cofactor-deficient phenotype in the presence of Mo. The FdxN- mutation resulted in reduced nitrogenase activities, especially when V was present. Dinitrogenase activity in extracts was similarly affected, suggesting a role of FdxN in iron-molybdenum cofactor synthesis. The NifO(-)-producing mutation did not affect any of the nitrogenases under standard diazotrophic conditions. The NifQ(-)-producing mutation resulted in an increased (approximately 1,000-fold) Mo requirement for Mo nitrogenase activity, a phenotype already observed with Klebsiella pneumoniae. No effect of the NifQ(-)-producing mutation on V or Fe nitrogenase was found; this is consistent with its very low expression under those conditions. Mutations in orf5 had no effect on nitrogenase activity.
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Affiliation(s)
- F Rodríguez-Quiñones
- Institut d'Estudis Avançats, Consejo Superior de Investigaciones Cientificas, Universitat de les Illes Balears, Ctra. de Valldemossa, Palma de Mallorca, Spain
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33
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Electrophoretic studies on the assembly of the nitrogenase molybdenum-iron protein from the Klebsiella pneumoniae nifD and nifK gene products. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)35937-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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34
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Bali A, Blanco G, Hill S, Kennedy C. Excretion of ammonium by a nifL mutant of Azotobacter vinelandii fixing nitrogen. Appl Environ Microbiol 1992; 58:1711-8. [PMID: 1622243 PMCID: PMC195662 DOI: 10.1128/aem.58.5.1711-1718.1992] [Citation(s) in RCA: 118] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A mutation in the gene upstream of nifA in Azotobacter vinelandii was introduced into the chromosome to replace the corresponding wild-type region. The resulting mutant, MV376, produced nitrogenase constitutively in the presence of 15 mM ammonium. When introduced into a nifH-lacZ fusion strain, the mutation permitted beta-galactosidase production in the presence of ammonium. The gene upstream of nifA is therefore designated nifL because of its similarity to the Klebsiella pneumoniae nifL gene in proximity to nifA, in mutant phenotype, and in amino acid sequence of the gene product. The A. vinelandii nifL mutant MV376 excreted significant quantities of ammonium (approximately 10 mM) during diazotrophic growth. In contrast, ammonium excretion during diazotrophy was much lower in a K. pneumoniae nifL deletion mutant (maximum, 0.15 mM) but significantly higher than in NifL+ K. pneumoniae. The expression of the A. vinelandii nifA gene, unlike that of K. pneumoniae, was not repressed by ammonium.
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Affiliation(s)
- A Bali
- Nitrogen Fixation Laboratory, University of Sussex, Brighton, United Kingdom
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35
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The dependence on iron availability of allocation of iron to nitrogenase components in Klebsiella pneumoniae and Escherichia coli. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)50437-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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36
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Lehman LJ, Roberts GP. Glycine 100 in the dinitrogenase reductase of Rhodospirillum rubrum is required for nitrogen fixation but not for ADP-ribosylation. J Bacteriol 1991; 173:6159-61. [PMID: 1917849 PMCID: PMC208365 DOI: 10.1128/jb.173.19.6159-6161.1991] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Dinitrogenase reductase (Rr2) is required for reduction of the molybdenum dinitrogenase in the nitrogen fixation reaction and is the target of posttranslational regulation in Rhodospirillum rubrum. This posttranslational regulation involves the ADP-ribosylation of Rr2. To study the structural requirements for these two functions of Rr2, i.e., activity and regulation, two site-directed mutations in nifH, the gene encoding Rr2, were constructed and analyzed. The mutations both affected a region of the protein known to be highly conserved in evolution and to be relevant to both of the above properties. These mutants were both Nif-, but one of the altered Rr2s was a substrate for ADP-ribosylation. This demonstrates that the ability of Rr2 to participate in nitrogen fixation can be separated from its ability to act as a substrate for ADP-ribosylation.
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Affiliation(s)
- L J Lehman
- Department of Bacteriology, University of Wisconsin-Madison 53706
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37
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Aguilar OM, Taormino J, Thöny B, Ramseier T, Hennecke H, Szalay AA. The nifEN genes participating in FeMo cofactor biosynthesis and genes encoding dinitrogenase are part of the same operon in Bradyrhizobium species. MOLECULAR & GENERAL GENETICS : MGG 1990; 224:413-20. [PMID: 2266945 DOI: 10.1007/bf00262436] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The nucleotide sequences of genes homologous to the Klebsiella pneumoniae nifEN genes have been determined in Bradyrhizobium japonicum 110. The coding regions for the nifE and nifN consist, respectively, of 1641 and 1407 nucleotides. The nifD gene (coding for the beta-subunit of dinitrogenase) and nifE are linked, and separated by 95 nucleotides. In the region of 12 nucleotides that separates nifE from nifN the stop codon for nifE overlaps the putative ribosome binding site for nifN. In contrast to Klebsiella and Azotobacter vinelandii, the B. japonicum nifEN genes are linked to the nifDK genes in the same operon. Comparison of dinitrogenase polypeptides (nifDK products) and the polypeptides of the nifE and nifN genes reveals considerable homology between nifD and nifE, and between nifK and nifN. Several protein domains, containing highly conserved cysteine residues, are conserved among the gene products of nifD, nifK, nifE and nifN. This result allows us to propose a probable evolutionary pathway for the common origin of these genes.
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Affiliation(s)
- O M Aguilar
- Plant Molecular Genetics and Biotechnology Center, University of Alberta, Edmonton, Canada
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38
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Harris G, White T, Flory J, Orme-Johnson W. Genes required for formation of the apoMoFe protein of Klebsiella pneumoniae nitrogenase in Escherichia coli. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)55485-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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39
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Fu H, Burris RH, Roberts GP. Reversible ADP-ribosylation is demonstrated to be a regulatory mechanism in prokaryotes by heterologous expression. Proc Natl Acad Sci U S A 1990; 87:1720-4. [PMID: 2106680 PMCID: PMC53554 DOI: 10.1073/pnas.87.5.1720] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The primary product of biological nitrogen fixation, ammonia, reversibly regulates nitrogenase activity in a variety of diazotrophs by a process called "NH4(+)-switch-off/on." Strong correlative evidence from work in Azospirillum lipoferum and Rhodospirillum rubrum indicates that this regulation involves both the inactivation of dinitrogenase reductase by dinitrogenase reductase ADP-ribosyltransferase and the reactivation by dinitrogenase reductase activating glycohydrolase. The genes encoding these two enzymes, draT and draG, have been cloned from these two organisms, so that direct genetic evidence can be marshaled to test this model in vivo. The draT/G system has been transferred to and monitored in the enteric nitrogen-fixing bacterium Klebsiella pneumoniae, an organism normally devoid of such a regulatory mechanism. The expressed draT and draG genes allowed K. pneumoniae to respond to NH4Cl with a reversible regulation of nitrogenase activity that was correlated with the reversible ADP-ribosylation of dinitrogenase reductase in vivo. Thus, the expression of draT and draG genes in K. pneumoniae is necessary and sufficient to support NH4(+)-switch-off/on, and ADP-ribosylation serves as a reversible regulatory mechanism for controlling nitrogenase activity in prokaryotes.
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Affiliation(s)
- H Fu
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison 53706
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40
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Gosink MM, Franklin NM, Roberts GP. The product of the Klebsiella pneumoniae nifX gene is a negative regulator of the nitrogen fixation (nif) regulon. J Bacteriol 1990; 172:1441-7. [PMID: 2155202 PMCID: PMC208618 DOI: 10.1128/jb.172.3.1441-1447.1990] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
An insertional mutation was made in the nifX gene of Klebsiella pneumoniae. This mutation had little effect on the nitrogenase activity of the strain, as measured by acetylene reduction. However, on the addition of NH4+ or O2 (conditions which block nif protein synthesis by transcriptional and posttranscriptional mechanisms), the NifX- mutant synthesized nitrogenase proteins longer and had more accumulated nifHDKTY mRNA than did the wild-type K. pneumoniae at all time points tested. Conversely, overexpression of the wild-type nifX region blocked nif protein synthesis, protein accumulation, and nifHDKTY mRNA accumulation. These complementary results indicate that a product of the nifX region has a role in the negative regulation of nif regulation in response to NH4+ and O2.
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Affiliation(s)
- M M Gosink
- Department of Bacteriology, College of Agricultural and Life Sciences, University of Wisconsin-Madison 53706
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41
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Fu HA, Wirt HJ, Burris RH, Roberts GP. Functional expression of a Rhodospirillum rubrum gene encoding dinitrogenase reductase ADP-ribosyltransferase in enteric bacteria. Gene 1989; 85:153-60. [PMID: 2515993 DOI: 10.1016/0378-1119(89)90475-7] [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: 01/01/2023]
Abstract
The function of the cloned draT gene of Rhodospirillum rubrum was studied by placing it under the control of the tac promoter in the vector, pKK223-3. After induction with isopropyl-beta-D-thiogalactopyranoside, dinitrogenase reductase ADP-ribosyltransferase (DRAT) activity was detected in crude extracts of the heterologous hosts Escherichia coli and Klebsiella pneumoniae. In addition, the expression of draT produced a Nif- phenotype in the otherwise wild-type K. pneumoniae strains, the result of the ADP-ribosylation of accumulated dinitrogenase reductase (DR). DR from a nifF- background was also susceptible to ADP-ribosylation, indicating that the oxidized form of DR will serve as a substrate for DRAT in vivo. A mutation that changes the Arg-101 residue of DR, the ADP-ribose attaching site, eliminates the ADP-ribosylation of DR in vivo, confirming the necessity of this residue for modification.
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Affiliation(s)
- H A Fu
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison 53706
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42
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Govezensky D, Zamir A. Structure-function relationships in the alpha subunit of Klebsiella pneumoniae nitrogenase MoFe protein from analysis of nifD mutants. J Bacteriol 1989; 171:5729-35. [PMID: 2676989 PMCID: PMC210421 DOI: 10.1128/jb.171.10.5729-5735.1989] [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: 01/02/2023] Open
Abstract
Crude extracts of wild-type, nitrogenase-derepressed Klebsiella pneumoniae fractionated by nondenaturing gel electrophoresis contain, in addition to the major form of the MoFe protein, two minor variants of lower electrophoretic mobility. Of seven Nif- mutants of K. pneumoniae with nonpolar point mutations in nifD (encoding the alpha subunit of Kp1), three exhibit a wild-type-like electrophoretic pattern, whereas in the remaining four, the slowest-migrating form becomes the predominant species. Amino acid substitutions in mutants of the first type are located in the N terminus of NifD and include Gly-85 to Arg (UN1661), Glu-121 to Lys (UN1649), and Gly-161 to Asp (UN1683). Mutations of the second type are Gly-186 to Asp (UN1648), Gly-195 to Glu (UN1680), Ser-443 to Pro (UN1793), and Gly-455 to Asp (UN1650). Six of the mutated residues show interspecies conservation, three are close to conserved cysteines, and two are located next to conserved histidines. Based on evidence pointing to the possibility that the lowest-mobility form lacks the iron-molybdenum cofactor, these results provide insights into the functional significance of specific sites in the alpha subunit of the MoFe protein.
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Affiliation(s)
- D Govezensky
- Biochemistry Department, Weizmann Institute of Science, Rehovot, Israel
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43
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Paustian TD, Shah VK, Roberts GP. Purification and characterization of the nifN and nifE gene products from Azotobacter vinelandii mutant UW45. Proc Natl Acad Sci U S A 1989; 86:6082-6. [PMID: 2668954 PMCID: PMC297779 DOI: 10.1073/pnas.86.16.6082] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The nifN and -E gene products are involved in the synthesis of the iron-molybdenum cofactor of dinitrogenase, the enzyme responsible for the reduction of dinitrogen to ammonia. By using the in vitro iron-molybdenum cofactor biosynthesis assay, we have followed the purification of these gene products 450-fold to greater than 95% purity. An overall recovery of 20% was obtained with the purified protein having a specific activity of 6900 units/mg of protein. The protein (hereafter referred to as NIFNE) was found to contain equimolar amounts of the nifN and -E gene products and have a native molecular mass of 200 +/- 10 kDa, which indicates an alpha 2 beta 2 structure. NIFNE was oxygen labile with a half-life of 1 min in air. A UV-visible spectrum of the dye-oxidized protein showed an absorption maximum at 425 nm that could be bleached by reduction of NIFNE with sodium dithionite, suggesting the presence of an Fe center in NIFNE.
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Affiliation(s)
- T D Paustian
- Department of Bacteriology, College of Agricultural and Life Sciences, University of Wisconsin-Madison 53706
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44
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Liang J, Burris RH. N2O reduction and HD formation by nitrogenase from a nifV mutant of Klebsiella pneumoniae. J Bacteriol 1989; 171:3176-80. [PMID: 2656643 PMCID: PMC210033 DOI: 10.1128/jb.171.6.3176-3180.1989] [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: 01/02/2023] Open
Abstract
Dinitrogenase from a nifV mutant of Klebsiella pneumoniae contains an altered form of iron-molybdenum cofactor (FeMoco) that lacks a biologically active homocitric acid molecule. Change in the composition of FeMoco led to substantial variation in the kinetics of nitrogenase action. The KmS of the mutant enzyme for N2 and N2O were 0.244 and 0.175 atm (24,714 and 17,726 kPa), respectively. The km for N2 was higher and the Km for N2O was lower than that for the wild-type enzyme. The mutant enzyme was ineffective in N2 fixation, in N2O reduction, and in HD formation, as indicated by the low Vmax of these reactions with saturating levels of substrate and under conditions of saturating electron flux. These observations provide further support for the concept that N2, N2O, and D2 interact with the same form of dinitrogenase. H2 evolution by the mutant enzyme is only partially inhibited by CO. Observation that different numbers of electrons are stored in CO-inhibited than in noninhibited dinitrogenase before H2 is released suggests that the mutant enzyme has more sites responsible for H2 evolution than the wild-type enzyme, whose H2 evolution is not inhibited by CO.
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Affiliation(s)
- J Liang
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison 53706
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45
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Kreutzer R, Singh M, Klingmüller W. Identification and characterization of the nifH and nifJ promoter regions located on the nif-plasmid pEA3 of Enterobacter agglomerans 333. Gene 1989; 78:101-9. [PMID: 2504647 DOI: 10.1016/0378-1119(89)90318-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Small restriction fragments of the plasmid-borne Enterobacter agglomerans 333 nif region were cloned into a promoter probe plasmid as transcriptional fusions with the lacZ gene. Identification of NifA-dependent promoters was accomplished by using a compatible plasmid which constitutively expresses the Klebsiella pneumoniae nifA gene. beta-Galactosidase assays showed strong activation of the cloned E. agglomerans promoters in Escherichia coli by the heterologous K. pneumoniae nifA gene product. The positions of the promoter fragments on the corresponding restriction map were determined by Southern hybridization. As confirmed by sequencing data, the nifH and nifJ promoters are situated at opposite end-points of the nif gene group and their -24 to -12 nucleotide sequences are similar to the consensus sequence of NtrA-dependent promoters. Also, typical NifA-binding motifs are present in both promoters. The agreement of the promoter proximal regions of nifH and nifJ with the corresponding K pneumoniae sequences is about 80%. Also the upstream regions of these genes are in agreement to some extent.
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Affiliation(s)
- R Kreutzer
- Lehrstuhl für Genetik, Universität Bayreuth, F.R.G
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46
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Prakash RK, Cummings B. Creation of novel nitrogen-fixing actinomycetes by protoplast fusion of Frankia with streptomyces. PLANT MOLECULAR BIOLOGY 1988; 10:281-289. [PMID: 24277522 DOI: 10.1007/bf00027405] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/1987] [Accepted: 12/07/1987] [Indexed: 06/02/2023]
Abstract
Protoplast fusion was used for the creation of a novel actinomycete capable of fixing atmospheric nitrogen. Protoplasts of Streptomyces griseofuscus, a fast-growing actinomycete, and Frankia, a slow-growing actinomycete which fixes atmospheric nitrogen in culture and in symbiotic association with alders, were allowed to fuse and regenerate on media without supplied nitrogen. Colonies which regenerated acquired the fast-growing characteristic of Streptomyces and the ability to grow on nitrogen-deficient media from Frankia. These colonies resembled Streptomyces in their morphology and fixed atmospheric nitrogen in culture. They contained both the parent Streptomyces DNA sequences and the Frankia DNA sequences homologous to nif structural genes HDK of K. pneumoniae. In addition to in vitro nitrogen-fixing capacity, one out of 20 colonies also formed nitrogen-fixing root nodules on Alnus rubra, the host plant for the Frankia strain. Examination of the root nodules induced by the hybrids showed only the presence of hyphae-like structures. The typical vesicle-like structures present in Frankia were absent.
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Affiliation(s)
- R K Prakash
- NPI, University Research Park, 417 Wakara Way, 84108, Salt Lake City, UT, USA
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47
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Hoover TR, Imperial J, Ludden PW, Shah VK. Homocitrate cures the NifV- phenotype in Klebsiella pneumoniae. J Bacteriol 1988; 170:1978-9. [PMID: 3127384 PMCID: PMC211064 DOI: 10.1128/jb.170.4.1978-1979.1988] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Dinitrogenase was isolated from a culture of a Klebsiella pneumoniae NifV- strain derepressed for nitrogenase in the presence of homocitrate. The enzyme isolated from this culture was identical to the wild-type dinitrogenase. These data provide in vivo evidence that the absence of homocitrate is responsible for the NifV- phenotype.
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Affiliation(s)
- T R Hoover
- Department of Biochemistry, College of Agriculture and Life Sciences, University of Wisconsin-Madison 53706
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48
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Abstract
Oxygen can be either beneficial or detrimental for diazotrophy in organisms capable of an aerobic catabolism. It supports the production of a substrate for nitrogenase (ATP), but it can also inhibit the activity and repress the synthesis of this enzyme. Here, aspects of the relevant physiology are reviewed with particular emphasis on those relating to the mechanism of O2 regulation of nitrogenase synthesis.
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Affiliation(s)
- S Hill
- AFRC-IPSR Division of Nitrogen Fixation, University of Sussex, Brighton, U.K
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49
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Aguilar OM, Reiländer H, Arnold W, Pühler A. Rhizobium meliloti nifN (fixF) gene is part of an operon regulated by a nifA-dependent promoter and codes for a polypeptide homologous to the nifK gene product. J Bacteriol 1987; 169:5393-400. [PMID: 3316182 PMCID: PMC213963 DOI: 10.1128/jb.169.12.5393-5400.1987] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
An essential gene for symbiotic nitrogen fixation (fixF) is located near the common nodulation region of Rhizobium meliloti. A DNA fragment carrying fixF was characterized by hybridization with Klebsiella pneumoniae nif DNA and by nucleotide sequence analysis. The fixF gene was found to be related to K. pneumoniae nifN and was therefore renamed as the R. meliloti nifN gene. Upstream of the nifN coding region a second open reading frame was identified coding for a putative polypeptide of 110 amino acids (ORF110). By fragment-specific Tn5 mutagenesis it was shown that the nifN gene and ORF110 form an operon. The control region of this operon contains a nif promoter and also the putative nifA-binding sequence. For the deduced amino acid sequence of the nifN gene product a striking homology to the R. meliloti nifK protein was found. One cysteine residue and its adjacent amino acid sequence, which are highly conserved in the R. meliloti nifK, R. meliloti nifN, and K. pneumoniae nifN proteins, may play a role in binding the FeMo cofactor.
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Affiliation(s)
- O M Aguilar
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Federal Republic of Germany
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50
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Hoover TR, Robertson AD, Cerny RL, Hayes RN, Imperial J, Shah VK, Ludden PW. Identification of the V factor needed for synthesis of the iron-molybdenum cofactor of nitrogenase as homocitrate. Nature 1987; 329:855-7. [PMID: 3313054 DOI: 10.1038/329855a0] [Citation(s) in RCA: 120] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nitrogenase catalyses the ATP-dependent reduction of N2 to NH3, and is composed of two proteins, dinitrogenase (MoFe protein or component I) and dinitrogenase reductase (Fe protein or component II). Dinitrogenase contains a unique prosthetic group (iron-molybdenum cofactor, FeMoco) comprised of Fe, Mo and S, which has been proposed as the site of N2 reduction. Biochemical and genetic studies of Nif- (nitrogen fixation) mutants of Klebsiella pneumoniae which are defective in nitrogen fixation, have shown that the nifB, nifQ, nifN, nifE and nifV genes are required for the biosynthesis of FeMo-co. Recently, a system for in vitro synthesis of FeMoco was described. The assay requires at least the nifB, nifN and nifE gene products, and a low-molecular-weight factor (V factor) produced in the presence of the nifV gene product. We have used this system to study FeMoco biosynthesis. We report here the isolation of V factor and identify it as homocitric acid ([R]2-hydroxy-1,2,4-butanetricarboxylic acid).
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Affiliation(s)
- T R Hoover
- Department of Biochemistry, University of Wisconsin-Madison 53706
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