Regulation of Nitrogen Fixation Genes

Gussin, Gary N.; Ronson, Clive W.; Ausubel, Frederick M.

doi:10.1146/annurev.ge.20.120186.003031

Cited by 324 publications

(101 citation statements)

References 59 publications

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“…1). Several nif-encoded proteins are involved in regulation, including NifI 1 I 2 , NifA, and NifL (12,47,48). While the distributions of nifI 1 and nifI 2 in gene clusters were strongly and inversely correlated with the ability to use O 2 in metabolism (Pearson R, Ϫ0.79), the distributions of nifA and nifL exhibited positive correlations with the ability to use O 2 in metabolism (Pearson R, 0.42 and 0.26, respectively).…”

Section: Resultsmentioning

confidence: 99%

Evolution of Molybdenum Nitrogenase during the Transition from Anaerobic to Aerobic Metabolism

Boyd¹,

Costas²,

Hamilton³

et al. 2015

J. Bacteriol.

117

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Molybdenum nitrogenase (Nif), which catalyzes the reduction of dinitrogen to ammonium, has modulated the availability of fixed nitrogen in the biosphere since early in Earth's history. Phylogenetic evidence indicates that oxygen (O 2 )-sensitive Nif emerged in an anaerobic archaeon and later diversified into an aerobic bacterium. Aerobic bacteria that fix N 2 have adapted a number of strategies to protect Nif from inactivation by O 2 , including spatial and temporal segregation of Nif from O 2 and respiratory consumption of O 2 . Here we report the complement of Nif-encoding genes in 189 diazotrophic genomes. We show that the evolution of Nif during the transition from anaerobic to aerobic metabolism was accompanied by both gene recruitment and loss, resulting in a substantial increase in the number of nif genes. While the observed increase in the number of nif genes and their phylogenetic distribution are strongly correlated with adaptation to utilize O 2 in metabolism, the increase is not correlated with any of the known O 2 protection mechanisms. Rather, gene recruitment appears to have been in response to selective pressure to optimize Nif synthesis to meet fixed N demands associated with aerobic productivity and to more efficiently regulate Nif under oxic conditions that favor protein turnover. Consistent with this hypothesis, the transition of Nif from anoxic to oxic environments is associated with a shift from posttranslational regulation in anaerobes to transcriptional regulation in obligate aerobes and facultative anaerobes. Given that fixed nitrogen typically limits ecosystem productivity, our observations further underscore the dynamic interplay between the evolution of Earth's oxygen, nitrogen, and carbon biogeochemical cycles. IMPORTANCEMolybdenum nitrogenase (Nif), which catalyzes the reduction of dinitrogen to ammonium, has modulated the availability of fixed nitrogen in the biosphere since early in Earth's history. Nif emerged in an anaerobe and later diversified into aerobes. Here we show that the transition of Nif from anaerobic to aerobic metabolism was accompanied by both gene recruitment and gene loss, resulting in a substantial increase in the number of nif genes. While the observed increase in the number of nif genes is strongly correlated with adaptation to utilize O 2 in metabolism, the increase is not correlated with any of the known O 2 protective mechanisms. Rather, gene recruitment was likely a response to more efficiently regulate Nif under oxic conditions that favor protein turnover.A ll life requires fixed nitrogen (N), and its availability often limits ecosystem productivity (1, 2). Most of the N on Earth is in the form of dinitrogen (N 2 ), which is unreactive, bio-unavailable, and must be chemically reduced to ammonium (NH 4 ϩ ) before it can be incorporated into biological molecules, such as proteins or nucleic acids. The primary enzyme that catalyzes the reduction of N 2 to NH 4 ϩ is the molybdenum (Mo)-dependent nitrogenase Nif (3, 4). Our recent phylogenetic studies...

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Section: Resultsmentioning

confidence: 99%

Evolution of Molybdenum Nitrogenase during the Transition from Anaerobic to Aerobic Metabolism

Boyd¹,

Costas²,

Hamilton³

et al. 2015

J. Bacteriol.

117

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“…Transcription of the nifoperons of Klebsiella pneumoniae is also dependent on Ea'M (7). The activator protein NIFA also binds to upstream sites (8,9) and is functionally and structurally similar to NRI (10,11).…”

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confidence: 99%

Role of integration host factor in the regulation of the glnHp2 promoter of Escherichia coli.

Claverie-Martı́n

Magasanik

1991

Proc. Natl. Acad. Sci. U.S.A.

120

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The glnHPQ operon of Escherichia coli encodes components of the high-affinity glutamine transport system. One of the two promoters of this operon, glnHp2, is responsible for expression of the operon under nitrogenlimiting conditions. The general nitrogen regultory protein (NRO) is also dependent on Ea'M (7). The activator protein NIFA also binds to upstream sites (8,9) and is functionally and structurally similar to NRI (10,11). In contrast to NRI, NIFA has not been purified in active form (12,13). Integration host factor (IHF) binds just upstream from the nifI and nifU promoters and stimulates NIFA-mediated activation (13-15). IHF is a sequence-specific DNA-bending protein, which is involved in gene expression and other processes in E. coli and some of its bacteriophages and plasmids (16).The glnHPQ operon of E. coli, which encodes the components of the high-affinity glutamine transport system, is among the operons whose expression is induced under nitrogen-limiting conditions (17, 18). A promoter with homology to the v.54 promoters, glnHp2, has been identified (19). In this study, we present evidence for the existence of overlapping binding sites for NR1 upstream from the gInHp2 promoter. We also found that IHF binds between the glnHp2 promoter and the NRI binding sites. This system allowed us to study the role of IHF in the activation of transcription by NR1 by using purified components. MATERIALS AND METHODSProteins, Primers, and Materials. Core RNA polymerase, or54, NRI, and NRI1 were purified as described (1,20,21). IHF was a gift from C. Robertson and H. Nash (National Institutes of Health). Primers FC5 (5'-CCACATCATCACA-CAATCG-3'), FC6 (5'-CAGACTTCATAGCATTTCC-3'), and FC7 (5'-GCATCTTCAGGGTATTGCC-3') hybridizing at -217, +50, and -103 (5' position), respectively, and primer FC1 (5'-GCGAGAGATATTCGTGG-3'), which hybridizes to T7 sequences close to the HindIII site of plasmid pTE103 (22), were synthesized at the Biopolymers Laboratory, Howard Hughes Medical Institute, Massachusetts Institute of Technology. The following materials were used: DNase I, Mae II, alkaline phosphatase, and bovine serum albumin, from Boehringer Mannheim; Klenow and other restriction endonucleases or DNA modifying enzymes, from New England Biolabs; radiolabels and Protosol, from DuPont/NEN; ultrapure solution ribonucleotides and Sephadex G-25, from Pharmacia LKB.Construction of Plasmids. All transcription templates were derived from plasmid pTE103, which contains the multicloning site from pUC8 placed upstream from a bacteriophage T7 transcriptional terminator (22). Plasmid pFC50 was constructed by inserting the 540-base-pair (bp) EcoRV/Sac II fragment from pTN240 (18), into the Sma I site of pTE103. The sticky ends of this fragment and of those mentioned below were made blunt by using T4 DNA polymerase. The 540-bp fragment contains the glnHp2 promoter with the upstream regulatory sequences and 66 nucleotides of the glnH coding region. Plasmid pFC54 was constructed by inserting the 180-bp Mae II/Sac II fragment from pTN240 ...

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“…These include proteins such as OmpR, which controls porin expression (11), NtrC, which controls responses to nitrogen depletion (12), PhoB, which controls phosphate assimilation (13), and SpoOA, which controls sporulation in response to nutrient deprivation (14). Most members of this family appear to be regulated by a second component that functions as a sensor for environmental change (10).…”

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confidence: 99%

CheA protein, a central regulator of bacterial chemotaxis, belongs to a family of proteins that control gene expression in response to changing environmental conditions.

Stock

Chen

Welsh

et al. 1988

Proc. Natl. Acad. Sci. U.S.A.

142

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During bacterial chemotaxis, the binding of stimulatory ligands to chemoreceptors at the cell periphery leads to a response at the flagellar motor. Three proteins appear to be required for receptor-mediated control of swimming behavior, the products of the cheA, cheW, and cheY genes. Here we present the complete nucleotide sequence of the Salmonella lyphimurium cheA gene together with the purification and characterization of its protein product. The protein is a 73,000 M, cytoplasmic constituent. Amino acid-sequence comparisons indicate that it belongs to a family of bacterial regulatory proteins including the products of the cpxA, deWf, envZ, ntrB, phoR, phoM, and virA genes. Each member of this family has a conserved domain of -200 residues within its C terminus. We have previously shown that another chemotaxis protein, CheY, represents a domain of protein structure that has been conserved within a second large family of bacterial regulatory proteins. Each protein of the CheA family seems to function as a regulator of a different CheY homologue. Although each pair of proteins appears to produce a specialized response to a distinct type of stimulus, the relationships in primary structure suggest that a similar molecular mechanism may be involved.During bacterial chemotaxis, receptor proteins at the cell surface modulate motor behavior in response to binding of extracellular ligands (for reviews, see refs.

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Regulation of Nitrogen Fixation Genes

Cited by 324 publications

References 59 publications

Evolution of Molybdenum Nitrogenase during the Transition from Anaerobic to Aerobic Metabolism

Evolution of Molybdenum Nitrogenase during the Transition from Anaerobic to Aerobic Metabolism

Role of integration host factor in the regulation of the glnHp2 promoter of Escherichia coli.

CheA protein, a central regulator of bacterial chemotaxis, belongs to a family of proteins that control gene expression in response to changing environmental conditions.

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