The NIFL regulatory protein controls transcriptional activation of nitrogen fixation (nif) genes in Azotobacter vinelandii The high energetic requirements for nitrogen fixation and the extreme oxygen sensitivity of the nitrogenase enzyme impose physiological constraints on diazotrophy, which necessitate stringent control of nitrogen fixation (nif) gene expression at the transcriptional level (1). In both Azotobacter vinelandii and Klebsiella pneumoniae, the NIFL protein regulates nif gene transcription in response to environmental oxygen and fixed nitrogen (2, 3). This control by NIFL is achieved through modulation of the activity of the transcriptional activator NIFA, an enhancer binding protein that catalyzes the formation of open promoter complexes by the alternative holoenzyme form of RNA polymerase containing the sigma factor eN (Eo4N) (4). Stimulation of open promoter complex formation by NIFA requires nucleoside triphosphate hydrolysis catalyzed by the central domain of this activator (5).Sequence analysis of NIFL indicates that this protein is composed of two domains separated by a glutamine-rich flexible linker. The amino-terminal domain shows homology to the bat gene product from Halobacterium halobium, which potentially has an oxygen-sensing function and also to the rhizobial FixL family of heme-based oxygen sensors, although the significance of these homologies is at present unknown (2). The carboxyl-terminal domain of NIFL shares characteristic features with the histidine protein kinase family of twocomponent regulatory proteins, and in the case of the A. vinelandii protein possesses all five of the conserved regions found in other transmitter domains. However, although A.The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.vinelandii NIFL contains a conserved histidine residue known to be the site of autophosphorylation in other members of this family, a number of substitutions of this residue do not impair function, implying that sensory transduction by NIFL does not involve phosphorylation of this residue (6). Moreover, neither autophosphorylation of NIFL nor phosphotransfer to NIFA has so far been detected in vitro (7,8). Inhibition of NIFA activity by NIFL apparently requires stoichiometric amounts of the two proteins, implying direct protein-protein interaction rather than catalytic modification of NIFA activity. Since the nucleoside triphosphatase activity of A. vinelandii NIFA decreases when the inhibitory complex between NIFL and NIFA is formed, NIFL may block NIFA activity by inhibiting its catalytic function. Moreover, inhibition by A. vinelandii NIFL is stimulated by the presence of adenosine nucleotides, particularly ADP, suggesting that formation of the inhibitory complex might be regulated by the ATP/ADP ratio (9).When NIFL is overexpressed aerobically in nitrogen-rich medium and purified under aerobic conditions, it is c...

Transcriptional control of the nitrogen fixation (nif) genes in response to oxygen in Azotobacter vinelandii is mediated by nitrogen fixation regulatory protein L (NifL), a regulatory flavoprotein that modulates the activity of the transcriptional activator nitrogen fixation regulatory protein A (NifA). CD spectra of purified NifL indicate that FAD is bound to NifL in an asymmetric environment and the protein is predominantly α-helical. The redox potential of NifL is -226 mV at pH 8 as determined by the enzymic reduction of NifL by xanthine oxidase/xanthine in the presence of appropriate mediators. The reduction of NifL by xanthine oxidase prevented NifL from acting as an inhibitor of NifA. In the absence of electron mediators NifL could also be reduced by Escherichia coli flavohaemoprotein (Hmp) with NADH as reductant. Hmp contains a globin-like domain with haem B as prosthetic group and an FAD-containing oxidoreductase module. The carboxyferrohaem form of Hmp was competent to reduce NifL, suggesting that electron donation to NifL originates from the flavin in Hmp rather than by direct electron transfer from the haem. Spinach ferredoxin:NAD(P) oxidoreductase, which adopts a folding similar to the FAD- and NAD-binding domains of Hmp, also reduced NifL with NADH as reductant. Re-oxidation of NifL occurs rapidly in the presence of air, raising the possibility that NifL might sense intracellular oxygen. We propose a physiological redox cycle in which the oxidation of NifL by oxygen and hence the activation of its inhibitory properties occurs rapidly, in contrast with the switch from the active to the reduced form of NifL, which occurs more slowly.

The enhancer-binding protein NIFA is required for transcriptional activation of nif promoters by the alternative holoenzyme form of RNA polymerase, which contains the sigma factor 54 ( N ). NIFA hydrolyzes nucleoside triphosphates to catalyze the isomerization of closed promoter complexes to transcriptionally competent open complexes. The activity of NIFA is antagonized by the regulatory protein NIFL in response to oxygen and fixed nitrogen in vivo. We have investigated the requirement for nucleotides in the formation and stability of open promoter complexes by NIFA and inhibition of its activity by NIFL at the Klebsiella pneumoniae nifH promoter. Open complexes formed by 54 -containing RNA polymerase are considerably more stable to heparin challenge in the presence of GTP than in the presence of ATP. This differential stability is most probably a consequence of GTP being the initiating nucleotide at this promoter. Adenosine nucleosides are specifically required for Azotobacter vinelandii NIFL to inhibit open complex formation by native NIFA, and the nucleoside triphosphatase activity of NIFA is strongly inhibited by NIFL under these conditions. We propose a model in which NIFL modulates the activity of NIFA via an adenosine nucleotide switch.A distinct mechanism of transcriptional activation is observed among the family of prokaryotic enhancer-binding proteins which interact with the holoenzyme form of RNA polymerase containing the alternative sigma factor 54 (E 54 ) (19,26). The nitrogen fixation regulatory protein NIFA is a member of this family which binds to upstream activator sequences (UAS) and catalyzes the isomerization of closed promoter complexes to the open complex in a reaction which requires hydrolysis of a nucleoside triphosphate (25). Productive interactions between NIFA and E 54 are enabled by DNA loop formation, which is facilitated by the binding of integration host factor (IHF) (18,30). The amino acid sequence of NIFA conforms to the three-domain model for the structure of pneumoniae NIFA activates transcription in the absence of specific DNA binding and possesses nucleoside triphosphatase activity (6). In contrast to its K. pneumoniae counterpart, the native Azotobacter vinelandii NIFA protein has been purified in a soluble form, and its properties with respect to DNA binding and catalysis of open complex formation have been characterized in vitro (2).In both K. pneumoniae and A. vinelandii, the activity of NIFA is controlled by a second regulatory protein, NIFL, in response to the environmental effectors oxygen and fixed nitrogen (7,22). Although NIFL proteins show homology in their C-terminal domains to the histidine protein kinase family of two-component regulatory proteins (14), NIFL and NIFA appear to interact at stoichiometric levels (5, 15), and phosphotransfer between the two proteins has not been detected in vitro (2, 21). Moreover, although A. vinelandii NIFL shows greater homology to the canonical histidine protein kinases than does K. pneumoniae NIFL and contains a conserved...

In Azotobacter vinelandii, activation ofnif gene expression by the transcriptional regulatory enhancer binding protein NIFA is controlled by the sensor protein NIFL in response to changes in levels of oxygen and fixed nitrogen in vivo. NIFL is a novel redox-sensing flavoprotein which is also responsive to adenosine nucleotides in vitro. Inhibition of NIFA activity by NIFL requires stoichiometric amounts of the two proteins, implying that the mechanism of inhibition is by direct protein-protein interaction rather than by catalytic modification of the NIFA protein. The formation of the inhibitory complex between NIFL and NIFA may be regulated by the intracellular ATP/ADP ratio. We show that adenosine nucleotides promote complex formation between purified NIFA and NIFL in vitro, allowing isolation of the NIFL-NIFA complex. The complex can also be isolated from cell extracts containing coexpressed NIFL and NIFA in the presence of MgADP. Removal of the nucleotide causes dissociation of the complex. Experiments with truncated proteins demonstrate that the amino-terminal domain of NIFA and the C-terminal region of NIFL potentiate the ADP-dependent stimulation of NIFL-NIFA complex formation.

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