Construction of chimeric proteins from the sigma N-associated transcriptional activators VnfA and AnfA of Azotobacter vinelandii shows that the determinants of promoter specificity lie outside the 'recognition' helix of the HTH motif in the C-terminal domain

Effect of nitric oxide on VnfA, a transcriptional activator of VFe-nitrogenase in Azotobacter vinelandii

The transcriptional activator, VnfA, is necessary for the expression of the structural genes encoding vanadium-dependent nitrogenase in Azotobacter vinelandii. We have previously reported that VnfA harbours a Fe-S cluster as a prosthetic group, presumably a 3Fe-4S type, which is vital for the transcriptionally active VnfA. A plausible effector molecule is a reactive oxygen species (ROS), which disassembles the Fe-S cluster switching the active VnfA to become fully inactive. This finding prompted us to investigate the effect of nitric oxide (NO), another physiologically important radical species on the VnfA activity. Unlike ROS, the VnfA activity was moderately inhibited and converged to 70% of the maximum by NO irrespective of its concentration. The Fe-S cluster of VnfA was found to react with NO to form a dinitrosyl-iron complex, either in the dimeric or monomeric form, dependent on the relative stoichiometry of NO to the Fe-S cluster. The VnfA species harbouring the dinitrosyl-iron complexes in each form exhibited 50% ATPase activity compared to the active VnfA. The findings of this study would open an argument about a biological effect of NO on nitrogenase in light of its transcriptional regulatory system.

The role of the GAF and central domains of the transcriptional activator VnfA in Azotobacter vinelandii

VnfA is a transcriptional activator that is required for the expression of the structural genes encoding nitrogenase-2 in Azotobacter vinelandii. VnfA consists of three domains: an N-terminal regulatory domain termed GAF, including a Cys-rich motif; a central domain from the AAA+ family; and a C-terminal domain for DNA binding. Previously, we reported that transcriptionally active VnfA harboring an Fe-S cluster (presumably of the 3Fe-4S type) as a prosthetic group and the Cys-rich motif were possibly associated with coordination of the Fe-S cluster. In the present study, we have investigated the roles of the GAF and central domains in the regulatory function of VnfA using truncated variants: ΔN15(VnfA) and ΔGAF(VnfA) that lack the N-terminal 15 residues and whole GAF domain, respectively, and GAF(VnfA) consisting of only the GAF domain. ΔN15(VnfA) and ΔGAF(VnfA) lost the ability to bind the Fe-S cluster, whereas GAF(VnfA) was still able to bind to the cluster, consistent with the hypothesis that the Cys-rich motif is essential for Fe-S cluster binding. The GAF domain showed an inhibitory effect on the transcriptional activity of VnfA, which was reversed in the presence of the Fe-S cluster, and reactivated upon disassembly of the cluster. The inhibitory activity of the GAF domain acts on the NTPase activity of the central domain, whereas the binding ability of VnfA to DNA was not significantly affected, when VnfA retains its tetrameric conformation. The results imply that a major pathway, by which VnfA function is regulated, operates via the control of NTPase activity by the GAF domain.

In vivo and in vitro activities of the Escherichia coli sigma54 transcription activator, PspF, and its DNA-binding mutant, PspFDeltaHTH

Transcription of the phage-shock protein (psp) operon in Escherichia coli is driven by a sigma54 promoter, stimulated by integration host factor and dependent on an upstream, cis-acting sequence and an activator protein, PspF. PspF belongs to the enhancer binding protein family but lacks an N-terminal regulatory domain. Purified PspF is not modified and has an ATPase activity that is increased twofold in the presence of DNA carrying the psp cis-acting sequence. Purified mutant His-tagged PspF that lacks the C-terminal DNA-binding motif has a DNA-independent ATPase activity when present at 30-fold the concentration of the wild-type protein. Both proteins oligomerize in solution in an ATP and DNA-independent manner. The wild-type activator protein, but not the DNA-binding mutant, binds specifically to the cis-acting sequence. Analysis of the sequence protected by PspF demonstrates the presence of two upstream binding sites within the sequence, UAS I and UAS II, which together constitute the psp enhancer. Protection at low protein concentrations is more pronounced and more extensive on a supercoiled DNA than on a linear template. Full expression of the psp operon upon hyperosmotic shock depends on wild-type PspF, but only partially requires the presence of the psp enhancer.

Promoters controlling expression of the alternative nitrogenase and the molybdenum uptake system in Rhodobacter capsulatus are activated by NtrC, independent of sigma54, and repressed by molybdenum

The alternative nitrogenase of Rhodobacter capsulatus is expressed only under conditions of nitrogen and molybdenum depletion. The analysis of anfA-lacZ fusions demonstrated that this dual control occurred at the level of transcription of anfA, which encodes a transcriptional activator specific for the alternative nitrogenase. The anfA promoter was found to be activated under nitrogen-limiting conditions by NtrC in a sigma54-independent manner. In addition, anfA transcription was repressed by traces of molybdenum. This molybdenum-dependent repression of anfA was released in R. capsulatus mutants carrying either lesions in the high-affinity molybdenum uptake system (modABCD) or a double deletion of mopA and mopB, two genes encoding molybdenum-pterin-binding proteins. The expression of the molybdenum transport system itself was shown to be negatively regulated by molybdenum and, unexpectedly, to be also regulated by NtrC. This finding is in line with the presence of two tandemly arranged DNA motifs located in front of the R. capsulatus mopA-modABCD operon, which are homologous to R. capsulatus NtrC binding sites. Mapping of the transcriptional initiation sites of mopA and anfA revealed promoter sequences exhibiting significant homology to each other but no homology to known prokaryotic promoters. In addition, a conserved DNA sequence of dyad symmetry overlapping the transcriptional initiation sites of mopA and anfA was found. Deletions within this element resulted in molybdenum-independent expression of anfA, indicating that this DNA sequence may be the target of MopA/MopB-mediated repression.

Expression from the nifB promoter of Azotobacter vinelandii can be activated by NifA, VnfA, or AnfA transcriptional activators

In Azotobacter vinelandii, nifB is required for the activity of all three nitrogenases. Expression of a nifB-lacZ fusion was examined to determine which regulatory gene products are important for nifB expression and how its transcription is regulated in response to metals. In all conditions, expression in A. vinelandii was eliminated by an rpoN mutation, confirming the absolute requirement for sigma N. In the wild type, nifB-lacZ expression was approximately twofold higher in cells grown with Mo than without. Expression was negligible in a nifA mutant grown with Mo but was much higher in Mo-free medium, suggesting that in these conditions, another sigma N-dependent activator was responsible for nifB expression, possibly VnfA, AnfA, or NtrC. Although expression of the nifB-lacZ fusion in A. vinelandii vnfA, anfA, and ntrC mutants was little different from that in the wild type, nifB transcription could be activated by NifA, VnfA, or a truncated form of AnfA in Escherichia coli. The two potential NifA binding sites centered at -87 and -129 bp upstream of the transcription start site each overlapped a VnfA recognition sequence, motifs also found in Azotobacter chroococcum in two exactly conserved regions. Deletion analysis showed that both regions are important for nifB expression. Activation of the full-length promoter by AnfA was impaired by overexpressing the DNA-binding domain of NifA, suggesting that binding of NifA and AnfA can be competitive.

Identification of sequences important for recognition of vnf genes by the VnfA transcriptional activator in Azotobacter vinelandii

To analyze regulation of the vanadium-dependent nitrogenase of Azotobacter vinelandii, plasmids carrying vnfE-, vnfH-, or vnfD-lacZ fusions were transferred to Escherichia coli. These genes were expressed only if VnfA was present. Deletions of the vnfE upstream region were constructed and comparison of a region necessary for expression with sequences upstream of other vnf genes indicated a substantially conserved motif, GTAC-N6-GTAC, hypothesized to be the binding site for VnfA. This motif was duplicated with 17 or 18 bases lying between each in the vnfH and vnfD promoters. Deletion analysis of the vnfH promoter indicated that both motifs were necessary for full expression. In footprinting experiments, VnfA significantly protected from methylation the guanine residues within or immediately adjacent to the proposed VnfA recognition motifs. The active form of VnfA is probably interacting dimers, a tetramer, or a higher order oligomer since two regions of dyad symmetry are required for its interaction with the DNA.

Specific binding of the replication protein of plasmid pPS10 to direct and inverted repeats is mediated by an HTH motif

The initiator protein of the plasmid pPS10, RepA, has a putative helix-turn-helix (HTH) motif at its C-terminal end. RepA dimers bind to an inverted repeat at the repA promoter (repAP) to autoregulate RepA synthesis. [D. García de Viedma, et al. (1996) EMBO J. in press]. RepA monomers bind to four direct repeats at the origin of replication (oriV) to initiate pPS10 replication This report shows that randomly generated mutations in RepA, associated with defficiencies in autoregulation, map either at the putative HTH motif or in its vicinity. These mutant proteins do not promote pPS10 replication and are severely affected in binding to both the repAP and oriV regions in vitro. Revertants of a mutant that map in the vicinity of the HTH motif have been obtained and correspond to a second amino acid substitution far upstream of the motif. However, reversion of mutants that map in the helices of the motif occurs less frequently, at least by an order of magnitude. All these data indicate that the helices of the HTH motif play an essential role in specific RepA-DNA interactions, although additional regions also seem to be involved in DNA binding activity. Some mutations have slightly different effects in replication and autoregulation, suggesting that the role of the HTH motif in the interaction of RepA dimers or monomers with their respective DNA targets (IR or DR) is not the same.

Chimeric transcriptional activators generated in vivo from VnfA and AnfA of Azotobacter vinelandii: N-terminal domain of AnfA is responsible for dependence on nitrogenase Fe protein

In vivo recombinants generating chimeras between the transcriptional activators VnfA and AnfA of Azotobacter vinelandii were constructed by cloning their structural genes in tandem and selecting against a conditionally lethal gene inserted between them. The parent molecules differ in their promoter specificities and in that AnfA, but not VnfA, requires the Fe protein of nitrogenase for its activity. Chimeras with fusion junctions in the N-terminal half of the central domain were found to be inactive, probably as a result of misfolding. All chimeras carrying the C-terminal domain of AnfA showed the corresponding promoter specificity, supporting the model which ascribes promoter specificity to the DNA-binding properties of the C-terminal domain. None of the chimeras showed the dependence on Fe protein typical of AnfA, including one which composed 82% of AnfA with only a short segment of VnfA at the N terminus. Deleting the N-terminal domain of AnfA gave a fully active protein which was also independent of Fe protein. This indicates that the N-terminal domain has an inhibitory effect on activity which is relieved by Fe protein.

Effect of amino acid substitutions in a potential metal-binding site of AnfA on expression from the anfH promoter in Azotobacter vinelandii

AnfA, an activator required for transcription of the structural genes encoding nitrogenase 3 (anfHDGK) in Azotobacter vinelandii, has a potential metal-binding site [(S19)H(C21)FTGE(C26)R] in its N terminus. Growth studies and expression of an anfH-lacZ fusion in mutants containing amino acid substitutions in this site indicate that Ser-19 is not required for AnfA activity whereas Cys-21 and Cys-26 are required. Residual expression of the anfH-lacZ fusion in AnfA- mutants was found to be due to activation by VnfA, the activator required for expression of genes encoding nitrogenase 2.

Rhizobium meliloti DctD, a sigma 54-dependent transcriptional activator, may be negatively controlled by a subdomain in the C-terminal end of its two-component receiver module

Rhizobium meliloti DctD is believed to have three functional domains: an N-terminal, two-component receiver domain; and like other sigma 54-dependent activators, C-terminal and central domains for DNA binding and transcription activation. We have characterized a progressive series of N-terminal deletions of R. meliloti DctD. The N-terminal domain was not needed for binding the dctA upstream activation sequence. Only 25% of the C-terminal end of the receive domain was needed to significantly inhibit the central domain, and proteins lacking up to 60% of the N-terminal end of the receiver domain were 'inducible' in R. meliloti cells. We hypothesize that the N-terminal two-thirds of the DctD receiver domain augments and controls an adjacent subdomain for inhibiting the central domain.