Nobuyuki Takatani

Regulation of nitrate assimilation in cyanobacteria

Nitrate assimilation by cyanobacteria is inhibited by the presence of ammonium in the growth medium. Both nitrate uptake and transcription of the nitrate assimilatory genes are regulated. The major intracellular signal for the regulation is, however, not ammonium or glutamine, but 2-oxoglutarate (2-OG), whose concentration changes according to the change in cellular C/N balance. When nitrogen is limiting growth, accumulation of 2-OG activates the transcription factor NtcA to induce transcription of the nitrate assimilation genes. Ammonium inhibits transcription by quickly depleting the 2-OG pool through its metabolism via the glutamine synthetase/glutamate synthase cycle. The P(II) protein inhibits the ABC-type nitrate transporter, and also nitrate reductase in some strains, by an unknown mechanism(s) when the cellular 2-OG level is low. Upon nitrogen limitation, 2-OG binds to P(II) to prevent the protein from inhibiting nitrate assimilation. A pathway-specific transcriptional regulator NtcB activates the nitrate assimilation genes in response to nitrite, either added to the medium or generated intracellularly by nitrate reduction. It plays an important role in selective activation of the nitrate assimilation pathway during growth under a limited supply of nitrate. P(II) was recently shown to regulate the activity of NtcA negatively by binding to PipX, a small coactivator protein of NtcA. On the basis of accumulating genome information from a variety of cyanobacteria and the molecular genetic data obtained from the representative strains, common features and group- or species-specific characteristics of the response of cyanobacteria to nitrogen is summarized and discussed in terms of ecophysiological significance.

Role of NtcB in Activation of Nitrate Assimilation Genes in the Cyanobacterium Synechocystis sp. Strain PCC 6803

In Synechocystis sp. strain PCC 6803, the genes encoding the proteins involved in nitrate assimilation are organized into two transcription units, nrtABCD-narB and nirA, the expression of which was repressed by ammonium and induced by inhibition of ammonium assimilation, suggesting involvement of NtcA in the transcriptional regulation. Under inducing conditions, expression of the two transcription units was enhanced by nitrite, suggesting regulation by NtcB, the nitrite-responsive transcriptional enhancer we previously identified in Synechococcus sp. strain PCC 7942. The slr0395 gene, which encodes a protein 47% identical to Synechococcus NtcB, was identified as the Synechocystis ntcB gene, on the basis of the inability of an slr0395 mutant to rapidly accumulate the transcripts of the nitrate assimilation genes upon induction and to respond to nitrite. While Synechococcus NtcB strictly requires nitrite for its action, Synechocystis NtcB enhanced transcription significantly even in the absence of nitrite. Whereas the Synechococcus ntcB mutant expresses the nitrate assimilation genes to a significant level in an NtcA-dependent manner, the Synechocystis ntcB mutant showed only low-level expression of the nitrate assimilation genes, indicating that NtcA by itself cannot efficiently promote expression of these genes in Synechocystis. Activities of the nitrate assimilation enzymes in the Synechocystis ntcB mutant were consequently low, being 40 to 50% of the wild-type level, and the cells grew on nitrate at a rate approximately threefold lower than that of the wild-type strain. These results showed that the contribution of NtcB to the expression of nitrate assimilation capability varies considerably among different strains of cyanobacteria.

Dual modification of a triple-stranded β-helix nanotube with Ru and Re metal complexes to promote photocatalytic reduction of CO2

We have constructed a robust β-helical nanotube from the component proteins of bacteriophage T4 and modified this nanotube with Ru(II)(bpy)(3) and Re(I)(bpy)(CO)(3)Cl complexes. The photocatalytic system arranged on the tube catalyzes the reduction of CO(2) with higher reactivity than that of the mixture of the monomeric forms.

Posttranslational Regulation of Nitrate Assimilation in the Cyanobacterium Synechocystis sp. Strain PCC 6803

Posttranslational regulation of nitrate assimilation was studied in the cyanobacterium Synechocystis sp. strain PCC 6803. The ABC-type nitrate and nitrite bispecific transporter encoded by the nrtABCD genes was completely inhibited by ammonium as in Synechococcus elongatus strain PCC 7942. Nitrate reductase was insensitive to ammonium, while it is inhibited in the Synechococcus strain. Nitrite reductase was also insensitive to ammonium. The inhibition of nitrate and nitrite transport required the PII protein (glnB gene product) and the C-terminal domain of NrtC, one of the two ATP-binding subunits of the transporter, as in the Synechococcus strain. Mutants expressing the PII derivatives in which Ala or Glu is substituted for the conserved Ser49, which has been shown to be the phosphorylation site in the Synechococcus strain, showed ammonium-promoted inhibition of nitrate uptake like that of the wild-type strain. The S49A and S49E substitutions in GlnB did not affect the regulation of the nitrate and nitrite transporter in Synechococcus either. These results indicated that the presence or absence of negative electric charge at the 49th position does not affect the activity of the PII protein to regulate the cyanobacterial ABC-type nitrate and nitrite transporter according to the cellular nitrogen status. This finding suggested that the permanent inhibition of nitrate assimilation by an S49A derivative of PII, as was previously reported for Synechococcus elongatus strain PCC 7942, is likely to have resulted from inhibition of nitrate reductase rather than the nitrate and nitrite transporter.

Effects of High CO2 on Growth and Metabolism of Arabidopsis Seedlings During Growth with a Constantly Limited Supply of Nitrogen

Elevated CO2 has been reported to stimulate plant growth under nitrogen-sufficient conditions, but the effects of CO2 on growth in a constantly nitrogen-limited state, which is relevant to most natural habitats of plants, remain unclear. Here, we maintained Arabidopsis seedlings under such conditions by growing a mutant with reduced nitrate uptake activity on a medium containing nitrate as the sole nitrogen source. Under nitrogen-sufficient conditions (i.e. in the presence of ammonium), growth of shoots and roots of both the wild type (WT) and the mutant was increased approximately 2-fold by elevated CO2. Growth stimulation of shoots and roots by elevated CO2 was observed in the WT growing with nitrate as the sole nitrogen source, but in the mutant grown with nitrate, the high-CO2 conditions stimulated only the growth of roots. In the mutant, elevated CO2 caused well-known symptoms of nitrogen-starved plants, including decreased shoot/root ratio, reduced nitrate content and accumulation of anthocyanin, but also had an increased Chl content in the shoot, which was contradictory to the known effect of nitrogen depletion. A high-CO2-responsive change specific to the mutant was not observed in the levels of the major metabolites, although CO2 responses were observed in the WT and the mutant. These results indicated that elevated CO2 causes nitrogen limitation in the seedlings grown with a constantly limited supply of nitrogen, but the Chl content and the root biomass of the plant increase to enhance the activities of both photosynthesis and nitrogen uptake, while maintaining normal metabolism and response to high CO2.

Engineering of Thermus thermophilus Cytochrome C552 : Thermally Tolerant Artificial Peroxidase

Application of peroxidases as catalysts for the oxidation of a wide spectrum of organic compounds has been a major focus in industrial sectors such as food processing, bioremediation, and biorefinement of oil because they use hydrogen peroxide (H2O2), an environmentally low-load oxidant. The full-scale use of peroxidases is, however, restricted by poor thermal and environmental stability, as is the case with many commercially available enzymes. Therefore, peroxidases with improved thermal stabilities are highly desired. Their detection in thermophilic bacteria by screening techniques is a popular approaches to finding thermally tolerant enzymes, and several such peroxidases have been isolated and characterized. 3] Although these peroxidases show remarkable stabilities and enzymatic activities at elevated temperatures in their host strains or cell lysates, the properties of the purified enzymes are still not sufficient for industrial applications. Some of the enzymes undergo rapid loss of activity in the presence of H2O2 over physiological levels. Partial compensation for the reduced thermoACHTUNGTRENNUNGstabilities and activities of the purified enzymes might be achievable by random mutagenesis achieved through evolutionary engineering. However, there are difficulties in elucidating the obtained variations in chemical terms, which prevents further tuning to improve the desired properties. Here we demonstrate that cytochrome c552 (Cyt c552) from Thermus thermophilus HB8 can be transformed into a thermally stable artificial peroxidase by rational modification based on the molecular mechanisms of natural peroxidases. Cyt c552 is an electron transfer protein containing His15 and Met69 as heme axial ligands, and it has characteristically high stability against thermal denaturation. In this study, two amino acid residues in Cyt c552 were chosen for mutagenesis in line with the peroxidase mechanism and three-dimensional structure of the protein (PDB ID: 1C52). One was Met69, which was replaced with alanine in order to provide a reaction site immediately above the heme iron (M69A). Another was the mutagenesis of Val49 to aspartic acid (V49D), which would be expected to introduce general acid–base catalyst, a fundamental element of the peroxidase mechanism, in the heme cavity. Although weak peroxidase activity is a natural property of cytochrome c, a variant bearing both mutations (M69A/V49D) exerts enhanced activity, which is observed neither for the wild-type nor for variants bearing only the M69A mutation. Figure 1 shows the temperature dependence of CD spectra recorded at 222 nm for the Cyt c552 variants (M69A/V49D and M69A) together with the wild-type and the H64D myoglobin variant (Mb H64D), an engineered sperm whale myoglobin

Essential Role of Acyl-ACP Synthetase in Acclimation of the Cyanobacterium Synechococcus elongatus Strain PCC 7942 to High-Light Conditions

Most organisms capable of oxygenic photosynthesis have an aas gene encoding an acyl-acyl carrier protein synthetase (Aas), which activates free fatty acids (FFAs) via esterification to acyl carrier protein. Cyanobacterial aas mutants are often used for studies aimed at photosynthetic production of biofuels because the mutation leads to intracellular accumulation of FFAs and their secretion into the external medium, but the physiological significance of the production of FFAs and their recycling involving Aas has remained unclear. Using an aas-deficient mutant of Synechococcus elongatus strain PCC 7942, we show here that remodeling of membrane lipids is activated by high-intensity light and that the recycling of FFAs is essential for acclimation to high-light conditions. Unlike wild-type cells, the mutant cells could not increase their growth rate as the light intensity was increased from 50 to 400 µmol photons m(-2) s(-1), and the high-light-grown mutant cells accumulated FFAs and the lysolipids derived from all the four major classes of membrane lipids, revealing high-light-induced lipid deacylation. The high-light-grown mutant cells showed much lower PSII activity and Chl contents as compared with the wild-type cells or low-light-grown mutant cells. The loss of Aas accelerated photodamage of PSII but did not affect the repair process of PSII, indicating that PSII is destabilized in the mutant. Thus, Aas is essential for acclimation of the cyanobacterium to high-light conditions. The relevance of the present finding s to biofuel production using cyanobacteria is discussed.

The role of the Fe-S cluster in the sensory domain of nitrogenase transcriptional activator VnfA from Azotobacter vinelandii.

Transcriptional activator VnfA is required for the expression of a second nitrogenase system encoded in the vnfH and vnfDGK operons in Azotobacter vinelandii. In the present study, we have purified full‐length VnfA produced in E. coli as recombinant proteins (Strep‐tag attached and tag‐less proteins), enabling detailed characterization of VnfA for the first time. The EPR spectra of whole cells producing tag‐less VnfA (VnfA) show distinctive signals assignable to a 3Fe‐4S cluster in the oxidized form ([Fe3S4]+). Although aerobically purified VnfA shows no vestiges of any Fe‐S clusters, enzymatic reconstitution under anaerobic conditions reproduced [Fe3S4]+ dominantly in the protein. Additional spectroscopic evidence of [Fe3S4]+in vitro is provided by anaerobically purified Strep‐tag attached VnfA. Thus, spectroscopic studies both in vivo and in vitro indicate the involvement of [Fe3S4]+ as a prosthetic group in VnfA. Molecular mass analyses reveal that VnfA is a tetramer both in the presence and absence of the Fe‐S cluster. Quantitative data of iron and acid‐labile sulfur in reconstituted VnfA are fitted with four 3Fe‐4S clusters per a tetramer, suggesting that one subunit bears one cluster. In vivoβ‐gal assays reveal that the Fe‐S cluster which is presumably anchored in the GAF domain by the N‐terminal cysteine residues is essential for VnfA to exert its transcription activity on the target nitrogenase genes. Unlike the NifAL system of A. vinelandii, O2 shows no effect on the transcriptional activity of VnfA but reactive oxygen species is reactive to cause disassembly of the Fe‐S cluster and turns active VnfA inactive.

Evaluation of the effects of PII deficiency and the toxicity of PipX on growth characteristics of the PII-less mutant of the cyanobacterium Synechococcus elongatus

Among the known functions of the P(II) protein (the glnB gene product) in the cyanobacterium Synechococcus elongatus, negative regulation of the activity of PipX, a transcriptional co-activator of the NtcA regulon, has been thought to be essential for cell viability, because all the P(II)-less mutants thus far constructed carry spontaneous mutations in pipX. PipX is thus deduced to be a toxic protein, but its toxicity has not been clearly defined because of the lack of P(II)-deficient mutants carrying wild-type pipX. In this study, we developed a method to construct a targeted P(II)-less mutant of S. elongatus without the pipX mutation and determined the contribution of PipX to the detrimental effects of P(II) deficiency. Growth defects of the mutant were severe under nitrogen-replete conditions, i.e. in the presence of ammonium, but were also apparent under nitrogen-limited conditions. Genetic analyses indicated that the growth impairment observed under the nitrogen-limited conditions is largely due to the toxicity of PipX. Some of the phenotypes observed under the nitrogen-replete conditions, including reduced pigmentation and death of most of the cells after transfer from nitrogen-limited conditions to nitrogen-replete conditions, were ascribed to the toxicity of PipX, but inactivation of pipX only partially rescued the growth defect observed in the presence of ammonium, indicating the presence of an as yet unknown P(II) function(s) required for normal growth. Effects of ammonium addition on the nitrite uptake activity of the glnB mutant revealed a new function for P(II) in regulation of the activity of the ABC-type cyanate/nitrite transporter.

Cytochrome c(552) from Thermus thermophilus engineered for facile substitution of prosthetic group.

The facile replacement of heme c in cytochromes c with non-natural prosthetic groups has been difficult to achieve due to two thioether linkages between cysteine residues and the heme. Fee et al. demonstrated that cytochrome c(552) from Thermus thermophilus, overproduced in the cytosol of E. coli, has a covalent linkage cleavable by heat between the heme and Cys11, as well as possessing the thioether linkage with Cys14 [Fee, J. A. (2004) Biochemistry 43, 12162-12176]. Prompted by this result, we prepared a C14A mutant, anticipating that the heme species in the mutant was bound to the polypeptide solely through the thermally cleavable linkage; therefore, the removal of the heme would be feasible after heating the protein. Contrary to this expectation, C14A immediately after purification (as-purified C14A) possessed no covalent linkage. An attempt to extract the heme using a conventional acid-butanone method was unsuccessful due to rapid linkage formation between the heme and polypeptide. Spectroscopic analyses suggested that the as-purified C14A possessed a heme b derivative where one of two peripheral vinyl groups had been replaced with a group containing a reactive carbonyl. A reaction of the as-purified C14A with [BH(3)CN](-) blocked the linkage formation on the carbonyl group, allowing a quantitative yield of heme-free apo-C14A. Reconstitution of apo-C14A was achieved with ferric and ferrous heme b and zinc protoporphyrin. All reconstituted C14As showed spontaneous covalent linkage formation. We propose that C14A is a potential source for the facile production of an artificial cytochrome c, containing a non-natural prosthetic group.