Glutamine synthetase gene of Bacillus subtilis

Formation of a stable RNase Y-RicT (YaaT) complex requires RicA (YmcA) and RicF (YlbF)

In Bacillus subtilis , the RicT (YaaT), RicA (YmcA) and RicF (YlbF) proteins, which form a stable ternary complex, are needed together with RNase Y (Rny), to cleave and thereby stabilize several key transcripts encoding enzymes of intermediary metabolism. We show here that RicT, but not RicA or RicF, forms a stable complex with Rny, and that this association requires the presence of RicA and RicF. We propose that RicT is handed off from the ternary complex to Rny. We show further that the two iron-sulfur clusters carried by the ternary Ric complex are required for the formation of the stable RicT-Rny complex. We demonstrate that proteins of the degradosome-like network of B. subtilis , which also interact with Rny, are dispensable for processing of the gapA operon. Thus, Rny participates in distinct RNA-related processes, determined by its binding partners, and a RicT-Rny complex is likely the functional entity for gapA mRNA maturation.

IMPORTANCE

The action of nucleases on RNA is universal and essential for all forms of life and includes processing steps that lead to the mature and functional forms of certain transcripts. In B. subtilis it has been shown that key transcripts for energy producing steps of glycolysis, for nitrogen assimilation and for oxidative phosphorylation, all of them crucial processes of intermediary metabolism, are cleaved at specific locations, resulting in mRNA stabilization. The proteins required for these cleavages in B. subtilis (Rny (RNase Y), RicA (YmcA), RicF (YlbF) and RicT (YaaT)) are broadly conserved among the firmicutes, including in several important pathogens, hinting that regulatory mechanisms they control may also be conserved. Several aspects of these regulatory events have been explored: phenotypes associated with the absence of these proteins have been described, the impact of these absences on the transcriptome has been documented, and there has been significant exploration of the biochemistry and structural biology of Rny and the Ric proteins. The present study further advances our understanding of the association of Ric proteins and Rny and shows that a complex of Rny with RicT is probably the entity that carries out mRNA maturation.

6S-1 RNA function leads to a delay in sporulation in Bacillus subtilis

We have discovered that 6S-1 RNA (encoded by bsrA) is important for appropriate timing of sporulation in Bacillus subtilis in that cells lacking 6S-1 RNA sporulate earlier than wild-type cells. The time to generate a mature spore once the decision to sporulate has been made is unaffected by 6S-1 RNA, and, therefore, we propose that it is the timing of onset of sporulation that is altered. Interestingly, the presence of cells lacking 6S-1 RNA in coculture leads to all cell types exhibiting an early-sporulation phenotype. We propose that cells lacking 6S-1 RNA modify their environment in a manner that promotes early sporulation. In support of this model, resuspension of wild-type cells in conditioned medium from ΔbsrA cultures also resulted in early sporulation. Use of Escherichia coli growth as a reporter of the nutritional status of conditioned media suggested that B. subtilis cells lacking 6S-1 RNA reduce the nutrient content of their environment earlier than wild-type cells. Several pathways known to impact the timing of sporulation, such as the skf- and sdp-dependent cannibalism pathways, were eliminated as potential targets of 6S-1 RNA-mediated changes, suggesting that 6S-1 RNA activity defines a novel mechanism for altering the timing of onset of sporulation. In addition, 6S-2 RNA does not influence the timing of sporulation, providing further evidence of the independent influences of these two related RNAs on cell physiology.

Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli

BACKGROUND

The assimilation of nitrogen in bacteria is achieved through only a few metabolic conversions between alpha-ketoglutarate, glutamate and glutamine. The enzymes that catalyze these conversions are glutamine synthetase, glutaminase, glutamate dehydrogenase and glutamine alpha-ketoglutarate aminotransferase. In low-GC Gram-positive bacteria the transcriptional control over the levels of the related enzymes is mediated by four regulators: GlnR, TnrA, GltC and CodY. We have analyzed the genomes of all species belonging to the taxonomic families Bacillaceae, Listeriaceae, Staphylococcaceae, Lactobacillaceae, Leuconostocaceae and Streptococcaceae to determine the diversity in central nitrogen metabolism and reconstructed the regulation by GlnR.

RESULTS

Although we observed a substantial difference in the extent of central nitrogen metabolism in the various species, the basic GlnR regulon was remarkably constant and appeared not affected by the presence or absence of the other three main regulators. We found a conserved regulatory association of GlnR with glutamine synthetase (glnRA operon), and the transport of ammonium (amtB-glnK) and glutamine/glutamate (i.e. via glnQHMP, glnPHQ, gltT, alsT). In addition less-conserved associations were found with, for instance, glutamate dehydrogenase in Streptococcaceae, purine catabolism and the reduction of nitrite in Bacillaceae, and aspartate/asparagine deamination in Lactobacillaceae.

CONCLUSIONS

Our analyses imply GlnR-mediated regulation in constraining the import of ammonia/amino-containing compounds and the production of intracellular ammonia under conditions of high nitrogen availability. Such a role fits with the intrinsic need for tight control of ammonia levels to limit futile cycling.

Feedback-resistant mutations in Bacillus subtilis glutamine synthetase are clustered in the active site

The feedback-inhibited form of Bacillus subtilis glutamine synthetase regulates the activity of the TnrA transcription factor through a protein-protein interaction that prevents TnrA from binding to DNA. Five mutants containing feedback-resistant glutamine synthetases (E65G, S66P, M68I, H195Y, and P318S) were isolated by screening for colonies capable of cross-feeding Gln(-) cells. In vitro enzymatic assays revealed that the mutant enzymes had increased resistance to inhibition by glutamine, AMP, and methionine sulfoximine. The mutant proteins had a variety of enzymatic alterations that included changes in the levels of enzymatic activity and in substrate K(m) values. Constitutive expression of TnrA- and GlnR-regulated genes was seen in all five mutants. In gel mobility shift assays, the E65G and S66P enzymes were unable to inhibit TnrA DNA binding, while the other three mutant proteins (M68I, H195Y, and P318S) showed partial inhibition of TnrA DNA binding. A homology model of B. subtilis glutamine synthetase revealed that the five mutated amino acid residues are located in the enzyme active site. These observations are consistent with the hypothesis that glutamine and AMP bind at the active site to bring about feedback inhibition of glutamine synthetase.

Cross-regulation of the Bacillus subtilis glnRA and tnrA genes provides evidence for DNA binding site discrimination by GlnR and TnrA

Two Bacillus subtilis transcriptional factors, TnrA and GlnR, regulate gene expression in response to changes in nitrogen availability. These two proteins have similar amino acid sequences in their DNA binding domains and bind to DNA sites (GlnR/TnrA sites) that have the same consensus sequence. Expression of the tnrA gene was found to be activated by TnrA and repressed by GlnR. Mutational analysis demonstrated that a GlnR/TnrA site which lies immediately upstream of the -35 region of the tnrA promoter is required for regulation of tnrA expression by both GlnR and TnrA. Expression of the glnRA operon, which contains two GlnR/TnrA binding sites (glnRAo1 and glnRAo2) in its promoter region, is repressed by both GlnR and TnrA. The glnRAo2 site, which overlaps the -35 region of the glnRA promoter, was shown to be required for regulation by both GlnR and TnrA, while the glnRAo1 site which lies upstream of the -35 promoter region is only involved in GlnR-mediated regulation. Examination of TnrA binding to tnrA and glnRA promoter DNA in gel mobility shift experiments showed that TnrA bound with an equilibrium dissociation binding constant of 55 nM to the GlnR/TnrA site in the tnrA promoter region, while the affinities of TnrA for the two GlnR/TnrA sites in the glnRA promoter region were greater than 3 muM. These results demonstrate that GlnR and TnrA cross-regulate each other's expression and that there are differences in their DNA-binding specificities.

Bacillus subtilis glutamine synthetase controls gene expression through a protein-protein interaction with transcription factor TnrA

Bacillus subtilis TnrA, a global regulator of transcription, responds to nitrogen availability, but the specific signal to which it responds has been elusive. Genetic studies indicate that glutamine synthetase is required for the regulation of TnrA activity in vivo. We report here that the feedback-inhibited form of glutamine synthetase directly interacts with TnrA and blocks the DNA binding activity of TnrA. Mutations in the tnrA gene (tnrA(C)) that allow constitutive high level expression of tnrA-activated genes were isolated and characterized. Feedback-inhibited glutamine synthetase had a significantly reduced ability to block the in vitro DNA binding by three of the TnrA(C) proteins. Thus, glutamine synthetase, an enzyme of central metabolism, directly interacts with and regulates the DNA binding activity of TnrA.

Transcriptional activation of the Bacillus subtilis ackA promoter requires sequences upstream of the CcpA binding site

Carbon catabolite protein A (CcpA) is a global regulator of carbon metabolism in gram-positive bacteria, repressing transcription of genes for the utilization of secondary carbon sources in the presence of a readily metabolized carbon source and activating transcription of genes, such as ackA and pta, that are required for carbon excretion. The promoter region of the Bacillus subtilis ackA gene contains two catabolite responsive elements (cre sites), of which only the site closest to the promoter (cre2) binds CcpA to activate transcription. A region immediately upstream of the cre2 site is also important for transcriptional activation. The required elements in this region were further defined by mutagenesis. CcpA binds to the ackA promoter region in gel shift assays even in the presence of mutations in the upstream element that block transcriptional activation, indicating that this region has a function other than promoting binding of CcpA.

Role of TnrA in nitrogen source-dependent repression of Bacillus subtilis glutamate synthase gene expression

Synthesis of glutamate, the cell's major donor of nitrogen groups and principal anion, occupies a significant fraction of bacterial metabolism. In Bacillus subtilis, the gltAB operon, encoding glutamate synthase, requires a specific positive regulator, GltC, for its expression. In addition, the gltAB operon was shown to be repressed by TnrA, a regulator of several other genes of nitrogen metabolism and active under conditions of ammonium (nitrogen) limitation. TnrA was found to bind directly to a site immediately downstream of the gltAB promoter. As is true for other genes, the activity of TnrA at the gltAB promoter was antagonized by glutamine synthetase under certain growth conditions.

Bacillus subtilis ccpA gene mutants specifically defective in activation of acetoin biosynthesis

A large number of carbon source utilization pathways are repressed in Bacillus subtilis by the global regulator CcpA, which also acts as an activator of carbon excretion pathways during growth in media containing glucose. In this study, CcpA mutants defective in transcriptional activation of the alsSD operon, which is involved in acetoin biosynthesis, were identified. These mutants retained normal glucose repression of amyE, encoding alpha-amylase, and acsA, encoding acetyl-coenzyme A synthetase, and normal activation of ackA, which is involved in acetate excretion; in these ccpA mutants the CcpA functions of activation of the acetate and acetoin excretion pathways appear to be separated.

Sensing of nitrogen limitation by Bacillus subtilis: comparison to enteric bacteria

Previous studies showed that Salmonella typhimurium apparently senses external nitrogen limitation as a decrease in the concentration of the internal glutamine pool. To determine whether the inverse relationship observed between doubling time and the glutamine pool size in enteric bacteria was also seen in phylogenetically distant organisms, we studied this correlation in Bacillus subtilis, a gram-positive, sporulating bacterium. We measured the sizes of the glutamine and glutamate pools for cells grown in batch culture on different nitrogen sources that yielded a range of doubling times, for cells grown in ammonia-limited continuous culture, and for mutant strains (glnA) in which the catalytic activity of glutamine synthetase was lowered. Although the glutamine pool size of B. subtilis clearly decreased under certain conditions of nitrogen limitation, particularly in continuous culture, the inverse relationship seen between glutamine pool size and doubling time in enteric bacteria was far less obvious in B. subtilis. To rule out the possibility that differences were due to the fact that B. subtilis has only a single pathway for ammonia assimilation, we disrupted the gene (gdh) that encodes the biosynthetic glutamate dehydrogenase in Salmonella. Studies of the S. typhimurium gdh strain in ammonia-limited continuous culture and of gdh glnA double-mutant strains indicated that decreases in the glutamine pool remained profound in strains with a single pathway for ammonia assimilation. Simple working hypotheses to account for the results with B. subtilis are that this organism refills an initially low glutamine pool by diminishing the utilization of glutamine for biosynthetic reactions and/or replenishes the pool by means of macromolecular degradation.

Transcriptional activation of the Bacillus subtilis ackA gene requires sequences upstream of the promoter

Transcriptional activation of the Bacillus subtilis ackA gene, encoding acetate kinase, was previously shown to require catabolite control protein A (CcpA) and sequences upstream of the ackA promoter. CcpA, which is responsible for catabolite repression of a number of secondary carbon source utilization genes in B. subtilis and other gram-positive bacteria, recognizes a cis-acting consensus sequence, designated cre (catabolite response element), generally located within or downstream of the promoter of the repressed gene. Two sites resembling this sequence are centered at positions -116.5 and -56.5 of the ackA promoter and have been termed cre1 and cre2, respectively. Synthesis of acetate kinase, which is involved in the conversion of acetyl coenzyme A to acetate, is induced when cells are grown in the presence of an easily metabolized carbon source such as glucose. In this study, cre2, the site closer to the promoter, and the region upstream of cre2 were shown to be indispensable for CcpA-dependent transcriptional activation of ackA, whereas cre1 was not required. In addition, insertion of 5 bp between cre2 and the promoter disrupted activation, while 10 bp was tolerated, suggesting face-of-the-helix dependence of the position of cre2 and/or upstream sequences. DNase footprinting experiments demonstrated binding of CcpA in vitro to cre2 but not cre1, consistent with the genetic data. Activation of ackA transcription was blocked in a ptsH1/crh double mutant, suggesting involvement of this pathway in CcpA-mediated transcriptional activation.

TnrA, a transcription factor required for global nitrogen regulation in Bacillus subtilis

Expression of the Bacillus subtilis nrgAB operon is derepressed during nitrogen-limited growth. We have identified a gene, tnrA, that is required for the activation of nrgAB expression under these growth conditions. Analysis of the DNA sequence of the tnrA gene revealed that it encodes a protein with sequence similarity to GlnR, the repressor of the B. subtilis glutamine synthetase operon. The tnrA mutant has a pleiotropic phenotype. Compared with wild-type cells, the tnrA mutant is impaired in its ability to utilize allantoin, gamma-aminobutyrate, isoleucine, nitrate, urea, and valine as nitrogen sources. During nitrogen-limited growth, transcription of the nrgAB, nasB, gabP, and ure genes is significantly reduced in the tnrA mutant compared with the levels seen in wild-type cells. In contrast, the level of glnRA expression is 4-fold higher in the, tnrA mutant than in wild-type cells during nitrogen restriction. The phenotype of the tnrA mutant indicates that a global nitrogen regulatory system is present in B. subtilis and that this system is distinct from the Ntr regulatory system found in enteric bacteria.

Autogenous regulation of the Bacillus subtilis glnRA operon

Purified Bacillus subtilis GlnR was shown to bind with high affinity to a specific region that overlaps with the glnRA promoter site. The GlnR binding site includes four copies of a repeated sequence that may be the recognition site for the protein. GlnR inhibited transcription from the glnRA promoter in vitro.

Bacillus subtilis glnR mutants defective in regulation

The Bacillus subtilis glnR gene (part of the glnRA operon) encodes a 135-amino-acid (aa) repressor, GlnR, that regulates glnRA transcription in response to nitrogen levels in the growth medium. Two glnR mutants unable to repress under nitrogen excess conditions were obtained by mutagenesis. Lesions were found at Leu77 and Ala80, aa that lie within a region (between aa 59-83) thought to form the alpha-helix-turn-alpha-helix (HTH) motif common among a class of regulatory proteins. Alteration of Gly72 by site-directed mutagenesis also affected regulation, suggesting that aa within the putative HTH region are critical for GlnR function and may be involved in DNA binding. However, other replacements within the aa 59-83 sequence failed to support the HTH structure proposed for this region. Mutations within the C-terminal region of GlnR were also found to affect regulation. Introduction of an ochre stop codon at aa 110, 116, 123 and 129 resulted in the production of truncated proteins that were constitutively repressed, strongly suggesting that a signal recognition site residues within the last seven aa of GlnR. Substituting Asp129 with Asn led to loss of repression, indicating that Asp129 may be directly involved in interacting with either positive or negative effector molecules, or is a target for post-translational modification.

Nitrogen regulation of nasA and the nasB operon, which encode genes required for nitrate assimilation in Bacillus subtilis

The divergently transcribed nasA gene and nasB operon are required for nitrate and nitrite assimilation in Bacillus subtilis. The beta-galactosidase activity of transcriptional lacZ fusions from the nasA and nasB promoters was high when cells were grown in minimal glucose medium containing poor nitrogen sources such as nitrate, proline, or glutamate. The expression was very low when ammonium or glutamine was used as the sole nitrogen source. The repression of the genes during growth on good sources of nitrogen required wild-type glutamine synthetase (GlnA), but not GlnR, the repressor of the glnRA operon. Primer extension analysis showed that the -10 region of each promoter resembles those of sigma A-recognized promoters. Between the divergently oriented nasA and nasB promoters is a region of dyad symmetry. Mutational analysis led to the conclusion that this sequence is required in cis for the activation of both nasA and nasB. The derepression of these genes in a glnA mutant also required this sequence. These results suggest that an unidentified transcriptional activator and glutamine synthetase function in the regulation of nasA and the nasB operon.

Catabolite regulation of Bacillus subtilis acetate and acetoin utilization genes by CcpA

The Bacillus subtilis acsA (acetyl coenzyme A synthetase) and acuABC (acetoin utilization) genes were previously identified in the region downstream from the ccpA gene, which encodes a protein required for catabolite repression of the amyE (alpha-amylase) gene. The acsA and acuABC genes are divergently transcribed, with only 20 bp separating the -35 sequences of their promoters. Expression of these genes was maximal in stationary phase and was repressed by the addition of glucose to the growth medium. Two sites resembling amyO, the cis-acting regulatory target site for amyE, were identified in the acsA and acuABC promoter regions. Glucose repression of acsA and acuABC transcription was dependent on both CcpA and the amyO-like sequences.

Regulation of the Bacillus subtilis acetate kinase gene by CcpA

The Bacillus subtilis gene encoding acetate kinase was identified on the basis of sequence similarity to the Escherichia coli ackA gene and to a second E. coli gene closely related to ackA. Insertional inactivation of this region of the B. subtilis chromosome resulted in the disappearance of acetate kinase enzyme activity in cell extracts. The ackA gene was mapped to a site close to the ccpA gene, at 263 degrees. The transcriptional start site for B. subtilis ackA was located 90 bp upstream from the start of the coding region, and expression was increased by growth in the presence of excess glucose. Growth of the AckA- mutant was inhibited by glucose, suggesting that acetate kinase is important for excretion of excess carbohydrate. The stimulation of ackA expression by glucose was blocked in a CcpA- mutant, indicating that CcpA, which is required for glucose repression of certain carbon source utilization genes, including amyE, may also be involved in activation of carbon excretion pathways. Two sequences resembling the amyO operator site were identified upstream of the ackA promoter; removal of this region resulted in loss of glucose activation of ackA expression.

Identification of genes involved in utilization of acetate and acetoin in Bacillus subtilis

The Bacillus subtilis ccpA gene has previously been shown to be involved in repression of amyE expression when cells are grown in excess glucose. The region of the B. subtilis chromosome downstream from ccpA was characterized to determine if additional genes involved in carbohydrate metabolism were present. Two open reading frames that exhibited sequence similarity to the Escherichia coli and B. subtilis motA and motB motility genes were found immediately downstream from ccpA; disruption of this region had no effect on growth, sporulation or motility. Two divergent transcriptional units containing the acsA and acuABC genes were also found in this region. The acsA gene encodes acetyl-CoA synthetase, and inactivation of this gene resulted in loss of the ability to utilize acetate as a carbon source for growth or sporulation. Disruption of the acuABC genes resulted in poor growth or sporulation on acetoin or butanediol. The acsA and acuABC promoter sequences were identified by primer extension, and are in close proximity. Two sequences resembling the amyO regulatory target site necessary for glucose repression of amyE were identified in the acsA-acuABC promoter regions.

Recent developments on the regulation and structure of glutamine synthetase enzymes from selected bacterial groups

The structure of glutamine synthetase (GS) enzymes from diverse bacterial groups fall into three distinct classes. GSI is the typical bacterial GS, GSII is similar to the eukaryotic GS and is found together with GSI in plant symbionts and Streptomyces, while GSIII has been found in two unrelated anaerobic rumen bacteria. In most cases, the structural gene for GS enzyme is regulated in response to nitrogen. However, different regulatory mechanisms, to ensure optimal utilization of nitrogen substrates, control the GS enzyme in each class.

Altered regulation of the glnRA operon in a Bacillus subtilis mutant that produces methionine sulfoximine-tolerant glutamine synthetase

A Bacillus subtilis mutant that produced glutamine synthetase (GS) with altered sensitivity to DL-methionine sulfoximine was isolated. The mutation, designated glnA33, was due to a T.A-to-C.G transition, changing valine to alanine at codon 190 within the active-site C domain. Altered regulation was observed for GS activity and antigen and mRNA levels in a B. subtilis glnA33 strain. The mutant enzyme was 28-fold less sensitive to DL-methionine sulfoximine and had a 13.0-fold-higher Km for hydroxylamine and a 4.8-fold-higher Km for glutamate than wild-type GS did.

Organization and nucleotide sequence of the glutamine synthetase (glnA) gene from Lactobacillus delbrueckii subsp. bulgaricus

A 3.3-kb BamHI fragment of Lactobacillus delbrueckii subsp. bulgaricus DNA was cloned and sequenced. It complements an Escherichia coli glnA deletion strain and hybridizes strongly to a DNA containing the Bacillus subtilis glnA gene. DNA sequence analysis of the L. delbrueckii subsp. bulgaricus DNA showed it to contain the glnA gene encoding class I glutamine synthetase, as judged by extensive homology with other prokaryotic glnA genes. The sequence suggests that the enzyme encoded in this gene is not controlled by adenylylation. Based on a comparison of glutamine synthetase sequences, L. delbrueckii subsp. bulgaricus is much closer to gram-positive eubacteria, especially Clostridium acetobutylicum, than to gram-negative eubacteria and archaebacteria. The fragment contains another open reading frame encoding a protein of unknown function consisting of 306 amino acids (ORF306), which is also present upstream of glnA of Bacillus cereus. In B. cereus, a repressor gene, glnR, is found between the open reading frame and glnA. Two proteins encoded by the L. delbrueckii subsp. bulgaricus gene were identified by the maxicell method; the sizes of these proteins are consistent with those of the open reading frames of ORF306 and glnA. The lack of a glnR gene in the L. delbrueckii subsp. bulgaricus DNA in this position may indicate a gene rearrangement or a different mechanism of glnA gene expression.

The effect of various culture conditions on the levels of ammonia assimilatory enzymes of Corynebacterium callunae

Corynebacterium callunae (NCIB 10338) grows faster on glutamate than ammonia when used as sole nitrogen sources. The levels of glutamine synthetase (GS; EC 6.3.1.2) and glutamate synthase (GOGAT; EC 1.4.1.13) of C. callunae were found to be influenced by the nitrogen source. Accordingly, the levels of GS and GOGAT activities were decreased markedly under conditions of ammonia excess and increased under low nitrogen conditions. In contrast, glutamate dehydrogenase (GDH; EC 1.4.1.4) activities were not significantly affected by the type or the concentration of the nitrogen source supplied. The carbon source in the growth medium could also affect GDH, GS and GOGAT levels. Of the carbon sources tested in the presence of 2 mM or 10 mM ammonium chloride as the nitrogen source pyruvate, acetate, fumarate and malate caused a decrease in the levels of all three enzymes as compared with glucose. GDH, GS and GOGAT levels were slightly influenced by aeration. Also, the enzyme levels varied with the growth phase. Methionine sulfoximine, an analogue of glutamine, markedly inhibited both the growth of C. callunae cells and the transferase activity of GS. The apparent Km values of GDH for ammonia and glutamate were 17.2 mM and 69.1 mM, respectively. In the NADPH-dependent reaction of GOGAT, the apparent Km values were 0.1 mM for alpha-ketoglutarate and 0.22 mM for glutamine.

Interaction of the Bacillus subtilis glnRA repressor with operator and promoter sequences in vivo

In vivo dimethyl sulfate footprinting of the Bacillus subtilis glnRA regulatory region under repressing and derepressing conditions demonstrated that the GlnR protein, encoded by glnR, interacts with two sites situated within and adjacent to the glnRA promoter. One site, glnRAo1, between positions -40 and -60 relative to the start point of transcription, is a 21-bp symmetrical element that has been identified as essential for glnRA regulation (H. J. Schreier, C. A. Rostkowski, J. F. Nomellini, and K. D. Hirschi, J. Mol. Biol. 220:241-253, 1991). The second site, glnRAo2, is a quasisymmetrical element having partial homology to glnRAo1 and is located within the promoter between positions -17 and -37. The symmetry and extent of modifications observed for each site during repression and derepression indicated that GlnR interacts with the glnRA regulatory region by binding to both sites in approximately the same manner. Experiments using potassium permanganate to probe open complex formation by RNA polymerase demonstrated that transcriptional initiation is inhibited by GlnR. Furthermore, distortion of the DNA helix within glnRAo2 occurred upon GlnR binding. While glutamine synthetase, encoded by glnA, has been implicated in controlling glnRA expression, analyses with dimethyl sulfate and potassium permanganate ruled out a role for glutamine synthetase in directly influencing transcription by binding to operator and promoter regions. Our results suggested that inhibition of transcription from the glnRA promoter involves GlnR occupancy at both glnRAo1 and glnRAo2. In addition, modification of bases within the glnRAo2 operator indicated that control of glnRA expression under nitrogen-limiting (derepressing) conditions included the involvement of a factor(s) other than GlnR.

Analysis of the Bacillus subtilis tyrS gene: conservation of a regulatory sequence in multiple tRNA synthetase genes

The Bacillus subtilis tyrS gene, which encodes tyrosyl-tRNA synthetase (TyrTS), was isolated, and its nucleotide sequence was determined. The cloned gene was shown to complement an Escherichia coli tyrS (Ts) mutant. The predicted amino acid sequence exhibited 70% identity to that of Bacillus stearothermophilus TyrTS and 55% identity to that of E. coli TyrTS, while identity to a second cryptic B. subtilis TyrTS gene, designated tyrZ, was only 27%. Primer extension analysis indicated that tyrS transcription initiated at a vegetative promoter sequence located 300 nucleotides upstream of the AUG start codon. The mRNA leader region was found to contain an inverted repeat sequence resembling a transcriptional terminator. Expression of a transcriptional tyrS-lacZ fusion was found to be induced by starvation for tyrosine in a tyrosine auxotroph (tyrA1). Transcription initiation was unaffected by tyrosine starvation. Deletion of the terminator region in a tyrS-lacZ fusion resulted in high-level constitutive expression. Immediately preceding the putative terminator was sequence element found to be conserved in the upstream region of a number of Bacillus tRNA synthetase genes as well as in the ilv-leu biosynthetic operon; mutation of this element in tyrS resulted in low-level uninducible expression. The conservation of this sequence element suggests that aminoacyl-tRNA synthetase genes and the ilv-leu operon may be regulated by a common mechanism in Bacillus spp.

Identification and cloning of the glnR locus, which is required for transcription of the glnA gene in Streptomyces coelicolor A3(2)

Six Streptomyces coelicolor mutants that required glutamine for growth at the wild-type rate on all nitrogen sources (Gln-) were isolated. The phenotypes of all six mutants were similar. The glutamine synthetase (GS) levels were 20- to 100-fold lower in extracts of the Gln- mutants than in extracts of their parents. The reduced levels of GS activity in the Gln- mutants were not due to adenylylation of the GS protein, because GS activity in Gln- extracts did not increase after snake venom phosphodiesterase treatment. No transcripts of the GS structural gene (glnA) could be detected in RNA isolated from the Gln- mutants in primer extension experiments. All six gln mutations mapped adjacent to adeA. S. coelicolor chromosomal DNA complementing the Gln- mutants was isolated from a library of S. coelicolor chromosomal DNA constructed in the low-copy-number S. coelicolor plasmid pIJ922. Subcloning experiments showed that a 1.45-kb DNA fragment could complement all six Gln- mutants. This DNA fragment did not hybridize with either the cloned S. coelicolor glnA gene or the cloned S. viridochromogenes GSII gene in Southern blots. Since glnA transcription was restored in the Gln- mutants containing the complementing DNA, the gln mutations appear to lie in one or more closely linked genes that are required for glnA transcription in S. coelicolor.

The Bacillus subtilis sigL gene encodes an equivalent of sigma 54 from gram-negative bacteria

The levanase operon in Bacillus subtilis is expressed from a -12, -24 promoter and transcription is stimulated by the regulator LevR, which contains a domain homologous with the central domain of the NifA and NtrC family of regulators. We isolated mutants defective in the expression of the levanase operon. These strains contain mutations that define a gene, called sigL, located between cysB and sacB on the genetic map. The sigL gene was cloned and sequenced. It encodes a polypeptide containing 436 residues with a molecular weight of 49,644. The amino acid sequence of SigL is homologous with all sigma 54 factors from Gram-negative bacteria, including Rhizobium meliloti (32% identity) and Klebsiella pneumoniae (30% identity). B. subtilis sigL mutants have a pleiotropic phenotype: (i) the transcription of the levanase operon is strongly reduced and (ii) in minimal medium lacking ammonia, sigL mutants cannot grow when arginine, ornithine, isoleucine, or valine is the sole nitrogen source. These results indicate that the sigL gene encodes an equivalent of the sigma 54 factor in B. subtilis, to our knowledge, the first of this type to be identified in Gram-positive bacteria.

Identification of DNA sequences involved in regulating Bacillus subtilis glnRA expression by the nitrogen source

The DNA binding protein, GlnR, encoded by glnR, is believed to be directly responsible for regulating glnRA expression in Bacillus subtilis. Identification of cis-acting loci involved in glnRA control is the focus of this study. Analysis of glnRA-lacZ transcriptional fusions harboring deletions extending into the promoter region demonstrated that sequences upstream from position -35, relative to the transcription start-point, were necessary for nitrogen source regulation. These sequences included a 21 base-pair (bp) element, from positions -40 to -60, having 2-fold symmetry; the element shares homology to certain binding sites utilized by proteins having the alpha-helix-turn-alpha-helix motif, of which GlnR is a member. Involvement of this element in regulation was examined by using synthetic DNA fragments containing the promoter and upstream sequences driving lacZ expression. Fragments extending from positions -63 to -8 and from positions -52 to -8 yielded full and partial regulation, respectively. Regulation from a fragment containing a 5 bp insertion between positions -36 and -37 was impaired. A T.A to A.T transversion mutation at position -41 did not have any detectable effect on regulation, whereas a T.A to C.G transition mutation at the same site resulted in constitutive expression. Using a gel electrophoresis mobility shift assay, it was found that purified GlnR bound to a glnRA restriction fragment that extended from positions -104 to +83; binding was abolished after digestion with HinfI, which cleaves between positions -52 and -48. Furthermore, HinfI digestion was inhibited by the presence of GlnR. Thus, the GlnR binding site extends from the vicinity of position -35 upstream to position -63. We suggest that the glnRA operator is the 21 bp sequence lying within this region.

The Bacillus subtilis outB gene is highly homologous to an Escherichia coli ntr-like gene

The Bacillus subtilis outB gene was found to have strong similarities to an Escherichia coli gene complementing ntr-like mutations in Rhodobacter capsulatus. The deduced gene products had 52% identical amino acids (65% similar residues). The phenotype of strains affected in the OutB function indicates that this B. subtilis gene may be involved in nitrogen utilization.

Cloning and nucleotide sequence of an archaebacterial glutamine synthetase gene: phylogenetic implications

The glnA gene of the thermophilic sulphur-dependent archaebacterium Sulfolobus solfataricus was identified by hybridization with the corresponding gene of the cyanobacterium Spirulina platensis and cloned in Escherichia coli. The nucleotide sequence of the 1696 bp DNA fragment containing the structural gene for glutamine synthetase was determined, and the derived amino acid sequence (471 residues) was compared to the sequences of glutamine synthetases from eubacteria and eukaryotes. The homology between the archaebacterial and the eubacterial enzymes is higher (42%-49%) than that found with the eukaryotic counterpart (less than 20%). This was true also when the five most conserved regions, which it is possible to identify in both eubacterial and eukaryotic glutamine synthetases, were analysed.

Regulation of Bacillus subtilis glutamine synthetase gene expression by the product of the glnR gene

Transcription of the Bacillus subtilis gene coding of glutamine synthetase (glnA) is regulated by the nitrogen source. The glnA gene lies in an operon in which it is preceded by an open reading frame with the potential to encode a polypeptide of approximately 16,000 Mr. We have now shown that this open reading frame is utilized in vivo, that its product (GlnR) acts as a diffusible, negative regulator of gln transcription, and that GlnR is likely to be a DNA-binding protein. Certain mutations in glnR, including a large, in-frame deletion and a start codon mutation, led to high-level constitutivity of the operon; other mutations caused low-level constitutivity. These latter mutations, which affected the C terminus of GlnR, seemed to disrupt response to the nitrogen source without eliminating the ability of GlnR to bind to DNA. Wild-type GlnR by itself, however, did not impose nitrogen-dependent regulation; such regulation also required the product of glnA. A model is presented in which glutamine synthetase monitors the availability of nitrogen and imposes negative regulation by interaction with or modification of GlnR.

Positive regulation of glutamate biosynthesis in Bacillus subtilis

Nitrogen source regulation of glutamate synthase activity in Bacillus subtilis occurs at the level of transcription of the gltA and gltB genes, which encode the two subunits of the enzyme. We show here that transcription of gltA requires the product of gltC, a gene whose transcription is divergent from that of gltA and whose transcriptional control sequences overlap those of gltA. gltC mutants had decreased, aberrantly regulated levels of glutamate synthase activity and decreased gltA mRNA. The gltC gene product could act in trans to complement both these defects. In addition, the gltC gene product repressed its own transcription. The DNA sequence of gltC revealed that its putative product is very similar to a number of positive regulatory proteins from gram-negative bacteria (the LysR family).

Glutamine auxotrophs of Bacillus subtilis that overproduce glutamine synthetase antigen have altered conserved amino acids in or near the active site

A number of mutations within the Bacillus subtilis glutamine synthetase (GS) gene result in altered catalytic properties and overproduction of the GS antigen. The restriction fragments containing mutations from three such mutants were sequenced, and they all had amino acid changes in conserved residues found either within or near sequences contributing to the active site of the Salmonella typhimurium GS.

Regulation of glutamine synthetase in Streptomyces coelicolor

Glutamine synthetase (GS) in Streptomyces coelicolor was shown to be regulated at two levels. First, the S. coelicolor GS protein is subject to a posttranslational covalent modification which is likely to involve adenylylation. Adenylylation is important in regulating GS activity both after sudden changes in ammonium availability and during steady-state growth. Since higher levels of adenylylated GS were seen in S. coelicolor mutants deficient in glutamate synthase than in wild-type cells, glutamine or a metabolite derived from glutamine is likely to be involved in the metabolic signal that regulates GS adenylylation. Second, the GS structural gene (glnA) is transcriptionally regulated in response to nitrogen availability during steady-state growth. Transcription of the glnA gene occurred from the same promoter during vegetative growth, stationary phase, and sporulation. The nucleotide sequence of this promoter has significant homology with the -10, but not the -35, region of the consensus sequence of Streptomyces vegetative promoters. The glnA gene is transcribed as a monocistronic mRNA.

Sequence of the Bacillus subtilis glutamine synthetase gene region

The nucleotide sequence of the glutamine synthetase (GS) region of Bacillus subtilis has been determined and found to contain several unique features. An open reading frame (ORF) upstream of the GS structural gene is part of the same operon as GS and is involved in regulation. Two downstream ORFs are separated from glnA by an apparent Rho-independent termination site. One of the downstream ORFs encodes a very hydrophobic polypeptide and contains its own potential RNA polymerase and ribosome-binding sites. The derived amino acid (aa) sequence of B. subtilis GS is similar to that of several other prokaryotes, especially to the GS of Clostridium acetobutylicum. The B. subtilis and C. acetobutylicum enzymes differ from the others in the lack of a stretch of about 25 aa as well as the presence of extra cysteine residues in a region known to contain regulatory as well as catalytic mutations. The region around the tyrosine residue that is adenylylated in GS from many species is fairly similar in the B. subtilis GS despite its lack of adenylylation.

Early-blocked sporulation mutations alter expression of enzymes under carbon control in Bacillus subtilis

The physiological roles of the gene subset defined by early-blocked sporulation mutations (spo0) and their second-site suppressor alleles (rvtA11 and crsA47) remain cryptic for both vegetative and sporulating Bacillus subtilis cells. To test the hypothesis that spo0 gene products affect global regulation, we assayed the levels of carbon- and nitrogen-sensitive enzymes in wild-type and spo0 strains grown in a defined minimal medium containing various carbon and nitrogen sources. All the spo0 mutations (except spo0J) affected both histidase and arabinose isomerase levels in an unexpected way: levels of both carbon-sensitive enzymes were two- to six-fold higher in spo0 strains compared to wild type, when cells were grown on the derepressing carbon sources arabinose or maltose. There was no difference in enzyme levels with glucose-grown cells, nor was there a significant difference in levels of the carbon-independent enzymes glutamine synthetase and glucose-6-phosphate dehydrogenase. This effect was not due to a slower growth rate for the spo0 mutants on the poor carbon and nitrogen sources used. The levels of carbon-sensitive enzymes were not simply correlated with sporulation ability in genetically suppressed spo0 mutants, but the rvtA and crsA suppressors each had such marked effects on wild-type growth and enzyme levels that these results were difficult to interpret. We conclude that directly or indirectly the spo0 mutations, although blocking the sporulation process, increase levels of carbon-sensitive enzymes, possibly at the level of gene expression.

Role of glutamate dehydrogenase in ammonia assimilation in nitrogen-fixing Bacillus macerans

Pathways of ammonia assimilation into glutamic acid in Bacillus macerans were investigated by measurements of the specific activities of glutamate dehydrogenase (GDH), glutamine synthetase, and glutamate synthase. In ammonia-rich medium, GDH was the predominant pathway of ammonia assimilation. In nitrogen-fixing cells in which the intracellular NH4+ concentration was 1.4 +/- 0.5 mM, the activity of GDH with a Km of 2.2 mM for NH4+ was found to be severalfold higher than that of glutamate synthase. The result suggests that GDH plays a significant role in the assimilation of NH4+ in N2-fixing B. macerans.

Nucleotide sequence of the glutamine synthetase gene and its controlling region from the acidophilic autotroph Thiobacillus ferrooxidans

A 2089-bp chromosomal DNA segment containing the Thiobacillus ferrooxidans glnA gene has been sequenced. Putative glnAp1-type promoter sequences, a consensus ntrC-gene-product-binding site and a catabolite-activating protein consensus recognition sequence were detected upstream of the structural gene. The glnA gene was followed by a sequence resembling a Rho-independent termination sequence. The complete amino acid sequence (468 residues) of the glutamine synthetase (GS) has been deduced, and comparisons are made with reported amino acid sequences of GS from other organisms.

Nucleotide sequence of the Azospirillum brasilense Sp7 glutamine synthetase structural gene

The complete nucleotide sequence of the glnA gene, encoding the glutamine synthetase subunit of Azospirillum brasilense Sp7, was established. This is the first Azospirillum gene sequenced. The gene encodes a 468 residue polypeptide of MW 51,917. The similarity coefficient (SAB) between the polypeptidic sequence of Azospirillum and Anabaena 7120, which is the only other glnA sequence available, is 58%. No significant homology with E. coli canonical and ntr promoters, or with the promoter region of the Anabaena glnA gene was found. When fused to an E. coli promoter, the gene could be translated in E. coli, despite a very biased codon usage and an atypical Shine-Dalgarno sequence.

Cloning, Expression, and Purification of Glutamine Synthetase from Clostridium acetobutylicum

A glutamine synthetase (GS) gene, glnA , from the gram-positive obligate anaerobe Clostridium acetobutylicum was cloned on recombinant plasmid pHZ200 and enabled Escherichia coli glnA deletion mutants to utilize (NH 4 ) 2 SO 4 as a sole source of nitrogen. The cloned C. acetobutylicum gene was expressed from a regulatory region contained within the cloned DNA fragment. glnA expression was subject to nitrogen regulation in E. coli . This cloned glnA DNA did not enable an E. coli glnA ntrB ntrC deletion mutant to utilize arginine or low levels of glutamine as sole nitrogen sources, and failed to activate histidase activity in this strain which contained the Klebsiella aerogenes hut operon. The GS produced by pHZ200 was purified and had an apparent subunit molecular weight of approximately 59,000. There was no DNA or protein homology between the cloned C. acetobutylicum glnA gene and GS and the corresponding gene and GS from E. coli . The C. acetobutylicum GS was inhibited by Mg 2+ in the γ-glutamyl transferase assay, but there was no evidence that the GS was adenylylated.

Altered regulation of the glnA gene in glutamine synthetase mutants of Bacillus subtilis

Expression of beta-galactosidase by Bacillus subtilis strains carrying transcriptional fusions of the glnA promoter region to the Escherichia coli lacZ gene was found to be regulated by the nitrogen source in glnA+ strains. The pattern of regulation was the same as that for glutamine synthetase (GS); the strongest repression was seen when glutamine was present in the medium. To see this regulation it was necessary for the fusion to be in low copy number, a condition achieved by forcing integration into the chromosome. We constructed a strain carrying a deletion mutation (glnA200) that removes part of the 5' end of the glnA structural gene. This strain did not produce any detectable GS activity or measurable GS antigen. We introduced this mutation and other glnA mutations (glnA73, glnA93, and glnA100) into strains carrying glnA-lacZ fusions. When the strains were grown with glutamine as the nitrogen source, beta-galactosidase activity was found to be derepressed. These results indicate that functional glnA gene product is required for the regulation of transcription from the glnA promoter. This supports the conclusion of our previous studies of the B. subtilis glnA gene cloned in E. coli. Additional factors may also be involved in glnA control. In particular, our results suggest that a 500-base-pair sequence of DNA between the promoter region and the start of the glnA structural gene plays a role in regulation; strains carrying this region within the glnA-lacZ fusion and unable to produce functional GS exhibited only partially derepressed beta-galactosidase levels when grown in the presence of glutamine.

Transcriptional control of the Bacillus subtilis spoIID gene

We cloned the wild-type allele of the spoIID locus of Bacillus subtilis. This DNA region was shown to be transcribed beginning within an hour after the onset of sporulation. The amount of spoIID mRNA present in cells at 1 h after the end of growth was more than 50-fold greater than it was growing cells; the pool of this mRNA decreased steadily after 1.5 h after the end of growth. spoIID mRNA was present in stationary-phase cells of sporulation mutants with lesions in the spo0J and spoIIB genes but was absent in cells carrying spo0B, spo0H, spoIIA, spoIIE, spoIIG, or spoIIIA mutations. In vitro runoff transcription with the E sigma 55, E sigma 37, E sigma 32, and E sigma 29 forms of RNA polymerase indicated that only the E sigma 29 form was able to transcribe the spoIID gene. This result is consistent with results of studies with the Spo- mutants, because only mutants that produced E sigma 29 were able to produce spoIID mRNA in vivo. In the course of this work, two additional transcription units were discovered in the DNA region neighboring the spoIID gene. One of these was expressed during vegetative growth; the other was expressed early during sporulation and corresponded to an in vitro transcript produced by the E sigma 29 forms of RNA polymerase.

Bacillus subtilis citB gene is regulated synergistically by glucose and glutamine

The activity of aconitase in Bacillus subtilis is greatly reduced in cells cultured in media containing rapidly metabolized carbon sources (e.g., glucose). Thus, expression of this enzyme appears to be subject to a form of catabolite repression. Since the product of the citB gene of B. subtilis is required for aconitase activity, we cloned the wild-type allele of this gene and used this DNA as a probe for transcription of citB in cells grown in various media. The steady-state level of RNA that hybridized to this probe was about 10-fold higher in B. subtilis cells grown in citrate-glutamine medium than in cells grown in glucose-glutamine medium. This result correlates well with the steady-state levels of aconitase activity. Two transcripts were shown to initiate within the cloned DNA; the steady-state level of one of these transcripts varied in the same way as did aconitase activity when cells were grown in media containing different carbon sources. This is the first demonstration of regulation by the carbon source of the level of a vegatative-cell transcript in B. subtilis.

Regulation of Bacillus subtilis glutamate synthase genes by the nitrogen source

The wild-type alleles of the gltA292 and gltB1 mutations of Bacillus subtilis have been identified in banks of B. subtilis DNA cloned in phage lambda. These mutations are thought to define the genes for the two subunits of glutamate synthase. Sequences having transforming activity for each allele were subcloned in plasmids and used as hybridization probes for measurements of the rates of synthesis and steady-state levels of glt mRNAs under different growth conditions. For both gltA and gltB, the level of mRNA varied according to the nitrogen source in the growth medium, to an extent sufficient to explain the variation in glutamate synthase activity under the same conditions. Two start points for mRNA synthesis were detected within the cloned DNA, one of which corresponded to the gltA locus. The other start point appears to define a transcription unit, separate from gltA and gltB, within which mutations cause loss of glutamate synthase activity.

Regulation of expression from the glnA promoter of Bacillus subtilis requires the glnA gene product

Expression of the cloned glnA gene [coding for glutamine synthetase (EC 6.3.1.2)] of Bacillus subtilis was 10-fold higher in an Escherichia coli strain grown under nitrogen-limiting conditions than in the same strain under nitrogen-excess conditions. Mutations in the E. coli glnA, glnB, glnD, glnE, glnF, glnG, and glnL genes had no effect on the observed regulation. To test whether sequences within the B. subtilis DNA (3.2 kilobase pairs) were responsible for the observed regulation, a plasmid carrying a transcriptional fusion of the B. subtilis glnA promoter with E. coli lacZ was constructed. beta-Galactosidase levels coded for by this plasmid were found to be negatively regulated in trans by a plasmid carrying the entire B. subtilis glnA gene. Analysis of various deletion plasmids showed that the 1.4-kilobase-pair region encoding glutamine synthetase was necessary for the observed regulation of beta-galactosidase. Plasmids coding for 67% or more of the glutamine synthetase polypeptide gave at least partial repression, but a plasmid carrying 30% of the structural gene, as well as a plasmid carrying a deletion internal to glnA, gave no repression. DNA downstream from glnA (to within 130 base pairs of the end of the gene) was not required for the observed regulation. These results suggest that the glnA gene of B. subtilis is autoregulated, supporting the model for glnA control proposed by Dean et al. [Dean, D. R., Hoch, J. A. & Aronson, A. I. (1977) J. Bacteriol. 131, 981-987].