Prolyl oligopeptidase from Pyrococcus furiosus.
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Base Sequence↗
Biomedical subjects
H J Schreier
Publications and source records attributed to H J Schreier.
beta-Glutamate as a substrate for glutamine synthetase.
The conversion of beta-glutamate to beta-glutamine by archaeal and bacterial glutamine synthetase (GS) enzymes has been examined. The GS from Methanohalophilus portucalensis (which was partially purified) is capable of catalyzing the amidation of this substrate with a rate sevenfold less than the rate obtained with alpha-glutamate. Recombinant GS from the archaea Methanococcus jannaschii and Archaeoglobus fulgidus were considerably more selective for alpha-glutamate than beta-glutamate as a substrate. All the archaeal enzymes were much less selective than the two bacterial GS (from Escherichia coli and Bacillus subtilis), whose specific activities towards beta-glutamate were much smaller than rates with the alpha-isomer. These results are discussed in light of the observation that beta-glutamate is accumulated as an osmolyte in many archaea while beta-glutamine (produced by glutamine synthetase) is used as an osmolyte only in M. portucalensis.
Animals↗
Transcriptional regulation of phosphoenolpyruvate synthase by maltose in the hyperthermophilic archaeon, Pyrococcus furiosus.
The phosphoenolpyruvate synthase (EC 2.7.9.2) from the hyperthermophilic archaeon Pyrococcus furiosus catalyzes the Pi-dependent formation of pyruvate, ATP and water from phosphoenolpyruvate and AMP [Sakuraba, H., Arch. Biochem. Biophys., 364, 125-128 (1999)]. In this study, the P. furiosus phosphoenolpyruvate synthase was purified to homogeneity and the N-terminal amino acid sequence was determined to be AYRFIKWFEELS. The sequence coincided completely with the N-terminal amino acid sequence of the translation product of the mlrA gene that was found to be upregulated at the transcriptional level by the alpha-linked glucose disaccharide maltose [Robinson, K.A. and Schreier, H.J., Gene, 151, 173-176 (1994)]. The mlrA gene was cloned and expressed in Escherichia coli. The recombinant cells produced a hyperthermostable phosphoenolpyruvate synthase. This indicates that the mlrA gene encodes the enzyme. When P. furiosus was grown on the medium supplemented with maltose, the specific activity of the enzyme markedly increased (about 10-fold) compared with that produced by the cells grown on the medium without maltose. Northern blot analysis revealed enhanced transcription of the mlrA gene in the presence of maltose. These results indicate that transcriptional regulation of phosphoenolpyruvate synthase by maltose is present in P. furiosus.
Journal Article↗
Control of Bacillus subtilis glutamine synthetase expression by glnR from Staphylococcus aureus.
GlnR plays a major role in regulation in Bacillus subtilis by directly controlling expression of glutamine synthetase (GS) as well as several genes involved in nitrogen metabolism. A GlnR homolog from Staphylococcus aureus was found to complement a B. subtilis glnR mutant, regulating GS levels and glnRA expression in a nitrogen-dependent manner. In a GS null mutant, S. aureus GlnR was not able to influence glnRA transcription, indicating that the S. aureus protein is able to respond to the same signals as its B. subtilis counterpart. This is the first demonstration of a relationship between GS and GlnR from a heterologous system and suggests the presence of a regulatory network in S. aureus that responds to changes in environmental nitrogen similar to that described for B. subtilis.
Bacillus subtilis↗
Heterologous expression in the Archaea: transcription from Pyrococcus furiosus gdh and mlrA promoters in Haloferax volcanii.
Multicopy plasmids containing the promoter regions for gdh and mlrA genes from Pyrococcus furiosus were propagated in Haloferax volcanii. High-level expression was detected from gdh promoter sequences, with transcription initiating at the same start-site as that found in P. furiosus. For mlrA, several transcripts were detected, with one initiating at the P. furiosus start-site; removal or disruption of the likely P. furiosus boxA element resulted in the disappearance of this transcript, indicating that these sequences were utilized by the H. volcanii RNA polymerase for initiation. This is the first demonstration of the utilization of promoters from a hyperthermophilic archaeon in a mesophilic haloarchaeon and provides further evidence for the unity of transcription processes in the domain Archaea.
Archaeal Proteins↗
Gene transfer systems for the Archaea.
The recent focus on exobiology and the potential for life in extreme environments has generated a great deal of interest in the Archaea because of their adaptation to extremes of temperature, salinity and anaerobicity. Recent advances in the development of genetic transfer systems for the Archaea provide the first glimpse of their genetic mechanisms and have the potential to serve as powerful tools for studying their unique adaptive strategies.
Adaptation, Physiological↗
Overexpression and characterization of a prolyl endopeptidase from the hyperthermophilic archaeon Pyrococcus furiosus.
The maltose-regulated mlr-2 gene from the hyperthermophilic archaeon Pyrococcus furiosus having homology to bacterial and eukaryal prolyl endopeptidase (PEPase) was cloned and overexpressed in Escherichia coli. Extracts from recombinant cells were capable of hydrolyzing the PEPase substrate benzyloxycarbonyl-Gly-Pro-p-nitroanilide (ZGPpNA) with a temperature optimum between 85 and 90 degrees C. Denaturing gel electrophoresis of purified PEPase showed that enzyme activity was associated with a 70-kDa protein, which is consistent with that predicted from the mlr-2 sequence. However, an apparent molecular mass of 59 kDa was obtained from gel permeation studies. In addition to ZGPpNA (K(Mapp) of 53 microM), PEPase was capable of hydrolyzing azocasein, although at a low rate. No activity was detected when ZGPpNA was replaced by substrates for carboxypeptidase A and B, chymotrypsin, subtilisin, and neutral endopeptidase. N-[N-(L-3-trans-Carboxirane-2-carbonyl)-L-Leu]-agmatine (E-64) and tosyl-L-Lys chloromethyl ketone did not inhibit PEPase activity. Both phenylmethylsulfonyl fluoride and diprotin A inhibited ZGPpNA cleavage, the latter doing so competitively (K(lapp) of 343 microM). At 100 degrees C, the enzyme displayed some tolerance to sodium dodecyl sulfate treatment. Stability of PEPase over time was dependent on protein concentration; at temperatures above 65 degrees C, dilute samples retained most of their activity after 24 h while the activity of concentrated preparations diminished significantly. This decrease was found to be due, in part, to autoproteolysis. Partially purified PEPase from P. furiosus exhibited the same temperature optimum, molecular weight, and kinetic characteristics as the enzyme overexpressed in E. coli. Extracts from P. furiosus cultures grown in the presence of maltose were approximately sevenfold greater in PEPase activity than those grown without maltose. Activity could not be detected in clarified medium obtained from maltose-grown cultures. We conclude that mlr-2, now called prpA, encodes PEPase; the physiological role of this protease is presently unknown.
Archaea↗
Identification and characterization of the pckA gene from Staphylococcus aureus.
The Staphylococcus aureus pckA gene was identified and characterized. A pckA mutant lacked detectable phosphoenolpyruvate carboxykinase activity and grew poorly in the absence of glucose. Both enzymatic activity and pckA promoter activity in wild-type cells grown in the absence of glucose were at least 22-fold greater than activities in cells grown in the presence of glucose.
Amino Acid Sequence↗
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.
Amino Acid Sequence↗
A gene from the hyperthermophile Pyrococcus furiosus whose deduced product is homologous to members of the prolyl oligopeptidase family of proteases.
The mlr-2 gene from the hyperthermophilic archaeum Pyrococcus furiosus was identified from a family of clones whose expression was influenced by the presence of maltose in the medium. The sequence of 2100 bp of DNA containing mlr-2 and its flanking regions revealed a 616-amino-acid (71 kDa) open reading frame (ORF). The ORF's initiation codon appeared 10 nt into the mlr-2 message and was not preceded by any apparent ribosome-binding site. The deduced product shared homology with prolyl endopeptidases from both eukaryotic and eubacterial sources (52-57% similarity, 30-37% identity) and signature domains containing the Ser-Asp-His triad, which is characteristic of this family of proteases, were present. Northern blot experiments revealed the presence of an approx. 2.0-kb transcript in P. furiosus extracts, corresponding in length to that expected from mlr-2 expression. Initiation of transcription occurred 23 bp downstream from a putative BoxA promoter element.
Amino Acid Sequence↗
Isolation, sequence and characterization of the maltose-regulated mlrA gene from the hyperthermophilic archaeum Pyrococcus furiosus.
The mlrA (maltose regulated) gene from the hyperthermophilic archaeum Pyrococcus furiosus was identified from a family of clones whose expression was influenced by the presence of maltose in the medium. Sequencing of the 2276 bp of DNA containing mlrA and flanking regions revealed a 753-amino-acid (aa) (88 kDa) open reading frame (ORF). The ORF is preceded by a bacterial-like ribosome-binding site. The deduced product shared extensive homology with pyruvate dikinases (PDK) from both eukaryal and eubacterial sources (35-61% similarity) and the signature domains characteristic of this class of proteins were present. Northern blot experiments demonstrated the presence of an approx. 2.4-kb transcript in P. furiosus extracts, corresponding in length to that expected from expression of mlrA. P. furiosus cultures grown in the presence of maltose were found to contain approx. 5-10-fold greater mlrA mRNA than those grown without maltose. Initiation of transcription under both cultural conditions occurred at the same transcription start point (tsp), 23 bp downstream from a putative BoxA promoter element.
Amino Acid Sequence↗
Isolation of maltose-regulated genes from the hyperthermophilic archaeum, Pyrococcus furiosus, by subtractive hybridization.
The hyperthermophilic archaeum, Pyrococcus furiosus, utilizes maltose as a preferred carbon source for growth. 32P-labeled complementary DNA (cDNA) probes representing maltose-regulated genes were obtained by a subtractive hybridization procedure that minimized retrieval of ribosomal RNA (rRNA) sequences during screening. Genomic DNA clones were isolated by positive hybridization to these probes. Genes whose expression varied both in the level of transcription, relative to rRNA, as well as in the degree of regulation were obtained; the extent of regulation varied over a wide range, from as little as fivefold to as high as 50-100-fold. DNA sequence analysis of several of these regulated genes indicated that the subtraction library included gene products required for maltose utilization (e.g., pyruvate dikinase), as well as growth-rate-related genes such as those encoding ribosomal proteins and RNA polymerase subunits. Our approach is applicable to studying gene regulation in organisms that are not amenable to classical genetic techniques.
Archaea↗
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.
Bacillus subtilis↗
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.
Bacillus subtilis↗
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.
Bacillus subtilis↗
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.
Amino Acid Sequence↗
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.
Amino Acid Sequence↗
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.
Bacillus subtilis↗