Structure and organisation of the pyrimidine biosynthesis pathway genes in Lactobacillus plantarum: a PCR strategy for sequencing without cloning

Elagöz, Aram; Abdi, Akila; Hubert, J.; Kammerer, B.

doi:10.1016/s0378-1119(96)00461-1

Cited by 42 publications

(43 citation statements)

References 33 publications

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“…In this case, only a single attenuation region in the 5Ј leader is used to control pyr operon expression, but the attenuation mechanism is still the same as in B. subtilis. L. plantarum pyr genes are also found in a single operon in the same order as in Bacillus, but the pyrP (uracil permease) gene is absent and only two attenuation regions are found (5Ј leader and pyrR-pyrB intercistronic regions) (33); the mechanism of regulation by PyrR is essentially the same in L. plantarum as in B. subtilis (125). Thus, pyr operons can apparently be adequately regulated in arrangements involving one, two, or three attenuation regions.…”

Section: Pyrr-mediated Transcription Attenuation Of Pyr Operonsmentioning

confidence: 99%

Regulation of Pyrimidine Biosynthetic Gene Expression in Bacteria: Repression without Repressors

Turnbough

Switzer

2008

Microbiol Mol Biol Rev

157

172

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SUMMARY DNA-binding repressor proteins that govern transcription initiation in response to end products generally regulate bacterial biosynthetic genes, but this is rarely true for the pyrimidine biosynthetic (pyr) genes. Instead, bacterial pyr gene regulation generally involves mechanisms that rely only on regulatory sequences embedded in the leader region of the operon, which cause premature transcription termination or translation inhibition in response to nucleotide signals. Studies with Escherichia coli and Bacillus subtilis pyr genes reveal a variety of regulatory mechanisms. Transcription attenuation via UTP-sensitive coupled transcription and translation regulates expression of the pyrBI and pyrE operons in enteric bacteria, whereas nucleotide effects on binding of the PyrR protein to pyr mRNA attenuation sites control pyr operon expression in most gram-positive bacteria. Nucleotide-sensitive reiterative transcription underlies regulation of other pyr genes. With the E. coli pyrBI, carAB, codBA, and upp-uraA operons, UTP-sensitive reiterative transcription within the initially transcribed region (ITR) leads to nonproductive transcription initiation. CTP-sensitive reiterative transcription in the pyrG ITRs of gram-positive bacteria, which involves the addition of G residues, results in the formation of an antiterminator RNA hairpin and suppression of transcription attenuation. Some mechanisms involve regulation of translation rather than transcription. Expression of the pyrC and pyrD operons of enteric bacteria is controlled by nucleotide-sensitive transcription start switching that produces transcripts with different potentials for translation. In Mycobacterium smegmatis and other bacteria, PyrR modulates translation of pyr genes by binding to their ribosome binding site. Evidence supporting these conclusions, generalizations for other bacteria, and prospects for future research are presented.

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Section: Pyrr-mediated Transcription Attenuation Of Pyr Operonsmentioning

confidence: 99%

Regulation of Pyrimidine Biosynthetic Gene Expression in Bacteria: Repression without Repressors

Turnbough

Switzer

2008

Microbiol Mol Biol Rev

157

172

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“…The mechanism by which PyrR regulates the expression of pyr genes has been studied in Bacillus (17-19, 35, 36), Enterococcus (13), Lactococcus (20,21), and Lactobacillus (4,12,25) species. In these organisms PyrR acts by mediating a nucleotide-regulated transcription attenuation mechanism, which has been well characterized in genetic and biochemical studies with Bacillus subtilis (33) and Bacillus caldolyticus (8,14).…”

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Regulation of pyr Gene Expression in Mycobacterium smegmatis by PyrR-Dependent Translational Repression

Fields

Switzer

2007

J Bacteriol

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Regulation of pyrimidine biosynthetic (pyr) genes by a transcription attenuation mechanism that is mediated by the PyrR mRNA-binding regulatory protein has been demonstrated for numerous gram-positive bacteria. Mycobacterial genomes specify pyrR genes and contain obvious PyrR-binding sequences in the initially transcribed regions of their pyr operons, but transcription antiterminator and attenuation terminator sequences are absent from their pyr 5 leader regions. This work demonstrates that repression of pyr operon expression in Mycobacterium smegmatis by exogenous uracil requires the pyrR gene and the pyr leader RNA sequence for binding of PyrR. Plasmids containing the M. smegmatis pyr promoter-leader region translationally fused to lacZ also displayed pyrR-dependent repression, but transcriptional fusions of the same sequences to a lacZ gene that retained the lacZ ribosome-binding site were not regulated by PyrR plus uracil. We propose that PyrR regulates pyr expression in M. smegmatis, other mycobacteria, and probably in numerous other bacteria by a translational repression mechanism in which nucleotide-regulated binding of PyrR occludes the first ribosomebinding site of the pyr operon.

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“…In order to coregulate expression, genes are often found to be organized in operons in procaryotes. The pyrimidine biosynthetic genes (pyr genes) have been found to constitute a single operon in a number of different gram-positive organisms including Bacillus subtilis (37), Bacillus caldolyticus (13), Enterococcus faecalis (23), and Lactobacillus plantarum (9). In addition a pyrimidine biosynthetic operon is found in Mycobacterium tuberculosis (6).…”

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confidence: 99%

The Pyrimidine Operon pyrRPB-carA from Lactococcus lactis

et al. 2001

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The four genes pyrR, pyrP, pyrB, and carA were found to constitute an operon in Lactococcus lactis subsp. lactis MG1363. The functions of the different genes were established by mutational analysis. The first gene in the operon is the pyrimidine regulatory gene, pyrR, which is responsible for the regulation of the expression of the pyrimidine biosynthetic genes leading to UMP formation. The second gene encodes a membrane-bound high-affinity uracil permease, required for utilization of exogenous uracil. The last two genes in the operon, pyrB and carA, encode pyrimidine biosynthetic enzymes; aspartate transcarbamoylase (pyrB) is the second enzyme in the pathway, whereas carbamoyl-phosphate synthetase subunit A (carA) is the small subunit of a heterodimeric enzyme, catalyzing the formation of carbamoyl phosphate. The carA gene product is shown to be required for both pyrimidine and arginine biosynthesis. The expression of the pyrimidine biosynthetic genes including the pyrRPB-carA operon is subject to control at the transcriptional level, most probably by an attenuator mechanism in which PyrR acts as the regulatory protein.The de novo synthesis of pyrimidines is universal. The pathway consists of six enzymatic steps leading to the formation of UMP, which is further converted into UTP, CTP, dCTP, and dTTP. In order to coregulate expression, genes are often found to be organized in operons in procaryotes. The pyrimidine biosynthetic genes (pyr genes) have been found to constitute a single operon in a number of different gram-positive organisms including Bacillus subtilis (37), Bacillus caldolyticus (13), Enterococcus faecalis (23), and Lactobacillus plantarum (9). In addition a pyrimidine biosynthetic operon is found in Mycobacterium tuberculosis (6). The pyrimidine metabolism in Lactococcus lactis has been studied for a number of years. Surprisingly it was found that the pyr genes of L. lactis are scattered on the chromosome in small operons, the pyrKDbF operon (2), the carB gene (35), the pyrEC operon (5), and the pyrDa gene (1). This paper describes the genomic organization of the pyrimidine biosynthetic genes of L. lactis, since we demonstrate the presence of an operon including pyrB, encoding aspartate transcarbamoylase, and carA, encoding the small subunit of the carbamoyl-phosphate (CP) synthetase (CPSase). Moreover, the operon includes pyrR, the regulatory gene controlling expression of the pyr genes, and pyrP, encoding the uracil transporter.Regulation of the expression of the pyr genes of L. lactis has not been subject to a detailed analysis. It has, however, been shown that the transcription of the carB gene is repressed by addition of uracil to the growth medium (35). Moreover, in front of both the carB gene (35) and the pyrKDbF operon (2) a putative attenuator similar to those found in B. subtilis (41) can be identified. These findings suggest that the expression of the pyr genes of L. lactis is regulated by the same attenuator mechanism as that suggested for B. subtilis (41). An RNA binding protein, Pyr...

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Structure and organisation of the pyrimidine biosynthesis pathway genes in Lactobacillus plantarum: a PCR strategy for sequencing without cloning

Cited by 42 publications

References 33 publications

Regulation of Pyrimidine Biosynthetic Gene Expression in Bacteria: Repression without Repressors

Regulation of Pyrimidine Biosynthetic Gene Expression in Bacteria: Repression without Repressors

Regulation of pyr Gene Expression in Mycobacterium smegmatis by PyrR-Dependent Translational Repression

The Pyrimidine Operon pyrRPB-carA from Lactococcus lactis

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