Cloning and characterization of the pyrF operon of Salmonella typhimurium

Independent component analysis of Corynebacterium glutamicum transcriptomes reveals its transcriptional regulatory network

Gene expression in bacteria is regulated by multiple transcription factors. Clarifying the regulation mechanism of gene expression is necessary to understand bacterial physiological activities. To further understand the structure of the transcriptional regulatory network of Corynebacterium glutamicum, we applied independent component analysis, an unsupervised machine learning algorithm, to the high-quality C. glutamicum gene expression profile which includes 263 samples from 29 independent projects. We obtained 87 robust independent regulatory modules (iModulons). These iModulons explain 76.7% of the variance in the expression profile and constitute the quantitative transcriptional regulatory network of C. glutamicum. By analyzing the constituent genes in iModulons, we identified potential targets for 20 transcription factors. We also captured the changes in iModulon activities under different growth rates and dissolved oxygen concentrations, demonstrating the ability of iModulons to comprehensively interpret transcriptional responses to environmental changes. In summary, this study provides a genome-scale quantitative transcriptional regulatory network for C. glutamicum and informs future research on complex changes in the transcriptome.

Nucleotides, Nucleosides, and Nucleobases

We review literature on the metabolism of ribo- and deoxyribonucleotides, nucleosides, and nucleobases in Escherichia coli and Salmonella,including biosynthesis, degradation, interconversion, and transport. Emphasis is placed on enzymology and regulation of the pathways, at both the level of gene expression and the control of enzyme activity. The paper begins with an overview of the reactions that form and break the N-glycosyl bond, which binds the nucleobase to the ribosyl moiety in nucleotides and nucleosides, and the enzymes involved in the interconversion of the different phosphorylated states of the nucleotides. Next, the de novo pathways for purine and pyrimidine nucleotide biosynthesis are discussed in detail.Finally, the conversion of nucleosides and nucleobases to nucleotides, i.e.,the salvage reactions, are described. The formation of deoxyribonucleotides is discussed, with emphasis on ribonucleotidereductase and pathways involved in fomation of dUMP. At the end, we discuss transport systems for nucleosides and nucleobases and also pathways for breakdown of the nucleobases.

Characterization of Treponema denticola pyrF encoding orotidine-5'-monophosphate decarboxylase

The Treponema denticola ATCC 35405 genome annotation contains most of the genes for de novo pyrimidine biosynthesis. To initiate characterization of pyrimidine synthesis in Treponema, we focused on TDE2110 (the putative pyrF, encoding orotidine-5'-monophosphate decarboxlyase). Unlike the parent strain, an isogenic pyrF mutant was resistant to 5-fluoroorotic acid. In complex medium, growth of the pyrF mutant was independent of added uracil, indicating activity of a uracil uptake/salvage pathway. Transcription of pyrF was greatly reduced in T. denticola grown in excess uracil, demonstrating that de novo pyrimidine synthesis is regulated and suggesting a feedback mechanism. Treponema denticola PyrF complemented uracil auxotrophy in an Escherichia coli pyrF mutant. This study provides biochemical confirmation of T. denticola genome predictions of de novo and salvage pyrimidine pathways and provides proof of concept that pyrF has potential as a selectable marker in T. denticola.

Isolation and sequence analysis of the orotidine-5'-phosphate decarboxylase gene (URA3) of Candida utilis. Comparison with the OMP decarboxylase gene family

The URA3 gene of Candida utilis encoding orotidine-5'-phosphate decarboxylase enzyme was isolated by complementation in Escherichia coli pyrF mutation. The deduced amino-acid sequence is highly similar to that of the Ura3 proteins from other yeast and fungal species. An extensive analysis of the family of orotidine-5'-phosphate decarboxylase is shown. The URA3 gene of C. utilis was able to complement functionally the ura3 mutation of Saccharomyces cerevisiae.

Genetic map of Salmonella typhimurium, edition VIII

We present edition VIII of the genetic map of Salmonella typhimurium LT2. We list a total of 1,159 genes, 1,080 of which have been located on the circular chromosome and 29 of which are on pSLT, the 90-kb plasmid usually found in LT2 lines. The remaining 50 genes are not yet mapped. The coordinate system used in this edition is neither minutes of transfer time in conjugation crosses nor units representing "phage lengths" of DNA of the transducing phage P22, as used in earlier editions, but centisomes and kilobases based on physical analysis of the lengths of DNA segments between genes. Some of these lengths have been determined by digestion of DNA by rare-cutting endonucleases and separation of fragments by pulsed-field gel electrophoresis. Other lengths have been determined by analysis of DNA sequences in GenBank. We have constructed StySeq1, which incorporates all Salmonella DNA sequence data known to us. StySeq1 comprises over 548 kb of nonredundant chromosomal genomic sequences, representing 11.4% of the chromosome, which is estimated to be just over 4,800 kb in length. Most of these sequences were assigned locations on the chromosome, in some cases by analogy with mapped Escherichia coli sequences.

Orotidine-5'-monophosphate decarboxylase from Pseudomonas aeruginosa PAO1: cloning, overexpression, and enzyme characterization

Orotidine-5'-monophosphate decarboxylase (OMPdecase) catalyzes the final step in pyrimidine biosynthesis, the conversion of orotidine-5'-monophosphate (OMP) to uridine-5'-monophosphate. The pyrF gene, encoding OMPdecase, was isolated from a chromosomal library of Pseudomonas aeruginosa PAO1 by screening for complementation of an Escherichia coli and a P. aeruginosa pyrF mutant. The nucleotide sequence of a 2510-bp chromosomal DNA fragment, complementing both strains, was determined (EMBL accession number X65613). On this a 696-bp open reading frame capable of encoding the 24 kDa OMPdecase was identified. Despite a generally good correspondence to other OMPdecase sequences, the P. aeruginosa gene was unique in that it did not constitute part of an operon. The pyrF gene was amplified by polymerase chain reaction, overexpressed in the pT7-7/E. coli BL21(DE3) system and purified to near electrophoretic homogeneity by anion exchange chromatography. Characterization of the purified enzyme revealed the following data, a Km value for OMP of 9.91 microM and an isoelectric point of 6.65. No major decrease in enzyme activity was observed in a pH range between 7.8 and 10.2. Gel electrophoresis under nondenaturing conditions suggested that the native form of OMPdecase is the dimer.

The tus gene of Escherichia coli: autoregulation, analysis of flanking sequences and identification of a complementary system in Salmonella typhimurium

The tus gene of Escherichia coli encodes a DNA-binding protein that, when bound to terminator sites, blocks replication forks. One of these sites, TerB, is immediately upstream from tus, and we have determined that the 5' end of tus mRNA is in the TerB site, that tus is autoregulated and that pTus is a very low efficiency promoter. Analysis of the DNA upstream from tus and TerB indicates a set of sensor/regulator genes which are comparable to envZ/ompR. Although tus mutants exhibit no growth phenotype in laboratory conditions, Salmonella typhimurium and E. coli have nevertheless maintained similar termination systems. Sequence homology can be demonstrated by Southern hybridizations, and the systems also exhibit functional complementation: the Tus protein of S. typhimurium blocks DNA replication at the TerA site of E. coli.

Isolation and molecular analysis of the orotidine-5'-phosphate decarboxylase gene (pyrG) of Phycomyces blakesleeanus

The pyrG gene of Phycomyces was isolated from a Phycomyces genomic library, constructed in the cosmid pHS255, by hybridization with a 170 bp fragment of the pyrG gene of Aspergillus niger. This fragment includes a consensus sequence found in almost all species in which the orotidine-5'-phosphate decarboxylase (OMPdecase) gene has been sequenced. The complete nucleotide sequence of the cloned pyrG gene from Phycomyces was determined and the transcription start sites mapped. In the predicted amino acid sequence there are regions of strong homology to the equivalent genes of Saccharomyces cerevisiae, A. niger, Schizophyllum commune and Homo sapiens. Analysis of the sequence revealed the presence of two introns. The precise length and location of these introns was determined by sequencing the pyrG cDNA and comparing it with the genomic clone. Non-coding flanking regions showed obvious homology to the consensus TATA and CAAT boxes, and the polyadenylation signal "AATAAA". The pyrG gene is the second Phycomyces gene that has been cloned and analysed. This is the first time that introns have been reported in Phycomyces.

Translational coupling in the pyrF operon of Salmonella typhimurium

The pyrF gene, encoding the sixth enzyme of pyrimidine biosynthesis in Salmonella typhirmurium, appears to be the first gene of an operon. The second gene, orfF, encodes a 11.5 kDa polypeptide of unknown function. To study the regulation of orfF expression directly, transcriptional and translational fusions of orfF to galK and lacZ, respectively, were constructed and the level of expression of the reporter genes was determined under different growth conditions. The results obtained show that the synthesis of OrfF and orotidine 5'-phosphate decarboxylase is coordinately controlled by pyrimidines, and that this control occurs at the level of transcription. The orfF translational start codon overlaps the pyrF translational stop codon, suggesting that the two genes are translationally coupled. This was investigated by studying how frameshift mutations, which cause premature termination of pyrF translation at different points, affect orfF expression. All mutations reduced orfF expression markedly without interfering with transcription of the gene. Thus, expression of pyrF and orfF are translationally coupled. Inspection of the nucleotide sequence of the pyrF/orfF junction region suggests that formation of secondary structures on the naked mRNA may explain the low level of orfF expression in the absence of translation of the pyrF terminal region.

Cloning of the pyr4 gene encoding orotidine-5'-phosphate decarboxylase in Cephalosporium acremonium

We have cloned the Cephalosporium acremonium pyr4 gene by cross-hybridization with the equivalent gene from Neurospora crassa, the closest relative from which this gene is available. The C. acremonium pyr4 gene complements an E. coli pyrF mutant lacking orotidine-5'-phosphate decarboxylase (OMPdecase), and most probably does not contain introns. Maxicell analysis in E. coli shows that it encodes a 46 kDa polypeptide. The C. acremonium OMPdecase contains a highly conserved pentadecapeptide characteristic for this category of enzyme. Extensive sequence comparison suggests an important role of this region in enzymatic activity.

Pyrimidine regulation of tandem promoters for carAB in Salmonella typhimurium

The carAB operon of Salmonella typhimurium encodes the two subunits of the enzyme carbamoylphosphate synthetase. Transcription of the operon is initiated at tandem promoters that are subject to control by pyrimidines and arginine. Pyrimidine regulation was examined by quantitative primer extension experiments under conditions in which densitometric measurements of the transcripts were linear with the amount of RNA. RNA was obtained from mutant strains that permit manipulations of pyrimidine nucleotide pools. The data showed that a uridine nucleotide repressed the upstream promoter (Pl), whereas arginine repressed the downstream promoter (P2). Exogenous cytidine, which increased the intracellular CTP pool in certain mutant strains, did not affect either promoter. However, CTP limitation resulted in derepression of the pyrimidine-specific promoter as well as the downstream arginine-specific promoter. The effect of pyrimidines on P2 was confirmed in a carA::lacZ transcriptional fusion in which the activity of the pyrimidine-specific promoter was abolished. Primer extension experiments with an argR::Tn10 derivative showed that repression of Pl by uridine nucleotides did not require a functional arginine repressor and that repression of P2 by arginine did not interfere with elongation of transcripts initiated at the upstream Pl promoter.

Sequence and transcript analysis of the C. albicans URA3 gene encoding orotidine-5'-phosphate decarboxylase

The human pathogen Candida albicans grows either as a yeast or in filamentous form. We have determined the sequence of a 1.365 kb genomic C. albicans fragment that complements Saccharomyces cerevisiae ura3 and Escherichia coli pyrF mutations. An open reading frame within this fragment corresponds to a protein of 270 amino acids that shows homology to orotidine-5'-phosphate decarboxylases (ODCases) of other fungal species. The C. albicans ODCase is most closely related to the ODCases of the budding yeasts Kluyveromyces lactis and S. cerevisiae (74% and 71% homology, respectively). Most 5' ends of URA3 transcripts in the authentic host and in the heterologous host S. cerevisiae were found to be identical. These results demonstrate a close taxonomic relationship between non-pathogenic budding yeasts and C. albicans.

Nucleotide sequence of the carA gene and regulation of the carAB operon in Salmonella typhimurium

The carAB operon of Salmonella typhimurium encoding carbamoyl-phosphate synthetase (CPSase) has been cloned, and the nucleotide sequence of the first gene of the operon, carA, together with 760 base pairs of the 5'-flanking region was determined. The product of the carA gene is the small subunit of CPSase. It catalyzes the transfer of the amide group from glutamine to an NH3-site on the heavy subunit. Primer extension and S1 nuclease mapping of in vivo carAB transcripts revealed that transcription is similar to that of Escherichia coli [Piette, J. et al. (1984) Proc. Natl Acad. Sci. USA 81, 4134-4138] in its initiation at two promoters, P1 and P2, controlled by pyrimidines and arginine, respectively. The arginine control is mediated through binding to the arginine repressor (argR). The involvement of titratable regulatory elements is indicated by the escape from both arginine and pyrimidine control, when the operon is present in multicopies on a plasmid. Measurements of CPSase levels in mutants which allows independent manipulation of the intracellular uracil and cytosine nucleotide pools show, that both uracil and cytosine nucleotides are required for full repression and that limitation of either nucleotide results in derepression of CPSase synthesis. Deletion analyses indicate that regions upstream of the P1 promoter are required for normal expression from this promoter but not from P2.

Regulation of pyrC expression in Salmonella typhimurium: identification of a regulatory region

Deletion analysis of a plasmid carrying the entire pyrC gene of Salmonella typhimurium served to localize the regulatory region within a 120 base pair DNA fragment comprising the promoter-leader region and the first 10 codons of pyrC. A region of dyad symmetry is present in the leader DNA and may result in the formation of a stable hairpin in the transcript with part of the Shine-Dalgarno sequence included in the stem. Four independently-isolated regulatory mutants, overexpressing pyrC, were found to have point mutations within the symmetry region and, significantly, the mutations occurred in sequences pertaining to either side of the stem of the putative hairpin of the transcript. All four mutations would decrease the stability of the hairpin, suggesting that pyrC expression is controlled at the level of translation. Additional evidence for translational control was provided by the finding that synthesis of galactokinase mediated from a pyrC-galK transcriptional fusion is not regulated by pyrimidines. The importance of the symmetry region in the leader was further emphasized by showing that pyrC expression is strongly affected when this region is deleted, inverted, or structured as a tandem duplication.

Sequence analysis of the DdPYR5-6 gene coding for UMP synthase in Dictyostelium discoideum and comparison with orotate phosphoribosyl transferases and OMP decarboxylases

A Dictyostelium discoideum DNA fragment that complements the ura3 and the ura5 mutants of Saccharomyces cerevisiae has been sequenced. It contains an open reading frame of 478 codons capable of encoding a polypeptide of molecular weight 52475. This gene, named DdPYR5-6, encodes a bifunctional protein composed of the orotate phosphoribosyl transferase (OPRTase) and the orotidine-5'-phosphate decarboxylase (OMPdecase) domains described for UMP synthase in mammals. The existence of separate domains for the two activities was suspected because deletion of the N-terminal coding segment of the gene eliminated the ura5 but not the ura3 complementing activity. We have now confirmed that the two parts of the open reading frame share homology with known OPRTase and OMPdecase sequences. Several blocks of sequence are conserved among OPRTase from bacteria, fungi and slime mold and one of them corresponds to the consensus sequence for phosphoribosylbinding sites. The OMPdecase domain shows extensive similarity with the yeast and Neurospora crassa enzymes, suggesting that they have evolved from an ancestral gene which was fused to the OPRTase gene in D. discoideum. It is less related to the bacterial enzyme but all these sequences present conserved blocks of homology which could identify the active site. The codon usage is strongly biased in a manner similar to that found for other D. discoideum genes. The flanking DNA contains homopolymers of A and T and alternating sequences that are characteristic of the gene organization in D. discoideum.