Evidence for transcriptional regulation of dihydroorotic acid dehydrogenase in Saccharomyces cerevisiae

How transcription circuits explore alternative architectures while maintaining overall circuit output

This review by Dalal and Johnson focuses on the evolutionary rewiring of transcription regulators and the conservation of patterns of gene expression. They describe how preservation of gene expression patterns in the wake of extensive rewiring is a general feature of transcription circuit evolution.

Transcription regulators bind to cis-regulatory sequences and thereby control the expression of target genes. While transcription regulators and the target genes that they regulate are often deeply conserved across species, the connections between the two change extensively over evolutionary timescales. In this review, we discuss case studies where, despite this extensive evolutionary rewiring, the resulting patterns of gene expression are preserved. We also discuss in silico models that reach the same general conclusions and provide additional insights into how this process occurs. Together, these approaches make a strong case that the preservation of gene expression patterns in the wake of extensive rewiring is a general feature of transcription circuit evolution.

Activation of transcription by metabolic intermediates of the pyrimidine biosynthetic pathway

Saccharomyces cerevisiae responds to pyrimidine starvation by increasing the expression of four URA genes, encoding the enzymes of de novo pyrimidine biosynthesis, three- to eightfold. The increase in gene expression is dependent on a transcriptional activator protein, Ppr1p. Here, we investigate the mechanism by which the transcriptional activity of Ppr1p responds to the level of pyrimidine biosynthetic intermediates. We find that purified Ppr1p is unable to promote activation of transcription in an in vitro system. Transcriptional activation by Ppr1p can be observed, however, if either dihydroorotic acid (DHO) or orotic acid (OA) is included in the transcription reactions. The transcriptional activation function and the DHO/OA-responsive element of Ppr1p localize to the carboxyl-terminal 134 amino acids of the protein. Thus, Ppr1p directly senses the level of early pyrimidine biosynthetic intermediates within the cell and activates the expression of genes encoding proteins required later in the pathway. These results are discussed in terms of (i) regulation of the pyrimidine biosynthetic pathway and (ii) a novel mechanism of regulating gene expression.

Sequence of the URA1 gene encoding dihydroorotate dehydrogenase from the basidiomycete fungus Agrocybe aegerita

The URA1 gene encoding dihydroorotate dehydrogenase (DHOdehase) from the edible basidiomycete, Agrocybe aegerita, has been cloned by complementation of the Escherichia coli pyrD mutation. The nucleotide sequence of a 1531-bp genomic fragment carrying URA1 revealed two uninterrupted open reading frames (ORFs) separated by 61 bp. The larger ORF can encode a 328-amino acid (aa) DHOdehase that has 53% homology with the corresponding protein from E. coli. Comparison with other DHOdehase aa sequences showed essentially conservation of the cofactor-binding site of flavoproteins.

Nucleotide sequence of the URA1 gene of Saccharomyces cerevisiae

The complete nucleotide sequence of the URA1 gene encoding dihydroorotic acid dehydrogenase (DHOdehase) is presented. This enzyme catalyses the conversion of DHO to orotic acid and plays a major role in the pyrimidine pathway, as DHO is the effector of the positive control of the transcription of at least four genes, URA1, URA3, URA4 and URA10. Comparisons between the amino acid sequence of the yeast DHOdehase and sequences of DHOdehases previously isolated from Dictyostellum discoïdum, Escherichia coli and Bacillus subtilis reveal no obvious homologies.

Yeast promoters URA1 and URA3. Examples of positive control

Transcription of the two unlinked structural genes URA1 and URA3 of Saccharomyces cerevisiae is positively regulated by the gene product PPR1. We have used S1 digestion and primer extension mapping to investigate the RNAs produced in different genetic backgrounds: wild-type, ppr1 deletion mutants, constitutively induced and non-inducible ppr1 mutants. Results show that each structural gene specifies multiple messenger RNA classes with different 5'-terminal sequences. The basal level of these transcripts does not require a functional PPR1 gene. Induction of URA1 results from an even increase of the level of synthesis of all the transcripts in contrast to that of URA3 which is effected by selectively increasing the levels of synthesis of one subset of transcripts. The PPR1-mediated control was also studied in the foreign genetic background of Schizosaccharomyces pombe using autonomously replicating hybrid plasmids carrying the gene URA1 or URA3 along with the regulatory gene PPR1, either in a constitutive or non-inducible allelic form. The 5' ends of the transcripts URA1 and URA3 made in S. pombe map upstream from the initiation sites used in S. cerevisiae. In contrast to S. cerevisiae, in S. pombe the URA3 but not URA1 transcripts respond to the PPR1-induction. We have identified a minimal control region for the PPR1-specific induction of URA1, that includes sequences located between the T-A-T-A box and the translation start codon. This region contains sequence features in common with URA3. There is an extensive alternating Pu:Py region including the T-A-T-A box of both promoters and an eight base-pair exact homology; further downstream, there is another 11 base-pair highly conserved sequence which either overlaps or lies in close proximity to the unregulated start sites of URA1 in S. pombe and of URA3 in S. cerevisiae. A positive regulatory model taking into accounts all these observations is presented.

The expression of the MET25 gene of Saccharomyces cerevisiae is regulated transcriptionally

The MET25 gene of Saccharomyces cerevisiae was cloned by functional complementation after transformation of a yeast met25 mutant. Subcloning of the DNA fragment bearing MET25 located the gene on a 2.3 kb region. The gene was formally identified by integration at the chromosomal MET25 locus. The cloned MET25 gene was used as a probe to measure the MET25 messenger RNA in a wild-type strain grown under conditions which promoted or failed to promote repression of MET25 expression. It was found that, under repression conditions, MET25 messenger RNA was reduced tenfold when compared with non-repression conditions. This suggests that the expression of MET25 is regulated transcriptionally. The direction of transcription, the size of the transcript and the position of the transcribed part of the gene were determined. Deletion mapping of the regulatory region was carried out. Deleted plasmids were introduced back into yeast cells and tested for their ability to complement met25 mutations and to promote regulation of expression of the MET25 gene by exogenous methionine. By this method the regulatory region was found to be confined to a 130 bp region.

Sequence analysis of a Dictyostelium discoideum gene coding for an active dihydroorotate dehydrogenase in yeast

A Dictyostelium discoideum DNA fragment isolated on the basis of its ability to complement the ural mutation of yeast, codes for a dihydroorotate dehydrogenase activity. The complete nucleotide sequence of this 1898 bp fragment has been determined and reveals an open reading frame capable of coding for a 369 amino acid polypeptide of molecular mass 47.000. The gene shows preferential use of codons with weak pairing forces. Eleven codons, mainly those with a G in the third position, are absent. The flanking sequences are unusually rich in A + T (80%). Several direct and inverted repeats exist in the 5' flanking sequence.

Transcriptional regulation of the MET3 gene of Saccharomyces cerevisiae

The MET3 gene, coding for ATP sulfurylase (ATPS), an enzyme implicated in methionine biosynthesis in Saccharomyces cerevisiae, was cloned by functional complementation, after transformation, of a yeast met3 mutant strain. The cloned MET3 gene was used as a probe to measure the specific MET3 messenger RNA in a wild-type strain grown under conditions which promote or fail to promote repression of ATPS synthesis. It was found that the level of MET3 messenger RNA is reduced ten-fold when the strain is grown under conditions where ATPS synthesis is repressed, suggesting that the MET3 expression is regulated transcriptionally. The direction of transcription and the size of the transcript have been determined.

Yeast regulatory gene PPR1. II. Chromosomal localization, meiotic map, suppressibility, dominance/recessivity and dosage effect

The Saccharomyces cerevisiae gene PPR1 encodes a positive regulator of the expression of the two unlinked structural genes URA1 and URA3. The gene has been mapped to a position 6.5 cM from the centromere of chromosome XII. Uninducible alleles have been selected and used to establish a meiotic map. Suppressible alleles have been identified. The sequencing of a suppressible allele confirms the nonsense nature of the mutation as well as the reading frame deduced from the nucleotide sequence. No evidence of intracistronic complementation was found, and enzymatic analysis of leaky mutants did not reveal any mutations dissociating regulation of URA1 from that of URA3. Three in vitro-constructed deletions of PPR1 have been integrated at the chromosomal locus, giving strains with a completely negative phenotype. These deletion mutants display the wild-type basal level of URA1 and URA3 expression and show a semi-dominant phenotype in heteroallelic ppr1+/ppr1-delta diploids. Amplifying PPR1 by introduction into yeast on a multicopy vector increases the induction factor of URA1 and URA3 expression. These results show that the extent of regulation of the two structural genes is dependent on the concentration of the active PPR1 protein.

Yeast regulatory gene PPR1. I. Nucleotide sequence, restriction map and codon usage

The PPR1 gene of Saccharomyces cerevisiae controls the transcription of two unlinked structural genes URA1 and URA3. The primary structure of this eukaryotic regulatory gene and its flanking regions has been established by the dideoxynucleotide chain termination method. Our data show an open reading frame of 2712 nucleotides, corresponding to 904 amino acid residues. The 3' untranslated messenger RNA region presents consensus yeast termination and polyadenylation sequences. The pattern of codon usage in the gene is clearly random. This result is discussed in relation to protein abundance and is compared with the codon usage in 20 yeast structural and regulatory genes and with that found for Escherichia coli genes.

The Dhod locus of Drosophila: mutations and interrelationships with other loci controlling de novo pyrimidine biosynthesis

Mutations at the Dhod locus have been isolated following ethylmethanesulfonate mutagenesis. These mutants express those phenotypes common to other mutations of the de novo pyrimidine pathway: specific wing and leg defects and female sterility. Dihydroorotate dehydrogenase activity is severely reduced in all Dhod mutants, whereas levels of the other pathway enzymes are largely unaffected. The twelve Dhod mutations described here comprise a single complementation group. All of these mutations are nonlethal and the collection includes apparent amorphic as well as hypomorphic alleles. These results are discussed relative to the properties of the complex loci that encode the other steps of de novo pyrimidine biosynthesis.

Cloning of a eukaryotic regulatory gene

From a pool of hybrid plasmids carrying Sau3A fragments representing the entire yeast (S. cerevisiae) genome, a DNA fragment containing the regulatory gene PPRI was cloned by complementation of a non-inducible ppr1 mutation which confers to the cells an increased sensitivity to 6-azauracil. Cells containing the cloned DNA regained the ability to induce the synthesis of URA1 and URA3 gene products controlled by PPR1. A physical map has been constructed and the study of subcloned restriction endonuclease fragments from the original yeast DNA fragment allowed us to localize the wile-type PPR1 regulatory gene within a 3 kilobase-pair region. The ppr1 RNA level was measured and the hybridization data indicate in a wild-type strain a low efficiency of transcription of PPR1 as compared to the structural URA3 gene, without effect of inducing conditions.

Expression of a cloned Saccharomyces cerevisiae gene (URA1) is controlled by a bacterial promoter in E. coli and by a yeast promoter in S. cerevisiae

The expression of a cloned yeast URA1 gene in Escherichia coli and in Saccharomyces cerevisiae was studied. In E. coli, only one orientation of the cloned yeast DNA segment inserted into the bacterial vector (pBR322) allows URA1 expression. Moreover, the permissive orientation changes with the cloning site. The absence of URA1 expression in E. coli can be corrected by the spontaneous integration into the cloned yeast DNA of a 0.9-kb bacterial DNA. Several copies of such a bacterial IS element have been detected in the host E. coli genome. The results strongly suggest that, in E. coli, transcription of the yeast URA1 needs a prokaryotic promoter for its initiation. In S. cerevisiae, the expression of non-chromosomally cloned URA1 does not depend on the orientation of the cloned fragment. Furthermore, it remains under the control of a nuclear regulatory gene (pprX-1) which constitutively enhances the expression of URA1 as well as URA3 at the transcriptional level. Therefore, in S. cerevisiae, transcription of non-chromosomally cloned URA1 involves a physiological yeast promoter cloned along with the structural part of the gene.