The molecular characterization of three transcriptional mutations in the yeast iso-2-cytochrome c gene

DNA insertions which affect the expression of the yeast iso-2-cytochrome c gene

The plasmid YCpCYC7(2) was constructed containing the Saccharomyces cerevisiae CYC7 gene, encoding the iso-2-cytochrome c protein, replicative sequences and selective markers from both E. coli and yeast, and the centromere of yeast chromosome III. The expression of the plasmid-CYC7 gene in yeast was similar to the low level expression characteristic of the chromosomal CYC7 gene. A number of insertions into the sequences 5' to the gene were constructed in vitro. The insertion at 142 by 5' to the coding sequence of a 400 by fragment which lies 5' to the CYC1 gene and is known to be essential for the high rates of CYC1 transcription increased transcription of the CYC7 gene to levels characteristic of CYC1 transcription. On the other hand, the insertion of random DNA fragments at the same position gave mostly decreased CYC7 transcription. In addition to these in vitro constructions, a mutant plasmid was selected which had increased CYC7 transcription. This mutation was caused by the insertion of the bacterial IS1 element 313 by 5' to the CYC7 coding sequence. The significance of these results is discussed in terms of two alternative models for CYC7 gene expression.

Delta sequence of Ty1 transposon can initiate transcription of the distal part of the URA2 gene complex in Saccharomyces cerevisiae

Expression of a silent aspartate transcarbamylase (ATCase) domain can occur by insertion of a Tyl retrotransposon within the coding sequence of a mutated ura2 allele. This unusual type of Ty-mediated gene activation is possible as the URA2 gene product is a multifunctional protein containing the carbamoyl phosphate synthetase (CPSase), the ATCase and a cryptic dihydroorotase (DHOase) domain. The region in which transcription of the corresponding allele is initiated was determined by RT-PCR experiments. Expression is initiated by a sequence located in the delta element of the Tyl and not by a sequence of the URA2 gene itself. This situation differs with the Ty-mediated gene activation described thus far, in which the transposon substitutes only the 5' regulatory sequences and in which the normal transcription start point is used. The corresponding protein carries both the DHOase-like domain and the ATCase domain, suggesting that the DHOase-like domain is at least involved in the architecture of the protein and necessary to render the ATCase domain functional.

CYP1 (HAP1) regulator of oxygen-dependent gene expression in yeast. II. Missense mutation suggests alternative Zn fingers as discriminating agents of gene control

In the accompanying paper, we present and analyse the sequence of a "superactivator" mutant allele of the CYP1 (HAP1) gene. This locus encodes a trans-acting pleiotropic positive regulator of the transcription of both isocytochrome c structural genes. In this paper, we present the genetic localization of the mutation and the sequence of the wild-type fragment that includes the mutation. The mutated phenotype that commutes the expression of the two isocytochrome structural genes (superactivation of CYP3 and inhibition of CYC1) results from a transversion in an AGT codon (serine) in the wild-type to an AGG codon (arginine) in the mutant. Moreover, we show that the missense mutation that affects the amino acid preceding the first cysteine of the "Zn finger" is responsible on its own account for the entire mutated phenotype. In all seven yeast regulatory proteins analysed so far, this position is occupied by a neutral amino acid (serine, alanine or glycine), thus the serine-arginine replacement is a radical one. This result is consistent with the hypothesis of alternative and mutually exclusive Zn fingers, formed either at low or high redox potential, recognizing the target sequences identified in the upstream regions of the CYC1 and CYP3 isocytochrome c structural genes.

CYP1 (HAP1) regulator of oxygen-dependent gene expression in yeast. I. Overall organization of the protein sequence displays several novel structural domains

In the yeast Saccharomyces cerevisiae the CYP1 gene that modulates the expression of iso1-(CYC1) and iso2-cytochrome c (CYP3) structural genes gives rise to two classes of mutated alleles; one class, represented by CYP1-18, has opposite effects on CYC1 and CYP3, it reduces the expression of CYC1 while it stimulates that of CYP3. The other class, represented by cyp1-23 or the related allele hap1-1, reduces the expression of both CYC1 and CYP3 genes. Genetic data suggested that the CYP1 product is a positive regulator of the cytochrome c genes. The CYP1-18 allele has been cloned. We show here that the iso2 overproducer function of CYP1-18 is included in a 5300 base XhoI-PstI fragment. The sequence of this fragment reveals a unique, long, uninterrupted open reading frame of 4449 nucleotides able to encode a protein of 1483 amino acid residues. The predicted product of this open reading frame contains several interesting features. The N-terminal part of the protein resembles a nucleic acid-binding domain, in which two domains can be distinguished. The first is similar to a "finger" DNA binding motif, as found in TFIIIA and other regulatory proteins. The second consists of seven tandemly repeated sequences with a KCPVDH motif. Because of its structure, it is tempting to speculate that this region may act as a "redox sensor" folded around a metal atom or heme and involved in recognition of respiratory effectors. These two domains are separated by an "opa" sequence of 13 Gln residues. Implication of these domains for the function of CYP1-18 is discussed.

Three nuclear genes suppress a yeast mitochondrial splice defect when present in high copy number

A gene bank of a yeast wild type DNA in the high copy number vector YEp13 was screened for recombinant plasmids which suppress the mitochondrial RNA splice defect exerted by mutant M1301, a -1 bp deletion in the first intron of the mitochondrial COB gene (bI1). A total of 17 recombinant plasmids with similar suppressor activity were found. Restriction mapping and cross-hybridization of the inserts revealed that these 17 plasmids contain three different inserts, all lacking any extended sequence homology. Each of the inserts, when present in high copy number, has a similar suppressor activity: high in the presence of mutation M1301 in bI1, a group II intron, and low but significant with the presence of few mutants in bI2 and bI3 of the COB gene, both of which are group I introns.

Yeast HAP1 activator binds to two upstream activation sites of different sequence

We show that the HAP1 protein binds in vitro to the upstream activation site (UAS) of the yeast CYC7 gene. Strikingly, this sequence bears no obvious similarity to the sequence bound by HAP1 at UAS1 of the CYC1 gene. The CYC1 and CYC7 sites compete for binding to HAP1 and have comparable affinities for the protein. The gross features of the interaction of HAP1 with the two sites are similar: multiple major and minor groove contacts, spanning 23 bp, on one helical face, with a back-side major groove contact toward one end. The precise positions of the contacts differ, however. A mutant form of HAP1, HAP1-18, abolishes the ability of the protein to bind to UAS1 but not CYC7 DNA. Possible mechanisms for how a single protein recognizes two sequences are discussed.

Sequence and structural features associated with translational initiator regions in yeast--a review

We have compared the translational initiator regions of 131 yeast genes. 95% utilize the first AUG from the 5' end of the message as the start codon for translation. Yeast leader regions in general are rich in adenine nucleotides (nt), have an average length of 52 nt, and are void of significant secondary structure. Sequences immediately adjacent to AUG start codons are preferred, however, the bias in nucleotide distribution (5'-A-YAA-UAAUGUCU-3') does not reflect a higher eukaryotic consensus (5'-CACCAUGG-3') with the exception of an adenine nucleotide preference at the -3 position. A minority of yeast mRNAs that contain AUG codons in the leader region that do not serve as the start codon for the primary gene product differ from the majority of mRNAs by one or more of these general properties. This analysis appears to indicate that basic features associated with yeast leader regions are consistent with a general mechanism of initiation of protein synthesis in eukaryotes, as proposed by the ribosomal 'scanning' model, but perhaps only basic features associated with ribosomal recognition of an AUG start codon are intact.

Regulation of the expression of iso 2-cytochrome c gene in S. cerevisiae: cloning of the positive regulatory gene CYP1 and identification of the region of its target sequence on the structural gene CYP3

CYP1 is a trans acting regulatory locus modulating both iso 1- and iso 2-cytochrome c synthesis. Genetical analysis of various mutated alleles has allowed us to identify the gene product as a positive regulatory element. The region of the target sequence of the CYP1 product on the iso 2-cytochrome c structural gene was located by molecular and genetic analysis of two cis acting mutations located at the CYP3 locus: CYP3-36 and CYP3-4, which have been shown to arise from the integration of TY1 elements near the promoter site. Determination of the amount of iso 2-cytochrome c synthesized by strains bearing various genetic constructions, in which the cis acting mutations were associated with different alleles of the CYP1 trans acting locus, showed that TY1 inserted into CYP3-36 extinguishes the activation function due to a mutated overproducer allele CYP1-18, while CYP3-4 amplifies this function. This result identifies at least a part of the target sequence of the CYP1 product within the region separating the two TY1 insertions. To clone the CYP1 gene, we took advantage of the iso 2-cytochrome c overproducer phenotype of the mutated allele CYP1-18, which confers a Lactate+ phenotype on an iso 1-cytochrome c-deficient strain. Such a phenotype allowed the isolation of a recombinant plasmid YEpJFM1 carrying the mutated allele, able to complement on lactate medium a lactate- recipient strain. The identity of the YEpJFM1 sequence with the chromosomal gene was confirmed by homologous recombination at the CYP1 locus.

Localization of the upstream regulatory sites of yeast iso2-cytochrome c gene

In order to study the regulation of expression of the iso2-cytochrome c gene, we have constructed a fused gene between the 5'flanking region of the gene coding for the yeast iso2-cytochrome c and the coding region of the E. coli beta-galactosidase lacZ gene. When introduced in yeast cells this hybrid gene is expressed and regulated like the production of iso2-cytochrome c: it is under the control of the general catabolic repression and of the unlinked trans-acting CYP1 gene whose CYP1-18 allele causes an overproduction of iso2-cytochrome c. The expression of hybrid genes whose upstream region has been progressively shortened or altered by internal deletions was studied either in wild-type CYP1+ cells or in cells carrying the CYP1-18 allele grown either on glucose or on glycerol. It appears that the expression and the regulation of the iso2-cytochrome c gene is controlled by an upstream regulatory site composed of a positive and a negative element. This site is the target of regulation by the CYP1 gene product and, directly or through this gene, of the control by the general catabolic repression.

Preferential integration of yeast transposable element Ty into a promoter region

Mobile genetic elements have been identified in several eukaryotic organisms and some classes have been found to share common structural features with the proviral forms of animal retroviruses. The representatives of this class of mobile elements in the yeast Saccharomyces cerevisiae are called Ty elements, which could be a useful model system for studying the transposition of retrovirus-like elements. Here we have attempted to answer two questions often raised in discussions of the biological importance of transposition: what is the frequency of spontaneous Ty transposition, and are there certain chromosomal regions into which Ty elements preferentially integrate? We chose the LYS2 gene to investigate these questions because it allows direct selection of both mutants and revertants. We have found that 2% of spontaneous lys2 mutants are caused by Ty transposition with a preferential integration into the transcription initiation region.

The expression in yeast of the Escherichia coli galK gene on CYC1::galK fusion plasmids

A set of gene fusions have been constructed between the transcriptional and translational initiation signals of the yeast CYC1 gene, encoding iso-1-cytochrome c, and the coding sequence of the Escherichia coli galK gene encoding galactokinase. These fusions are contained on plasmids which have both yeast and E. coli replication origins and selectable markers and, therefore, can be used to transform either yeast or E. coli cells. When galactokinase-deficient (gall-) yeasts were transformed with these plasmids the resulting Gal+ transformants were heterogeneous with respect to their galactokinase levels. The galactokinase levels in all were subject to glucose repression, characteristic of the transcriptional regulation of the CYC1 gene. The fusion points for representative plasmids were determined by DNA sequence analysis, and from these data, the differential expression of the galK gene could be explained. One fusion plasmid, YRpR1, which gave the highest level of galK expression, was characterized further. As an additional demonstration that galactokinase expression from the fusion was under CYC1 transcriptional control, a cis-dominant, CYC1-linked mutation known to drastically reduce CYC1 gene transcription was introduced into YRpR1 and shown to similarly effect galK expression. The galK mRNA produced from the fused gene of YCpR1, a centromere-containing derivative of YRpR1, consisted of the mRNA leader sequence plus the first four codons of the CYC1 gene, the galK coding sequence, then the remainder of the CYC1 coding sequence and the 175 nucleotide non-translated 3' sequence. As a demonstration of the usefulness of these plasmids for the selection of regulatory mutants, two mutants capable of greatly enhanced levels of galactokinase expression were isolated. Preliminary characterization of these mutations indicates that they likewise affect the expression of the chromosomal CYC1 gene.