Saccharomyces cerevisiae BUF protein binds to sequences participating in DNA replication in addition to those mediating transcriptional repression (URS1) and activation.

The heteromeric BUF protein was originally shown to bind to URS1 elements which are situated upstream of many genes in Saccharomyces cerevisiae and mediate negative control of their transcription. Among the genes regulated through the URS1 site and the proteins interacting with it are those participating in carbon, nitrogen, and inositol metabolism; electron transport; meiosis; sporulation; and mating-type switching. We show here that pure BUF protein, in addition to binding to the negatively acting URS1 site, also binds to CAR1 sequences supporting transcriptional activation (upstream activation sequences). To determine the BUF protein structure, we cloned and sequenced the BUF1 and BUF2 genes and found them to be identical to the RF-A (RP-A) gene whose products participate in yeast DNA replication as single-stranded DNA binding proteins. These data argue that BUF protein-binding sites serve multiple roles in transcription and replication.

Regulation of the urea active transporter gene (DUR3) in Saccharomyces cerevisiae.

The DUR3 gene, which encodes a component required for active transport of urea in Saccharomyces cerevisiae, has been isolated, and its sequence has been determined. The deduced DUR3 protein profile possesses alternating hydrophobic and hydrophilic regions characteristics of integral membrane proteins. Strong negative complementation observed during genetic analysis of the DUR3 locus suggests that the DUR3 product may polymerize to carry out its physiological function. Expression of DUR3 is regulated in a manner similar to that of other genes in the allantoin pathway. High-level expression is inducer dependent, requiring functional DAL81 and DAL82 genes. Maintenance of DUR3 mRNA at uninduced, nonrepressed basal levels requires the negatively acting DAL80 gene product. DUR3 expression is highly sensitive to nitrogen catabolite repression and also has a partial requirement for the GLN3 product.

Role of DNA-protein interactions in bacteriophage phi X174 DNA injection.

Like most bacteriophages, phi X174 transfers its DNA through the cell wall, leaving an empty capsid on the cell surface. The process begins with ejection of the genome at its host-receptor site. The rate of this event can be measured, so detailed structure/function analysis of the mechanism is possible now that an atomic structure of the phi X174 protein shell has been obtained. Amino acid substitutions at two arginine residues near the DNA-binding pocket of F capsid protein decrease the eclipse rate, while deletion of 27 bases from the J-F non-coding region increases the rate. An alanine to serine change in the N-terminal region of the phi X174 H "spike" protein has suppressor activity in that this mutation also increases the eclipse rate when the complete genome is present within both mutant and wild-type F capsids. These results suggest that a portion of H protein is inside the capsid, and disruption of DNA-protein interactions is involved in the ejection mechanism.

Nitrogen catabolite repression of arginase (CAR1) expression in Saccharomyces cerevisiae is derived from regulated inducer exclusion.

Expression of the Saccharomyces cerevisiae arginase (CAR1) gene is regulated by induction and nitrogen catabolite repression (NCR). Arginine was demonstrated to be the native inducer. CAR1 sensitivity to NCR has long been accepted to be accomplished through a negative control mechanism, and cis-acting sites for it have been hypothesized. In search of this negatively acting site, we discovered that CAR1 sensitivity to NCR derives from regulated inducer (arginine) exclusion. The route of catabolic entry of arginine into the cell, the general amino acid permease (GAP1), is sensitive to NCR. However, CAR1 expression in the presence of sufficient intracellular arginine is NCR insensitive.

Localization of protective epitopes within the pilin subunit of the Vibrio cholerae toxin-coregulated pilus.

From a collection of monoclonal antibodies (MAbs) that recognize the native structure of the toxin-coregulated pilus of Vibrio cholerae, two protective MAbs (16.1 and 169.1) were used to localize the corresponding epitopes on the pilus. These MAbs were shown to specifically recognize the carboxyl half of the TcpA pilin subunit, as determined by their recognition of proteolytic fragments and hybrid pilin proteins. The positions of the epitopes were precisely determined through the use of overlapping synthetic peptides corresponding to this region of the pilin. The MAbs were found to recognize adjacent peptides, delineating a region between residues 157 and 199. Since the protective nature is specific for these two antibodies, the findings suggest that this region defines a domain that participates in toxin-coregulated pilus-mediated colonization and therefore represents a target for studies of its potential as an immunogen for incorporation into a component cholera vaccine.

Fast atom bombardment mass spectrometric quantitative analysis of methionine-enkephalin in human pituitary tissues.

Picomole amounts of endogenous methionine-enkephalin (ME = YGGFM) were quantified in 11 individual human pituitaries by fast atom bombardment mass spectrometry methods. Quantification was based either upon the comparison of the molecular ion (MH+) current of endogenous ME versus the current of a deuterated ME internal standard (d5-ME) or, similarly, upon the unimolecular decomposition MH+----YGGF-+ In the first field-free region to produce the unique tetrapeptide fragment ion. The latter method used the multiple reaction monitoring (MRM) mode. Native ME was purified with an octadecylsilyl (ODS) disposable cartridge and with multidimensional reversed-phase high-performance liquid chromatography. The amounts of ME determined were 18.26 +/- 19.98 ng of ME/mg of protein with the MH+ method and 15.28 +/- 16.59 ng of ME/mg of protein with the MRM method. A fraction (ca. 4%) of the total amount of ME from one pituitary was used to acquire these quantitative data, and ca. half of the remaining amount of a separate sample (no d5-ME added) was used to obtain a linked scan at constant B/E (B, magnetic field; E, electric field) of the ME MH+ at 574 u to produce the amino acid sequence determining fragment ions at m/z 297, 354, 411, 397, 278, and 425 u corresponding to Y2", Y3", Y4", A4, B3, and B4, respectively. That product ion spectrum was similar to a scan of 100 ng of synthetic ME. We calculated that the amount of pentapeptide for the MRM experiments corresponded to a total of 30 ng (52 pmol) of ME on the probe tip during quantification. On the other hand, we estimated that 3 times more, or 90 ng (156 pmol), ME was on the probe tip during acquisition of the product ion spectrum.

Multiple positive and negative cis-acting elements mediate induced arginase (CAR1) gene expression in Saccharomyces cerevisiae.

Expression of the arginase (CAR1) gene in Saccharomyces cerevisiae is induced by arginine or its analog homoarginine. Induction has been previously shown to require a negatively acting upstream repression sequence, which maintains expression of the gene at a low level in the absence of inducer. The objective of this work was to identify the cis-acting elements responsible for CAR1 transcriptional activation and response to inducer. We identified three upstream activation sequences (UASs) that support transcriptional activation in a heterologous expression vector. Two of these UAS elements function in the absence of inducer, whereas the third functions only when inducer is present. One of the inducer-independent UAS elements exhibits significant homology to the Sp1 factor-binding sites identified in simian virus 40 and various mammalian genes.

A cis-acting element present in multiple genes serves as a repressor protein binding site for the yeast CAR1 gene.

Induction of the arginase (CAR1) gene expression in Saccharomyces cerevisiae has previously been shown to require participation of a cis-dominantly regulated upstream repression sequence (URS). Deletion of this element results in high-level expression of the CAR1 gene without inducer. To determine the structure of the CAR1 URS element, we performed a saturation mutagenesis. Results of the mutagenic analysis indicated that the CAR1 URS was a 9-base-pair palindromic sequence, 5'-AGCCGCCGA-3'. A DNA fragment containing this sequence was shown to bind one or more proteins by a gel shift assay. DNA fragments containing point mutations that completely eliminated URS function were not effective competitors in this assay, whereas those which supported URS function were effective competitors. Sequences in the 5'-flanking regions of 14 other genes were found to be homologous to the CAR1 URS. These sequences were shown to support varying degrees of URS function in the expression vector assay, to bind protein as demonstrated by the gel shift assay, and to compete with a DNA fragment containing the CAR1 URS for protein binding. These results indicate that the CAR1 URS element possesses the characteristics of a repressor binding site. Further, they are consistent with the suggestion that sites homologous to the CAR1 URS may be situated in the 5'-flanking regions of multiple unrelated yeast genes. The widespread occurrence of this element raises the possibility that it is the target site for one or more negatively acting general transcription factors.

Identification of sequences responsible for transcriptional activation of the allantoate permease gene in Saccharomyces cerevisiae.

DAL5 is a constitutively expressed allantoin system gene whose product is required for allantoate transport. Its simple pattern of expression prompted us to use this gene for identifying the element(s) that mediates transcriptional activation of allantoin system genes. Deletion analysis of the DAL5 5'-flanking sequences resulted in identification of two small regions required for DAL5 expression. Analysis of these two regions with synthetic oligonucleotides localized the sequences supporting transcriptional activation to two DNA fragments of 10 to 12 base pairs, each containing one copy of the pentanucleotide 5'-GATAA-3'. The 5'-flanking region of DAL5 contained eight copies of this sequence. Synthetic constructions containing single copies of these fragments were unable to support transcriptional activation, while those containing two or more copies supported high-level activation. The 5'-GATAA-3' sequence was also found beneath the footprint of a DNA-binding protein. These observations are consistent with the suggestion that DNA fragments containing the sequence 5'-GATAA-3' play an important role in DAL5 gene expression, probably representing a portion of the binding site for a transcriptional activation factor.

Ubiquitous upstream repression sequences control activation of the inducible arginase gene in yeast.

Expression of the yeast arginase gene (CAR1) responds to both induction and nitrogen catabolite repression. Regulation is mediated through sequences that both positively and negatively modulate CAR1 transcription. A short sequence, 5'-TAGCCGCCGAGGG-3', possessing characteristics of a repressor binding site, plays a central role in the induction process. A fragment containing this upstream repression sequence (URS1) repressed gene expression when placed either 5' or 3' to the upstream activation sequences of the heterologous gene CYC1. Action of the URS and its cognate repressor was overcome by CAR1 induction when the URS was situated cis to the CAR1 flanking sequences. This was not observed, however, when it was situated downstream of a heterologous CYC1 upstream activation sequence indicating that URS function is specifically neutralized by cis-acting elements associated with CAR1 induction. Searches of sequences in various gene banks revealed that URS1-like sequences occur ubiquitously in genetic regulatory regions including those of bacteriophage lambda, yeast, mammalian, and viral genes. In a significant number of cases the sequence is contained in a region associated with negative control of yeast gene regulation. These data suggest the URS identified in this work is a generic repressor target site that apparently has been conserved during the evolution of transcriptional regulatory systems.

Point mutation generates constitutive expression of an inducible eukaryotic gene.

We describe the analysis of two cis-dominant mutations that result in constitutive expression of the inducible CAR1 gene from yeast. One mutation results from insertion of a Ty element just upstream from the point where CAR1-specific transcription begins. The other mutation is a C-to-G transversion at position -153. Isolation of this point mutation, outside of the transcribed region of CAR1, suggests that expression of this gene is regulated at transcription. It also demonstrates the feasibility and usefulness of analyzing the regulatory sequences of eukaryotic genes on a nucleotide-by-nucleotide basis.

Nucleotide sequence of the Saccharomyces cerevisiae arginase gene (CAR1) and its transcription under various physiological conditions.

We have determined the nucleotide sequence of the yeast CAR1 gene along with its 5' and 3' flanking sequences. The structural portion of this gene encodes a protein of 333 amino acid residues with a calculated Mr value of 35,616. The transcripts produced from this gene are modestly heterogeneous at their 5' and 3' termini. Most 5' termini map to a position 42 to 49 base pairs upstream from the ATG at the beginning of the open reading frame. The 3' termini map to a position 108 to 127 base pairs downstream of the amber codon which terminates the open reading frame. A variety of potentially significant sequences were identified in the regions flanking the structural portion of the gene.

What is the function of nitrogen catabolite repression in Saccharomyces cerevisiae?

In contrast to the previously held notion that nitrogen catabolite repression is primarily responsible for the ability of yeast cells to use good nitrogen sources in preference to poor ones, we demonstrate that this ability is probably the result of other control mechanisms, such as metabolite compartmentation. We suggest that nitrogen repression is functionally a long-term adaptation to changes in the nutritional environment of yeast cells.

Isolation of the CAR1 gene from Saccharomyces cerevisiae and analysis of its expression.

We isolated the CAR1 gene from Saccharomyces cerevisiae on a recombinant plasmid and localized it to a 1.58-kilobase DNA fragment. The cloned gene was used as a probe to analyze polyadenylated RNA derived from wild-type and mutant cells grown in the presence and absence of an inducer. Wild-type cells grown without the inducer contained very little polyadenylated RNA capable of hybridizing to the isolated CAR1 gene. A 1.25-kilobase CAR1-specific RNA species was markedly increased, however, in wild-type cells grown in the presence of inducer and in constitutive, regulatory mutants grown without it. No CAR1-specific RNA was observed when one class of constitutive mutant was grown in medium containing a good nitrogen source, such as asparagine. Two other mutants previously shown to be resistant to nitrogen repression contained large quantities of CAR1 RNA regardless of the nitrogen source in the medium. These data point to a qualitative correlation between the steady-state levels of CAR1-specific, polyadenylated RNA and the degree of arginase induction and repression observed in the wild type and in strains believed to carry regulatory mutations. Therefore, they remain consistent with our earlier suggestion that arginase production is probably controlled at the level of gene expression.

Urea carboxylase and allophanate hydrolase are components of a multifunctional protein in yeast.

Saccharomyces cerevisiae can use urea as sole nitrogen source by degrading it in two steps (urea carboxylase and allophanate hydrolase) to ammonia and carbon dioxide. We previously demonstrated that: 1) the enzymatic functions required for degradation are encoded in two tightly linked genetic loci and 2) pleiotropic mutations each resulting in the loss of both activities are found in both loci. These and other observations led to the hypothesis that urea degradation might be catalyzed by a multifunctional polypeptide. Waheed and Castric (1977) J. Biol. Chem. 252, 1628-1632), on the other hand, purified urea amidolyase from Candida utilis and reported it to be a tetramer composed of nonidentical 70- and 170-kilodalton subunits. To resolve the differing views of urea amidolyase structure, we purified the protein using rapid methods designed to avoid proteolytic cleavage. Application of these methods resulted in the isolation of a single, inducible and repressible, 204-kilodalton species. We observed no evidence for the existence of nonidentical subunits. A similar inducible, high molecular weight species was also detected in C. utilis. These biochemical results support our earlier hypothesis that urea degradation is carried out in yeast by an inducible and repressible protein composed of identical, multifunctional subunits.

Post-translational processing of urea amidolyase in Saccharomyces cerevisiae.

Urea amidolyase catalyzes the two reactions (urea carboxylase and a allophanate hydrolase) associated with urea degradation in Saccharomyces cerevisiae. Past work has shown that both reactions are catalyzed by a 204-kilodalton, multifunctional protein. In view of these observations, it was surprising to find that on induction at 22 degrees C, approximately 2 to 6 min elapsed between the appearance of allophanate hydrolase and urea carboxylase activities. In search of an explanation for this apparent paradox, we determined whether or not a detectable period of time elapsed between the appearance of allophanate hydrolase activity and activation of the urea carboxylase domain by the addition of biotin. We found that a significant portion of the protein produced immediately after the onset of induction lacked the prosthetic group. A steady-state level of biotin-free enzyme was reached 16 min after induction and persisted indefinitely thereafter. These data are consistent with the suggestion that sequential induction of allophanate hydrolase and urea carboxylase activities results from the time required to covalently bind biotin to the latter domain of the protein.

Oxalurate transport in Saccharomyces cerevisiae.

Oxalurate, the gratuitous inducer of the allantoin degradative enzymes, was taken into the cell by an energy-dependent active transport system with an apparent Km of 1.2 mM. Efflux of previously accumulated oxalurate was rapid, with a half-life of about 2 min. The oxalurate uptake system appears to be both constitutively produced and insensitive to nitrogen catabolite repression. The latter observations suggest that failure of oxalurate to bring about induction of allophanate hydrolase in cultures growing under repressive conditions does not result from inducer exclusion, but rather from repression of dur1,2 gene expression.

Addition of basic amino acids prevents G-1 arrest of nitrogen-starved cultures of Saccharomyces cerevisiae.

Arginase-minus mutants of Saccharomyces cerevisiae were arrested in growth and accumulated at the unbudded G-1 stage of the cell cycle when starved for nitrogen. If, however, arginine was added to the culture medium at the time of starvation, growth ceased but the cells did not collect at the unbudded G-1 stage. We suggest that arginine addition prevented the cells from collecting at the G-1 stage by starving them for histidine and lysine, thereby inhibiting synthesis of proteins needed to complete the cell cycle.

Control of vacuole permeability and protein degradation by the cell cycle arrest signal in Saccharomyces cerevisiae.

Saccharomyces cerevisiae responds to deperivation of nutrients by arresting cell division at the unbudded G1 stage. Cells situated outside of G1 at the time of deperivation complete the cell cycle before arresting. This prompted an investigation of the source of nutrients used by these cells to complete division and the mechanisms controlling their availability. We found a close correlation between accumulation of unbudded cells and loss of previously formed allophanate hydrolase activity after nutrient starvation. These losses were not specific to the allantoin, system since they have been observed for a number of other enzymes and also when cellular protein levels were monitored with [3H]leucine. Loss of hydrolase activity was also observed when protein synthesis was inhibited either by addition of inhibitors or loss of the prtl gene product. We found that onset of nutrient starvation brought about release of large quantities of arginine and allantoin normally sequestered in the cell vacuole. Treatment of a cells with alpha-factor resulted in both the release of allantoin and arginine from the cell vacuole and the onset of intracellular protein degradation. These effects were not observed when either alpha cells or a/alpha diploid strains were treated with alpha-factor. These data suggest that release of vacuolar constitutents and protein turnover may be regulated by the G1 arrest signal.