Identification of sequence elements that confer cell-type-specific control of MF alpha 1 expression in Saccharomyces cerevisiae

Yeast Gal11 and transcription factor IIE function through a common pathway in transcriptional regulation

The global transcription regulator Gal11, a component of RNA polymerase II holoenzyme, is required for full expression of many genes in yeast. We previously reported that Gal11 binds the small (Tfa2) and large (Tfa1) subunits of the general transcription factor (TF) IIE through Gal11 functional domains A and B, respectively. Here we demonstrate that the C-terminal basic region in Tfa2 is responsible for binding to domain A, whereas both the N-terminal hydrophobic and internal glutamic acid-rich regions in Tfa1 are responsible for binding to domain B. Yeast cells bearing a C-terminal deletion encompassing the Gal11-interacting region in each of the two TFIIE subunits, being viable, exhibited no obvious phenotype. In contrast, combination of the two deletions (TFIIE-DeltaC) showed phenotypes similar to those of gal11 null mutations. The levels of mRNA from TATA-containing genes, but not from TATA-less genes, decreased in TFIIE-DeltaC to an extent comparable to that in the gal11 null mutant. Combination of TFIIE-DeltaC with a gal11 null mutation did not result in an enhanced effect, suggesting that both TFIIE and Gal11 act in a common regulatory pathway. In a reconstituted cell-free system, Gal11 protein stimulated basal transcription in the presence of wild-type TFIIE. Such a stimulation was not seen in the presence of TFIIE-DeltaC.

Promoter structure-dependent functioning of the general transcription factor IIE in Saccharomyces cerevisiae

General transcription factor (TF) IIE is an essential component of the basal transcription complex for protein-encoding genes, which is widely conserved in eukaryotes. Here we analyzed requirement for TFIIE for transcription in vivo by using yeast Saccharomyces cerevisiae cells harboring mutations in the TFA1 gene encoding the larger one of the two subunits of TFIIE. Deletion analysis indicated that the N-terminal half of Tfa1 protein has an essential function to support the cell growth. In a temperature-sensitive tfa1 mutant cell, the steady-state level of bulk poly(A)+ RNA decreased rapidly at the restrictive temperature. Surprisingly, levels of several mRNAs, whose transcription is directed by the promoters lacking the typical TATA sequence, were not affected in the mutant cells at that temperature. This promoter-specific functioning of TFIIE was reproduced in a cell-free system composed of TFIIE-depleted nuclear extracts. These results strongly suggest that requirement for TFIIE varies in each gene depending on the promoter structures in vivo.

Probing the limits of expression levels by varying promoter strength and plasmid copy number in Saccharomyces cerevisiae

Heterologous gene expression levels were measured in yeast using the Escherichia coli gusA gene (encoding beta-D-glucuronidase) as a reporter. The influence of two major parameters, promoter activity and plasmid copy number, was studied. (1) Promoters used in this study ranged from the very weak constitutive KEX2, the regulated CYC1 and PGK and the mating type-specific MF alpha 1 to the strong constitutive TEF1 and TDH promoters. Using centromeric vectors, gusA expression levels varied within three orders of magnitude. (2) Plasmid copy number was changed by shifting from a monocopy (centromeric plasmid) over a moderate copy number (2 mu-based plasmid) to a high copy number (2 mu associated with the URA3-d selection marker). gusA expression levels increased relatively with plasmid copy number in all cases studied, but did not exceed the equivalent of 2% of total soluble yeast proteins. Coupling these variables, a 5-log range in gene expression levels was covered. Taken together, these results provide a framework which allows a comparison of existing and new promoters. This framework will be useful for expressing genes to required levels.

A new signal peptide useful for secretion of heterologous proteins from yeast and its application for synthesis of hirudin

The BGL2 gene from Saccharomyces cerevisiae encodes a beta-glucanase which is localized to the yeast cell wall. The ability of a 23-amino acid (aa) signal peptide derived from the BGL2 gene to direct a heterologous protein to the secretory pathway of yeast has been compared to that of the MF alpha 1-encoded signal peptide in a series of gene fusions. As a model protein, the leech anticoagulant, recombinant hirudin variant 2-Lys47 (HIR) has been studied. From a multicopy plasmid chimaeric proteins were produced which carry the BGL2 signal peptide (or the artificial BGL2 pre-Val7 variant) (i) in front of the MF alpha 1 pro sequence (or modified versions of MF alpha 1 pro), i.e., a prepro signal, or (ii) joined directly to the heterologous protein. Accumulation of active HIR in yeast culture supernatants was observed when the BGL2 (or the BGL2 pre-Val7) signal peptide were used in combination with either of three versions of the MF alpha 1 pro peptide: the authentic MF alpha 1 pro, a partially deleted MF alpha 1 pro-delta 22-61, or a pro bearing an aa change (MF alpha 1 pro-Gly22). In each case the BGL2 signal peptide (or its variant) has proven equally productive to the corresponding MF alpha 1 peptide. Four times more active HIR was detected in the culture supernatant when either signal peptide was fused directly to the recombinant protein, as compared to a prepro protein version. Correct signal peptide cleavage was obtained when HIR was produced as a BGL2 pre-Val7::fusion protein.

Relative contributions of MCM1 and STE12 to transcriptional activation of a- and alpha-specific genes from Saccharomyces cerevisiae

We have examined the relative contributions of MCM1 and STE12 to the transcription of the a-specific STE2 gene by using a 367 bp fragment from the STE2 5'-noncoding region to drive expression of a reporter lacZ gene. Mutation of the MCM1 binding site destroyed MCM1.alpha 2-mediated repression in alpha cells and dramatically reduced expression in a cells. The residual expression was highly stimulated by exposure of cells to pheromone. Likewise, the loss of STE12 function reduced lacZ expression driven by the wild-type STE2 fragment. In the absence of both MCM1 and STE12 functions, no residual expression was observed. Thus, the STE2 fragment appears to contain two distinct upstream activation sequences (UASs), one that is responsible for the majority of expression in cells not stimulated by pheromone, and one that is responsible for increased expression upon pheromone stimulation. In further support of this idea, a chemically synthesized version of the STE2 MCM1 binding site had UAS activity, but the activity was neither stimulated by pheromone nor reduced in ste12 mutants. Although transcription of alpha-specific genes also requires both MCM1 and STE12, these genes differ from a-specific genes in that they have a single, MCM1-dependent UAS system. The activity of the minimal 26 bp UAS from the alpha-specific STE3 gene was both stimulated by pheromone and reduced in ste12 mutants. These data suggest that at alpha-specific genes STE12 and MCM1 exert their effects through a single UAS.

The glucoamylase multigene family in Saccharomyces cerevisiae var. diastaticus: an overview

Saccharomyces cerevisiae has been used widely both as a model system for unraveling the biochemical, genetic, and molecular details of gene expression and the secretion process, and as a host for the production of heterologous proteins of biotechnological interest. The potential of starch as a renewable biological resource has stimulated research into amylolytic enzymes and the broadening of the substrate range of S. cerevisiae. The enzymatic hydrolysis of starch, consisting of linear (amylose) and branched glucose polymers (amylopectin), is catalyzed by alpha- and beta-amylases, glucoamylases, and debranching enzymes, e.g., pullulanases. Starch utilization in the yeast S. cerevisiae var. diastaticus depends on the expression of the three unlinked genes, STA1 (chr. IV), STA2 (chr. II), and STA3 (chr. XIV), each encoding one of the extracellular glycosylated glucoamylases isozymes GAI, GAII, or GAIII, respectively. The restriction endonuclease maps of STA1, STA2, and STA3 are identical. These genes are absent in S. cerevisiae, but a related gene, SGA1, encoding an intracellular, sporulation-specific glucoamylase (SGA), is present. SGA1 is homologous to the middle and 3' regions of the STA genes, but lacks a 5' sequence that encodes the domain for secretion of the extracellular glucoamylases. The STA genes are positively regulated by the presence of three GAM genes. In addition to positive regulation, the STA genes are regulated negatively at three levels. Whereas strains of S. diastaticus are capable of expressing the STA genes, most strains of S. cerevisiae contain STA10, whose presence represses the expression of the STA genes in an undefined manner. The STA genes are also repressed in diploid cells, presumably by the MATa/MAT alpha-encoded repressor. STA gene expression is reduced in liquid synthetic media, it is carbon catabolite repressed by glucose, and is inhibited in petite mutants.

DNA binding-induced conformational change of the yeast transcriptional activator PRTF

Our studies using proteases to probe protein structure establish that binding to the upstream activating sequences (UASs) of two different yeast a-specific genes induces a conformational change in the pheromone/receptor transcription factor (PRTF), which is not observed upon binding to the UASs of either of two alpha-specific genes. We propose that this selective structural alteration exposes an activation region of PRTF when it binds a-specific genes, switching these genes on. The transcriptional activator MAT alpha 1 may activate alpha-specific genes by binding to the PRTF-alpha-specific UAS complex and unmasking the otherwise hidden activation surface of PRTF. We also show that the N-terminal third of PRTF is sufficient for specific DNA binding, while the middle third of the protein interacts with MAT alpha 1.

A regulatory hierarchy for cell specialization in yeast

The specialized sets of genes that determine different cell types in yeast are controlled by combinations of DNA-binding proteins some of which are present only in certain cell types whereas others are present in all cell types. Final differentiation requires an inductive signal that triggers both gene transcription and cell-cycle arrest. Synthesis of the proteins coded by the 'master regulatory' mating-type locus is regulated so as to generate a heterogeneous mitotic cell population containing a stem-cell lineage.

Synthesis and secretion of human nerve growth factor by Saccharomyces cerevisiae

The DNA coding for human nerve growth factor (hNGF) was chemically synthesized and introduced into Saccharomyces cerevisiae. Expression and secretion of hNGF was obtained by use of the yeast phosphoglycerate kinase-encoding gene promoter and the pre-pro sequence of the yeast alpha-mating factor. Immunoblotting with antiserum raised against a protein A-hNGF fusion protein, allowed the detection of an immunoreactive material secreted into the culture medium. A preparation from the culture medium, partially purified by ion-exchange column chromatography, stimulated neurite outgrowth from rat pheochromocytoma PC12h cells.

Hormone-induced expression of the CHS1 gene from Saccharomyces cerevisiae

When MATa cells of Saccharomyces cerevisiae have been treated with the mating hormone alpha-factor an increase in chitin synthase zymogen, as well as chitin content in the cell-wall fraction, have been reported. With a DNA probe derived from the cloned CHS1 gene that codes for chitin synthase I [Bulawa, C. E., Slater, M., Cabib, E., Au-Young, J., Sburlati, A., Adair, W. L. and Robbins, P. (1986) Cell 46, 213-225] a Northern analysis was conducted of CHS1-specific transcripts. alpha-Factor-treated MATa cells revealed more than sixfold elevated steady-state levels of CHS1 mRNA as compared to control cells. MAT alpha cells responded the same way when treated with a-factor although induction rate was somewhat smaller. After hormone application a rapid increase in CHS1 mRNA levels could be observed that occurred also in the absence of ongoing protein synthesis. In order to minimize possible side effects of CHS1-coding sequences on expression and mRNA stability a CHS1::SUC2 chimaeric gene was constructed where 730 bp of the CHS1 promoter region (+20 bp of the coding region) were fused in frame to a fragment of the SUC2 coding region. The fusion protein exhibits invertase activity that has been used to monitor CHS1 promoter activity. By analysis of shortened versions of the CHS1 promoter a 94-bp DNA fragment has been identified that confers hormone inducibility to the CHS1 promoter. According to the published sequence of the CHS1 gene, this fragment contains four repeats of a TGAAACA consensus sequence previously identified in the alpha-factor-inducible BAR1 promoter [Kronstad, J. W., Holly, J. A. and MacKay, V. L. (1987) Cell 50, 369-377]. This heptamer may represent the cis-acting element involved in mating-hormone-mediated gene expression in yeast.

The MF alpha 1 gene of Saccharomyces cerevisiae: genetic mapping and mutational analysis of promoter elements

The activity and cell-type specificity of the promoter of the MF alpha 1 gene of Saccharomyces cerevisiae were examined by measuring expression of an MF alpha 1-SUC2 gene fusion in MATa, MAT alpha, and MATa/MAT alpha cells. A high level of invertase activity was observed only in MAT alpha cells. Weak expression occurred in MATa cells when the hybrid gene was carried on a multicopy plasmid or on a centromere-containing plasmid, but not when the hybrid gene was integrated at the normal MF alpha 1 locus. Analysis of a set of 5'-deletions of the promoter region of the MF alpha 1-SUC2 gene on the multicopy plasmid indicated that sequences from -354 to -274 upstream of the translational start site were required for high level expression in MAT alpha cells. Smaller internal deletions and insertions within the promoter region of the MF alpha 1-SUC2 gene were inserted into the genome at the normal MF alpha 1 locus. These mutations further delineated four promoter domains important for expression: (1) two 26 bp elements (-365 to -340 and -312 to -287) with imperfect dyad symmetry; (2) a 40 bp segment (-264 to -226) that lies about 120 bp upstream of the TATA box; and (3) the TATA box itself (-128 to -122). The transcriptional start sites of the normal MF alpha 1 promoter and of a mutant lacking the TATA box were determined. The MF alpha 1 locus was mapped to the left arm of chromosome XVI, about 22 cM centromere-proximal to the PEP4 gene.