Efficient transcription of the glycolytic gene ADH1 and three translational component genes requires the GCR1 product, which can act through TUF/GRF/RAP binding sites

Differential activation mechanisms of two isoforms of Gcr1 transcription factor generated from spliced and un-spliced transcripts in Saccharomyces cerevisiae

Gcr1, an important transcription factor for glycolytic genes in Saccharomyces cerevisiae, was recently revealed to have two isoforms, Gcr1^U and Gcr1^S, produced from un-spliced and spliced transcripts, respectively. In this study, by generating strains expressing only Gcr1^U or Gcr1^S using the CRISPR/Cas9 system, we elucidate differential activation mechanisms of these two isoforms. The Gcr1^U monomer forms an active complex with its coactivator Gcr2 homodimer, whereas Gcr1^S acts as a homodimer without Gcr2. The USS domain, 55 residues at the N-terminus existing only in Gcr1^U, inhibits dimerization of Gcr1^U and even acts in trans to inhibit Gcr1^S dimerization. The Gcr1^S monomer inhibits the metabolic switch from fermentation to respiration by directly binding to the ALD4 promoter, which can be restored by overexpression of the ALD4 gene, encoding a mitochondrial aldehyde dehydrogenase required for ethanol utilization. Gcr1^U and Gcr1^S regulate almost the same target genes, but show unique activities depending on growth phase, suggesting that these isoforms play differential roles through separate activation mechanisms depending on environmental conditions.

A fast and tuneable auxin-inducible degron for depletion of target proteins in budding yeast

The auxin‐inducible degron (AID) is a useful technique to rapidly deplete proteins of interest in nonplant eukaryotes. Depletion is achieved by addition of the plant hormone auxin to the cell culture, which allows the auxin‐binding receptor, TIR1, to target the AID‐tagged protein for degradation by the proteasome. Fast depletion of the target protein requires good expression of TIR1 protein, but as we show here, high levels of TIR1 may cause uncontrolled depletion of the target protein in the absence of auxin. To enable conditional expression of TIR1 to a high level when required, we regulated the expression of TIR1 using the β‐estradiol expression system. This is a fast‐acting gene induction system that does not cause secondary effects on yeast cell metabolism. We demonstrate that combining the AID and β‐estradiol systems results in a tightly controlled and fast auxin‐induced depletion of nuclear target proteins. Moreover, we show that depletion rate can be tuned by modulating the duration of β‐estradiol preincubation. We conclude that TIR1 protein is a rate‐limiting factor for target protein depletion in yeast, and we provide new tools that allow tightly controlled, tuneable, and efficient depletion of essential proteins whereas minimising secondary effects.

Integrative random forest for gene regulatory network inference

Motivation: Gene regulatory network (GRN) inference based on genomic data is one of the most actively pursued computational biological problems. Because different types of biological data usually provide complementary information regarding the underlying GRN, a model that integrates big data of diverse types is expected to increase both the power and accuracy of GRN inference. Towards this goal, we propose a novel algorithm named iRafNet: integrative random forest for gene regulatory network inference.

Results: iRafNet is a flexible, unified integrative framework that allows information from heterogeneous data, such as protein–protein interactions, transcription factor (TF)-DNA-binding, gene knock-down, to be jointly considered for GRN inference. Using test data from the DREAM4 and DREAM5 challenges, we demonstrate that iRafNet outperforms the original random forest based network inference algorithm (GENIE3), and is highly comparable to the community learning approach. We apply iRafNet to construct GRN in Saccharomyces cerevisiae and demonstrate that it improves the performance in predicting TF-target gene regulations and provides additional functional insights to the predicted gene regulations.

Availability and implementation: The R code of iRafNet implementation and a tutorial are available at: http://research.mssm.edu/tulab/software/irafnet.html

Contact:zhidong.tu@mssm.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Developmental strategies and regulation of cell-free enzyme system for ethanol production: a molecular prospective

Most biomanufacturing systems developed for the production of biocommodities are based on whole-cell systems. However, with the advent of innovative technologies, the focus has shifted from whole-cell towards cell-free enzyme system. Since more than a century, researchers are using the cell-free extract containing the required enzymes and their respective cofactors in order to study the fundamental aspects of biological systems, particularly fermentation. Although yeast cell-free enzyme system is known since long ago, it is rarely been studied and characterized in detail. In this review, we hope to describe the major pitfalls encountered by whole-cell system and introduce possible solutions to them using cell-free enzyme systems. We have discussed the glycolytic and fermentative pathways and their regulation at both transcription and translational levels. Moreover, several strategies employed for development of cell-free enzyme system have been described with their potential merits and shortcomings associated with these developmental approaches. We also described in detail the various developmental approaches of synthetic cell-free enzyme system such as compartmentalization, metabolic channeling, protein fusion, and co-immobilization strategies. Additionally, we portrayed the novel cell-free enzyme technologies based on encapsulation and immobilization techniques and their development and commercialization. Through this review, we have presented the basics of cell-free enzyme system, the strategies involved in development and operation, and the advantages over conventional processes. Finally, we have addressed some potential directions for the future development and industrialization of cell-free enzyme system.

The transcription factor Gcr1 stimulates cell growth by participating in nutrient-responsive gene expression on a global level

Transcriptomic reprogramming is critical to the coordination between growth and cell cycle progression in response to changing extracellular conditions. In Saccharomyces cerevisiae, the transcription factor Gcr1 contributes to this coordination by supporting maximum expression of G1 cyclins in addition to regulating both glucose-induced and glucose-repressed genes. We report here the comprehensive genome-wide expression profiling of gcr1Delta cells. Our data show that reduced expression of ribosomal protein genes in gcr1Delta cells is detectable both 20 min after glucose addition and in steady-state cultures of raffinose-grown cells, showing that this defect is not the result of slow growth or growth on a repressing sugar. However, the large cell phenotype of the gcr1Delta mutant occurs only in the presence of repressing sugars. GCR1 deletion also results in aberrant derepression of numerous glucose repressed loci; glucose-grown gcr1Delta cells actively respire, demonstrating that this global alteration in transcription corresponds to significant changes at the physiological level. These data offer an insight into the coordination of growth and cell division by providing an integrated view of the transcriptomic, phenotypic, and metabolic consequences of GCR1 deletion.

Trehalose, glycogen and ethanol metabolism in the gcr1 mutant of Saccharomyces cerevisiae

Since Gcr1p is pivotal in controlling the transcription of glycolytic enzymes and trehalose metabolism seems to be one of the control points of glycolysis, we examined trehalose and glycogen synthesis in response to 2% glucose pulse during batch growth in gcr1 (glucose regulation-1) mutant lacking fully functional glycolytic pathway and in the wild-type strain. An increase in both trehalose and glycogen stores was observed 1 and 2 h after the pulse followed by a steady decrease in both the wild-type and the gcr1 mutant. The accumulation was faster while the following degradation was slower in gcr1 cells compared to wild-type ones. Although there was no distinct glucose consumption in the mutant cells it seemed that the glucose repression mechanism is similar in gcr1 mutant and in wild-type strain at least with respect to trehalose and glycogen metabolism.

Rap1p requires Gcr1p and Gcr2p homodimers to activate ribosomal protein and glycolytic genes, respectively

Efficient transcription of ribosomal protein (RP) and glycolytic genes requires the Rap1p/Gcr1p regulatory complex. A third factor, Gcr2p, is required for only the glycolytic (specialized) mode of transcriptional activation. It is recruited to the complex by Gcr1p and likely mediates a change in the phosphorylation state and/or conformation of the latter. We show here that leucine zipper motifs in Gcr1p and Gcr2p (1LZ and 2LZ) are each specific to one of the two activation mechanisms-mutations in 1LZ and 2LZ impair transcription of RP and glycolytic genes, respectively. Although neither class of mutations causes more than a mild growth defect, simultaneous impairment of 1LZ and 2LZ results in a severe synthetic defect and a reduction in the expression of both sets of genes. Intracistronic complementation by point mutations in the charged e and g positions confirmed that Gcr1p/Gcr1p and Gcr2p/Gcr2p homodimers are the forms required for the different roles of the activator complex. Direct heterodimerization between 1LZ and 2LZ apparently does not occur. Dichotomous Rap1p activation and its striking requirement for distinct homodimeric subunits give cells the capacity to switch between coordinated and uncoupled RP and glycolytic gene regulation.

Xylose utilisation: cloning and characterisation of the Xylose reductase from Candida tenuis

Xylose reductases catalyse the initial reaction in the xylose utilisation pathway, the NAD(P)H+H+ dependent reduction of xylose to xylitol. In this work, the xylose reductase gene from Candida tenuis CBS 4435 was cloned and successfully expressed in E. coli. From the purified and partially sequenced protein primers were deduced for PCR. The fragment obtained was used for Southern blot analysis and screening of a subgenomic library. The clone containing the open reading frame was sequenced; the gene consisted of 969 nucleotides coding for a 322 amino acids protein with a molecular mass of 36 kDa. Putative regulatory signals were identified with the help of a Saccharomyces cerevisiae regulatory sequence database. In order to express the xylose reductase in E. coli, the gene was placed under positive and negative control. At low temperatures, the xylose reductase was expressed in soluble and active form up to about 10% of the soluble protein; with rising temperatures formation of visible inclusion bodies occurred. In refolding experiments we were able to recover the major portion of xylose reductase activity from the pellet fraction.

Regulation of ribosome biogenesis by the rapamycin-sensitive TOR-signaling pathway in Saccharomyces cerevisiae

The TOR (target of rapamycin) signal transduction pathway is an important mechanism by which cell growth is controlled in all eucaryotic cells. Specifically, TOR signaling adjusts the protein biosynthetic capacity of cells according to nutrient availability. In mammalian cells, one branch of this pathway controls general translational initiation, whereas a separate branch specifically regulates the translation of ribosomal protein (r-protein) mRNAs. In Saccharomyces cerevisiae, the TOR pathway similarly regulates general translational initiation, but its specific role in the synthesis of ribosomal components is not well understood. Here we demonstrate that in yeast control of ribosome biosynthesis by the TOR pathway is surprisingly complex. In addition to general effects on translational initiation, TOR exerts drastic control over r-protein gene transcription as well as the synthesis and subsequent processing of 35S precursor rRNA. We also find that TOR signaling is a prerequisite for the induction of r-protein gene transcription that occurs in response to improved nutrient conditions. This induction has been shown previously to involve both the Ras-adenylate cyclase as well as the fermentable growth medium-induced pathways, and our results therefore suggest that these three pathways may be intimately linked.

Specialized Rap1p/Gcr1p transcriptional activation through Gcr1p DNA contacts requires Gcr2p, as does hyperphosphorylation of Gcr1p

The multifunctional regulatory factor Rap1p of Saccharomyces cerevisiae accomplishes one of its tasks, transcriptional activation, by complexing with Gcr1p. An unusual feature of this heteromeric complex is its apparent capacity to contact simultaneously two adjacent DNA elements (UASRPG and the CT box, bound specifically by Rap1p and Gcr1p, respectively). The complex can activate transcription through isolated UASRPG but not CT elements. In promoters that contain both DNA signals its activity is enhanced, provided the helical spacing between the two elements is appropriate; this suggests that at least transient DNA loop formation is involved. We show here that this CT box-dependent augmentation of Rap1p/Gcr1p activation requires the presence of a third protein Gcr2p; the Gcr2- growth defect appears to result from a genome-wide loss of the CT box effect. Interestingly, a hyperphosphorylated form of Gcr1p disappears in delta gcr2 cells but reappears if they harbor a doubly point-mutated GCR1 allele that bypasses the Gcr2- growth defect. Gcr2p therefore appears to induce a conformation change in Gcr1p and/or stimulate its hyperphosphorylation; one or both of these effects can be mimicked in the absence of GCR2 by mutation of GCR1. This improved view of Rap1p/Gcr1p/Gcr2p function reveals a new aspect of eukaryotic gene regulation: modification of an upstream activator, accompanied by at least transient DNA loop formation, mediates its improved capacity to activate transcription.

Mutations in GCR3, a gene involved in the expression of glycolytic genes in Saccharomyces cerevisiae, suppress the temperature-sensitive growth of hpr1 mutants

To study the functions of DNA topoisomerase I and Hpr1 protein, a suppressor mutant of the temperature-sensitive growth of an hpr1 top1-5ts double mutant was isolated. The isolated triple mutant showed cold-sensitive growth. By complementation of this phenotype, the suppressor gene was cloned. DNA sequencing showed it to be GCR3, a gene involved in the expression of glycolytic genes. Further analysis showed that gcr3 mutations also suppressed the temperature-sensitive growth of hpr1 single mutants. Experiments with gcr3 truncation mutants also suggested a genetic interaction between GCR3 and HPR1. The fact that top1 suppressed the growth defect of gcr3 suggested an interaction between those two genes also. Plasmid DNA isolated from gcr3 mutants was significantly more negatively supercoiled than normal, suggesting that Gcr3 protein, like topoisomerase I and Hpr1p, affects chromatin structure, perhaps during transcription.

The multifunctional transcription factors Abf1p, Rap1p and Reb1p are required for full transcriptional activation of the chromosomal PGK gene in Saccharomyces cerevisiae

We have identified two new transcription factor binding sites upstream of the previously defined UAS within the phosphoglycerate kinase (PGK) gene promoter in Saccharomyces cerevisiae. These sites are bound in vitro by the multifunctional factors Cpf1p and Reb1p. We have generated targeted deletions of Rap1p, Abf1p and Reb1p binding sites in the promoter of the chromosomal copy of the PGK gene. Northern blot analysis confirmed that most PGK promoter activity is mediated through the Rap1p binding site. However, significant effects are also mediated through both the Reb1p and Abf1p sites. In contrast, when the promoter is present on a high-copy-number plasmid, both the Abf1p and Reb1p sites play no role in transcriptional activation. The role of Cpf1p was examined using a cpf1 null strain. Cpf1p was found to have little if any, effect on activation of either the chromosomal or plasmid-borne PGK gene.

A new essential gene GCR4 located in the upstream region of GCR1

A new essential gene of Saccharomyces cerevisiae was found upstream of GCR1. Its cloning and sequencing predict a 280 amino acid protein (32,577 Da). The predicted protein is fairly hydrophobic, and a search of the database did not identify any homologous proteins. A LEU2 disruption at codon 104 was lethal, but disruption at codon 221 showed a temperature-sensitive conditional growth phenotype. Abnormalities were observed in some glycolytic enzyme levels.

The glucose-dependent transactivation activity of ABF1 on the expression of the TDH3 gene in yeast

Autonomously replicating sequence binding factor 1 (ABF1) has been implicated in the control of a variety of gene expressions in Saccharomyces cerevisiae. In this paper evidence is presented that ABF1 is involved in the glucose-dependent expression of the TDH3 gene which encodes glyceraldehyde-3-phosphate dehydrogenase. ABF1 binds to consensus sites located between -420 and -250, and between +77 and +200, and acts as a transactivator in an orientation-independent manner on both upstream and downstream sites. TDH3-lacZ fusions having an ABF1 consensus motif showed glucose-dependent expression of TDH3, whereas in the abf1 mutant strain JCA35 glucose-dependent expression disappeared. These findings suggest that ABF1 functions as a glucose-dependent transactivator for the expression of the TDH3 gene.

RAP1: a protean regulator in yeast

The yeast protein RAP1 is a sequence-specific DNA-binding protein that binds to many promoters, to two elements that silence mating-type genes, and to [(C)1-3A]n tracts at telomeres. RAP1 is essential for cell viability and can function as either an activator or a repressor of transcription, depending upon the context of its binding site. Recent experiments suggest that its function may be determined by different sets of protein-protein interactions at promoters and silencers. At the ends of chromosomes, RAP1 plays an important role in both silencing (telomere position effect) and telomere structure.

Importance of general regulatory factors Rap1p, Abf1p and Reb1p for the activation of yeast fatty acid synthase genes FAS1 and FAS2

The fatty acid synthase genes FAS1 and FAS2 of the yeast Saccharomyces cerevisiae are under transcriptional control of pathway-specific regulators of phospholipid biosynthesis. However, site-directed mutagenesis of the respective cis-acting elements upstream of FAS1 and FAS2 revealed that additional sequences activating both genes must exist. A deletion analysis of the FAS1 promoter lacking the previously characterized inositol/choline-responsive-element motif defined a region (nucleotides -760 to -850) responsible for most of the remaining activation potency. Gel-retardation experiments and in-vitro DNase footprint studies proved the binding of the general regulatory factors Rap1p, Abf1p and Reb1p to this FAS1 upstream region. Mutation of the respective binding sites led to a drop of gene activation to 8% of the wild-type level. Similarly, we also demonstrated the presence of a Reb1p-binding site upstream of FAS2 and its importance for gene activation. Thus, in addition to the previously characterized FAS-binding factor 1 interacting with the inositol/choline-responsive-element motif, a second motif common to the promoter regions of both FAS genes could be identified. Transcription of yeast fatty acid synthase genes is therefore subjected to both the pathway-specific control affecting genes of phospholipid biosynthesis and to the activation by general transcription factors allowing a sufficiently high level of constitutive gene expression.

A Reb1p-binding site is required for efficient activation of the yeast RAP1 gene, but multiple binding sites for Rap1p are not essential

The Saccharomyces cerevisiae RAP1 protein (Rap1p) is a key multifunctional transcription factor. Using gel retardation analysis, four binding sites for Rap1p have been identified within the promoter of the RAP1 gene. These sites are located downstream of a binding site for the transcription factor Reb1p. The Reb1p site and an associated AT-rich region are important for transcriptional activation, but deletion of three of the Rap1p-binding sites had little effect on promoter activity. The activity of the RAP1 promoter has been analysed in a yeast strain (YDS410) that contains a temperature-sensitive mutation in the RAP1 gene. This mutation renders the DNA-binding activity of Rap1p temperature dependent. When YDS410 was grown at a semi-permissive temperature (30 degrees C), the activity of the RAP1 promoter increased by approximately 170%, compared with the same strain grown at the permissive temperature (25 degrees C). A RAP1 promoter in which three of the four Rap1p-binding sites had been deleted, showed only a small increase in activity in the same experiment. These data confirm that Rap1p is not required for activation of the RAP1 gene, and suggest a role for Rap1p in negative autoregulation.

Saccharomyces cerevisiae ribosomal protein L37 is encoded by duplicate genes that are differentially expressed

A duplicate copy of the RPL37A gene (encoding ribosomal protein L37) was cloned and sequenced. The coding region of RPL37B is very similar to that of RPL37A, with only one conservative amino-acid difference. However, the intron and flanking sequences of the two genes are extremely dissimilar. Disruption experiments indicate that the two loci are not functionally equivalent: disruption of RPL37B was insignificant, but disruption of RPL37A severely impaired the growth rate of the cell. When both RPL37 loci are disrupted, the cell is unable to grow at all, indicating that rpL37 is an essential protein. The functional disparity between the two RPL37 loci could be explained by differential gene expression. The results of two experiments support this idea: gene fusion of RPL37A to a reporter gene resulted in six-fold higher mRNA levels than was generated by the same reporter gene fused to RPL37B, and a modest increase in gene dosage of RPL37B overcame the lack of a functional RPL37A gene.

Transcription regulation of ribosomal protein genes at different growth rates in continuous cultures of Kluyveromyces yeasts

We have investigated the relationship between the growth rate of two Kluyveromyces strains that differ in their maximum growth rate, namely K. lactis (mumax = 0.5 h-1) and K. marxianus (mumax = 1.1 h-1), and the transcription rate of ribosomal protein (rp) genes in these strains. The growth rate of either strain was varied by culturing the cells in a chemostat under conditions of glucose limitation at different dilution rates. Although the steady-state levels of transcription of the rp-genes of both Kluyveromyces strains were tightly coupled to the cellular growth rate, no clear relationship between the level of rp-gene transcription and the amount of in vitro binding of the RAP1- and ABF1-like proteins to the promoters of these rp-genes was observed. Upon a sudden increase in the growth rate of a steady-state culture, the transcription of rp-genes of K. lactis showed a different response from that in K. marxianus. Whereas a substantial overexpression of the K. lactis rp-genes was found during at least 4-5 h, the level of expression of the K. marxianus rp-genes was almost immediately adjusted to the new growth rate.

Saccharomyces cerevisiae multifunctional protein RAP1 binds to a conserved sequence in the Polyoma virus enhancer and is responsible for its transcriptional activity in yeast cells

The Polyoma virus enhancer (A + B domain) activates transcription in Saccharomyces cerevisiae when joined to appropriate yeast promoter elements. We demonstrate by DNase I footprints and inhibition of binding by specific antibody, that the yeast protein RAP1 binds to the B-domain of the Polyoma enhancer and, at least in some promoter contexts, is responsible for transcriptional activity of the enhancer B-domain in yeast. Close matches to a consensus RAP1-binding site are also present in other viral enhancers.

Growth-related expression of ribosomal protein genes in Saccharomyces cerevisiae

The rate of ribosomal protein gene (rp-gene) transcription in yeast is accurately adjusted to the cellular requirement for ribosomes under various growth conditions. However, the molecular mechanisms underlying this co-ordinated transcriptional control have not yet been elucidated. Transcriptional activation of rp-genes is mediated through two different multifunctional transacting factors, ABF1 and RAP1. In this report, we demonstrate that changes in cellular rp-mRNA levels during varying growth conditions are not parallelled by changes in the in vitro binding capacity of ABF1 or RAP1 for their cognate sequences. In addition, the nutritional upshift response of rp-genes observed after addition of glucose to a culture growing on a non-fermentative carbon source turns out not to be the result of increased expression of the ABF1 and RAP1 genes or of elevated DNA-binding activity of these factors. Therefore, growth rate-dependent transcription regulation of rp-genes is most probably not mediated by changes in the efficiency of binding of ABF1 and RAP1 to the upstream activation sites of these genes, but rather through other alterations in the efficiency of transcription activation. Furthermore, we tested the possibility that cAMP may play a role in elevating rp-gene expression during a nutritional shift-up. We found that the nutritional upshift response occurs normally in several mutants defective in cAMP metabolism.

Transcriptional control of yeast phosphoglycerate mutase-encoding gene

Yeast genes encoding enzymes of the glycolytic pathway are highly expressed due to transcriptional control elements in their promoters. We provide data on such elements in the 5'-noncoding sequences of the Saccharomyces cerevisiae GPM1 gene, encoding phosphoglycerate mutase. Using fusions to the lacZ reporter gene, a detailed deletion analysis was performed. A palindromic sequence was shown to function as an upstream activation site (UAS) and two upstream repressing sites (URS1 and URS2) were located. Western and Northern blot analyses were used to substantiate the data obtained in enzymatic measurements. The regulatory sequences were shown to be functional in the heterologous CYC1 promoter. In addition, a promoter region was detected which mediated general glycolytic control by the GCR1 regulatory factor.

Identification of three genes required for the glucose-dependent transcription of the yeast transcriptional activator ADR1

Glucose repression of the ADH2 gene from Saccharomyces cerevisiae is mediated by the synthesis and activity of the transcriptional activator ADR1. In this study, we isolated mutations in three new genes (SAF1, SAF2 and SAF3) that suppressed the glucose-insensitive expression of ADH2 caused by the ADR1-5c allele. The mechanism by which the SAF genes maintain ADR1-5c function was investigated. Each of the mutated SAF genes was found to suppress ADR1-5c activity by lowering ADR1-5c steady state mRNA levels 5- to 8-fold under glucose growth conditions. ADR1 mRNA levels were similarly affected by the saf mutations. In contrast, mutations in the SAF genes had little or no effect on ADR1-5c or ADR1 mRNA levels under ethanol growth conditions. The stability of ADR1-5c mRNA was unaffected by mutations in each of the SAF genes, implying that the SAF genes are required for the transcription of ADR1 mRNA under glucose growth conditions. The possible function of the three SAF genes in ADR1 expression is discussed.

Telomere-mediated plasmid segregation in Saccharomyces cerevisiae involves gene products required for transcriptional repression at silencers and telomeres

Plasmids that contain Saccharomyces cerevisiae TG1-3 telomere repeat sequences (TRS plasmids) segregate efficiently during mitosis. Mutations in histone H4 reduce the efficiency of TRS-mediated plasmid segregation, suggesting that chromatin structure is involved in this process. Sir2, Sir3 and Sir4 are required for the transcriptional repression of genes located at the silent mating type loci (HML and HMR) and at telomeres (telomere position effect) and are also involved in the segregation of TRS plasmids, indicating that TRS-mediated plasmid segregation involves factors that act at chromosomal telomeres. TRS plasmid segregation differes from the segregation of plasmids carrying the HMR E silencing region: HMR E plasmid segregation function is completely dependent upon Sir2, Sir3 and Sir4, involves Sir1 and is not influenced by mutations in RAP 1 that eliminate TRS plasmid segregation. Mutations in SIR1, SIN1, TOP1, TEL1 and TEL2 do not influence TRS plasmid segregation. Unlike transcriptional repression at telomeres, TRS plasmids retain partial segregation function in sir2, sir3, sir4, nat1 and ard1 mutant strains. Thus it is likely that TRS plasmid segregation involves additional factors that are not involved in telomere position effect.

GCR3 encodes an acidic protein that is required for expression of glycolytic genes in Saccharomyces cerevisiae

Screening of a mutagenized strain carrying a multicopy ENO1-'lacZ fusion plasmid revealed a new mutation affecting several glycolytic enzyme activities. The recessive single nuclear gene mutation, named gcr3, caused an extremely defective growth phenotype on fermentable carbon sources such as glucose, while growth on respiratory media was almost normal. The GCR3 gene was obtained by growth complementation from a genomic DNA library, and the complemented strains had normal enzyme levels. GCR3 gene was sequenced, and a 99,537-Da protein was predicted. The predicted GCR3 protein was fairly acidic (net charge, -34). The C-terminal region was highly charged, and an acidic stretch was found in it.

Global regulators of chromosome function in yeast

In the yeast Saccharomyces cerevisiae, several abundant, sequence-specific DNA binding proteins are involved in multiple aspects of chromosome function. In addition to functioning as transcriptional activators of a large number of yeast genes, they are also involved in transcriptional silencing, the initiation of DNA replication, centromere function and regulation of telomere length. This review will consider each of these proteins, focusing on what is known about the mechanisms of their multiple functions.

A multi-component upstream activation sequence of the Saccharomyces cerevisiae glyceraldehyde-3-phosphate dehydrogenase gene promoter

The majority of the activation potential of the Saccharomyces cerevisiae TDH3 gene promoter is contained within nucleotides -676 to -381 (relative to the translation initiation codon). An upstream activation sequence (UAS) in this region has been characterized by in vitro and in vivo assays and demonstrated to be composed of two small, adjacent DNA sequence elements. The essential determinant of this upstream UAS is a general regulatory factor 1 (GRF1) binding site at nucleotides -513 to -501. A synthetic DNA element comprising this sequence, or an analogue in which two of the degenerate nucleotides of the GRF1 site consensus sequence were altered, activated 5' deleted TDH3 and CYC1 promoters. The second DNA element of the UAS is a 7 bp sequence which is conserved in the promoters of several yeast genes encoding glycolytic enzymes and occurs at positions -486 to -480 of the TDH3 promoter. This DNA sequence represents a novel promoter element: it contains no UAS activity itself, yet potentiates the activity of a GRF1 UAS. The potentiation of the GRF1 UAS by this element occurs when placed upstream from the TATA box of either the TDH3 or CYC1 promoters. The characteristics of this element (termed GPE for GRF1 site potentiator element) indicate that it represents a binding site for a different yeast protein which increases the promoter activation mediated by the GRF1 protein. Site-specific deletion and promoter reconstruction experiments suggest that the entire activation potential of the -676 to -381 region of the TDH3 gene promoter may be accounted for by a combination of the GRF1 site and the GPE.

Optimization of Bacillus alpha-amylase production by Saccharomyces cerevisiae

Production of Bacillus amyloliquefaciens alpha-amylase by Saccharomyces cerevisiae using the multicopy plasmid pAAH5 and ways of improving the yields of secreted enzyme were studied. In standard non-buffered medium, alpha-amylase was rapidly inactivated but stabilization of the pH at 6 led to stable accumulation of alpha-amylase in the culture medium. Removal of 1100 bp of the upstream sequence of the ADH1 promoter present on pAAH5 resulted in delayed but increased alpha-amylase production: 29-fold in selective medium, two-fold in non-selective medium. With the original ADH1 promoter, accumulation of alpha-amylase in the medium started to level off before the cultures reached stationary phase and was very low when exponentially growing cells were transferred from glucose to ethanol. This coincided with the appearance of a mRNA larger than the alpha-amylase messenger. With the shortened promoter, the normal-size alpha-amylase mRNA was detected under all growth conditions and alpha-amylase was efficiently secreted into the medium also late in stationary phase and after transfer to ethanol. Highest total yields of alpha-amylase were obtained with the short promoter in non-selective glucose-containing medium; this may be explained by the greater final cell density obtained. However, the production of alpha-amylase per cell mass was higher in ethanol-containing selective medium. Seventy to eighty per cent of the alpha-amylase activity was secreted into the medium independent of the total amount produced.

Multifunctional DNA-binding proteins mediate concerted transcription activation of yeast ribosomal protein genes

Transcription activation of ribosomal protein genes (rp genes) in yeast is mediated through two different abundant transacting proteins, RAP1 and ABF1. These factors are multifunctional proteins playing a part in diverse cellular processes, all related to cellular growth.

Efficient expression of the Saccharomyces cerevisiae glycolytic gene ADH1 is dependent upon a cis-acting regulatory element (UASRPG) found initially in genes encoding ribosomal proteins

The glycolytic form of alcohol dehydrogenase (ADHI) is encoded by the ADH1 gene of Saccharomyces cerevisiae. We found that efficient expression of the ADH1 gene requires a sequence between bp -635 and -615 with respect to the +1 mRNA start point; removal of this sequence reduced ADH1 mRNA levels 25-fold but did not affect carbon-source regulation. DNaseI footprinting analysis of the ADH1 promoter revealed the specific protection of a perfect match to UASRPG at -630 to -615. UASRPG is thought to be responsible for activation of transcription, via binding of the translation upstream factor (TUF), of genes encoding components of the translational apparatus. In band retardation assays, the promoters for the elongation factor 1 alpha-encoding genes (TEF1 and TEF2) competed for binding of the protein to the copy of UASRPG in the ADH1 promoter. We conclude that TUF is probably involved in activation of the bulk of ADH1 transcription. Further, we propose that TUF has a role in the activation of many or most glycolytic genes. If so, it is essential for efficient expression of a wide variety of functionally disparate products that are required by yeast cells for rapid growth.