Biosynthesis of branched-chain amino acids in yeast: effect of carbon source on leucine biosynthetic enzymes

Replicative and chronological aging in Saccharomyces cerevisiae

Saccharomyces cerevisiae has directly or indirectly contributed to the identification of arguably more mammalian genes that affect aging than any other model organism. Aging in yeast is assayed primarily by measurement of replicative or chronological life span. Here, we review the genes and mechanisms implicated in these two aging model systems and key remaining issues that need to be addressed for their optimization. Because of its well-characterized genome that is remarkably amenable to genetic manipulation and high-throughput screening procedures, S. cerevisiae will continue to serve as a leading model organism for studying pathways relevant to human aging and disease.

Identification by functional analysis of the gene encoding alpha-isopropylmalate synthase II (LEU9) in Saccharomyces cerevisiae

The function of the open reading frame (ORF) YOR108w of Saccharomyces cerevisiae has been analysed. The deletion of this ORF from chromosome XV did not give an identifiable phenotype. A mutant in which both ORF YOR108w and LEU4 gene have been deleted proved to be leucine auxotrophic and alpha-isopropylmalate synthase (alpha-IPMS)-negative. This mutant recovered alpha-IPMS activity and a Leu(+) phenotype when transformed with a plasmid copy of YOR108w. These data and the sequence homology indicated that YOR108w is the structural gene for alpha-IPMS II, responsible for the residual alpha-IPMS activity found in a leu4Delta strain. The leu4Delta strain appeared to be very sensitive to the leucine analogue trifluoroleucine. In the absence of leucine, its growth was not much impaired in glucose but more on non-fermentable carbon sources.

Cloning and expression analysis of beta-isopropylmalate dehydrogenase from potato

A full-length cDNA clone for beta-isopropylmalate dehydrogenase from potato has been isolated and sequenced. The open reading frame is 1071 bp in length encoding a protein of 357 amino acids which includes a 29 amino acid, putative chloroplastic transit peptide. The amino acid sequence shows 33.3% and 28.6% identity to beta-isopropylmalate dehydrogenases from rape and Bacillus subtilis, respectively. Southern analysis shows that the gene is present in low copy number in potato, and in single copy in tomato and Arabidopsis. The gene is expressed in all tissues of the potato plant and its expression is increased by leucine, and leucine plus threonine, in contrast to the situation in yeast and prokaryotes. The gene is also induced by sucrose in a manner similar to that seen with genes involved in carbohydrate metabolism, which indicates that there may be some interaction at the transcriptional level between genes involved in carbon and nitrogen metabolism.

The upstream activating sequence for L-leucine gene regulation in Saccharomyces cerevisiae

The upstream activating sequence (UAS) conferring leucine-specific regulation of transcription in Saccharomyces cerevisiae was identified by analysis of the LEU2 promoter and by comparison to other genes regulated by leucine. The UAS was localized with deletions and cloned synthetic DNA. Point mutations and sequence rearrangements were used to identify important basepairs and to construct an improved UAS with increased regulation and expression. The improved UAS contains a core ten basepair, GC-rich, palindromic sequence, which is sufficient to confer minimal levels of activation and regulation, within a 36 basepair palindromic sequence which confers maximal activation and regulation. Deletions downstream of the UAS indicated that the UAS must act in conjunction with at least one other site, perhaps a TATAA region, in order to confer high levels of activation. Tandem copies of the UAS in front of LEU2 increased expression and regulation. Tandem UAS elements in trans on a multi-copy 2 mu-based plasmid decreased expression and regulation. These results are consistent with a model that the UAS serves as the DNA-binding site for diffusible activation factor(s), possibly the LEU3 gene product.

Chromatin structure of the 5' flanking region of the yeast LEU2 gene

The chromatin structure of the LEU2 gene and its flanks has been studied by means of nuclease digestion, both with micrococcal nuclease and DNase I. The gene is organized in a array of positioned nucleosomes. Within the promoter region, the nucleosome positioning places the regulatory sequences, putative TATA box and upstream activator sequence outside the nucleosomal cores. The tRNA3Leu gene possesses a characteristic structure and is protected against nucleases. Most of the 5' flank is sensitive to DNase I digestion, although no clear hypersensitive sites were found. The chromatin structure is independent of either the transcriptional state of the gene or the chromosomal or episomal location. Finally, in the plasmid pJDB207, which lacks most of the promoter, we have found that the chromatin structure of the coding region is similar to that of the wild-type allele.

Regulation of isoleucine-valine biosynthesis in Saccharomyces cerevisiae

The threonine deaminase gene (ILV1) of Saccharomyces cerevisiae has been designated "multifunctional" since Bollon (1974) indicated its involvement both in the catalysis of the first step in isoleucine biosynthesis and in the regulation of the isoleucine-valine pathway. Its role in regulation is characterized by a decrease in the activity of the five isoleucine-valine enzymes when cells are grown in the presence of the three branched-chain amino acids, isoleucine, valine and leucine (multivalent repression). We have demonstrated that the regulation of AHA reductoisomerase (encoded by ILV5) and branched-chain amino acid transaminase is unaffected by the deletion of ILV1, subsequently revealing that the two enzymes can be regulated in the absence of threonine deaminase. Both threonine deaminase activity and ILV1 mRNA levels increase in mutants (gcd2 and gcd3) having constitutively depressed levels of enzymes under the general control of amino acid biosynthesis, as well as in response to starvation for tryptophan and branched-chain amino acid imbalance. Thus, the ILV1 gene is under general amino acid control, as is the case for both the ILV5 and the transaminase gene. Multivalent repression of reductoisomerase and transaminase can be observed in mutants defective in general control (gcn and gcd), whereas this is not the case for threonine deaminase. Our analysis suggests that repression effected by general control is not complete in minimal medium. Amino acid dependent regulation of threonine deaminase is only through general control, while the branched-chain amino acid repression of AHA reducto isomerase and the transaminase is caused both by general control and an amino acid-specific regulation.

LEU3 of Saccharomyces cerevisiae encodes a factor for control of RNA levels of a group of leucine-specific genes

Although the majority of genes for amino acid biosynthesis which have been examined are under general amino acid control, LEU1 and LEU2 of Saccharomyces cerevisiae respond specifically to leucine. We report here an analysis of LEU3, a putative leucine-specific regulatory locus. We show that LEU3 is necessary for expression of wild-type levels of LEU1- and LEU2-specific RNAs and, further, that the levels of LEU4-specific transcripts are also affected by LEU3. We cloned LEU3 and showed by DNA sequence analysis that it contained an open reading frame of 886 amino acids. A striking feature of the predicted LEU3 protein was a cluster of acidic amino acids (19 of 20) located in the C-terminal half of the coding region. The protein also had a repeated cysteine motif which was conserved in a number of other yeast proteins implicated in gene regulation. We show that whole-cell extracts contained a LEU3-dependent DNA-binding activity that interacted with the 5' region of LEU2. Subdivision of the LEU2 5' region established that the LEU3-dependent DNA-binding activity interacted with the segment which had the previously reported homology with LEU1.

LEU3 of Saccharomyces cerevisiae encodes a factor for control of RNA levels of a group of leucine-specific genes

Although the majority of genes for amino acid biosynthesis which have been examined are under general amino acid control, LEU1 and LEU2 of Saccharomyces cerevisiae respond specifically to leucine. We report here an analysis of LEU3, a putative leucine-specific regulatory locus. We show that LEU3 is necessary for expression of wild-type levels of LEU1- and LEU2-specific RNAs and, further, that the levels of LEU4-specific transcripts are also affected by LEU3. We cloned LEU3 and showed by DNA sequence analysis that it contained an open reading frame of 886 amino acids. A striking feature of the predicted LEU3 protein was a cluster of acidic amino acids (19 of 20) located in the C-terminal half of the coding region. The protein also had a repeated cysteine motif which was conserved in a number of other yeast proteins implicated in gene regulation. We show that whole-cell extracts contained a LEU3-dependent DNA-binding activity that interacted with the 5' region of LEU2. Subdivision of the LEU2 5' region established that the LEU3-dependent DNA-binding activity interacted with the segment which had the previously reported homology with LEU1.

The general control of amino acid biosynthetic genes in the yeast Saccharomyces cerevisiae

Enzymes in diverse amino acid biosynthetic pathways in Saccharomyces cerevisiae are subject to a general amino acid control in which starvation for any amino acid leads to increased levels of the mRNAs encoding these enzymes. The short nucleotide sequence TGACTC, found nontandemly repeated upstream from the coregulated structural genes, serves as a cis-acting site for positive regulation of transcription. Multiple trans-acting repressors and activators have been identified. Most of these factors act indirectly by regulating the level of an activator encoded by the GCN4 gene. This regulation occurs at the level of GCN4 translation and is mediated by sequences in the long 5' leader of GCN4 mRNA. The GCN4 protein is the most likely candidate for the transcriptional activator that interacts with the TGACTC sequences at the structural genes.

Total deletion of yeast LEU4: further evidence for a second alpha-isopropylmalate synthase and evidence for tight LEU4-MET4 linkage

Using a combination of restriction endonuclease digestion, nuclease BAL 31 treatment, and standard ligation procedures, a 4.4-kb DNA segment that carried the yeast LEU4 gene [encoding alpha-isopropylmalate synthase (IPMS) I] and adjoining sequences was excised from an appropriate plasmid and replaced with the yeast HIS3 gene. The new plasmid was digested to obtain a linear HIS3-carrying fragment flanked by remnants of the LEU4 region. Integrative transformation of a LEU4fbr LEU5+ his3- strain with this fragment resulted in the deletion of the LEU4 gene from the genome of some recipients, as demonstrated by transformant phenotype, genetic analysis and the absence of RNA capable of hybridizing to a LEU4 probe. The leu4 deletion strains remained Leu+. The extract of one such strain contained about 18% of the IPMS activity of wild-type cells. It is concluded that the residual activity is that of a second IPMS (IPMS II) that depends on an intact LEU5 locus. IPMS II was inhibited by leucine, but its sensitivity was about an order of magnitude lower than that of IPMS I. Deletion of the LEU4 region by the method utilized here resulted in an amino acid auxotrophy that could be satisfied by methionine, homocysteine, or cysteine. Complementation tests and genetic analysis demonstrated that the affected gene was MET4. Linkage to MET4 would place the LEU4 gene on the left arm of chromosome XIV.

Expression of galactokinase as a fusion protein in Escherichia coli and Saccharomyces cerevisiae

Plasmids are described that allow fusions between the Escherichia coli galK gene (coding for galactokinase) and any gene of interest. An example is given in which a galK gene, lacking the normal initiator methionine codon, is fused to various segments of the 5' end of the tetR gene of pBR322. The resulting plasmids complemented an E. coli galK mutant, and galactokinase activity was retained despite the addition of up to 250 foreign amino acids to the amino-terminus of the galactokinase polypeptide. In a second experiment, the galK gene was fused to the LEU2 gene of Saccharomyces cerevisiae. The resulting plasmid was able to complement a yeast GAL1-mutant and galactokinase synthesis in yeast was controlled, via the LEU2 regulatory system, by the levels of leucine and threonine in the growth medium. The galK fusion plasmids should facilitate analysis of the control systems of a wide variety of genes in different organisms.

Submitochondrial localization, cell-free synthesis, and mitochondrial import of 2-isopropylmalate synthase of yeast

2-Isopropylmalate synthase (EC 4.1.3.12) of yeast is a mitochondrial enzyme. We now provide evidence showing that a large part of the 2-isopropylmalate synthase activity that is associated with the mitochondria is located in the mitochondrial matrix. In vitro translation of total yeast RNA followed by immunoprecipitation with anti-2-isopropylmalate synthase antibody yields two polypeptides. The larger of these has an apparent molecular weight identical to that of purified 2-isopropylmalate synthase subunit (ca. 65,000). It is incorporated into isolated yeast mitochondria with no detectable change in molecular weight. The import requires energy. The smaller polypeptide migrates to a position corresponding to a molecular weight of 63,000-64,000. It is not taken up by mitochondria. Both polypeptides, which also can be obtained by immunoprecipitation of crude extracts, become labeled when in vitro translation is performed in the presence of N-formyl[35S]methionyl-tRNAf. Mutants with no detectable 2-isopropylmalate synthase activity are deficient in either one or both synthase-related polypeptides. These results are discussed in the light of recent evidence for two 2-isopropylmalate synthase-encoding genes in yeast.

Nucleotide sequence of yeast LEU2 shows 5'-noncoding region has sequences cognate to leucine

The LEU2 structural gene and its regulatory sequences were isolated on a 2200 bp Xho I-Sal I fragment. Sequencing of the 5'-noncoding region showed that at -151 there is an open reading frame of 23 codons of which six are for leucine. The leucine codon usage in this reading frame follows exactly that of other yeast genes. At the carboxy-terminal end and immediately after the peptide reading frame, a 14 bp hairpin (followed by a T-rich segment) can form in the putative mRNA; this arrangement closely resembles an RNA polymerase terminator. These and other features suggest a model for regulation. Preceding this is a gene (which starts at -463) for tRNALeu3, the major tRNALeu isoacceptor. RNA polymerase III transcription start and termination signals flank 5' and 3' ends, respectively, of the structural gene. The features noted above are in the same DNA strand that codes for the LEU2 gene product.

Evidence that alpha-isopropylmalate synthase of Saccharomyces cerevisiae is under the "general" control of amino acid biosynthesis

The specific activity and the immunoreactive amount of alpha-isopropylmalate synthase were more than three times above wild-type values in a Saccharomyces cerevisiae mutant (cdr1) with constitutively derepressed levels of enzymes known to be under the "general" control of amino acid biosynthesis. The specific activity was also higher in lysine- and arginine-leaky strains when these were grown under limiting conditions, and in wild-type cells grown in the presence of 5-methyltryptophan. A low specific activity was found in a mutant (ndr1) unable to derepress enzymes of the general control system. Neither isopropylmalate isomerase nor beta-isopropylmalate dehydrogenase responded to general control signals.

Glucose-induced inactivation of mitochondrial enzymes in the yeast Saccharomyces cerevisiae

1. Addition of glucose induced an inactivation of mitochondrial enzymes in the yeast Saccharomyces cerevisiae containing normal mitochondrial particles. 2. The glucose-induced inactivation of mitochondrial enzymes was inhibited by the presence of cycloheximide. 3. Pepstatin also inhibited the inactivation, but phenylmethanesulphonyl fluoride accelerated the inactivation. 4. The specific activities of fructose 1,6-bisphosphatase and cytoplasmic malate dehydrogenase were decreased on the exposure to glucose, as well as those of the mitochondrial enzymes. However, the glucose-induced inactivation of cytoplasmic enzymes was not inhibited by the presence of pepstatin. 5. The specific activities of hexokinase and phosphofructokinase, which are cytoplasmic enzymes were increased by the addition of glucose, and this effect was not affected by pepstatin. 6. Addition of glucose resulted in an increase in the synthesis of proteins of the mitochondria and the cytosol, and simultaneously in degradation of these mitochondrial and cytoplasmic proteins.

Transposed LEU2 gene of Saccharomyces cerevisiae is regulated normally

The repression of beta-isopropylmalate dehydrogenase, the LEU2 gene product, by leucine and leucine plus threonine was unaffected by the transposition of LEU2 from its original locus on chromosome III to a new locus within the ribosomal deoxyribonucleic acid gene cluster on chromosome XII. Since the expression of the LEU2 gene is probably controlled at a pretranslational level, we conclude that the recombinant plasmid used for transformation carries regulatory information in addition to LEU2 structural information.

The use of phenylmethylsulfonyl fluoride in the study of catabolite inactivation and repression in intact cells of Saccharomyces cervisiae

Catabolite inactivation of fructose-1,6-bisphosphatase, isocitrate lyase, phosphoenolpruvate carboxykinase and malate dehydrogenase in intact cells could be prevented by phenylmethylsulfonyl fluoride added 40 min prior to the addition of glucose. Protein synthesis, fermentative and respiratory activity and catabolite repression were not affected. Elimination of catabolite inactivation by the addition of PMSF revealed that catabolite repression started at different times for different enzyme.

Increased antimetabolite sensitivity with variation of carbon source during growth

In Serratia marcescens, analogs of leucine (norleucine), methionine (alpha-methylmethionine), histidine (3-amino-1,2,4-triazolealanine), tyrosine (p-aminophenylalanine), and tryptophan (7-methylindole) are conditional inhibitors of growth; inhibition occurs during the metabolism of some carbon sources but not with others. A further increase in sensitivity to growth inhibition by these analogs can be accomplished through the use of particular combinations of carbon sources present in the inoculum and in the subsequent analog-containing culture medium. Variable sensitivity to analog-mediated inhibition of growth observed during growth on glucose, glycerol, fructose, or citrate correlated inversely with the intracellular pool sizes of the amino acids cognate to the analogs used. The above-cited results, in conjunction with previous results obtained with Pseudomonas aeruginosa and Bacillus subtilis, involve diverse biochemical pathways and suggest that nutritional manipulation to alter the pattern of carbon flow in microorganisms is a generally useful means to accomplish increased sensitivity to growth inhibition by metabolite analogs.

Effect of glucose starvation on the nicotinamide adenine dinucleotide phosphate-dependent glutamate dehydrogenase of yeast

Yeast cells growing on mineral medium plus ammonia and glucose contained high levels of nicotinamide adenine dinucleotide phosphate-dependent glutamate dehydrogenase activity, as measured in crude extracts. After suspension of cells in fresh medium lacking glucose, there was a loss of the glutamate dehydrogenase activity. Loss of activity was inhibited by 2,4-dinitrophenol, sodium azide, iodoacetic acid, and cycloheximide. The enzyme activity was restored when glucose was added back to the medium, and this recovery was fully prevented in the presence of cycloheximide.

The regulation of glutamate metabolism in Candida utilis. Evidence for two interconvertible forms of NAD-dependent glutamate dehydrogenase

An earlier observation from this laboratory (J. Gen. Microbiol. 64, 423--427) that NAD-dependent glutamate dehydrogenase activity is modulated by rapid inactivation has been extended to show that this mechanism is completely reversible. Changes in properties of the enzyme accompany inactivation and two different forms active (a) and inactive (b) of the enzyme with distinctive properties have been isolated. Incubation of the inactive enzyme with magnesium in vitro produced a rapid increase of activity; this was accompanied by a change in the properties of the enzyme to those of the a form. This control mechanism of enzyme interconversion appears widespread among yeasts. Its probable role in modulating glutamate synthesis and degration is discussed.

Effects of glucose and nitrogen source on the levels of proteinases, peptidases, and proteinase inhibitors in yeast

In Saccharomyces cerevisiae harvested from early exponential growth on glucose-containing media, the specifc activities of proteinases A and B, carboxypeptidase Y, and the inhibitors IA, IB, IC of these three proteinases, respectively, are found to be 10-30% of the specific activities observed in media without glucose, containing acetate as a carbon source; the activities of two aminopeptidases in glucose-grown cells were 30-50% of those in acetate-grown cells. In contrast to fructose-biphosphatase, phosoenolpyruvate carboxykinase, and cytoplasmic malate dehydrogenase, which are inactivated after the addition of glucose to derepressed cells, the proteinases and inhibitors are not inactivated after glucose addition, but appear to be repressed. Growth of the yeast on poor nitrogen sources or starvation for nitrogen results in 2-3 fold increases in the levels of most proteinases and peptidases, but this effect is not observed with glucose as the carbon source.