Reversible, coenzyme-A-mediated inactivation of biosynthetic condensing enzymes in yeast: a possible regulatory mechanism

The metabolic growth limitations of petite cells lacking the mitochondrial genome

Eukaryotic cells can survive the loss of their mitochondrial genome, but consequently suffer from severe growth defects. 'Petite yeasts', characterized by mitochondrial genome loss, are instrumental for studying mitochondrial function and physiology. However, the molecular cause of their reduced growth rate remains an open question. Here we show that petite cells suffer from an insufficient capacity to synthesize glutamate, glutamine, leucine and arginine, negatively impacting their growth. Using a combination of molecular genetics and omics approaches, we demonstrate the evolution of fast growth overcomes these amino acid deficiencies, by alleviating a perturbation in mitochondrial iron metabolism and by restoring a defect in the mitochondrial tricarboxylic acid cycle, caused by aconitase inhibition. Our results hence explain the slow growth of mitochondrial genome-deficient cells with a partial auxotrophy in four amino acids that results from distorted iron metabolism and an inhibited tricarboxylic acid cycle.

The chemical mechanisms of the enzymes in the branched-chain amino acids biosynthetic pathway and their applications

l-Valine, l-isoleucine, and l-leucine are three key proteinogenic amino acids, and they are also the essential amino acids required for mammalian growth, possessing important and to some extent, special physiological and biological functions. Because of the branched structures in their carbon chains, they are also named as branched-chain amino acids (BCAAs). This review will highlight the advance in studies of the enzymes involved in the biosynthetic pathway of BCAAs, concentrating on their chemical mechanisms and applications in screening herbicides and antibacterial agents. The uses of some of these enzymes in lab scale organic synthesis are also discussed.

Overexpression of the peroxin Pex34p suppresses impaired acetate utilization in yeast lacking the mitochondrial aspartate/glutamate carrier Agc1p

PEX34, encoding a peroxisomal protein implicated in regulating peroxisome numbers, was identified as a high copy suppressor, capable of bypassing impaired acetate utilization of agc1∆ yeast. However, improved growth of agc1∆ yeast on acetate is not mediated through peroxisome proliferation. Instead, stress to the endoplasmic reticulum and mitochondria from PEX34 overexpression appears to contribute to enhanced acetate utilization of agc1∆ yeast. The citrate/2-oxoglutarate carrier Yhm2p is required for PEX34 stimulated growth of agc1∆ yeast on acetate medium, suggesting that the suppressor effect is mediated through increased activity of a redox shuttle involving mitochondrial citrate export. Metabolomic analysis also revealed redirection of acetyl-coenzyme A (CoA) from synthetic reactions for amino acids in PEX34 overexpressing yeast. We propose a model in which increased formation of products from the glyoxylate shunt, together with enhanced utilization of acetyl-CoA, promotes the activity of an alternative mitochondrial redox shuttle, partially substituting for loss of yeast AGC1.

A moonlighting metabolic protein influences repair at DNA double-stranded breaks

Catalytically active proteins with divergent dual functions are often described as ‘moonlighting’. In this work we characterize a new, chromatin-based function of Lys20, a moonlighting protein that is well known for its role in metabolism. Lys20 was initially described as homocitrate synthase (HCS), the first enzyme in the lysine biosynthetic pathway in yeast. Its nuclear localization led to the discovery of a key role for Lys20 in DNA damage repair through its interaction with the MYST family histone acetyltransferase Esa1. Overexpression of Lys20 promotes suppression of DNA damage sensitivity of esa1 mutants. In this work, by taking advantage of LYS20 mutants that are active in repair but not in lysine biosynthesis, the mechanism of suppression of esa1 was characterized. First we analyzed the chromatin landscape of esa1 cells, finding impaired histone acetylation and eviction. Lys20 was recruited to sites of DNA damage, and its overexpression promoted enhanced recruitment of the INO80 remodeling complex to restore normal histone eviction at the damage sites. This study improves understanding of the evolutionary, structural and biological relevance of independent activities in a moonlighting protein and links metabolism to DNA damage repair.

Inactivation of homocitrate synthase causes lysine auxotrophy in copper/zinc-containing superoxide dismutase-deficient yeast Schizosaccharomyces pombe

The fission yeast Schizosaccharomyces pombe lacking copper/zinc-containing superoxide dismutase (CuZn-SOD) is auxotrophic for lysine and sulfurous amino acids under aerobic growth conditions. A multicopy suppressor gene (phx1+) that restored the growth of CuZn-SOD-deficient cells on minimal medium was isolated. It encodes a putative DNA-binding protein with a conserved homeobox domain. Overproduction of Phx1 increased the amount of several proteins, and one of those turned out to be a putative homocitrate synthase (HCS) encoded by the lys4+ gene in S. pombe as judged by mass spectrometric analysis. Consistent with this observation, overexpression of the lys4+ gene increased HCS enzyme activity and was sufficient to suppress the lysine requirement of the CuZn-SOD-deficient cells. Enzyme activity and Western blot analyses revealed that the activity and protein level of HCS were dramatically reduced upon depletion of CuZn-SOD. Treatment of exponentially growing S. pombe cells with paraquat, a superoxide generator, caused a decrease in the amount of Lys4 protein as expected. These results led us to conclude that HCS, the first enzyme in the alpha-aminoadipate-mediated pathway for lysine synthesis common in fungi and some bacteria, is a labile target of oxidative stress caused by CuZn-SOD depletion and that its synthesis is positively regulated by the putative transcriptional regulator Phx1.

Regulatory mechanism of histidine-tagged homocitrate synthase from Saccharomyces cerevisiae. II. Theory

In this study, rate equations that predict the regulatory kinetic behavior of homocitrate synthase were derived, and simulation of the predicted behavior was carried out over a range of values for the kinetic parameters. The data obtained allow application of the resulting expressions to enzyme systems that exhibit activation and inhibition as a result of the interaction of effectors at multiple sites in the free enzyme. Homocitrate synthase was used as an example in terms of its activation by Na+ binding to the active enzyme conformer at an allosteric site, inhibition by binding to the active site, and inhibition by lysine binding to the less active enzyme conformer.

Regulatory mechanism of histidine-tagged homocitrate synthase from Saccharomyces cerevisiae. I. Kinetic studies

Homocitrate synthase (HCS) catalyzes one of the regulated steps of the alpha-aminoadipate pathway for lysine biosynthesis in fungi. The kinetic mechanism of regulation of HCS from Saccharomyces cerevisiae by Na+ and the feedback inhibitor lysine was studied by measuring the initial rate in the absence and presence of the effectors. The data suggest that Na+ is an activator at low concentrations and an inhibitor at high concentrations and that these effects occur as a result of the monovalent ion binding to two different sites in the free enzyme. Inhibition and activation by Na+ can occur simultaneously, with the net rate of the enzyme determined by Na+/K(iNa+) and Na+/K(act), where K(iNa+) and K(act) are the inhibition and activation constants, respectively. The inhibition by Na+ was eliminated at high concentrations of acetyl-CoA, the second substrate bound, but the activation remained. Fluorescence binding studies indicated that lysine bound with high affinity to its binding site as an inhibitor. The inhibition by lysine was competitive versus alpha-ketoglutarate and linear in the physiological range of lysine concentrations up to 5 mm. The effects of Na+ and lysine were independent of one another. A model is developed for regulation of HCS that takes into account all of the effects discussed above.

Stabilization and characterization of histidine-tagged homocitrate synthase from Saccharomyces cerevisiae

Histidine-tagged homocitrate synthase from Saccharomyces cerevisiae was purified to about 98% using a Ni-NTA resin and stabilized using a combination of 100 mM guanidine hydrochloride, 100 mM alpha-cyclodextrin, and 600 mM ammonium sulfate. The enzyme was assayed using dichlorophenol indophenol (DCPIP) as an oxidant to oxidize the CoASH produced in the reaction. A stoichiometry of 1:1 was obtained between DCPIP and CoASH. Kinetic parameters for the stable enzyme at pH 7.5 are: Km (AcCoA), 24 microM: Km (alpha-kg), 1.3 mM; and kcat, 37 min(-1). The enzyme, in the absence of reactants, self-associates, as suggested by size exclusion chromatography. Fluorescence and circular dichroic spectra suggested a partially exposed tryptophan residue and a mixed (alpha/beta) secondary structure for the enzyme. Fluorescence quenching studies with KI, CsCl, and acrylamide suggest that the microenvironment around the single tryptophan residue of the enzyme has some positive charge.

Leucine biosynthesis in fungi: entering metabolism through the back door

After exploring evolutionary aspects of branched-chain amino acid biosynthesis, the review focuses on the extended leucine biosynthetic pathway as it operates in Saccharomyces cerevisiae. First, the genes and enzymes specific for the leucine pathway are considered: LEU4 and LEU9 (encoding the alpha-isopropylmalate synthase isoenzymes), LEU1 (isopropylmalate isomerase), and LEU2 (beta-isopropylmalate dehydrogenase). Emphasis is given to the unusual distribution of the branched-chain amino acid pathway enzymes between mitochondrial matrix and cytosol, on the newly defined role of Leu5p, and on regulatory mechanisms governing gene expression and enzyme activity, including new evidence for the metabolic importance of the regulation of alpha-isopropylmalate synthase by coenzyme A. Next, structure-function relationships of the transcriptional regulator Leu3p are addressed, defining its dual role as activator and repressor and discussing evidence in support of the self-masking model. Recent data pointing at a more extended Leu3p regulon are discussed. An overview of the layered controls of the extended leucine pathway is provided that includes a description of the newly recognized roles of Ilv5p and Bat1p in maintaining mitochondrial integrity. Finally, branched-chain amino acid biosynthesis and its regulation in other fungi are summarized, the question of leucine as metabolic signal is addressed, and possible directions of future research in this area are outlined.

Homocitrate synthase is located in the nucleus in the yeast Saccharomyces cerevisiae

We have generated monoclonal antibodies against nuclear proteins from the yeast Saccharomyces cerevisiae. The monoclonal antibodies react with proteins of 47 and 49 kDa on immunoblots and with partially overlapping sets of proteins on two-dimensional nonequilibrium pH gradient electrophoresis-SDS blots. Immunofluorescence localization shows a nuclear staining pattern. Immunoscreening a yeast expression library yielded five independent full-length clones of two open reading frames from chromosome IV, corresponding to YDL182w (LYS20) and YDL131w in the Saccharomyces genome data base. These two open reading frames are predicted to encode homocitrate synthase isozymes of 47 and 49 kDa, respectively. A clone carrying YDL182w was sequenced in its entirety and directs the expression of a 47-kDa protein in Escherichia coli. A clone carrying YDL131w expresses a 49-kDa protein in E. coli. Yeast grown in minimal medium plus lysine show significant reductions in nuclear immunofluorescence staining. Cell fractionation studies localize the 47- and 49-kDa proteins to the nucleus. Nuclear fractionation studies reveal that a portion of the 47- and 49-kDa proteins can only be extracted with DNase digestion and high salt. The localization of homocitrate synthase to the nucleus is unexpected given previous reports that homocitrate synthase is present in mitochondria and the cytoplasm in S. cerevisiae.

Cloning and sequencing of the LYS1 gene encoding homocitrate synthase in the yeast Yarrowia lipolytica

The alpha-aminoadipate pathway for the biosynthesis of lysine is present only in fungi and euglena. The first step in the pathway is the condensation of acetyl-CoA and alpha-ketoglutarate into homocitrate, and this step is carried out by the enzyme homocitrate synthase (EC 4.1.3.21). In spite of extensive genetic analysis, no mutation affecting this step has been isolated until now in model organisms such as Saccharomyces cerevisiae or Neurospora crassa, although identification of mutations affecting the structural gene (LYS1) for homocitrate synthase was reported in the yeast Yarrowia lipolytica several years ago. Here we used these mutants for the cloning and sequencing of the Yarrowia LYS1 gene. The LYS1 gene encodes a predicted 446 amino acid polypeptide, with a molecular mass of 48442 Da. The Lys1p sequence displays two regions, one near the N-terminal section and the other in the central region, that contain conserved signatures found in prokaryotic homocitrate synthases (nifV genes of Azotobacter vinelandii and Klebsiella pneumoniae), as well as in all alpha-isopropyl malate synthases so far described. A putative mitochondrial targeting signal of 41-45 amino acids is predicted at the N-terminus. The Lys1p sequence shows 84% identity at the amino acid level with the putative product of open reading frame D1298 of S. cerevisiae. Northern blot hybridizations revealed a LYS1 transcript of approximately 1.7 kb in Y. lipolytica. Deletion of the LYS1 gene resulted in a Lys- phenotype. Our results indicate that we cloned the structural gene for homocitrate synthase in Y. lipolytica, and that the enzyme is encoded by a single gene in this yeast.

Identification of a gene encoding a homocitrate synthase isoenzyme of Saccharomyces cerevisiae

In Saccharomyces cerevisiae, most of the LYS structural genes have been identified except the genes encoding homocitrate synthase and alpha-aminoadipate aminotransferase. Expression of several LYS genes responds to an induction mechanism mediated by the product of LYS14 and an intermediate of the pathway, alpha-aminoadipate semialdehyde (alpha AASA) as an inducer. This activation is modulated by the presence of lysine in the growth medium leading to an apparent repression. Since the first enzyme of the pathway, homocitrate synthase, is feedback inhibited by lysine, it could be a major element in the control of alpha AASA supply. During the sequencing of chromosome IV of S. cerevisiae, the sequence of ORF D1298 showing a significant similarity with the nifV gene of Azotobacter vinelandii was reported. Disruption and overexpression of ORF D1298 demonstrate that this gene, named LYS20, encodes a homocitrate synthase. The disrupted segregants are able to grow on minimal medium and exhibit reduced but significant homocitrate synthase indicating that this activity is catalysed by at least two isoenzymes. We have also shown that the product of LYS20 is responsible for the greater part of the lysine production. The different isoforms are sensitive to inhibition by lysine but only the expression of LYS20 is strongly repressed by lysine. The N-terminal end of homocitrate synthase isoform coded by LYS20 contains no typical mitochondrial targeting sequence, suggesting that this enzyme is not located in the mitochondria.

Homocitrate synthase from Penicillium chrysogenum. Localization, purification of the cytosolic isoenzyme, and sensitivity to lysine

Subcellular fractionation of cell-free extracts obtained by nitrogen cavitation showed that Penicillium chrysogenum Q176 contains a cytosolic as well as a mitochondrial homocitrate synthase activity. The cytosolic isoenzyme was purified about 500-fold, and its kinetic and molecular properties were investigated. Native homocitrate synthase shows a molecular mass of 155 +/- 10 kDa as determined by gel filtration and a pH of 4.9 +/- 0.1 as determined by chromatofocusing. The kinetic behaviour towards 2-oxoglutarate is hyperbolic, with Km = 2.2 mM; with respect to acetyl-CoA the enzyme shows sigmoidal saturation kinetics, with [S]0.5 = 41 microM and h = 2.6. The enzyme was inhibited strongly by L-lysine (Ki = 8 +/- 2 microM; 50% inhibition by 53 microM at 6 mM-2-oxoglutarate), competitively with 2-oxoglutarate, in protamine sulphate-treated and desalted cell-free extracts and in partially purified preparations. The extent of this inhibition was strongly pH-dependent. Both isoenzymes are equally susceptible to inhibition by lysine. The same inhibition pattern is shown by the enzyme from strain D6/1014A, which is a better producer of penicillin than strain Q176.

Mutation affecting the specific regulatory control of lysine biosynthetic enzymes in Saccharomyces cerevisiae

A Saccharomyces cerevisiae mutant which exhibits a considerably increased cellular lysine pool has been isolated and characterized. Assay of enzymes of the lysine and arginine pathways shows that the mutation harboured by this mutant alters the specific repression of lysine but does not influence the general control of amino acid biosynthesis. Because it is recessive to the wild-type allele and acts pleiotropically on the synthesis of several lysine pathway enzymes, this regulatory mutation has been denominated lys80-1 (or lysR--1). It is believed to affect the synthesis or the structure of a factor which plays a negative role in the control of LYS gene expression.

alpha-Aminoadipate pathway for the biosynthesis of lysine in lower eukaryotes

Bacteria and green plants use the diaminopimelate pathway for the biosynthesis of the essential amino acid, lysine; however, yeast and other higher fungi use the alpha-aminoadipate (AA) pathway. The AA pathway has been investigated in detail biochemically, genetically, and in terms of regulatory mechanisms in the baker's yeast Saccharomyces cerevisiae. The genetic analysis of lysine auxotrophs of S. cerevisiae revealed that there are more than 12 lysine genes for 8 enzyme-catalyzed steps. Lysine genes are not linked to each other and seven of the genes are mapped on six different linkage groups (chromosomes). The gene-enzyme relationships have been determined for ten of the lysine loci which include two unlinked gene functions required for each of AA reductase (LYS2 and LYS5) and Saccharopine reductase (LYS9 and LYS14). Five of the lysine enzymes are localized in mitochondria and three in cytosol. The lysine pathway of S. cerevisiae is regulated by feedback inhibition and end product repression. Two, and possibly three, of the enzymes exhibit general control of amino acid biosynthesis and at least five of the enzymes coded for, by unlinked genes, are simultaneously depressed in a regulatory (repressor) gene-mutant.

The sub-cellular localisation of pyruvate carboxylase and of some other enzymes in Aspergillus nidulans

The sub-cellular localisation of enzymes has been defined by latency analysis, and fractionation by differential centrifugation, in cell-free extracts prepared from the mycelium of Aspergillus nidulans by growth in the presence of 2-deoxyglucose followed by treatment with a mixture of beta-glucuronidase, sulphatase and beta-glucanase and exposure to N2 cavitation at 5.2 PMa. In such extracts pyruvate carboxylase and NAD-dependent and NADP-dependent glutamate dehydrogenases are exclusively localised in the cytosol whereas all the other enzymes studied have sub-cellular localisation patterns similar to those described for mammalian liver. Electrophoretic analysis has established the presence of unique mitochondrial and cytosolic isoenzymes for many of the enzymes, e.g. NAD--malate dehydrogenase, NADP--isocitrate dehydrogenase, glutamate/oxaloacetate transaminase, fumarase, which show a marked extent of incomplete latency and the presence of significant activity in the mitochondrial and cytosolic fractions prepared by differential centrifugation. A novel method is described for detection of citrate synthase activity following electrophoresis of the cell-free extract. Application of this method confirms the absence of a unique cytosolic isoenzyme of citrate synthase and hence shows that citrate synthase activity detected in the soluble fraction results from damage to the mitochondria during isolation. A scheme is proposed on the basis of these data to describe the organisation of lipid and amino acid synthesis from glucose in an organism which possesses a cytosolic pyruvate carboxylase.

Intramitochondrial ATP and cell functions: yeast cells depleted of intramitochondrial ATP lose the ability to grow and multiply

Cells of the yeast Saccharomyces cerevisiae could be depleted of their intramitochondrial ATP bu culturing on glucose in the presence of antimycin A, which prevents production of ATP in mitochondria, along with bongkrekic acid, which prevents transport of ATP from the cytosol into mitochondria. Alternatively, the depletion could be achieved by culturing respiration-deficient mutants in the presence of bongkrekic acid. The depleted cells of the respiration-deficient mutant did not grow on glucose in a synthetic medium and growth for a few generations was made possible by adding peptone, yeast extract or some amino acids into the medium. The depleted cells did not differ from control cells in their content of amino acids, proteins, nucleic acids and major phospholipids and had preserved the ability to carry on protein and nucleic acid syntheses and to mate to other cells. No conspicuous cytological differences were found between the control and depleted cells. After culturing in a semi-synthetic medium in the presence of bongkrekic acid the cells of the respiration-deficient mutant exhibited almost no cytochrome c in their spectra and their azide-sensitive ATPase activity was drastically reduced. The results suggest that intramitochondrial syntheses of some low-molecular compounds as well as import and/or assembly of some cytoplasmically synthesized mitochondrial proteins into mitochondria may be impaired in cells lacking intramitochondrial ATP and this may be responsible for their inability to grow and multiply.

Regulation of activity and synthesis of N-acetylglutamate synthase from Saccharomyces cerevisiae

Feedback inhibition of N-acetylgutamate synthase in a particulate fraction from Saccharomyces cerevisiae by L-arginine was synergistically enhanced by N-actylglutamate, whereas coenzyme A let to an additive enhancement of arginine inhibition. N-acetylglutamate synthase was not inhibited by polyamines, nor was the enzyme inactivated by incubation in the presence of coenzyme A and zinc ions. Evidence was obtained for the involvement of at least three different regulatory mechanisms in the expression of N-acetylglutamate synthase: arginine-specific repression, glucose repression and general amino acid control. The combined action of these control mechanisms led to a 90-fold variation in the specific activity of the enzyme.

Evidence for mutations in the structural gene for homocitrate synthase in Saccharomycopsis lipolytica

Eight strains devoid of homocitrate synthase activity were found among lysine requiring mutants of the yeast Saccharomycopsis lipolytica. Genetic analysis of these strains showed that they were all affected at the same locus LYS 1. Three lines of evidence suggest that this locus defines a structural gene for homocitrate synthase. First, the mutations show various degrees of intragenic complementation; it could be shown in some cases that the hybrid enzyme formed in vivo displayed modified properties in vitro. Second, reversion of some of these mutations can result in a modified enzyme (desensitized). Third, a feedback mutant of homocitrate synthase was directly isolated from the wild type strain, and shown to carry a single mutation at of near LYS 1. We also present here the first attempts at genetic fine mapping in Saccharomycopsis lipolytica.

Arginine metabolism in Saccharomyces cerevisiae: subcellular localization of the enzymes

Subcellular localization of enzymes of arginine metabolism in Saccharomyces cerevisiae was studied by partial fractionation and stepwise homogenization of spheroplast lysates. These enzymes could clearly be divided into two groups. The first group comprised the five enzymes of the acetylated compound cycle, i.e., acetylglutamate synthase, acetylglutamate kinase, acetylglutamyl-phosphate reductase, acetylornithine aminotransferase, and acetylornithine-glutamate acetyltransferase. These enzymes were exclusively particulate. Comparison with citrate synthase and cytochrome oxidase, and results from isopycnic gradient analysis, suggested that these enzymes were associated with the mitochondria. By contrast, enzymatic activities going from ornithine to arginine, i.e., arginine pathway-specific carbamoylphosphate synthetase, ornithine carbamoyltransferase, argininosuccinate synthetase, and argininosuccinate lyase, and the two first catabolic enzymes, arginase and ornithine aminotransferase, were in the "soluble" fraction of the cell.

alpha-Isopropylmalate synthase from Alcaligenes eutrophus H 16. II. Substrate specificity and kinetics

The purified isopropylmalate synthase of Alcaligenes eutrophus H 16 reacted with the following alpha-keto acids and acyl-coenzyme A derivatives (in the sequence of decreasing affinities): alpha-ketoisovalerate, alpha-keto-n-valerate, alpha-ketobutyrate and pyruvate; acetyl-CoA, propionyl-CoA, butyryl-CoA, malonyl-CoA, valeryl-CoA, and crotonyl0CoA. alpha-Ketoisocaproate, however, is a strong inhibitor of the enzyme. All reactions catalyzed by isopropylmalate synthase were inhibited to the same extent by the endproduct L-leucine. The substrate saturation curves of alpha-ketoisovalerate or other alpha-keto acids and of acetyl-coenzyme A or other acyl-CoA derivatives had intermediary plateau regions; the Hill coefficient alternated between nH-values higher and lower than 1.0, indicating changes from positive to negative and from negative to positive cooperativity for the substrates. The products, isopropylmalate and free coenzyme A, showed competitive inhibition patterns against both substrates (alpha-ketoisovalerate and acetyl-CoA). Free coenzyme A (1 micronM) inactivated the enzyme irreversibly. The 3'-phosphate of coenzyme A and the free carboxyl group of alpha-ketoisovalerate were involved in optimal binding of these substrates, but 3'-dephospho-acetyl-coenzyme A and the methylester of alpha-keto-isovalerate were also converted by this enzyme. A CH3--CH2-grouping of the alpha-keto acids seemed to be necessary for binding this substrate.

Carnitine acetyltransferase: candidate for the transfer of acetyl groups through the mitochondrial membrane of yeast

On the basis of its specific activity and its affinity for acetyl-coenzyme A, carnitine acetyltransferase appears to be the most likely candidate for acetyl group transfer out of yeast mitochondria.