The effect of amino acids on growth and phosphate metabolism in a prototrophic yeast strain

Determination of the Global Pattern of Gene Expression in Yeast Cells by Intracellular Levels of Guanine Nucleotides

This paper investigates whether, independently of the supply of any specific nutrient, gene transcription responds to the energy status of the cell by monitoring ATP and GTP levels. Short pathways for the inducible and futile consumption of ATP or GTP were engineered into the yeast Saccharomyces cerevisiae, and the effect of an increased demand for these purine nucleotides on gene transcription was analyzed. The resulting changes in transcription were most consistently associated with changes in GTP and GEC levels, although the reprogramming in gene expression during glucose repression is sensitive to adenine nucleotide levels. The results show that GTP levels play a central role in determining how genes act to respond to changes in energy supply and that any comprehensive understanding of the control of eukaryotic gene expression requires the elucidation of how changes in guanine nucleotide abundance are sensed and transduced to alter the global pattern of transcription.

Correlations between gene transcription and the abundance of high-energy purine nucleotides in Saccharomyces cerevisiae have often been noted. However, there has been no systematic investigation of this phenomenon in the absence of confounding factors such as nutrient status and growth rate, and there is little hard evidence for a causal relationship. Whether transcription is fundamentally responsive to prevailing cellular energetic conditions via sensing of intracellular purine nucleotides, independently of specific nutrition, remains an important question. The controlled nutritional environment of chemostat culture revealed a strong correlation between ATP and GTP abundance and the transcription of genes required for growth. Short pathways for the inducible and futile consumption of ATP or GTP were engineered into S. cerevisiae, permitting analysis of the transcriptional effect of an increased demand for these nucleotides. During steady-state growth using the fermentable carbon source glucose, the futile consumption of ATP led to a decrease in intracellular ATP concentration but an increase in GTP and the guanylate energy charge (GEC). Expression of transcripts encoding proteins involved in ribosome biogenesis, and those controlled by promoters subject to SWI/SNF-dependent chromatin remodelling, was correlated with these nucleotide pool changes. Similar nucleotide abundance changes were observed using a nonfermentable carbon source, but an effect on the growth-associated transcriptional programme was absent. Induction of the GTP-cycling pathway had only marginal effects on nucleotide abundance and gene transcription. The transcriptional response of respiring cells to glucose was dampened in chemostats induced for ATP cycling, but not GTP cycling, and this was primarily associated with altered adenine nucleotide levels.

Uridine 5'-polyphosphates (p4U and p5U) and uridine(5')polyphospho(5')nucleosides (Up(n)Ns) can be synthesized by UTP:glucose-1-phosphate uridylyltransferase from Saccharomyces cerevisiae

UTP:glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) from Saccharomyces cerevisiae can transfer the uridylyl moiety from UDP-glucose onto tripolyphosphate (P(3)), tetrapolyphosphate (P(4)), nucleoside triphosphates (p(3)Ns) and nucleoside 5'-polyphosphates (p(4)Ns) forming uridine 5'-tetraphosphate (p(4)U), uridine 5'-pentaphosphate (p(5)U) and dinucleotides, such as Ap(4)U, Cp(4)U, Gp(4)U, Up(4)U, Ap(5)U and Gp(5)U. Unlike UDP-glucose, UDP-galactose was not a UMP donor and ADP was not a UMP acceptor. This is the first example of an enzyme that may be responsible for accumulation of dinucleoside tetraphosphates containing two pyrimidine nucleosides in vivo. Occurrence of such dinucleotides in S. cerevisiae and Escherichia coli has been previously reported (Coste et al., J. Biol. Chem. 262 (1987) 12096-12103).

Plant acquisition of organic nitrogen in boreal forests

Research on plant nitrogen (N) uptake and metabolism has more or less exclusively concerned inorganic N, particularly nitrate. Nevertheless, recent as well as older studies indicate that plants may have access to organic N sources. Laboratory studies have shown that ectomycorrhizal and ericoid mycorrhizal plants can degrade polymeric N and absorb the resulting products. Recent studies have also shown that some non-mycorrhizal plants are able to absorb amino acids. Moreover, amino acid transporters have been shown to be present in both plant roots and in mycorrhizal hyphae. Although both mycorrhizal and non-mycorrhizal plants appear to have a capacity for absorbing a range of organic N compounds, is this capacity realized in the field? Several lines of evidence show that plants are outcompeted by microorganisms for organic N sources. Such studies, however, have not addressed the issue of spatial and temporal separation between plants and microorganisms. Moreover, competition studies have not been able to separate uptake by symbiotic and non-symbiotic microorganisms. Qualitative assessment of organic N uptake by plants has been performed with dual-labelled glycine in several studies. These studies arrive at different conclusions: some indicate that plants do not absorb this organic N source when competing with other organisms in soil, while others conclude that significant fractions of amino acid N are absorbed as intact amino acid. These variable results may reflect species differences in the ability to absorb glycine as well as differences in experimental conditions and analytical techniques. Although theoretical calculations indicate that organic N might add significant amounts of N to plant N uptake, direct quantitative assessment of the fraction of plant N derived from uptake by organic N sources is a challenge for future research.

SHC1, a high pH inducible gene required for growth at alkaline pH in Saccharomyces cerevisiae

In this study, we carried out a large-scale transposon tagging screening to identify genes whose expression is regulated by ambient pH. Of 35,000 transformants, two strains carrying the genes whose expression is strictly dependent on pH of growth medium were identified. One of the genes with 20-fold induction by alkali pH was identified as SHC1 gene in the Yeast Genome Directory and its expression was the highest at alkaline pH and moderately induced by osmotic stress. However, the gene was expressed neither at acidic pH nor by other stress conditions. The haploid mutant with truncated shc1 gene showed growth retardation and an abnormal morphology at alkaline pH. On the other hand, the mutant strain carrying the wild-type SHC1 gene reverted to the mutant phenotype. To confirm that Shc1p is an alkali-inducible protein, a monoclonal antibody to Shc1p was produced. While a 55-kDa protein band appeared on the Western blot of cells grown at alkaline pH, Shc1p was barely detectable on the blots of cells grown in YPD. Our results indicate that yeast cells have an efficient system adapting to large variations in ambient pH and SHC1 is one of the genes required for the growth at alkaline pH.

New aspects of inorganic polyphosphate metabolism and function

The review analyzes the results of recent studies on the biochemistry of high-molecular inorganic poly-phosphates (PolyPs). The data obtained lead to the following main conclusions. PolyPs are polyfunctional compounds. The main role of PolyPs is their participation in the regulation of metabolism both at the genetic and metabolic levels. Among the functions of PolyPs known at present, the most important are the following: phosphate and energy storage; regulation of the levels of ATP and other nucleotide and nucleoside-containing coenzymes; participation in the regulation of homeostasis and storage of inorganic cations and other positively charged solutes in an osmotically inert form; participation in membrane transport processes mediated by poly-beta-Ca2+-hydroxybutyrate complexes; participation in the formation and functions of cell surface structures; control of gene activity; and regulation of activities of the enzymes and enzyme assemblies involved in the metabolism of nucleic acids and other acid biopolymers. However, the functions of PolyPs vary among organisms of different evolutionary levels. The metabolism and functions of PolyPs in each cellular compartment of procaryotes (cell wall, plasma membrane, cytosol) and eucaryotes (nuclei, vacuoles, mitochondria, plasma membrane, cell wall, mitochondria, cytosol) are unique. The synthesis and degradation of PolyPs in the organelles of eucaryotic cells are possibly mediated by different sets of enzymes. This is consistent with of the endosymbiotic hypothesis of eucaryotic cell origin. Some aspects of the biochemistry of high-molecular PolyPs are considered to be of great significance to the approach to biotechnological, ecological and medical problems.

Characterization of the stringent and relaxed responses of Streptococcus equisimilis

The 739-codon rel(Seq) gene of Streptococcus equisimilis H46A is bifunctional, encoding a strong guanosine 3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (ppGppase) and a weaker ribosome-independent ATP:GTP 3'-pyrophosphoryltransferase [(p)ppGpp synthetase]. To analyze the function of this gene, (p)ppGpp accumulation patterns as well as protein and RNA synthesis were compared during amino acid deprivation and glucose exhaustion between the wild type and an insertion mutant carrying a rel(Seq) gene disrupted at codon 216. We found that under normal conditions, both strains contained basal levels of (p)ppGpp. Amino acid deprivation imposed by pseudomonic acid or isoleucine hydroxamate triggered a rel(Seq)-dependent stringent response characterized by rapid (p)ppGpp accumulation at the expense of GTP and abrupt cessation of net RNA accumulation in the wild type but not in the mutant. Tetracycline added to block (p)ppGpp synthesis caused the accumulated (p)ppGpp to degrade rapidly, with a concomitant increase of the GTP pool (decay constant of ppGpp, approximately 0.7 min(-1)). Simultaneous addition of pseudomonic acid and tetracycline to mimic a relaxed response caused wild-type RNA synthesis to proceed at rates approximating those seen under either condition in the mutant. Glucose exhaustion provoked the (p)ppGpp accumulation response in both the wild type and the rel(Seq) insertion mutant, consistent with the block of net RNA accumulation in both strains. Although the source of (p)ppGpp synthesis during glucose exhaustion remains to be determined, these findings reinforce the idea entertained previously that rel(Seq) fulfils functions that reside separately in the paralogous reL4 and spoT genes of Escherichia coli. Analysis of (p)ppGpp accumulation patterns was complicated by finding an unknown phosphorylated compound that comigrated with ppGpp under two standard thin-layer chromatography conditions. Unlike ppGpp, this compound did not adsorb to charcoal and did not accumulate appreciably during isoleucine deprivation. Like ppGpp, the unknown compound did accumulate during energy source starvation.

In situ 31P nuclear magnetic resonance for observation of polyphosphate and catabolite responses of chemostat-cultivated Saccharomyces cerevisiae after alkalinization

The proposed pH buffering and phosphagenic functions of polyphosphate were investigated by subjecting chemostat-cultivated Saccharomyces cerevisiae to alkalinization (NaOH addition) and anaerobiosis. The subsequent changes in intracellular phosphate-containing species were observed in situ by nuclear magnetic resonance (NMR) spectroscopy by using the NMR cultivator we developed. For the alkalinization experiments, changes in catabolite secretion were also measured in parallel experiments. Additionally, a range of potential neutralization capacity was investigated: a dilute culture and concentrated cultures with low or high polyphosphate content. The concentrated cultures displayed increased cytosolic pH and rapid polyphosphate degradation to small chains. The pH changes and extent of polyphosphate degradation depended inversely on initial polyphosphate content. The dilute culture restored extracellular pH rapidly and secreted acetate. The concentrated culture with low polyphosphate reserves also secreted acetate. In contrast to the alkalinization-induced polyphosphate dynamics, anaerobiosis resulted in the complete hydrolysis of polyphosphate to P(i), as opposed to small chains, and reduced cytosolic pH. The results and calculations suggest that the bulk of NMR-observable polyphosphate (vacuolar) degradation to short polymers conceivably contributes to neutralizing added alkalinity. In other circumstances, such as anaerobiosis, degradation serves other functions, such as phosphorylation potential regulation.

Development of yeast strains for the efficient utilisation of starch: evaluation of constructs that express alpha-amylase and glucoamylase separately or as bifunctional fusion proteins

Eight constructions involving the Bacillus subtilis alpha-amylase gene (amyE), a mouse pancreatic alpha-amylase cDNA (AMY2) and an Aspergillus awamori glucoamylase cDNA (glaA) were prepared: three fusion genes, involving one alpha-amylase and the glucoamylase, two double-cassette plasmids (expressing one or other alpha-amylase and the glucoamylase) and three single-cassette plasmids, expressing the individual coding sequences. Following transformation of each plasmid into Saccharomyces cerevisiae, a plate test revealed that the largest starch hydrolysis halo was produced by the strain bearing the B. subtilis alpha-amylase/glucoamylase fusion (BsAAase/GAase), and the smallest halo by the one expressing the mouse pancreatic alpha-amylase/glucoamylase fusion (MAAase/GAase). When assayed for enzymatic activity in liquid medium, the strains bearing the fusion and the double-cassette plasmids involving B. subtilis alpha-amylase and the glucoamylase exhibited both enzymic activities. Moreover, the BsAAase/GAase hybrid was able to adsorb and digest raw starch. The MAAse/GAase fusion protein was found to exhibit only alpha-amylase activity. Finally, the capacity to grow on soluble and corn starch was tested in liquid medium for the strains bearing plasmids coding for the fusion proteins and the separate enzymes. The strain carrying the double-cassette BsAAase + GAase, which produced one of the smallest hydrolysis haloes in the place test, showed the best performance, not only in digesting soluble and corn starch but also in using all of the hydrolysis products for growth. The transformant bearing the BsAAase/GAase fusion was able to grow on soluble starch, but not on corn starch.

Lack of production of (p)ppGpp in Halobacterium volcanii under conditions that are effective in the eubacteria

The stringent halobacterial strain Haloferax volcanii was subjected to a set of physiological conditions different from amino acid starvation that are known to cause production of guanosine polyphosphates [(p)pp Gpp] in eubacteria via the relA-independent (spoT) pathway. The conditions used were temperature upshift, treatment with cyanide, and total starvation. Under none of these conditions were detectable levels of (p)ppGpp observed. This result, in conjunction with our previous finding that (p)ppGpp synthesis does not occur under amino acid starvation, leads to the conclusion that in halobacteria both growth rate control and stringency are probably governed by mechanisms that operate in the absence of ppGpp. During exponential growth, a low level of phosphorylated compounds with electrophoretic mobilities similar, but not identical, to that of (p)ppGpp were observed. The intracellular concentration of these compounds increased considerably during the stationary phase of growth and with all of the treatments used. The compounds were identified as short-chain polyphosphates identical to those found under similar conditions in Saccharomyces cerevisiae.

Functional expression of the yeast Mn-superoxide dismutase gene in Escherichia coli requires deletion of the signal peptide sequence

Oligodeoxyribonucleotide-directed mutagenesis has been used to delete the leader sequence-coding region from the yeast gene specifying Mn-superoxide dismutase and thus enable its expression in Escherichia coli. The deletion of this leader was demonstrated to be an absolute requirement for the synthesis of an active yeast enzyme in the bacterium. Complementation analysis in E. coli has confirmed that the product of the truncated yeast gene is active in vivo as well as in vitro.

A downstream activator sequence regulates the expression of the yeast transposon

The regulation of transcription of the class II yeast transposon Ty 1-17 has been examined using a Ty::LEU2 fusion gene. Deletion analysis has defined a 251 bp region within the coding sequence of the TY A gene which is essential for Ty transcription and is also required for diploid control of Ty expression. This downstream activator sequence (DAS) contains two sequence blocks which show homology to the SV40 enhancer core and three with homology to the diploid-regulation-site from the yeast MAT gene.

Physical separation and functional interaction of Kluyveromyces lactis and Saccharomyces cerevisiae ARS elements derived from killer plasmid DNA

Two DNA fragments which have autonomously replicating sequence (ARS) activity in both Saccharomyces cerevisiae and Kluyveromyces lactis have been isolated from the K. lactis kl killer plasmid. One fragment (Kla1) is 700 base pairs (bp) in length and plasmids carrying it are mitotically unstable in both hosts. In K. lactis, this instability leads to colonies having a 'nibbled' phenotype when grown on selective media and appears to be the result of inefficient plasmid segregation. The other fragment (Kla2) is an artificial junction fragment of 1100 bp which was produced during the cloning procedure. Kla2 has been divided into two sub-fragments Kla2A and Kla2B which have, respectively, ARS activity in K. lactis and S. cerevisiae but not the other species. This indicates that these two closely related yeasts have different sequence requirements for ARS activity. Kla2B contains a perfect match to the S. cerevisiae ARS consensus but Kla2A does not. Both Kla2A and Kla1 share a 10 bp sequence as the sole region of homology between them. This sequence, 5'TCATAATATA3', is tentatively offered as defining the ARS consensus sequence for K. lactis.

An E. coli-yeast shuttle cosmid with positive selection for inserted fragments

We describe the construction of a cosmid cloning vector, pMT555, which allows positive selection for the presence of an inserted DNA fragment. The vector contains sequences which enable its replication and selection in either E. coli or Saccharomyces cerevisiae. We demonstrate that pMT555 may be used for the efficient construction of total genomic banks from small quantities of donor DNA. The positive selection permits the stable maintenance of the cosmid in E. coli and the faithful replication of inserted sequences.

[Nucleoside polyphosphates: occurrence, metabolism and function]

Procaryotes have regulatory systems allowing to vary the metabolism in response to nutritional variations, to reduce the growth, and to start development. Nucleoside polyphosphates are mediators of coordinated alterations of metabolism. In this review, after a brief recall of the characteristics of the stringent response, the occurrence, determinations, and the metabolism of the nucleoside polyphosphates are presented. The representation of the pleiotropic effects includes the regulation of the protein synthesis and of the protein synthesis apparatus, of the protein turnover, of the N- and carbohydrate metabolism, of the formation of cell membranes and cell walls as well as the possible function of the development.

Levels of acid-soluble polyphosphate in growing cultures of Saccharomyces cerevisiae

Short-chain acid-soluble polyphosphates were extracted from growing cultures of Saccharomyces cerevisiae, and the changes in the levels of these compounds were determined. The production of acid-soluble polyphosphates correlated with the mitochondrial activities since it occurred in two bursts in respiration-competent yeast cells and in only one burst in respiration-deficient yeast cells. The possible role of these compounds is discussed.

The metabolic properties of acid soluble polyphosphates in Saccharomyces cerevisiae

Tripolyphosphate was found to be the predominant species of soluble polyphosphate in yeast. Evidence is presented which shows that under normal growth conditions tripolyphosphate had little or no turnover. The amounts of the various polyphosphates decreased as the chain length increased. Tetrapolyphosphate was shown to be synthesized more rapidly than tripolyphosphate. These observations suggest that short chain polyphosphates arise by degradation of longer chain length polyphosphates with tripolyphosphate the ultimate degradation product. During nitrogen starvation, the normal accumulation of tripolyphosphate rapidly ceased even though the cells continued normal growth for at least two hours. After the addition of L-amino acids or (NH4)2SO4 to nitrogen starved cells, there was a dramatic increase in the accumulation of tripolyphosphate and tetrapolyphosphate which occurred at the same time as the increase in growth rate. Implications of this result are discussed in terms of possible functions of polyphosphate.

Incorporation of 32Pi into nucleotides, polyphosphates, and other acid-soluble compounds by Myxococcus xanthus during myxospore formation

When glycerol was used to induce myxospore formation in Myxococcu xanthus in the presence of 32Pi, the label was incorporated into a variety of acid-soluble compounds. Incorporation into ribonucleotides was approximately fivefold greater than in vegetative cells or noninducible mutants grown in glycerol. The label was also incorporated into some unknown compounds and material tentatively identified as guanosine tetraphosphate. Marked accumulation into polyphosphates, which were present mainly in culture supernatants, occurred relatively late during myxospore formation. The kinetics of accumulation of some of these compounds and their distribution into acid-soluble cell extracts and culture supernatants are described and compared with those in vegetative cells and noninducible mutants.