Aging and the survival of quiescent and non-quiescent cells in yeast stationary-phase cultures.

In this chapter, we argue that with careful attention to cell types in stationary-phase cultures of the yeast, S. cerevisiae provide an excellent model system for aging studies and hold much promise in pinpointing the set of causal genes and mechanisms driving aging. Importantly, a more detailed understanding of aging in this single celled organism will also shed light on aging in tissue-complex model organisms such as C. elegans and D. melanogaster. We feel strongly that the relationship between aging in yeast and tissue-complex organisms has been obscured by failure to notice the heterogeneity of stationary-phase cultures and the processes by which distinct cell types arise in these cultures. Although several studies have used yeast stationary-phase cultures for chronological aging, the majority of these studies have assumed that cultures in stationary phase are homogeneously composed of a single cell type. However, genome-scale analyses of yeast stationary-phase cultures have identified two major cell fractions: quiescent and non-quiescent, which we discuss in detail in this chapter. We review evidence that cell populations isolated from these cultures exhibit population-specific phenotypes spanning a range of metabolic and physiological processes including reproductive capacity, apoptosis, differences in metabolic activities, genetic hyper-mutability, and stress responses. The identification, in S. cerevisiae, of multiple sub-populations having differentiated physiological attributes relevant to aging offers an unprecedented opportunity. This opportunity to deeply understand yeast cellular (and population) aging programs will, also, give insight into genomic and metabolic processes in tissue-complex organism, as well as stem cell biology and the origins of differentiation.

Scalable learning of large networks.

Cellular networks inferred from condition-specific microarray data can capture the functional rewiring of cells in response to different environmental conditions. Unfortunately, many algorithms for inferring cellular networks do not scale to whole-genome data with thousands of variables. We propose a novel approach for scalable learning of large networks: cluster and infer networks (CIN). CIN learns network structures in two steps: (a) partition variables into smaller clusters, and (b) learn networks per cluster. We optionally revisit the cluster assignment of variables with poor neighbourhoods. Results on networks with known topologies suggest that CIN has substantial speed benefits, without substantial performance loss. We applied our approach to microarray compendia of glucose-starved yeast cells. The inferred networks had significantly higher number of subgraphs representing meaningful biological dependencies than random graphs. Analysis of subgraphs identified biological processes that agreed well with existing information about yeast populations under glucose starvation, and also implicated novel pathways that were previously not known to be associated with these populations. [Includes supplementary material].

Analysis of the pdx-1 (snz-1/sno-1) region of the Neurospora crassa genome: correlation of pyridoxine-requiring phenotypes with mutations in two structural genes.

We report the analysis of a 36-kbp region of the Neurospora crassa genome, which contains homologs of two closely linked stationary phase genes, SNZ1 and SNO1, from Saccharomyces cerevisiae. Homologs of SNZ1 encode extremely highly conserved proteins that have been implicated in pyridoxine (vitamin B6) metabolism in the filamentous fungi Cercospora nicotianae and in Aspergillus nidulans. In N. crassa, SNZ and SNO homologs map to the region occupied by pdx-1 (pyridoxine requiring), a gene that has been known for several decades, but which was not sequenced previously. In this study, pyridoxine-requiring mutants of N. crassa were found to possess mutations that disrupt conserved regions in either the SNZ or SNO homolog. Previously, nearly all of these mutants were classified as pdx-1. However, one mutant with a disrupted SNO homolog was at one time designated pdx-2. It now appears appropriate to reserve the pdx-1 designation for the N. crassa SNZ homolog and pdx-2 for the SNO homolog. We further report annotation of the entire 36,030-bp region, which contains at least 12 protein coding genes, supporting a previous conclusion of high gene densities (12,000-13,000 total genes) for N. crassa. Among genes in this region other than SNZ and SNO homologs, there was no evidence of shared function. Four of the genes in this region appear to have been lost from the S. cerevisiae lineage.

The highly conserved, coregulated SNO and SNZ gene families in Saccharomyces cerevisiae respond to nutrient limitation.

SNZ1, a member of a highly conserved gene family, was first identified through studies of proteins synthesized in stationary-phase yeast cells. There are three SNZ genes in Saccharomyces cerevisiae, each of which has another highly conserved gene, named SNO (SNZ proximal open reading frame), upstream. The DNA sequences and relative positions of SNZ and SNO genes have been phylogenetically conserved. This report details studies of the expression of the SNZ-SNO gene pairs under various conditions and phenotypic analysis of snz-sno mutants. An analysis of total RNA was used to determine that adjacent SNZ-SNO gene pairs are coregulated. SNZ2/3 and SNO2/3 mRNAs are induced prior to the diauxic shift and decrease in abundance during the postdiauxic phase, when SNZ1 and SNO1 are induced. In snz2 snz3 mutants, SNZ1 mRNA is induced prior to the diauxic shift, when SNZ2/3 mRNAs are normally induced. Under nitrogen-limiting conditions, SNZ1 mRNAs accumulate in tryptophan, adenine, and uracil auxotrophs but not in prototrophic strains, indicating that induction occurs in response to the limitation of specific nutrients. Strains carrying deletions in all SNZ-SNO gene pairs are viable, but snz1 and sno1 mutants are sensitive to 6-azauracil (6-AU), an inhibitor of purine and pyrimidine biosynthetic enzymes, and methylene blue, a producer of singlet oxygen. The conservation of sequence and chromosomal position, the coregulation and pattern of expression of SNZ1 and SNO1 genes, and the sensitivity of snz1 and sno1 mutants to 6-AU support the hypothesis that the associated proteins are part of an ancient response to nutrient limitation.

Yeast bcy1 mutants with stationary phase-specific defects.

Entry into the stationary phase requires the yeast BCY1 gene, which encodes the regulatory subunit of the cAMP-dependent protein kinase (cAPK). New bcy1 mutants, constructed by in vitro mutagenesis of the 3'-region encoding the cAMP-binding domains, were classified as early or late-acting mutants based on viability studies. The late-acting bcy1 mutants accumulated fewer stationary phase-specific Bcy1p isoforms and had decreased cAPK activity. This late-acting class is novel and dies after 7 days in culture, later than two previously reported stationary phase mutants, ubi4 and ard1.

Expressed sequences from conidial, mycelial, and sexual stages of Neurospora crassa.

In the Neurospora Genome Project at the University of New Mexico, expressed sequence tags (ESTs) corresponding to three stages of the life cycle of the filamentous fungus Neurospora crassa are being analyzed. The results of a pilot project to identify expressed genes and determine their patterns of expression are presented. 1,865 partial complementary DNA (cDNA) sequences for 1,409 clones were determined using single-pass sequencing. Contig analysis allowed the identification of 838 unique ESTs and 156 ESTs present in multiple cDNA clones. For about 34% of the sequences, highly or moderately significant matches to sequences (of known and unknown function) in the NCBI database were detected. Approximately 56% of the ESTs showed no similarity to previously identified genes. Among genes with assigned function, about 43.3% were involved in metabolism, 32.9% in protein synthesis and 8.4% in RNA synthesis. Fewer were involved in defense (6%), cell signalling (3.4%), cell structure (3.4%) and cell division (2.6%).

A stationary-phase gene in Saccharomyces cerevisiae is a member of a novel, highly conserved gene family.

The regulation of cellular growth and proliferation in response to environmental cues is critical for development and the maintenance of viability in all organisms. In unicellular organisms, such as the budding yeast Saccharomyces cerevisiae, growth and proliferation are regulated by nutrient availability. We have described changes in the pattern of protein synthesis during the growth of S. cerevisiae cells to stationary phase (E. K. Fuge, E. L. Braun, and M. Werner-Washburne, J. Bacteriol. 176:5802-5813, 1994) and noted a protein, which we designated Snz1p (p35), that shows increased synthesis after entry into stationary phase. We report here the identification of the SNZ1 gene, which encodes this protein. We detected increased SNZ1 mRNA accumulation almost 2 days after glucose exhaustion, significantly later than that of mRNAs encoded by other postexponential genes. SNZ1-related sequences were detected in phylogenetically diverse organisms by sequence comparisons and low-stringency hybridization. Multiple SNZ1-related sequences were detected in some organisms, including S. cerevisiae. Snz1p was found to be among the most evolutionarily conserved proteins currently identified, indicating that we have identified a novel, highly conserved protein involved in growth arrest in S. cerevisiae. The broad phylogenetic distribution, the regulation of the SNZ1 mRNA and protein in S. cerevisiae, and identification of a Snz protein modified during sporulation in the gram-positive bacterium Bacillus subtilis support the hypothesis that Snz proteins are part of an ancient response that occurs during nutrient limitation and growth arrest.

Stationary phase in Saccharomyces cerevisiae.

Like other microorganisms, the yeast Saccharomyces cerevisiae responds to starvation by arresting growth and entering stationary phase. Because most microorganisms exist under conditions of nutrient limitation, the ability to tolerate starvation is critical for survival. Molecular analyses have identified changes in transcription, translation, and protein modification in stationary-phase cells. At the level of translation, the pattern of newly synthesized proteins in stationary-phase cells is surprisingly similar to the pattern of proteins synthesized during exponential growth. When limited for different nutrients, yeast strains may not enter stationary phase but opt for pathways such as pseudohyphal growth. If nutrient limitation continues, the end-point is likely to be a stationary-phase cell. Based on the results of recent studies, we propose a model for entry into stationary phase in which G(o) arrest is separable from acquisition of the ability to survive long periods of time without added nutrients.

Protein synthesis in long-term stationary-phase cultures of Saccharomyces cerevisiae.

We are interested in characterizing the process of entry into and the maintenance of the stationary phase. To identify proteins that are induced during growth to stationary phase, we examined protein synthesis in long-term stationary-phase cultures using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Although the total rate of protein synthesis declined when growth ceased after the postdiauxic phase, the pattern of proteins synthesized remained similar throughout the experimental period (28 days), except at the diauxic shift. At the diauxic shift most proteins detectable by 2D-PAGE undergo a transient reduction in their relative rate of synthesis that ends when cells resume growth during the postdiauxic phase. We conclude from this that the transient repression of protein synthesis at the diauxic shift is not directly associated with stationary-phase arrest. A number of proteins that are synthesized after exponential phase have been identified by 2D-PAGE. These proteins could be divided into three temporal classes depending upon when their synthesis became detectable. One postexponential protein, designated p35, was induced later than all other proteins, and its relative rate of synthesis increased throughout stationary phase. Unlike most postexponential proteins, p35 was not regulated by heat shock or glucose repression. We also observed that a direct correlation between steady-state mRNA accumulation and protein synthesis for another postexponential protein (Ssa3p) or two closely related constitutive proteins (Ssa1p and Ssa2p) did not exist. We conclude from this result that synthesis of proteins in stationary phase is regulated by mechanisms other than the control of steady-state mRNA accumulation.

Isolation and characterization of AAP1. A gene encoding an alanine/arginine aminopeptidase in yeast.

The yeast AAP1 gene, encoding a putative amino-peptidase, was isolated based on its ability to suppress the temperature-sensitive growth on nonfermentable carbon sources of spr5, a stationary phase regulatory mutant. AAP1 was physically mapped to chromosome VIII between PUT2 and CUP1. Sequence analysis of the AAP1 gene showed a 1581-nucleotide open reading frame capable of encoding a 59-kilodalton protein. The protein encoded by this open reading frame exhibits approximately 40% sequence identity to human, rat, and mouse aminopeptidases. In limited regions, sequence identity between Aap1 and the mammalian aminopeptidases ranges from 53% to 93%. Insertional inactivation of the AAP1 gene resulted in a decrease in glycogen accumulation and the loss of the major band of arginine/alanine aminopeptidase activity. Strains carrying the AAP1 gene on a high copy plasmid show an increase in the major arginine/alanine aminopeptidase activity, a dramatic increase in glycogen accumulation, and an increase in transcription from a vector carrying lacZ fused to the promoter of a gene (SSA3) expressed during post-diauxic and stationary phases of the culture cycle. We conclude that although the AAP1 gene is not essential for viability, the Aap1 protein positively affects glycogen accumulation in yeast.

Stationary phase in the yeast Saccharomyces cerevisiae.

Growth and proliferation of microorganisms such as the yeast Saccharomyces cerevisiae are controlled in part by the availability of nutrients. When proliferating yeast cells exhaust available nutrients, they enter a stationary phase characterized by cell cycle arrest and specific physiological, biochemical, and morphological changes. These changes include thickening of the cell wall, accumulation of reserve carbohydrates, and acquisition of thermotolerance. Recent characterization of mutant cells that are conditionally defective only for the resumption of proliferation from stationary phase provides evidence that stationary phase is a unique developmental state. Strains with mutations affecting entry into and survival during stationary phase have also been isolated, and the mutations have been shown to affect at least seven different cellular processes: (i) signal transduction, (ii) protein synthesis, (iii) protein N-terminal acetylation, (iv) protein turnover, (v) protein secretion, (vi) membrane biosynthesis, and (vii) cell polarity. The exact nature of the relationship between these processes and survival during stationary phase remains to be elucidated. We propose that cell cycle arrest coordinated with the ability to remain viable in the absence of additional nutrients provides a good operational definition of starvation-induced stationary phase.

Heat shock-mediated cell cycle blockage and G1 cyclin expression in the yeast Saccharomyces cerevisiae.

For cells of the yeast Saccharomyces cerevisiae, heat shock causes a transient inhibition of the cell cycle-regulatory step START. We have determined that this heat-induced START inhibition is accompanied by decreased CLN1 and CLN2 transcript abundance and by possible posttranscriptional changes to CLN3 (WHI1/DAF1) cyclin activity. Persistent CLN2 expression from a heterologous promoter or the CLN2-1 or CLN3-1 alleles that are thought to encode cyclin proteins with increased stability eliminated heat-induced START inhibition but did not affect other aspects of the heat shock response. Heat-induced START inhibition was shown to be independent of functions that regulate cyclin activity under other conditions and of transcriptional regulation of SWI4, an activator of cyclin transcription. Cells lacking Bcy1 function and thus without cyclic AMP control of A kinase activity were inhibited for START by heat shock as long as A kinase activity was attenuated by mutation. We suggest that heat shock mediates START blockage through effects on the G1 cyclins.

The translation machinery and 70 kd heat shock protein cooperate in protein synthesis.

The function of the yeast SSB 70 kd heatshock proteins (hsp70s) was investigated by a variety of approaches. The SSB hsp70s (Ssb1/2p) are associated with translating ribosomes. This association is disrupted by puromycin, suggesting that Ssb1/2p may bind directly to the nascent polypeptide. Mutant ssb1 ssb2 strains grow slowly, contain a low number of translating ribosomes, and are hypersensitive to several inhibitors of protein synthesis. The slow growth phenotype of ssb1 ssb2 mutants is suppressed by increased copy number of a gene encoding a novel translation elongation factor 1 alpha (EF-1 alpha)-like protein. We suggest that cytosolic hsp70 aids in the passage of the nascent polypeptide chain through the ribosome in a manner analogous to the role played by organelle-localized hsp70 in the transport of proteins across membranes.

Bcy1, the regulatory subunit of cAMP-dependent protein kinase in yeast, is differentially modified in response to the physiological status of the cell.

The regulatory subunit of cAMP-dependent protein kinase in yeast, encoded by the BCY1 gene, is known to be required under certain conditions such as growth on nonfermentable carbon sources and entry into stationary phase. We have identified novel isoforms of Bcy1 in cells under these conditions. The isoforms are distinguishable by their migration on one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and 2-dimensional nonequilibrium pH gradient gel electrophoresis. The isoforms observed by one-dimensional SDS-PAGE bind cAMP, as determined by [32P]8-azido-cAMP labeling (diagnostic of Bcy1 protein). Proteins isolated from cells grown to stationary phase in rich medium exhibit five antibody-reactive bands, by one-dimensional SDS-PAGE immunoblot analysis, with apparent molecular masses of 50, 52, 55, 59 and 61 kDa. Total Bcy1 protein increases at least 8-fold between exponential and stationary phase. Analysis of proteins from a variety of yeast mutants indicated that 1) many of the observed modifications of Bcy1 are dependent upon the presence of the Ser-145 phosphorylation site; 2) the appearance of the 59- and 61-kDa bands is dependent upon the presence of Yak1 kinase; and 3) Bcy1 protein is modified even in the absence of cAMP-dependent protein kinase catalytic subunits. Cells carrying the bcy1(ala145) allele exhibit non-wild type growth, indicating that these modifications may be functionally significant.

SSC1, an essential member of the yeast HSP70 multigene family, encodes a mitochondrial protein.

SSC1 is an essential member of the yeast HSP70 multigene family (E. Craig, J. Kramer, and J. Kosic-Smithers, Proc. Natl. Acad. Sci. USA 84:4156-4160, 1987). Analysis of the SSC1 DNA sequence revealed that it could encode a 70,627-dalton protein that is more similar to DnaK, an Escherichia coli hsp70 protein, than other yeast hsp70s whose sequences have been determined. Ssc1p was found to have an amino-terminal extension of 28 amino acids, in comparison with either Ssa1p, another hsp70 yeast protein, or Dnak. This putative leader is rich in basic and hydroxyl amino acids, characteristic of many mitochondrial leader sequences. Ssc1p that was synthesized in vitro could be imported into mitochondria and was cleaved in the process. The imported protein comigrated with an abundant mitochondrial protein that reacted with hsp70-specific antibodies. We conclude that Ssc1p is a mitochondrial protein and that hsp70 proteins perform functions in many compartments of the cell.

Yeast Hsp70 RNA levels vary in response to the physiological status of the cell.

Yeast Hsp70 genes constitute a multigene family in which at least five of the nine members are heat inducible. Hsp70 RNA levels also vary dramatically during stationary arrest and sporulation. During growth to stationary phase, SSB1-SSB2 and SSC1 RNAs decreased in abundance as cell density increased. In contrast, SSA1-SSA2 RNA levels increased before the diauxic shift and then decreased as cells approach stationary phase. SSA3 RNA was detected only after the diauxic shift and accumulated to high levels as cells entered stationary phase. This accumulation was reversed by addition of glucose. Studies with cyr1 mutants indicated that SSA3 RNA accumulation is stimulated by decreasing intracellular cyclic AMP concentrations. When cells were incubated in sporulation medium, most Hsp70 RNAs, with the exception of SSA1-SSA2 RNA, decreased in abundance. This finding contrasted with the SSA1-SSA2 pattern observed during growth to stationary phase. SSA3 RNA was not detected during growth in acetate-based medium but accumulated after several hours. SSA3 RNA accumulation was higher in sporulating cells than in nonsporulating cells and was reversed by addition of glucose.

Expression of members of the Saccharomyces cerevisiae hsp70 multigene family.

The hsp70 multigene family of Saccharomyces cerevisiae is a complex multigene family, composed of members exhibiting complex patterns of regulation. Expression of some members is induced after a heat shock, whereas expression of others is repressed. Some members of the family are expressed during exponential growth. One gene, SSA3, shows an unusual pattern of expression during approach to stationary phase. While most RNAs decrease in abundance, SSA3 RNA levels dramatically increase. The constitutive expression of SSA3 in cells lacking adenylate cyclase activity suggests that cAMP modulates SSA3 expression.

A subfamily of stress proteins facilitates translocation of secretory and mitochondrial precursor polypeptides.

Depletion of a subset of 70K stress proteins in yeast mutants shows that they are involved in the post-translational import of precursor polypeptides into both mitochondria and the lumen of the endoplasmic reticulum. The identification of such a basic function may explain the remarkable evolutionary conservation of the gene family encoding these proteins.

Complex interactions among members of an essential subfamily of hsp70 genes in Saccharomyces cerevisiae.

Saccharomyces cerevisiae contains a large family of genes related to hsp70, the major heat shock-inducible gene of Drosophila melanogaster. One subfamily, identified by sequence homology, contains four genes, SSA1, SSA2, SSA3, and SSA4 (formerly YG100, YG102, YG106, and YG107, respectively). Previous studies showed that strains containing mutations in SSA1 and SSA2 are temperature sensitive for growth. SSA4, which is normally heat inducible and not expressed during vegetative growth, is expressed at high levels in ssa1 ssa2 strains at 23 degrees C. We constructed mutations in SSA3 and SSA4 and analyzed strains carrying mutations in the four genes. Strains carrying mutations in SSA3 SSA4 or SSA3 and SSA4 were indistinguishable from the wild type. However, ssa1 ssa2 ssa4 strains were inviable. SSA3, like SSA4, is a heat-inducible gene that is not normally expressed at 23 degrees C. Nevertheless, an intact copy of SSA3 regulated by the constitutive SSA2 promoter was capable of rescuing a ssa1 ssa2 ssa4 strain. This indicates that SSA3 encodes a functional protein and that the SSA1, SSA2, SSA3, and SSA4 gene products are functionally similar.

Adenine nucleotide translocase-dependent anion transport in pea chloroplasts.

Pea chloroplasts were found to take up actively ATP and ADP and exchange the external nucleotides for internal ones. Using carrier-free [14C]ATP, the rate of nucleotide transport in chloroplasts prepared from 12-14-day-old plants was calculated to be 330 mumol ATP/g chlorophyll/min, and the transport was not affected by light or temperature between 4 and 22 degrees C. Adenine nucleotide uptake was inhibited only slightly by carboxyatractylate, whereas bongkrekic acid was nearly as effective an inhibitor of the translocator in pea chloroplasts as it was in mammalian mitochondria. There was no counter-transport of adenine nucleotides with substrates carried on the phosphate translocator including inorganic phosphate, 3-phosphoglycerate and dihydroxyacetone phosphate. However, internal or external phosphoenolpyruvate, normally considered to be transported on the phosphate carrier in chloroplasts, was able to exchange readily with adenine nucleotides. Furthermore, inorganic pyrophosphate which is not transported by the phosphate carrier initiated efflux of phosphoenolpyruvate as well as ATP from the chloroplast. These findings illustrate some interesting similarities as well as differences between the various plant phosphate and nucleotide transport systems which may relate to their role in photosynthesis.