We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over time for almost every yeast gene, as cells responded to temperature shocks, hydrogen peroxide, the superoxide-generating drug menadione, the sulfhydryl-oxidizing agent diamide, the disulfide-reducing agent dithiothreitol, hyper- and hypo-osmotic shock, amino acid starvation, nitrogen source depletion, and progression into stationary phase. A large set of genes (approximately 900) showed a similar drastic response to almost all of these environmental changes. Additional features of the genomic responses were specialized for specific conditions. Promoter analysis and subsequent characterization of the responses of mutant strains implicated the transcription factors Yap1p, as well as Msn2p and Msn4p, in mediating specific features of the transcriptional response, while the identification of novel sequence elements provided clues to novel regulators. Physiological themes in the genomic responses to specific environmental stresses provided insights into the effects of those stresses on the cell.

/pdf/genomic-expression-programs-in-the-response-of-yeast-cells-4xrnicxf7t.pdf

Genomic expression programs in the response of yeast cells to environmental changes.

https://escholarship.org/content/qt0t31t1k9/qt0t31t1k9.pdf?t=ql3cnf

Dissection of TNF Receptor 1 Effector Functions: JNK Activation Is Not Linked to Apoptosis While NF-κB Activation Prevents Cell Death

Diploid cells of budding yeast produce haploid cells through the developmental program of sporulation, which consists of meiosis and spore morphogenesis DNA microarrays containing nearly every yeast gene were used to assay changes in gene expression during sporulation At least seven distinct temporal patterns of induction were observed The transcription factor Ndt80 appeared to be important for induction of a large group of genes at the end of meiotic prophase Consensus sequences known or proposed to be responsible for temporal regulation could be identified solely from analysis of sequences of coordinately expressed genes The temporal expression pattern provided clues to potential functions of hundreds of previously uncharacterized genes, some of which have vertebrate homologs that may function during gametogenesis

/pdf/the-transcriptional-program-of-sporulation-in-budding-yeast-4oqyqqmn64.pdf

The Transcriptional Program of Sporulation in Budding Yeast

The economics of ribosome biosynthesis in yeast.

The adenoviral oncoprotein E1A induces progression through the cell cycle by binding to the products of the p300/CBP and retinoblastoma gene families. A new cellular p300/CBP-associated factor (P/CAF) having intrinsic histone acetylase activity has been identified that competes with E1A. Exogenous expression of P/CAF in HeLa cells inhibits cell-cycle progression and counteracts the mitogenic activity of E1A. E1A disturbs the normal cellular interaction between p300/CBP and its associated histone acetylase.

A p300/CBP-associated factor that competes with the adenoviral oncoprotein E1A

We describe the identification of a new meiosis-specific gene of Saccharomyces cerevisiae, NDT80. The ndt80 null and point mutants arrest at the pachytene stage of meiosis, with homologs connected by full-length synaptonemal complexes and spindle pole bodies duplicated but unseparated. Meiotic recombination in an ndt80 delta mutant is relatively normal, although commitment to heteroallelic recombination is elevated two- to threefold and crossing over is decreased twofold compared with those of the wild type. ndt80 arrest is not alleviated by mutations in early recombination genes, e.g., SPO11 or RAD50, and thus cannot be attributed to an intermediate block in prophase chromosome metabolism like that observed in several other mutants. The ndt80 mutant phenotype during meiosis most closely resembles that of a cdc28 mutant, which contains a thermolabile p34, the catalytic subunit of maturation-promoting factor. Cloning and molecular analysis reveal that the NDT80 gene maps on the right arm of chromosome VIII between EPT1 and a Phe-tRNA gene, encodes a 627-amino-acid protein which exhibits no significant homology to other known proteins, and is transcribed specifically during middle meiotic prophase. The NDT80 gene product could be a component of the cell cycle regulatory machinery involved in the transition out of pachytene, a participant in an unknown aspect of meiosis sensed by a pachytene checkpoint, or a SPO11- and RAD50-independent component of meiotic chromosomes that is the target of cell cycle signaling.

NDT80, a meiosis-specific gene required for exit from pachytene in Saccharomyces cerevisiae.

https://www.cell.com/cell/pdf/0092-8674(94)90153-8.pdf

The UV response involving the Ras signaling pathway and AP-1 transcription factors is conserved between yeast and mammals.

Yeast ribosomal protein genes are coordinately regulated as a function of cell growth; RNA levels decrease during amino acid starvation but increase following a carbon source upshift. Binding sites for RAP1, a multifunctional transcription factor, are present in nearly all ribosomal protein genes and are associated with growth rate regulation. We show that ribosomal protein mRNA levels are increased twofold in strains that have constitutively high levels of cyclic AMP-dependent protein kinase (protein kinase A [PKA]) activity. The PKA-dependent induction requires RAP1 binding sites, and it reflects increased transcriptional activation by RAP1. Growth-regulated transcription of ribosomal protein genes strongly depends on the ability to regulate PKA activity. Cells with constitutively high PKA levels do not show the transcriptional decrease in response to amino acid starvation. Conversely, in cells with constitutively low PKA activity, ribosomal protein mRNAs levels are lower and largely uninducible upon carbon source upshift. We suggest that modulation of RAP1 transcriptional activity by PKA accounts for growth-regulated expression of ribosomal protein genes.

Protein kinase A mediates growth-regulated expression of yeast ribosomal protein genes by modulating RAP1 transcriptional activity.

The rate at which the TATA-binding protein (TBP) interacts with the TATA element and promotes transcription by RNA polymerase II was determined in yeast cells. A TBP derivative with altered TATA-element specificity was rapidly induced, and transcription from promoters with appropriately mutated TATA elements was measured. Without a functional activator protein, basal transcription was observed only after a lag of several hours. In contrast, GCN4-activated transcription occurred rapidly upon induction of the TBP derivative. These results suggest that accessibility of TBP to the chromatin template in vivo is rate limiting and that activation domains increase recruitment of TBP to the promoter.

http://science.sciencemag.org/content/sci/266/5183/280.full.pdf

Increased recruitment of TATA-binding protein to the promoter by transcriptional activation domains in vivo

it causes cells to become more resistant to themicromanipulationsinvolvedinthepedigreeanal-ysis(Fig.4,BandC).Thus,atransientinductionof NDT80 is sufficient to extend the life span ofreplicatively aged cells.To address how transient induction of Ndt80extends RLS, we monitored age-dependent cel-lular changes after NDT80 induction. NeitherERCs nor Hsp104-eGFP aggregates were re-duced after NDT80 induction, although it is pos-sible that they were reduced at later time points(fig. S8, A and B). Furthermore, NDT80 expres-sion extended life span in the absence of the au-tophagy gene ATG1 (fig. S8C). Together thesefindings suggest that life-span extension can oc-cur in the absence of ERC and Hsp104-aggregateelimination. Although ERCs and Hsp104-eGFPaggregates were not affected by transient NDT80expression, nucleolar morphology was. The per-centage of aged cells with enlarged nucleolar mor-phology decreased after NDT80 induction (Fig. 4,D and E, and fig. S8D). Thus, transient inductionof NDT80 causes a change in nucleolar and/orrDNA structure, which reverts to a state that re-sembles the morphology of young cells.We do not yet know whether NDT80-andsporulation-induced RLS resetting use the samemechanism(s). The findings that NDT80 is nec-essaryforlife-spanextensionduringsporulationand sufficient for life-span extension during veg-etative growth and that nucleolar morphology isaltered under both circumstances suggest that atleast some processes are shared. Irrespective ofthe relation between NDT80- and sporulation-induced RLS resetting, we note that resetting ofRLS provides an opportunity to dissect the mo-lecular causes of aging. For instance, eliminationof Hsp104 aggregates and ERCs seem unlikelyto be required for NDT80-dependent life-spanextension,butchangesinnucleolarfunctionand/orstructure may be important. Intriguingly, rDNAinstability and not ERCs per se appear to causeaging in yeast ( 23), and budding yeast cells elim-inate most of the nucleolar material during sporepackaging (24).It will be interesting to i nvestigate whether ourfindings extend to other species. In Caenorhabditiselegans, a number of longevity mutants exhibita soma-to-germline transformation that contrib-utes to their enhanced survival ( 25). In mice, re-introduction of telomerase rescues the age-relatedphenotypes of telomerase-deficient mice ( 26),which suggests that age-dependent cellular dam-age can be repaired. Our studies suggest that atransient induction of the gametogenesis programin somatic cells removes age-dependent cellulardamage and extends life span. Determining howgametogenesis causes the resetting of life spanwill provide insights into the mechanisms ofaging and could facilitate the development ofstrategies for longevity.

C. Klein

Papers

NDT80, a meiosis-specific gene required for exit from pachytene in Saccharomyces cerevisiae.

The UV response involving the Ras signaling pathway and AP-1 transcription factors is conserved between yeast and mammals.

Protein kinase A mediates growth-regulated expression of yeast ribosomal protein genes by modulating RAP1 transcriptional activity.

Increased recruitment of TATA-binding protein to the promoter by transcriptional activation domains in vivo

A Cell Cycle Phosphoproteome of the Yeast Centrosome