| Verghese J, et al. (2012) Biology of the Heat Shock Response and Protein Chaperones: Budding Yeast (Saccharomyces cerevisiae) as a Model System. Microbiol Mol Biol Rev 76(2):115-58 |
| Costa V and Moradas-Ferreira P (2001) Oxidative stress and signal transduction in Saccharomyces cerevisiae: insights into ageing, apoptosis and diseases. Mol Aspects Med 22(4-5):217-46 |
| Drobna E, et al. (2012) Overexpression of the YAP1, PDE2, and STB3 genes enhances the tolerance of yeast to oxidative stress induced by 7-chlorotetrazolo[5,1-c]benzo[1,2,4]triazine. FEMS Yeast Res 12(8):958-68 |
| Zheng J, et al. (2010) Epistatic relationships reveal the functional organization of yeast transcription factors. Mol Syst Biol 6():420 |
| Tsuzi D, et al. (2004) Regulation of the yeast phospholipid hydroperoxide glutathione peroxidase GPX2 by oxidative stress is mediated by Yap1 and Skn7. FEBS Lett 565(1-3):148-54 |
| Rojas M, et al. (2008) Selective inhibition of yeast regulons by daunorubicin: a transcriptome-wide analysis. BMC Genomics 9:358 |
| Yazgan O and Krebs JE (2012) Mitochondrial and nuclear genomic integrity after oxidative damage in Saccharomyces cerevisiae. Front Biosci 17():1079-93 |
| Teixeira MC, et al. (2006) Early transcriptional response of Saccharomyces cerevisiae to stress imposed by the herbicide 2,4-dichlorophenoxyacetic acid. FEMS Yeast Res 6(2):230-48 |
| Huebert DJ, et al. (2012) Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators. Mol Cell Biol 32(9):1645-53 |
| Drakulic T, et al. (2005) Involvement of oxidative stress response genes in redox homeostasis, the level of reactive oxygen species, and ageing in Saccharomyces cerevisiae. FEMS Yeast Res 5(12):1215-28 |
| Miller C, et al. (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7():458 |
| Zhao Y, et al. (2008) Development of a Novel Oligonucleotide Array-Based Transcription Factor Assay Platform for Genome-Wide Active Transcription Factor Profiling in Saccharomyces cerevisiae. J Proteome Res 7(3):1315-1325 |
| Lushchak VI (2010) Oxidative stress in yeast. Biochemistry (Mosc) 75(3):281-96 |
| Santos PM, et al. (2009) Insights into yeast adaptive response to the agricultural fungicide mancozeb: a toxicoproteomics approach. Proteomics 9(3):657-70 |
| Wu WS and Chen BS (2009) Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data. Bioinform Biol Insights 1():137-45 |
| Miermont A, et al. (2013) Severe osmotic compression triggers a slowdown of intracellular signaling, which can be explained by molecular crowding. Proc Natl Acad Sci U S A 110(14):5725-30 |
| Babbitt GA (2010) Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene 466(1-2):43-8 |
| Rodrigues-Pousada C, et al. (2005) The yeast stress response. Role of the Yap family of b-ZIP transcription factors. The PABMB Lecture delivered on 30 June 2004 at the 29th FEBS Congress in Warsaw. FEBS J 272(11):2639-47 |
| Zanton SJ and Pugh BF (2006) Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock. Genes Dev 20(16):2250-65 |
| Fry RC, et al. (2005) Genome-wide responses to DNA-damaging agents. Annu Rev Microbiol 59():357-77 |
| Guzy RD, et al. (2007) Mitochondrial complex III is required for hypoxia-induced ROS production and gene transcription in yeast. Antioxid Redox Signal 9(9):1317-28 |
| Ratnakumar S, et al. (2011) Phenomic and transcriptomic analyses reveal that autophagy plays a major role in desiccation tolerance in Saccharomyces cerevisiae. Mol Biosyst 7(1):139-49 |
| Okada N, et al. (2014) Comprehensive analysis of genes involved in the oxidative stress tolerance using yeast heterozygous deletion collection. FEMS Yeast Res 14(3):425-434 |
| Wu WS and Li WH (2008) Identifying gene regulatory modules of heat shock response in yeast. BMC Genomics 9:439 |
| Temple MD, et al. (2005) Complex cellular responses to reactive oxygen species. Trends Cell Biol 15(6):319-26 |
| Horan S, et al. (2006) Transcriptional response to nitrosative stress in Saccharomyces cerevisiae. Yeast 23(7):519-35 |
| Hasan R, et al. (2002) The control of the yeast H2O2 response by the Msn2/4 transcription factors. Mol Microbiol 45(1):233-41 |
| Madeo F and Rockenfeller P (2008) Apoptotic death of ageing yeast. Exp Gerontol 43(10):876-81 |
| Fomenko DE, et al. (2011) Thiol peroxidases mediate specific genome-wide regulation of gene expression in response to hydrogen peroxide. Proc Natl Acad Sci U S A 108(7):2729-34 |
| Chua G, et al. (2006) Identifying transcription factor functions and targets by phenotypic activation. Proc Natl Acad Sci U S A 103(32):12045-50 |
| Elemento O, et al. (2007) A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types. Mol Cell 28(2):337-50 |
| Wang YC and Chen BS (2010) Integrated cellular network of transcription regulations and protein-protein interactions. BMC Syst Biol 4():20 |
| Piper PW, et al. (2006) Preadaptation to efficient respiratory maintenance is essential both for maximal longevity and the retention of replicative potential in chronologically ageing yeast. Mech Ageing Dev 127(9):733-40 |
| Barreto L, et al. (2006) A Peroxisomal Glutathione Transferase of Saccharomyces cerevisiae Is Functionally Related to Sulfur Amino Acid Metabolism. Eukaryot Cell 5(10):1748-59 |
| Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35 |
| Bourges I, et al. (2005) Effect of inhibition of the bc1 complex on gene expression profile in yeast. J Biol Chem 280(33):29743-9 |
| Lai LC, et al. (2006) Metabolic-state-dependent remodeling of the transcriptome in response to anoxia and subsequent reoxygenation in Saccharomyces cerevisiae. Eukaryot Cell 5(9):1468-89 |
| Ernst J, et al. (2007) Reconstructing dynamic regulatory maps. Mol Syst Biol 3():74 |
| Middendorf M, et al. (2004) Predicting genetic regulatory response using classification. Bioinformatics 20 Suppl 1():i232-40 |
| Arino J (2010) Integrative Responses to High pH Stress in S. cerevisiae. OMICS 14(5):517-23 |
| Lopez-Garcia B, et al. (2010) A genomic approach highlights common and diverse effects and determinants of susceptibility on the yeast Saccharomyces cerevisiae exposed to distinct antimicrobial peptides. BMC Microbiol 10():289 |
| Tkach JM, et al. (2012) Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol 14(9):966-76 |
| Gasch AP, et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11(12):4241-57 |
| Ma M and Liu ZL (2010) Quantitative transcription dynamic analysis reveals candidate genes and key regulators for ethanol tolerance in Saccharomyces cerevisiae. BMC Microbiol 10():169 |
| Yu H and Gerstein M (2006) Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A 103(40):14724-31 |
| Lu CC, et al. (2008) Extracting transcription factor binding sites from unaligned gene sequences with statistical models. BMC Bioinformatics 9 Suppl 12:S7 |
| Ayer A, et al. (2012) A genome-wide screen in yeast identifies specific oxidative stress genes required for the maintenance of sub-cellular redox homeostasis. PLoS One 7(9):e44278 |
| Aung-Htut MT, et al. (2012) Oxidative stresses and ageing. Subcell Biochem 57():13-54 |
| Kim IS, et al. (2011) Decarbonylated cyclophilin A Cpr1 protein protects Saccharomyces cerevisiae KNU5377Y when exposed to stress induced by menadione. Cell Stress Chaperones 16(1):1-14 |
| Inoue Y, et al. (2011) Glyoxalase system in yeasts: structure, function, and physiology. Semin Cell Dev Biol 22(3):278-84 |
| Hosiner D, et al. (2009) Arsenic toxicity to Saccharomyces cerevisiae is a consequence of inhibition of the TORC1 kinase combined with a chronic stress response. Mol Biol Cell 20(3):1048-57 |
| Das D, et al. (2011) Potentized homeopathic drug Arsenicum Album 30C positively modulates protein biomarkers and gene expressions in Saccharomyces cerevisae exposed to arsenate. Zhong Xi Yi Jie He Xue Bao 9(7):752-60 |
| Wong CM, et al. (2003) Transcriptional regulation of yeast peroxiredoxin gene TSA2 through Hap1p, Rox1p, and Hap2/3/5p. Free Radic Biol Med 34(5):585-97 |
| Jungwirth H and Kuchler K (2006) Yeast ABC transporters-- a tale of sex, stress, drugs and aging. FEBS Lett 580(4):1131-8 |
| Izawa S, et al. (2007) Msn2p/Msn4p-activation is essential for the recovery from freezing stress in yeast. Biochem Biophys Res Commun 352(3):750-5 |
| Legras JL, et al. (2010) Activation of Two Different Resistance Mechanisms in Saccharomyces cerevisiae upon Exposure to Octanoic and Decanoic Acids. Appl Environ Microbiol 76(22):7526-35 |
| Saxena A and Sitaraman R (2014) Osmoregulation and the human mycobiome. Front Microbiol 5():167 |
| Mazumder A, et al. (2013) Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae. Nucleic Acids Res 41(20):9310-24 |
| Landstetter N, et al. (2010) Functional genomics of drug-induced ion homeostasis identifies a novel regulatory crosstalk of iron and zinc regulons in yeast. OMICS 14(6):651-63 |
| Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8 |
| Lelandais G and Devaux F (2010) Comparative functional genomics of stress responses in yeasts. OMICS 14(5):501-15 |
| Moye-Rowley WS (2003) Regulation of the transcriptional response to oxidative stress in fungi: similarities and differences. Eukaryot Cell 2(3):381-9 |
| Teixeira MC, et al. (2011) A genome-wide perspective on the response and tolerance to food-relevant stresses in Saccharomyces cerevisiae. Curr Opin Biotechnol 22(2):150-156 |
| Nevitt T, et al. (2004) YAP4 gene expression is induced in response to several forms of stress in Saccharomyces cerevisiae. Yeast 21(16):1365-74 |
| Gordan R, et al. (2011) Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol 12(12):R125 |
| Caspeta L, et al. (2015) Modifying Yeast Tolerance to Inhibitory Conditions of Ethanol Production Processes. Front Bioeng Biotechnol 3():184 |
| Boorsma A, et al. (2008) Inferring Condition-Specific Modulation of Transcription Factor Activity in Yeast through Regulon-Based Analysis of Genomewide Expression. PLoS One 3(9):e3112 |
| Murray DB, et al. (2011) Redox regulation in respiring Saccharomyces cerevisiae. Biochim Biophys Acta 1810(10):945-58 |
| Elsztein C, et al. (2011) The resistance of the yeast Saccharomyces cerevisiae to the biocide polyhexamethylene biguanide: involvement of cell wall integrity pathway and emerging role for YAP1. BMC Mol Biol 12(1):38 |
| Toone WM and Jones N (1998) Stress-activated signalling pathways in yeast. Genes Cells 3(8):485-98 |
| Molin M, et al. (2011) Life Span Extension and H(2)O(2) Resistance Elicited by Caloric Restriction Require the Peroxiredoxin Tsa1 in Saccharomyces cerevisiae. Mol Cell 43(5):823-33 |
| Hong SK, et al. (2002) Msn2p/Msn4p act as a key transcriptional activator of yeast cytoplasmic thiol peroxidase II. J Biol Chem 277(14):12109-17 |
| Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294 |
| Rautio JJ, et al. (2007) Monitoring yeast physiology during very high gravity wort fermentations by frequent analysis of gene expression. Yeast 24(9):741-60 |
| Wawrzycka D, et al. (2010) Vmr 1p is a novel vacuolar multidrug resistance ABC transporter in Saccharomyces cerevisiae. FEMS Yeast Res 10(7):828-38 |
| Jimenez A, et al. (2010) The biological activity of the wine anthocyanins delphinidin and petunidin is mediated through Msn2 and Msn4 in Saccharomyces cerevisiae. FEMS Yeast Res 10(7):858-69 |
| Swiecilo A (2016) Cross-stress resistance in Saccharomyces cerevisiae yeast-new insight into an old phenomenon. Cell Stress Chaperones () |
| Fujiwara H, et al. (2013) Significance of sulfiredoxin/peroxiredoxin and mitochondrial respiratory chain in response to and protection from 100% O(2) in Saccharomyces cerevisiae. Mitochondrion 13(1):52-8 |
| Siddharthan R, et al. (2005) PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput Biol 1(7):e67 |
| Maeta K, et al. (2007) Green tea polyphenols function as prooxidants to activate oxidative-stress-responsive transcription factors in yeasts. Appl Environ Microbiol 73(2):572-80 |
| Yu L, et al. (2010) Allicin-induced global gene expression profile of Saccharomyces cerevisiae. Appl Microbiol Biotechnol 88(1):219-29 |
| Jung PP, et al. (2011) Ploidy influences cellular responses to gross chromosomal rearrangements in Saccharomyces cerevisiae. BMC Genomics 12(1):331 |
| Kim IS, et al. (2013) Saccharomyces cerevisiae KNU5377 stress response during high-temperature ethanol fermentation. Mol Cells 35(3):210-8 |
| Koerkamp MG, et al. (2002) Dissection of transient oxidative stress response in Saccharomyces cerevisiae by using DNA microarrays. Mol Biol Cell 13(8):2783-94 |
| Toledano MB, et al. (2013) Functions and cellular compartmentation of the thioredoxin and glutathione pathways in yeast. Antioxid Redox Signal 18(13):1699-711 |
| de la Torre-Ruiz MA, et al. (2010) How budding yeast sense and transduce the oxidative stress signal and the impact in cell growth and morphogenesis. Curr Protein Pept Sci 11(8):669-79 |
| Farrugia G and Balzan R (2012) Oxidative stress and programmed cell death in yeast. Front Oncol 2():64 |
| de Lucena RM, et al. (2012) Participation of CWI, HOG and Calcineurin pathways in the tolerance of Saccharomyces cerevisiae to low pH by inorganic acid. J Appl Microbiol 113(3):629-40 |
| Gessler NN, et al. (2007) Reactive oxygen species in regulation of fungal development. Biochemistry (Mosc) 72(10):1091-109 |
| Kandror O, et al. (2004) Yeast adapt to near-freezing temperatures by STRE/Msn2,4-dependent induction of trehalose synthesis and certain molecular chaperones. Mol Cell 13(6):771-81 |
| Galganska H, et al. (2010) VDAC contributes to mRNA levels in Saccharomyces cerevisiae cells by the intracellular reduction/oxidation state dependent and independent mechanisms. J Bioenerg Biomembr 42(6):483-9 |
| Morano KA, et al. (2012) The response to heat shock and oxidative stress in Saccharomyces cerevisiae. Genetics 190(4):1157-95 |
| Estruch F (2000) Stress-controlled transcription factors, stress-induced genes and stress tolerance in budding yeast. FEMS Microbiol Rev 24(4):469-86 |
| Bussereau F, et al. (2006) The Kluyveromyces lactis repertoire of transcriptional regulators. FEMS Yeast Res 6(3):325-35 |
| Stanhill A, et al. (1999) The yeast ras/cyclic AMP pathway induces invasive growth by suppressing the cellular stress response. Mol Cell Biol 19(11):7529-38 |
| Cardona F, et al. (2012) Phylogenetic origin and transcriptional regulation at the post-diauxic phase of SPI1, in Saccharomyces cerevisiae. Cell Mol Biol Lett 17(3):393-407 |
| Orellana M, et al. (2014) Metabolic and transcriptomic response of the wine yeast Saccharomyces cerevisiae strain EC1118 after an oxygen impulse under carbon-sufficient, nitrogen-limited fermentative conditions. FEMS Yeast Res 14(3):412-424 |
| Alejandro-Osorio AL, et al. (2009) The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress. Genome Biol 10(5):R57 |
| Hong SY, et al. (2013) Oxidative stress-related transcription factors in the regulation of secondary metabolism. Toxins (Basel) 5(4):683-702 |
| Perrone GG, et al. (2008) Reactive oxygen species and yeast apoptosis. Biochim Biophys Acta 1783(7):1354-68 |
| Zhou J, et al. (2009) Loss of cardiolipin leads to longevity defects that are alleviated by alterations in stress response signaling. J Biol Chem 284(27):18106-14 |
| Lushchak VI (2011) Adaptive response to oxidative stress: Bacteria, fungi, plants and animals. Comp Biochem Physiol C Toxicol Pharmacol 153(2):175-90 |
| Lewis JA, et al. (2010) Exploiting Natural Variation in Saccharomyces cerevisiae to Identify Genes for Increased Ethanol Resistance. Genetics 186(4):1197-205 |
| Engelberg D, et al. (2014) Transmembrane signaling in Saccharomyces cerevisiae as a model for signaling in metazoans: state of the art after 25 years. Cell Signal 26(12):2865-78 |
| Bayliak MM, et al. (2014) Concentration-Dependent Effects of Rhodiola Rosea on Long-Term Survival and Stress Resistance of Yeast Saccharomyces Cerevisiae: The Involvement of YAP 1 and MSN2/4 Regulatory Proteins. Dose Response 12(1):93-109 |
| Ye Y, et al. (2009) Gaining insight into the response logic of Saccharomyces cerevisiae to heat shock by combining expression profiles with metabolic pathways. Biochem Biophys Res Commun 385(3):357-62 |
| Wang Y, et al. (2009) Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res 37(18):5943-58 |
| Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12 |
| Inoue Y, et al. (1998) Expression of the glyoxalase I gene of Saccharomyces cerevisiae is regulated by high osmolarity glycerol mitogen-activated protein kinase pathway in osmotic stress response. J Biol Chem 273(5):2977-83 |
| Molin M, et al. (2007) Ionizing radiation induces a Yap1-dependent peroxide stress response in yeast. Free Radic Biol Med 43(1):136-44 |
| Cuellar-Cruz M, et al. (2008) High resistance to oxidative stress in the fungal pathogen Candida glabrata is mediated by a single catalase, Cta1p, and is controlled by the transcription factors Yap1p, Skn7p, Msn2p, and Msn4p. Eukaryot Cell 7(5):814-25 |
| Haugen AC, et al. (2004) Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol 5(12):R95 |
| Fordyce PM, et al. (2010) De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat Biotechnol 28(9):970-5 |
| Yiu G, et al. (2008) Pathways change in expression during replicative aging in Saccharomyces cerevisiae. J Gerontol A Biol Sci Med Sci 63(1):21-34 |