- -

Different Mechanisms Confer Gradual Control and Memory at Nutrient- and Stress-Regulated Genes in Yeast

RiuNet: Institutional repository of the Polithecnic University of Valencia

Share/Send to

Cited by

Statistics

Different Mechanisms Confer Gradual Control and Memory at Nutrient- and Stress-Regulated Genes in Yeast

Show full item record

Rienzo, A.; Poveda Huertes, D.; Aydin, S.; Buchler, NE.; Pascual-Ahuir Giner, MD.; Proft, MH. (2015). Different Mechanisms Confer Gradual Control and Memory at Nutrient- and Stress-Regulated Genes in Yeast. Molecular and Cellular Biology. 35(21):3669-3683. doi:10.1128/MCB.00729-15

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/78703

Files in this item

Item Metadata

Title: Different Mechanisms Confer Gradual Control and Memory at Nutrient- and Stress-Regulated Genes in Yeast
Author:
UPV Unit: Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes
Universitat Politècnica de València. Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural - Escola Tècnica Superior d'Enginyeria Agronòmica i del Medi Natural
Issued date:
Abstract:
Cells respond to environmental stimuli by fine-tuned regulation of gene expression. Here we investigated the dose-dependent modulation of gene expression at high temporal resolution in response to nutrient and stress signals ...[+]
Subjects: RNA-polymerase-II , Graded transcriptional responses , Saccharomyces cerevisiae , In-vivo , MAP kinase , Expression program , Nuclear periphery , Oxidative stress , Cellular memory , Osmotic stress
Copyrigths: Reserva de todos los derechos
Source:
Molecular and Cellular Biology. (issn: 0270-7306 ) (eissn: 1098-5549 )
DOI: 10.1128/MCB.00729-15
Publisher:
American Society for Microbiology
Publisher version: http://dx.doi.org/10.1128/MCB.00729-15
Thanks:
This work was supported by grants from Ministerio de Economia y Competitividad (BFU2011-23326), Generalitat de Valencia (ACOMP2011/031), and the NIH Director's New Innovator Award (DP2 OD008654-01). Alessandro Rienzo was ...[+]
Type: Artículo

References

Gasch, A. P., & Werner-Washburne, M. (2002). The genomics of yeast responses to environmental stress and starvation. Functional & Integrative Genomics, 2(4-5), 181-192. doi:10.1007/s10142-002-0058-2

Hahn, S., & Young, E. T. (2011). Transcriptional Regulation inSaccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators. Genetics, 189(3), 705-736. doi:10.1534/genetics.111.127019

Dos Santos, S. C. (2012). Yeast toxicogenomics: genome-wide responses to chemical stresses with impact in environmental health, pharmacology, and biotechnology. Frontiers in Genetics, 3. doi:10.3389/fgene.2012.00063 [+]
Gasch, A. P., & Werner-Washburne, M. (2002). The genomics of yeast responses to environmental stress and starvation. Functional & Integrative Genomics, 2(4-5), 181-192. doi:10.1007/s10142-002-0058-2

Hahn, S., & Young, E. T. (2011). Transcriptional Regulation inSaccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators. Genetics, 189(3), 705-736. doi:10.1534/genetics.111.127019

Dos Santos, S. C. (2012). Yeast toxicogenomics: genome-wide responses to chemical stresses with impact in environmental health, pharmacology, and biotechnology. Frontiers in Genetics, 3. doi:10.3389/fgene.2012.00063

Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., … Brown, P. O. (2000). Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes. Molecular Biology of the Cell, 11(12), 4241-4257. doi:10.1091/mbc.11.12.4241

Martínez-Montañés, F., Pascual-Ahuir, A., & Proft, M. (2010). Toward a Genomic View of the Gene Expression Program Regulated by Osmostress in Yeast. OMICS: A Journal of Integrative Biology, 14(6), 619-627. doi:10.1089/omi.2010.0046

Morano, K. A., Grant, C. M., & Moye-Rowley, W. S. (2011). The Response to Heat Shock and Oxidative Stress in Saccharomyces cerevisiae. Genetics, 190(4), 1157-1195. doi:10.1534/genetics.111.128033

De Nadal, E., Ammerer, G., & Posas, F. (2011). Controlling gene expression in response to stress. Nature Reviews Genetics, 12(12), 833-845. doi:10.1038/nrg3055

Takahashi, S., & Pryciak, P. M. (2008). Membrane Localization of Scaffold Proteins Promotes Graded Signaling in the Yeast MAP Kinase Cascade. Current Biology, 18(16), 1184-1191. doi:10.1016/j.cub.2008.07.050

Cai, L., Dalal, C. K., & Elowitz, M. B. (2008). Frequency-modulated nuclear localization bursts coordinate gene regulation. Nature, 455(7212), 485-490. doi:10.1038/nature07292

Giorgetti, L., Siggers, T., Tiana, G., Caprara, G., Notarbartolo, S., Corona, T., … Natoli, G. (2010). Noncooperative Interactions between Transcription Factors and Clustered DNA Binding Sites Enable Graded Transcriptional Responses to Environmental Inputs. Molecular Cell, 37(3), 418-428. doi:10.1016/j.molcel.2010.01.016

Hao, N., & O’Shea, E. K. (2011). Signal-dependent dynamics of transcription factor translocation controls gene expression. Nature Structural & Molecular Biology, 19(1), 31-39. doi:10.1038/nsmb.2192

Stewart-Ornstein, J., Nelson, C., DeRisi, J., Weissman, J. S., & El-Samad, H. (2013). Msn2 Coordinates a Stoichiometric Gene Expression Program. Current Biology, 23(23), 2336-2345. doi:10.1016/j.cub.2013.09.043

Hao, N., Budnik, B. A., Gunawardena, J., & O’Shea, E. K. (2013). Tunable Signal Processing Through Modular Control of Transcription Factor Translocation. Science, 339(6118), 460-464. doi:10.1126/science.1227299

Lam, F. H., Steger, D. J., & O’Shea, E. K. (2008). Chromatin decouples promoter threshold from dynamic range. Nature, 453(7192), 246-250. doi:10.1038/nature06867

Dolz-Edo, L., Rienzo, A., Poveda-Huertes, D., Pascual-Ahuir, A., & Proft, M. (2013). Deciphering Dynamic Dose Responses of Natural Promoters and Single cis Elements upon Osmotic and Oxidative Stress in Yeast. Molecular and Cellular Biology, 33(11), 2228-2240. doi:10.1128/mcb.00240-13

Sellick, C. A., Campbell, R. N., & Reece, R. J. (2008). Chapter 3 Galactose Metabolism in Yeast—Structure and Regulation of the Leloir Pathway Enzymes and the Genes Encoding Them. International Review of Cell and Molecular Biology, 111-150. doi:10.1016/s1937-6448(08)01003-4

Kumar, P. R., Yu, Y., Sternglanz, R., Johnston, S. A., & Joshua-Tor, L. (2008). NADP Regulates the Yeast GAL Induction System. Science, 319(5866), 1090-1092. doi:10.1126/science.1151903

Thoden, J. B., Ryan, L. A., Reece, R. J., & Holden, H. M. (2008). The Interaction between an Acidic Transcriptional Activator and Its Inhibitor. Journal of Biological Chemistry, 283(44), 30266-30272. doi:10.1074/jbc.m805200200

Egriboz, O., Jiang, F., & Hopper, J. E. (2011). Rapid GAL Gene Switch of Saccharomyces cerevisiae Depends on Nuclear Gal3, Not Nucleocytoplasmic Trafficking of Gal3 and Gal80. Genetics, 189(3), 825-836. doi:10.1534/genetics.111.131839

Jiang, F., Frey, B. R., Evans, M. L., Friel, J. C., & Hopper, J. E. (2009). Gene Activation by Dissociation of an Inhibitor from a Transcriptional Activation Domain. Molecular and Cellular Biology, 29(20), 5604-5610. doi:10.1128/mcb.00632-09

Lavy, T., Kumar, P. R., He, H., & Joshua-Tor, L. (2012). The Gal3p transducer of the GAL regulon interacts with the Gal80p repressor in its ligand-induced closed conformation. Genes & Development, 26(3), 294-303. doi:10.1101/gad.182691.111

Bhaumik, S. R. (2001). SAGA is an essential in vivo target of the yeast acidic activator Gal4p. Genes & Development, 15(15), 1935-1945. doi:10.1101/gad.911401

Brown, C. E. (2001). Recruitment of HAT Complexes by Direct Activator Interactions with the ATM-Related Tra1 Subunit. Science, 292(5525), 2333-2337. doi:10.1126/science.1060214

Jeong, C.-J., Yang, S.-H., Xie, Y., Zhang, L., Johnston, S. A., & Kodadek, T. (2001). Evidence That Gal11 Protein Is a Target of the Gal4 Activation Domain in the Mediator†. Biochemistry, 40(31), 9421-9427. doi:10.1021/bi010011k

Koh, S. S., Ansari, A. Z., Ptashne, M., & Young, R. A. (1998). An Activator Target in the RNA Polymerase II Holoenzyme. Molecular Cell, 1(6), 895-904. doi:10.1016/s1097-2765(00)80088-x

Larschan, E. (2001). The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4. Genes & Development, 15(15), 1946-1956. doi:10.1101/gad.911501

Lemieux, K., & Gaudreau, L. (2004). Targeting of Swi/Snf to the yeast GAL1 UASG requires the Mediator, TAFIIs, and RNA polymerase II. The EMBO Journal, 23(20), 4040-4050. doi:10.1038/sj.emboj.7600416

De Nadal, E., & Posas, F. (2009). Multilayered control of gene expression by stress-activated protein kinases. The EMBO Journal, 29(1), 4-13. doi:10.1038/emboj.2009.346

Proft, M. (2001). Regulation of the Sko1 transcriptional repressor by the Hog1 MAP kinase in response to osmotic stress. The EMBO Journal, 20(5), 1123-1133. doi:10.1093/emboj/20.5.1123

Proft, M., & Struhl, K. (2002). Hog1 Kinase Converts the Sko1-Cyc8-Tup1 Repressor Complex into an Activator that Recruits SAGA and SWI/SNF in Response to Osmotic Stress. Molecular Cell, 9(6), 1307-1317. doi:10.1016/s1097-2765(02)00557-9

Brickner, D. G., Cajigas, I., Fondufe-Mittendorf, Y., Ahmed, S., Lee, P.-C., Widom, J., & Brickner, J. H. (2007). H2A.Z-Mediated Localization of Genes at the Nuclear Periphery Confers Epigenetic Memory of Previous Transcriptional State. PLoS Biology, 5(4), e81. doi:10.1371/journal.pbio.0050081

Kundu, S., Horn, P. J., & Peterson, C. L. (2007). SWI/SNF is required for transcriptional memory at the yeast GAL gene cluster. Genes & Development, 21(8), 997-1004. doi:10.1101/gad.1506607

Kundu, S., & Peterson, C. L. (2010). Dominant Role for Signal Transduction in the Transcriptional Memory of Yeast GAL Genes. Molecular and Cellular Biology, 30(10), 2330-2340. doi:10.1128/mcb.01675-09

Zacharioudakis, I., Gligoris, T., & Tzamarias, D. (2007). A Yeast Catabolic Enzyme Controls Transcriptional Memory. Current Biology, 17(23), 2041-2046. doi:10.1016/j.cub.2007.10.044

Winzeler, E. A. (1999). Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel Analysis. Science, 285(5429), 901-906. doi:10.1126/science.285.5429.901

Ghaemmaghami, S., Huh, W.-K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., … Weissman, J. S. (2003). Global analysis of protein expression in yeast. Nature, 425(6959), 737-741. doi:10.1038/nature02046

Mason, P. B., & Struhl, K. (2003). The FACT Complex Travels with Elongating RNA Polymerase II and Is Important for the Fidelity of Transcriptional Initiation In Vivo. Molecular and Cellular Biology, 23(22), 8323-8333. doi:10.1128/mcb.23.22.8323-8333.2003

Rienzo, A., Pascual-Ahuir, A., & Proft, M. (2012). The use of a real-time luciferase assay to quantify gene expression dynamics in the living yeast cell. Yeast, 29(6), 219-231. doi:10.1002/yea.2905

Alberti, S., Gitler, A. D., & Lindquist, S. (2007). A suite of Gateway®cloning vectors for high-throughput genetic analysis inSaccharomyces cerevisiae. Yeast, 24(10), 913-919. doi:10.1002/yea.1502

Mazo-Vargas, A., Park, H., Aydin, M., & Buchler, N. E. (2014). Measuring fast gene dynamics in single cells with time-lapse luminescence microscopy. Molecular Biology of the Cell, 25(22), 3699-3708. doi:10.1091/mbc.e14-07-1187

Kuras, L., & Struhl, K. (1999). Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme. Nature, 399(6736), 609-613. doi:10.1038/21239

Kvarnström, M., Logg, K., Diez, A., Bodvard, K., & Käll, M. (2008). Image analysis algorithms for cell contour recognition in budding yeast. Optics Express, 16(17), 12943. doi:10.1364/oe.16.012943

Acar, M., Becskei, A., & van Oudenaarden, A. (2005). Enhancement of cellular memory by reducing stochastic transitions. Nature, 435(7039), 228-232. doi:10.1038/nature03524

Acar, M., Pando, B. F., Arnold, F. H., Elowitz, M. B., & van Oudenaarden, A. (2010). A General Mechanism for Network-Dosage Compensation in Gene Circuits. Science, 329(5999), 1656-1660. doi:10.1126/science.1190544

Biggar, S. R. (2001). Cell signaling can direct either binary or graded transcriptional responses. The EMBO Journal, 20(12), 3167-3176. doi:10.1093/emboj/20.12.3167

Gandhi, S. J., Zenklusen, D., Lionnet, T., & Singer, R. H. (2010). Transcription of functionally related constitutive genes is not coordinated. Nature Structural & Molecular Biology, 18(1), 27-34. doi:10.1038/nsmb.1934

Abramczyk, D., Holden, S., Page, C. J., & Reece, R. J. (2011). Interplay of a Ligand Sensor and an Enzyme in Controlling Expression of the Saccharomyces cerevisiae GAL Genes. Eukaryotic Cell, 11(3), 334-342. doi:10.1128/ec.05294-11

Ahmed, S., & Brickner, J. H. (2007). Regulation and epigenetic control of transcription at the nuclear periphery. Trends in Genetics, 23(8), 396-402. doi:10.1016/j.tig.2007.05.009

Babazadeh, R., Adiels, C. B., Smedh, M., Petelenz-Kurdziel, E., Goksör, M., & Hohmann, S. (2013). Osmostress-Induced Cell Volume Loss Delays Yeast Hog1 Signaling by Limiting Diffusion Processes and by Hog1-Specific Effects. PLoS ONE, 8(11), e80901. doi:10.1371/journal.pone.0080901

Miermont, A., Waharte, F., Hu, S., McClean, M. N., Bottani, S., Leon, S., & Hersen, P. (2013). Severe osmotic compression triggers a slowdown of intracellular signaling, which can be explained by molecular crowding. Proceedings of the National Academy of Sciences, 110(14), 5725-5730. doi:10.1073/pnas.1215367110

Proft, M., & Struhl, K. (2004). MAP Kinase-Mediated Stress Relief that Precedes and Regulates the Timing of Transcriptional Induction. Cell, 118(3), 351-361. doi:10.1016/j.cell.2004.07.016

Guan, Q., Haroon, S., Bravo, D. G., Will, J. L., & Gasch, A. P. (2012). Cellular Memory of Acquired Stress Resistance inSaccharomyces cerevisiae. Genetics, 192(2), 495-505. doi:10.1534/genetics.112.143016

Pelet, S., Rudolf, F., Nadal-Ribelles, M., de Nadal, E., Posas, F., & Peter, M. (2011). Transient Activation of the HOG MAPK Pathway Regulates Bimodal Gene Expression. Science, 332(6030), 732-735. doi:10.1126/science.1198851

[-]

This item appears in the following Collection(s)

Show full item record