Dynamical Remodeling of the Transcriptome during Short-Term Anaerobiosis in Saccharomyces cerevisiae: Differential Response and Role of Msn2 and/or Msn4 and Other Factors in Galactose and Glucose Media Export

@article{citeulike:1531649, abstract = {In contrast to previous steady-state analyses of the O2-responsive transcriptome, here we examined the dynamics of the response to short-term anaerobiosis (2 generations) in both catabolite-repressed (glucose) and derepressed (galactose) cells, assessed the specific role that Msn2 and Msn4 play in mediating the response, and identified gene networks using a novel clustering approach. Upon shifting cells to anaerobic conditions in galactose medium, there was an acute ([\~{}]10 min) yet transient (<45 min) induction of Msn2- and/or Msn4-regulated genes associated with the remodeling of reserve energy and catabolic pathways during the switch from mixed respiro-fermentative to strictly fermentative growth. Concomitantly, MCB- and SCB-regulated networks associated with the G1/S transition of the cell cycle were transiently down-regulated along with rRNA processing genes containing PAC and RRPE motifs. Remarkably, none of these gene networks were differentially expressed when cells were shifted in glucose, suggesting that a metabolically derived signal arising from the abrupt cessation of respiration, rather than O2 deprivation per se, elicits this "stress response." By [\~{}]0.2 generation of anaerobiosis in both media, more chronic, heme-dependent effects were observed, including the down-regulation of Hap1-regulated networks, derepression of Rox1-regulated networks, and activation of Upc2-regulated ones. Changes in these networks result in the functional remodeling of the cell wall, sterol and sphingolipid metabolism, and dissimilatory pathways required for long-term anaerobiosis. Overall, this study reveals that the acute withdrawal of oxygen can invoke a metabolic state-dependent "stress response" but that acclimatization to oxygen deprivation is a relatively slow process involving complex changes primarily in heme-regulated gene networks. 10.1128/MCB.25.10.4075-4091.2005}, author = {Lai, Liang-Chuan and Kosorukoff, Alexander L. and Burke, Patricia V. and Kwast, Kurt E.}, citeulike-article-id = {1531649}, citeulike-linkout-0 = {http://dx.doi.org/10.1128/MCB.25.10.4075-4091.2005}, citeulike-linkout-1 = {http://mcb.asm.org/cgi/content/abstract/25/10/4075}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/15870279}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=15870279}, day = {15}, doi = {10.1128/MCB.25.10.4075-4091.2005}, journal = {Mol. Cell. Biol.}, keywords = {bioinformatics, biology, gene-expression, genomics}, month = {May}, number = {10}, pages = {4075--4091}, posted-at = {2007-08-03 01:28:23}, priority = {0}, title = {Dynamical Remodeling of the Transcriptome during Short-Term Anaerobiosis in Saccharomyces cerevisiae: Differential Response and Role of Msn2 and/or Msn4 and Other Factors in Galactose and Glucose Media}, url = {http://dx.doi.org/10.1128/MCB.25.10.4075-4091.2005}, volume = {25}, year = {2005} }

TY - JOUR ID - citeulike:1531649 L3 - citeulike-article-id:1531649 N2 - In contrast to previous steady-state analyses of the O2-responsive transcriptome, here we examined the dynamics of the response to short-term anaerobiosis (2 generations) in both catabolite-repressed (glucose) and derepressed (galactose) cells, assessed the specific role that Msn2 and Msn4 play in mediating the response, and identified gene networks using a novel clustering approach. Upon shifting cells to anaerobic conditions in galactose medium, there was an acute ([~]10 min) yet transient (<45 min) induction of Msn2- and/or Msn4-regulated genes associated with the remodeling of reserve energy and catabolic pathways during the switch from mixed respiro-fermentative to strictly fermentative growth. Concomitantly, MCB- and SCB-regulated networks associated with the G1/S transition of the cell cycle were transiently down-regulated along with rRNA processing genes containing PAC and RRPE motifs. Remarkably, none of these gene networks were differentially expressed when cells were shifted in glucose, suggesting that a metabolically derived signal arising from the abrupt cessation of respiration, rather than O2 deprivation per se, elicits this "stress response." By [~]0.2 generation of anaerobiosis in both media, more chronic, heme-dependent effects were observed, including the down-regulation of Hap1-regulated networks, derepression of Rox1-regulated networks, and activation of Upc2-regulated ones. Changes in these networks result in the functional remodeling of the cell wall, sterol and sphingolipid metabolism, and dissimilatory pathways required for long-term anaerobiosis. Overall, this study reveals that the acute withdrawal of oxygen can invoke a metabolic state-dependent "stress response" but that acclimatization to oxygen deprivation is a relatively slow process involving complex changes primarily in heme-regulated gene networks. 10.1128/MCB.25.10.4075-4091.2005 IS - 10 JF - Mol. Cell. Biol. EP - 4091 TI - Dynamical Remodeling of the Transcriptome during Short-Term Anaerobiosis in Saccharomyces cerevisiae: Differential Response and Role of Msn2 and/or Msn4 and Other Factors in Galactose and Glucose Media VL - 25 SP - 4075 KW - bioinformatics KW - biology KW - gene-expression KW - genomics AU - Lai, Liang-Chuan AU - Kosorukoff, Alexander AU - Burke, Patricia AU - Kwast, Kurt PY - 2005/05/15/ UR - http://dx.doi.org/10.1128/MCB.25.10.4075-4091.2005 ER -