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https://www.readbyqxmd.com/read/27690227/dynamic-control-of-gene-regulatory-logic-by-seemingly-redundant-transcription-factors
#1
Zohreh AkhavanAghdam, Joydeb Sinha, Omar P Tabbaa, Nan Hao
Many transcription factors co-express with their homologs to regulate identical target genes, however the advantages of such redundancies remain elusive. Using single-cell imaging and microfluidics, we study the yeast general stress response transcription factor Msn2 and its seemingly redundant homolog Msn4. We find that gene regulation by these two factors is analogous to logic gate systems. Target genes with fast activation kinetics can be fully induced by either factor, behaving as an 'OR' gate. In contrast, target genes with slow activation kinetics behave as an 'AND' gate, requiring distinct contributions from both factors, upon transient stimulation...
September 30, 2016: ELife
https://www.readbyqxmd.com/read/27628486/costs-benefits-and-redundant-mechanisms-of-adaption-to-chronic-low-dose-stress-in-yeast
#2
Marta Markiewicz-Potoczny, David Lydall
All organisms live in changeable, stressful environments. It has been reported that exposure to low-dose stresses or poisons can improve fitness. However, examining the effects of chronic low-dose chemical exposure is challenging. To address this issue we used temperature sensitive mutations affecting the yeast cell division cycle to induce low-dose stress for 40 generation times, or more. We examined cdc13-1 mutants, defective in telomere function, and cdc15-2 mutants, defective in mitotic kinase activity...
October 17, 2016: Cell Cycle
https://www.readbyqxmd.com/read/27618436/the-9aatad-transactivation-domains-from-gal4-to-p53
#3
Martin Piskacek, Marek Havelka, Martina Rezacova, Andrea Knight
The family of the Nine amino acid Transactivation Domain, 9aaTAD family, comprises currently over 40 members. The 9aaTAD domains are universally recognized by the transcriptional machinery from yeast to man. We had identified the 9aaTAD domains in the p53, Msn2, Pdr1 and B42 activators by our prediction algorithm. In this study, their competence to activate transcription as small peptides was proven. Not surprisingly, we elicited immense 9aaTAD divergence in hundreds of identified orthologs and numerous examples of the 9aaTAD species' convergence...
2016: PloS One
https://www.readbyqxmd.com/read/27478089/attenuation-of-transcriptional-and-signaling-responses-limits-viability-of-%C3%AF-0-saccharomyces-cerevisiae-during-periods-of-glucose-deprivation
#4
R Magnus N Friis, Michael C Schultz
BACKGROUND: The maintenance of viability during periods when a glycolytic carbon source is limited (or absent) is a major obstacle for cells whose mitochondrial DNA (mtDNA) has been damaged or lost. METHODS: We utilized genome wide transcriptional profiling and in gel mobility analyses to examine the transcriptional response and characterize defects in the phosphorylation dependent signaling events that occur during acute glucose starvation in ρ(0) cells that lack mtDNA...
November 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27325672/oma1-links-mitochondrial-protein-quality-control-and-tor-signaling-to-modulate-physiological-plasticity-and-cellular-stress-responses
#5
Iryna Bohovych, Stavroula Kastora, Sara Christianson, Danelle Topil, Heejeong Kim, Teresa Fangman, You J Zhou, Antoni Barrientos, Jaekwon Lee, Alistair J P Brown, Oleh Khalimonchuk
A network of conserved proteases known as the intramitochondrial quality control (IMQC) system is central to mitochondrial protein homeostasis and cellular health. IMQC proteases also appear to participate in establishment of signaling cues for mitochondrion-to-nucleus communication. However, little is known about this process. Here, we show that in Saccharomyces cerevisiae, inactivation of the membrane-bound IMQC protease Oma1 interferes with oxidative-stress responses through enhanced production of reactive oxygen species (ROS) during logarithmic growth and reduced stress signaling via the TORC1-Rim15-Msn2/Msn4 axis...
September 1, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27235439/evidence-for-a-role-for-the-plasma-membrane-in-the-nanomechanical-properties-of-the-cell-wall-as-revealed-by-an-atomic-force-microscopy-study-of-the-response-of-saccharomyces-cerevisiae-to-ethanol-stress
#6
Marion Schiavone, Cécile Formosa-Dague, Carolina Elsztein, Marie-Ange Teste, Helene Martin-Yken, Marcos A De Morais, Etienne Dague, Jean M François
UNLABELLED: A wealth of biochemical and molecular data have been reported regarding ethanol toxicity in the yeast Saccharomyces cerevisiae However, direct physical data on the effects of ethanol stress on yeast cells are almost nonexistent. This lack of information can now be addressed by using atomic force microscopy (AFM) technology. In this report, we show that the stiffness of glucose-grown yeast cells challenged with 9% (vol/vol) ethanol for 5 h was dramatically reduced, as shown by a 5-fold drop of Young's modulus...
August 1, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27092438/ionic-and-thermo-switchable-polymer-masked-mesoporous-silica-drug-nanocarrier-high-drug-loading-capacity-at-10%C3%A2-c-and-fast-drug-release-completion-at-40%C3%A2-c
#7
Mohamed Eltohamy, Jae-Won Seo, Ji-Young Hwang, Won-Cheoul Jang, Hae-Won Kim, Ueon Sang Shin
The preparation of the ideal smart drug-delivery systems were successfully achieved by the in situ co-polymerization of a vinyl group-functionalized mesoporous silica nanoparticle (f-MSN) with 1-butyl-3-vinyl imidazolium bromide (BVIm) and N-isopropylacrylamide (NIPAAm) monomers. The thickness of the capping copolymer layer, poly(NIPAAm-co-BVIm) (p-NIBIm), was controlled at between 2.5nm and 5nm, depending on the monomers/f-MSN ratio in the reaction solution. The finally obtained smart drug-delivery systems are named as p-MSN2...
August 1, 2016: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/26947009/the-signaling-pathways-underlying-starvation-induced-upregulation-of-%C3%AE-mannosidase-ams1-in-saccharomyces-cerevisiae
#8
Midori Umekawa, Masato Ujihara, Kazuki Makishima, Shohei Yamamoto, Hiromu Takematsu, Mamoru Wakayama
BACKGROUND: Cells have evolved the mechanisms to survive nutritional shortages in the environment. In Saccharomyces cerevisiae, α-mannosidase Ams1 is known to play a role in catabolism of N-linked free oligosaccharides in the cytosol. Although, this enzyme is also known to be transported selectively from the cytosol to the vacuoles by autophagy, the physiological significance of this transport has not been clarified. METHODS: To elucidate the regulatory mechanism of the activity of Ams1, we assessed the enzymatic activity of the cell free extract of the wild-type and various gene disruptants under different nutritional conditions...
June 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/26470684/the-c-terminal-region-of-the-hot1-transcription-factor-binds-gggacaaa-related-sequences-in-the-promoter-of-its-target-genes
#9
COMPARATIVE STUDY
Mercè Gomar-Alba, Catarina Amaral, Alejandro Artacho, Giuseppe D'Auria, Catarina Pimentel, Claudina Rodrigues-Pousada, Marcel lí del Olmo
Response to hyperosmotic stress in the yeast Saccharomyces cerevisiae involves the participation of the general stress response mediated by Msn2/4 transcription factors and the HOG pathway. One of the transcription factors activated through this pathway is Hot1, which contributes to the control of the expression of several genes involved in glycerol synthesis and flux, or in other functions related to adaptation to adverse conditions. This work provides new data about the interaction mechanism of this transcription factor with DNA...
December 2015: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/26466562/combinatorial-gene-regulation-by-modulation-of-relative-pulse-timing
#10
Yihan Lin, Chang Ho Sohn, Chiraj K Dalal, Long Cai, Michael B Elowitz
Studies of individual living cells have revealed that many transcription factors activate in dynamic, and often stochastic, pulses within the same cell. However, it has remained unclear whether cells might exploit the dynamic interaction of these pulses to control gene expression. Here, using quantitative single-cell time-lapse imaging of Saccharomyces cerevisiae, we show that the pulsatile transcription factors Msn2 and Mig1 combinatorially regulate their target genes through modulation of their relative pulse timing...
November 5, 2015: Nature
https://www.readbyqxmd.com/read/26446933/condition-specific-genetic-interaction-maps-reveal-crosstalk-between-the-camp-pka-and-the-hog-mapk-pathways-in-the-activation-of-the-general-stress-response
#11
Jenia Gutin, Amit Sadeh, Ayelet Rahat, Amir Aharoni, Nir Friedman
Cells must quickly respond and efficiently adapt to environmental changes. The yeast Saccharomyces cerevisiae has multiple pathways that respond to specific environmental insults, as well as a generic stress response program. The later is regulated by two transcription factors, Msn2 and Msn4, that integrate information from upstream pathways to produce fast, tunable, and robust response to different environmental changes. To understand this integration, we employed a systematic approach to genetically dissect the contribution of various cellular pathways to Msn2/4 regulation under a range of stress and growth conditions...
October 7, 2015: Molecular Systems Biology
https://www.readbyqxmd.com/read/26279577/cis-determinants-of-promoter-threshold-and-activation-timescale
#12
Anders S Hansen, Erin K O'Shea
Although the relationship between DNA cis-regulatory sequences and gene expression has been extensively studied at steady state, how cis-regulatory sequences affect the dynamics of gene induction is not known. The dynamics of gene induction can be described by the promoter activation timescale (AcTime) and amplitude threshold (AmpThr). Combining high-throughput microfluidics with quantitative time-lapse microscopy, we control the activation dynamics of the budding yeast transcription factor, Msn2, and reveal how cis-regulatory motifs in 20 promoter variants of the Msn2-target-gene SIP18 affect AcTime and AmpThr...
August 25, 2015: Cell Reports
https://www.readbyqxmd.com/read/26188548/pka-pho-and-stress-response-pathways-regulate-the-expression-of-udp-glucose-pyrophosphorylase-through-msn2-4-in-budding-yeast
#13
Dae-Gwan Yi, Won-Ki Huh
Ugp1, a UDP-glucose pyrophosphorylase, is essential for various cellular activities in Saccharomyces cerevisiae because its product, UDP-glucose, is a sole glucosyl donor in several metabolic pathways. Here, we report that Msn2/4 play a crucial role in the regulation of UGP1 expression. Msn2/4 bound to three stress response elements in the UGP1 promoter in a protein kinase A (PKA)-dependent manner. Several stresses induced UGP1 transcription, suggesting that the regulation of UGP1 mediated by Msn2/4 is involved in general stress response...
August 19, 2015: FEBS Letters
https://www.readbyqxmd.com/read/26182431/functional-role-of-histone-variant-htz1%C3%A2-in-the-stress-response-to-oleate-in-saccharomyces-cerevisiae
#14
Hongde Liu, Guanghui Li, Lingjie Liu, Yakun Wan
Chromatin structure is implicated in regulating gene transcription in stress response. Transcription factors, transferases and deacetylases, such as multicopy suppressor of SNF1 protein 2 (Msn2), SET domain-containing protein 1 (Set1) and sucrose NonFermenting protein 1 (Snf1), have been identified as key regulators in stress response. In the present study, we reported the dynamics of nucleosome occupancy, Histone Two A Z1 (Htz1) deposition and histone H3 lysine 4 dimethylation (H3K4me2) and histone H3 lysine 79 trimethylation (H3K79me3) in Saccharomyces cerevisiae under oleate stress...
2015: Bioscience Reports
https://www.readbyqxmd.com/read/26162967/a-novel-ras-gtpase-ras3-regulates-conidiation-multi-stress-tolerance-and-virulence-by-acting-upstream-of-hog1-signaling-pathway-in-beauveria-bassiana
#15
Yi Guan, Ding-Yi Wang, Sheng-Hua Ying, Ming-Guang Feng
Two Ras ATPases (Ras1 and Ras2) are well known to regulate antagonistically or cooperatively various cellular events in many fungi. Here we show the significance of a novel Ras homolog (Ras3) for Beauveria bassiana. Ras3 possesses five domains and two GTP/GDP switches typical for Ras family and was proven to localize to plasma membrane despite the position change of a membrane-targeting cysteine in C-terminal CAAX motif. Deletion of ras3 altered temporal transcription pattern of ras1 instead of ras2. Compared with wild-type, Δras3 grew significantly faster in a rich medium but slower in some minimal media, and produced far fewer conidia with impaired quality, which was evident with slower germination, attenuated virulence, reduced thermotolerance and decreased UV-B resistance...
September 2015: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/26158443/high-throughput-microfluidics-to-control-and-measure-signaling-dynamics-in-single-yeast-cells
#16
Anders S Hansen, Nan Hao, Erin K O'Shea
Microfluidics coupled to quantitative time-lapse fluorescence microscopy is transforming our ability to control, measure and understand signaling dynamics in single living cells. Here we describe a pipeline that incorporates multiplexed microfluidic cell culture, automated programmable fluid handling for cell perturbation, quantitative time-lapse microscopy and computational analysis of time-lapse movies. We illustrate how this setup can be used to control the nuclear localization of the budding yeast transcription factor Msn2...
August 2015: Nature Protocols
https://www.readbyqxmd.com/read/26068574/a-genetic-screen-for-saccharomyces-cerevisiae-mutants-that-fail-to-enter-quiescence
#17
Lihong Li, Shawna Miles, Linda L Breeden
Budding yeast begin the transition to quiescence by prolonging G1 and accumulating limited nutrients. They undergo asymmetric cell divisions, slow cellular expansion, acquire significant stress tolerance and construct elaborate cell walls. These morphologic changes give rise to quiescent (Q) cells, which can be distinguished from three other cell types in a stationary phase culture by flow cytometry. We have used flow cytometry to screen for genes that are required to obtain the quiescent cell fraction. We find that cell wall integrity is critical and these genes may help define quiescence-specific features of the cell wall...
August 2015: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/26048894/response-of-yeast-cells-to-high-glucose-involves-molecular-and-physiological-differences-when-compared-to-other-osmostress-conditions
#18
Mercè Gomar-Alba, Ma Ángeles Morcillo-Parra, Marcel Lí Del Olmo
Yeast cells can be affected by several causes of osmotic stress, such as high salt, sorbitol or glucose concentrations. The last condition is particularly interesting during natural processes where this microorganism participates. Response to osmostress requires the HOG (High Osmolarity Glycerol) pathway and several transcription factors, including Hot1, which plays a key role in high glucose concentrations. In this work, we describe how the yeast response to osmotic stress shows differences in accordance with the stress agent responsible for it...
August 2015: FEMS Yeast Research
https://www.readbyqxmd.com/read/26046481/the-transcription-factor-swi4-is-target-for-pka-regulation-of-cell-size-at-the-g1-to-s-transition-in-saccharomyces-cerevisiae
#19
Loredana Amigoni, Sonia Colombo, Fiorella Belotti, Lilia Alberghina, Enzo Martegani
To investigate the specific target of PKA in the regulation of cell cycle progression and cell size we developed a new approach using the yeast strain GG104 bearing a deletion in adenylate cyclase gene and permeable to cAMP ( cyr1Δ, pde2Δ, msn2Δ, msn4Δ). In this strain the PKA activity is absent and can be activated by addition of cAMP in the medium, without any other change of the growth conditions. In the present work we show that the activation of PKA by exogenous cAMP in the GG104 strain exponentially growing in glucose medium caused a marked increase of cell size and perturbation of cell cycle with a transient arrest of cells in G1, followed by an accumulation of cells in G2/M phase with a minimal change in the growth rate...
August 3, 2015: Cell Cycle
https://www.readbyqxmd.com/read/25990582/functional-role-of-histone-variant-htz1-in-the-stress-response-to-oleate-in-saccharomycescerevisiae
#20
Hongde Liu, Guanghui Li, Lingjie Liu, Yakun Wan
BACKGROUND: Chromatin structure is implicated in regulating gene transcription in stressresponse. Transcription factors, transferases, and deacetylases, such as Msn2, Set1, and Snf1,have been identified as key regulators in stress response. Here, we reported the dynamics ofnucleosome occupancy, Htz1 deposition, and histone H3 lysine 4 dimethylation (H3K4me2)and histone H3 lysine 79 trimethylation (H3K79me3) in Saccharomyces cerevisiae underoleate stress. RESULTS: Our results indicated that citrate cycle-associated genes are enhanced and ribosomegenes are repressed during the glucose-oleate shift...
May 20, 2015: Bioscience Reports
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