A global optimization strategy to identify quantitative design principles for gene expression in yeast adaptation to heat shock

2009 ◽  
pp. 1045-1050 ◽  
Author(s):  
Gonzalo Guillén-Gosálbez ◽  
Carlos Pozo ◽  
Laureano Jiménez ◽  
Albert Sorribas
Keyword(s):  
Gene Expression ◽  
Global Optimization ◽  
Heat Shock ◽  
Design Principles ◽  
Optimization Strategy ◽  
Adaptation To Heat ◽  
Quantitative Design

scholarly journals Metabolic constraints and quantitative design principles in gene expression during adaption of yeast to heat shock

2017 ◽  
Author(s):  
Tania Pereira ◽  
Ester Vilaprinyo ◽  
Gemma Belli ◽  
Enric Herrero ◽  
Baldiri Salvado ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Shock ◽  
Causal Relationships ◽  
Adaptive Responses ◽  
Protein Levels ◽  
Metabolic Adaptations ◽  
Modulation Of Gene Expression ◽  
Quantitative Design ◽  
Do So ◽  
Simplified Kinetic Model

AbstractMicroorganisms evolved adaptive responses that enable them to survive stressful challenges in ever changing environments by adjusting metabolism through the modulation of gene expression, protein levels and activity, and flow of metabolites. More frequent challenges allow natural selection ampler opportunities to select from a larger number of phenotypes that are compatible with survival. Understanding the causal relationships between physiological and metabolic requirements that are needed for cellular stress adaptation and gene expression changes that are used by organisms to achieve those requirements may have a significant impact in our ability to interpret and/or guide evolution.Here, we study those causal relationships during heat shock adaptation in the yeast Saccharomyces cerevisiae. We do so by combining dozens of independent experiments measuring whole genome gene expression changes during stress response with a nonlinear simplified kinetic model of central metabolism.This combination is used to create a quantitative, multidimensional, genotype-to-phenotype mapping of the metabolic and physiological requirements that enable cell survival to the feasible changes in gene expression that modulate metabolism to achieve those requirements. Our results clearly show that the feasible changes in gene expression that enable survival to heat shock are specific for this stress. In addition, they suggest that genetic programs for adaptive responses to desiccation/rehydration and to pH shifts might be selected by physiological requirements that are qualitatively similar, but quantitatively different to those for heat shock adaptation. In contrast, adaptive responses to other types of stress do not appear to be constrained by the same qualitative physiological requirements. Our model also explains at the mechanistic level how evolution might find different sets of changes in gene expression that lead to metabolic adaptations that are equivalent in meeting physiological requirements for survival. Finally, our results also suggest that physiological requirements for heat shock adaptation might be similar between unicellular ascomycetes that live in similar environments. Our analysis is likely to be scalable to other adaptive response and might inform efforts in developing biotechnological applications to manipulate cells for medical, biotechnological, or synthetic biology purposes.

scholarly journals Vibrionaceae core, shell and cloud genes are non-randomly distributed on Chr 1: An hypothesis that links the genomic location of genes with their intracellular placement

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Cecilie Bækkedal Sonnenberg ◽  
Tim Kahlke ◽  
Peik Haugen
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Fast Growth ◽  
Gene Copy ◽  
Distribution Data ◽  
Optimization Strategy ◽  
Gene Distribution ◽  
Fast Growing ◽  
Genomic Location ◽  
Growing Conditions

Abstract Background The genome of Vibrionaceae bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork replication results in higher gene copy numbers and increased expression of genes located close to the origin of replication of Chr 1 (ori1). This is believed to be a growth optimization strategy to satisfy the high demand of essential growth factors during fast growth. The relationship between ori1-proximate growth-related genes and gene expression during fast growth has been investigated by many researchers. However, it remains unclear which other gene categories that are present close to ori1 and if expression of all ori1-proximate genes is increased during fast growth, or if expression is selectively elevated for certain gene categories. Results We calculated the pangenome of all complete genomes from the Vibrionaceae family and mapped the four pangene categories, core, softcore, shell and cloud, to their chromosomal positions. This revealed that core and softcore genes were found heavily biased towards ori1, while shell genes were overrepresented at the opposite part of Chr 1 (i.e., close to ter1). RNA-seq of Aliivibrio salmonicida and Vibrio natriegens showed global gene expression patterns that consistently correlated with chromosomal distance to ori1. Despite a biased gene distribution pattern, all pangene categories contributed to a skewed expression pattern at fast-growing conditions, whereas at slow-growing conditions, softcore, shell and cloud genes were responsible for elevated expression. Conclusion The pangene categories were non-randomly organized on Chr 1, with an overrepresentation of core and softcore genes around ori1, and overrepresentation of shell and cloud genes around ter1. Furthermore, we mapped our gene distribution data on to the intracellular positioning of chromatin described for V. cholerae, and found that core/softcore and shell/cloud genes appear enriched at two spatially separated intracellular regions. Based on these observations, we hypothesize that there is a link between the genomic location of genes and their cellular placement.

scholarly journals Arabidopsis heat shock transcription factor HSFA7b positively mediates salt stress tolerance by binding to an E-box-like motif to regulate gene expression

2019 ◽  
Vol 70 (19) ◽  
pp. 5355-5374 ◽  
Author(s):  
Dandan Zang ◽  
Jingxin Wang ◽  
Xin Zhang ◽  
Zhujun Liu ◽  
Yucheng Wang
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Heat Shock ◽  
Salt Tolerance ◽  
Stress Responses ◽  
Ion Homeostasis ◽  
Cellulose Synthase ◽  
Regulate Gene Expression ◽  
E Box ◽  
Regulate Gene

Abstract Plant heat shock transcription factors (HSFs) are involved in heat and other abiotic stress responses. However, their functions in salt tolerance are little known. In this study, we characterized the function of a HSF from Arabidopsis, AtHSFA7b, in salt tolerance. AtHSFA7b is a nuclear protein with transactivation activity. ChIP-seq combined with an RNA-seq assay indicated that AtHSFA7b preferentially binds to a novel cis-acting element, termed the E-box-like motif, to regulate gene expression; it also binds to the heat shock element motif. Under salt conditions, AtHSFA7b regulates its target genes to mediate serial physiological changes, including maintaining cellular ion homeostasis, reducing water loss rate, decreasing reactive oxygen species accumulation, and adjusting osmotic potential, which ultimately leads to improved salt tolerance. Additionally, most cellulose synthase-like (CSL) and cellulose synthase (CESA) family genes were inhibited by AtHSFA7b; some of them were randomly selected for salt tolerance characterization, and they were mainly found to negatively modulate salt tolerance. By contrast, some transcription factors (TFs) were induced by AtHSFA7b; among them, we randomly identified six TFs that positively regulate salt tolerance. Thus, AtHSFA7b serves as a transactivator that positively mediates salinity tolerance mainly through binding to the E-box-like motif to regulate gene expression.

scholarly journals Global optimization of an encapsulated Si/SiO$$_2$$ L3 cavity with a 43 million quality factor

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
J. P. Vasco ◽  
V. Savona
Keyword(s):  
Global Optimization ◽  
Photonic Crystal ◽  
Quality Factor ◽  
State Of The Art ◽  
Optimization Strategy ◽  
High Quality ◽  
Optimal Value ◽  
Out Of Plane ◽  
Fabrication Tolerances ◽  
Structural Imperfections

AbstractWe optimize a silica-encapsulated silicon L3 photonic crystal cavity for ultra-high quality factor by means of a global optimization strategy, where the closest holes surrounding the cavity are varied to minimize out-of-plane losses. We find an optimal value of $$Q_c=4.33\times 10^7$$ Q c = 4.33 × 10 7 , which is predicted to be in the 2 million regime in presence of structural imperfections compatible with state-of-the-art silicon fabrication tolerances.

scholarly journals Heat Shock Protein 70 Improves In Vitro Embryo Yield and Quality from Heat Stressed Bovine Oocytes

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1794
Author(s):  
Konstantina Stamperna ◽  
Themistoklis Giannoulis ◽  
Eleni Dovolou ◽  
Maria Kalemkeridou ◽  
Ioannis Nanas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Heat Shock Protein 70 ◽  
Cumulus Cells ◽  
Intramolecular Interactions ◽  
Developmental Competence ◽  
Embryo Yield ◽  
Bovine Oocytes

Heat shock protein 70 (HSP70) is a chaperon that stabilizes unfolded or partially folded proteins, preventing inappropriate inter- and intramolecular interactions. Here, we examined the developmental competence of in vitro matured oocytes exposed to heat stress with or without HSP70. Bovine oocytes were matured for 24 h at 39 °C without (group C39) or with HSP70 (group H39) and at 41 °C for the first 6 h, followed by 16 h at 39 °C with (group H41) or without HSP70 (group C41). After insemination, zygotes were cultured for 9 days at 39 °C. Cleavage and embryo yield were assessed 48 h post insemination and on days 7, 8, 9, respectively. Gene expression was assessed by RT-PCR in oocytes, cumulus cells and blastocysts. In C41, blastocysts formation rate was lower than in C39 and on day 9 it was lower than in H41. In oocytes, HSP70 enhanced the expression of three HSP genes regardless of incubation temperature. HSP70 at 39 °C led to tight coordination of gene expression in oocytes and blastocysts, but not in cumulus cells. Our results imply that HSP70, by preventing apoptosis, supporting signal transduction, and increasing antioxidant protection of the embryo, protects heat stressed maturing bovine oocyte and restores its developmental competence.

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