Overexpression of Far1, a cyclin-dependent kinase inhibitor, induces a large transcriptional reprogramming in which RNA synthesis senses Far1 in a Sfp1-mediated way

Busti, Stefano; Gotti, Laura; Balestrieri, Chiara; Querin, Lorenzo; Drovandi, Guido; Felici, Giovanni; Mavelli, Gabriella; Bertolazzi, Paola; Alberghina, Lilia; Vanoni, Marco

doi:10.1016/j.biotechadv.2011.09.007

Cited by 7 publications

(12 citation statements)

References 94 publications

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“…For cytofluorimetric determination of DNA, RNA and protein intracellular content, samples were essentially processed as previously described6869.…”

Section: Methodsmentioning

confidence: 99%

“…GAPDH activity assay was performed essentially as described75, measuring the rate of NADH formation per minute, following the increase in absorbance at 340 nm. The assay for invertase activity was performed essentially as previously described68. The β- glucoronidase enzymatic assay was performed as described76.…”

Section: Methodsmentioning

confidence: 99%

“…The β- glucoronidase enzymatic assay was performed as described76. Glucose consumption and ethanol production were evaluated by standard enzymatic assays (Sigma-Aldrich; Megazyme), essentially as previously described68.…”

Section: Methodsmentioning

confidence: 99%

“…Fructose 1,5 bisphosphate, Dihydroxyacetone phosphate, Glyceraldehyde 3-phosphate, phosphoenolpyruvate and pyruvate intracellular content was determined by appropriate enzimatic methods, as described86. Quantification of glutathione levels was performed as previously described6887. For each metabolite, the intracellular concentration was estimated by dividing the measured values by the mean cellular volumes (as evaluated by Coulter counter analysis).…”

Section: Methodsmentioning

confidence: 99%

“…Total RNA was prepared as described previously68. qRT-PCR reactions were performed in a MiniOpticon detection system (BIO-RAD) using the SsoFast EvaGreen Supermix (BIO-RAD).…”

Section: Methodsmentioning

confidence: 99%

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Respiratory metabolism and calorie restriction relieve persistent endoplasmic reticulum stress induced by calcium shortage in yeast

Busti

Mapelli

Tripodi

et al. 2016

Sci Rep

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Calcium homeostasis is crucial to eukaryotic cell survival. By acting as an enzyme cofactor and a second messenger in several signal transduction pathways, the calcium ion controls many essential biological processes. Inside the endoplasmic reticulum (ER) calcium concentration is carefully regulated to safeguard the correct folding and processing of secretory proteins. By using the model organism Saccharomyces cerevisiae we show that calcium shortage leads to a slowdown of cell growth and metabolism. Accumulation of unfolded proteins within the calcium-depleted lumen of the endoplasmic reticulum (ER stress) triggers the unfolded protein response (UPR) and generates a state of oxidative stress that decreases cell viability. These effects are severe during growth on rapidly fermentable carbon sources and can be mitigated by decreasing the protein synthesis rate or by inducing cellular respiration. Calcium homeostasis, protein biosynthesis and the unfolded protein response are tightly intertwined and the consequences of facing calcium starvation are determined by whether cellular energy production is balanced with demands for anabolic functions. Our findings confirm that the connections linking disturbance of ER calcium equilibrium to ER stress and UPR signaling are evolutionary conserved and highlight the crucial role of metabolism in modulating the effects induced by calcium shortage.

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“…For cytofluorimetric determination of DNA, RNA and protein intracellular content, samples were essentially processed as previously described6869.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…Total RNA was prepared as described previously68. qRT-PCR reactions were performed in a MiniOpticon detection system (BIO-RAD) using the SsoFast EvaGreen Supermix (BIO-RAD).…”

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Respiratory metabolism and calorie restriction relieve persistent endoplasmic reticulum stress induced by calcium shortage in yeast

Busti

Mapelli

Tripodi

et al. 2016

Sci Rep

Self Cite

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Automated gene function prediction through gene multifunctionality in biological networks

Frasca

2015

Neurocomputing

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As the number of sequenced genomes rapidly grows, automated prediction of gene function (AFP) is now a challenging problem. Despite significant progresses in the last several years, the accuracy of gene function prediction still needs to be improved in order to be used effectively in practice. Two of the main issues of AFP problem are the imbalance of gene functional annotations and the 'multifunctional properties' of genes. While the former is a well studied problem in machine learning, the latter has recently emerged in bioinformatics and few studies have been carried out about it. Here we propose a method for AFP which appropriately handles the label imbalance characterizing biological taxonomies, and embeds in the model the property of some genes of being 'multifunctional'. We tested the method in predicting the functions of the Gene Ontology functional hierarchy for genes of yeast and fly model organisms, in a genome-wide approach. The achieved results show that cost-sensitive strategies and 'gene multifunctionality' can be combined to achieve significantly better results than the compared state-of-the-art algorithms for AFP.

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Differential Protein Expression in Set5p-Mediated Acetic Acid Stress Response and Novel Targets for Engineering Yeast Stress Tolerance

Zhang,

Yuan,

Wang

et al. 2024

J. Proteome Res.

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Acetic acid is a prevalent inhibitor in lignocellulosic hydrolysate, which represses microbial growth and bioproduction. Histone modification and chromatin remodeling have been revealed to be critical for regulating eukaryotic metabolism. However, related studies in chronic acetic acid stress responses remain unclear. Our previous studies revealed that overexpression of the histone H4 methyltransferase Set5p enhanced acetic acid stress tolerance of the budding yeast Saccharomyces cerevisiae. In this study, we examined the role of Set5p in acetic acid stress by analyzing global protein expression. Significant activation of intracellular protein expression under the stress was discovered, and the functions of the differential proteins were mainly involved in chromatin modification, signal transduction, and carbohydrate metabolism. Notably, a substantial increase of Set5p expression was observed in response to acetic acid stress. Functional studies demonstrated that the restriction of the telomere capping protein Rtc3p, as well as Ies3p and Taf14p, which are related to chromatin regulation, was critical for yeast stress response. This study enriches the understanding of the epigenetic regulatory mechanisms underlying yeast stress response mediated by histone-modifying enzymes. The results also benefit the development of robust yeast strains for lignocellulosic bioconversion.

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Overexpression of Far1, a cyclin-dependent kinase inhibitor, induces a large transcriptional reprogramming in which RNA synthesis senses Far1 in a Sfp1-mediated way

Cited by 7 publications

References 94 publications

Respiratory metabolism and calorie restriction relieve persistent endoplasmic reticulum stress induced by calcium shortage in yeast

Respiratory metabolism and calorie restriction relieve persistent endoplasmic reticulum stress induced by calcium shortage in yeast

Automated gene function prediction through gene multifunctionality in biological networks

Differential Protein Expression in Set5p-Mediated Acetic Acid Stress Response and Novel Targets for Engineering Yeast Stress Tolerance

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