Cargando…
Comparison of the Proteomes and Phosphoproteomes of S. cerevisiae Cells Harvested with Different Strategies
The budding yeast Saccharomyces cerevisiae is a powerful model system that is widely used to investigate many cellular processes. The harvesting of yeast cells is the first step in almost every experimental procedure. Here, yeast cells are isolated from their growth medium, collected, and used for s...
Autores principales: | , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10594529/ https://www.ncbi.nlm.nih.gov/pubmed/37873870 http://dx.doi.org/10.3390/proteomes11040028 |
_version_ | 1785124671490883584 |
---|---|
author | Rossio, Valentina Paulo, Joao A. |
author_facet | Rossio, Valentina Paulo, Joao A. |
author_sort | Rossio, Valentina |
collection | PubMed |
description | The budding yeast Saccharomyces cerevisiae is a powerful model system that is widely used to investigate many cellular processes. The harvesting of yeast cells is the first step in almost every experimental procedure. Here, yeast cells are isolated from their growth medium, collected, and used for successive experiments or analysis. The two most common methods to harvest S. cerevisiae are centrifugation and filtration. Understanding if and how centrifugation and filtration affect yeast physiology is essential with respect to downstream data interpretation. Here, we profile and compare the proteomes and the phosphoproteomes, using isobaric label-based quantitative mass spectrometry, of three common methods used to harvest S. cerevisiae cells: low-speed centrifugation, high-speed centrifugation, and filtration. Our data suggest that, while the proteome was stable across the tested conditions, hundreds of phosphorylation events were different between centrifugation and filtration. Our analysis shows that, under our experimental conditions, filtration may cause both cell wall and osmotic stress at higher levels compared to centrifugation, implying harvesting-method-specific stresses. Thus, considering that the basal activation levels of specific stresses may differ under certain harvesting conditions is an important, but often overlooked, aspect of experimental design. |
format | Online Article Text |
id | pubmed-10594529 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-105945292023-10-25 Comparison of the Proteomes and Phosphoproteomes of S. cerevisiae Cells Harvested with Different Strategies Rossio, Valentina Paulo, Joao A. Proteomes Article The budding yeast Saccharomyces cerevisiae is a powerful model system that is widely used to investigate many cellular processes. The harvesting of yeast cells is the first step in almost every experimental procedure. Here, yeast cells are isolated from their growth medium, collected, and used for successive experiments or analysis. The two most common methods to harvest S. cerevisiae are centrifugation and filtration. Understanding if and how centrifugation and filtration affect yeast physiology is essential with respect to downstream data interpretation. Here, we profile and compare the proteomes and the phosphoproteomes, using isobaric label-based quantitative mass spectrometry, of three common methods used to harvest S. cerevisiae cells: low-speed centrifugation, high-speed centrifugation, and filtration. Our data suggest that, while the proteome was stable across the tested conditions, hundreds of phosphorylation events were different between centrifugation and filtration. Our analysis shows that, under our experimental conditions, filtration may cause both cell wall and osmotic stress at higher levels compared to centrifugation, implying harvesting-method-specific stresses. Thus, considering that the basal activation levels of specific stresses may differ under certain harvesting conditions is an important, but often overlooked, aspect of experimental design. MDPI 2023-09-27 /pmc/articles/PMC10594529/ /pubmed/37873870 http://dx.doi.org/10.3390/proteomes11040028 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Rossio, Valentina Paulo, Joao A. Comparison of the Proteomes and Phosphoproteomes of S. cerevisiae Cells Harvested with Different Strategies |
title | Comparison of the Proteomes and Phosphoproteomes of S. cerevisiae Cells Harvested with Different Strategies |
title_full | Comparison of the Proteomes and Phosphoproteomes of S. cerevisiae Cells Harvested with Different Strategies |
title_fullStr | Comparison of the Proteomes and Phosphoproteomes of S. cerevisiae Cells Harvested with Different Strategies |
title_full_unstemmed | Comparison of the Proteomes and Phosphoproteomes of S. cerevisiae Cells Harvested with Different Strategies |
title_short | Comparison of the Proteomes and Phosphoproteomes of S. cerevisiae Cells Harvested with Different Strategies |
title_sort | comparison of the proteomes and phosphoproteomes of s. cerevisiae cells harvested with different strategies |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10594529/ https://www.ncbi.nlm.nih.gov/pubmed/37873870 http://dx.doi.org/10.3390/proteomes11040028 |
work_keys_str_mv | AT rossiovalentina comparisonoftheproteomesandphosphoproteomesofscerevisiaecellsharvestedwithdifferentstrategies AT paulojoaoa comparisonoftheproteomesandphosphoproteomesofscerevisiaecellsharvestedwithdifferentstrategies |