title: Absolute protein quantification of the yeast chaperome under conditions of heat shock.
abstract: Chaperones are fundamental to regulating the heat shock response, mediating protein recovery from thermal-induced misfolding and aggregation. Using the QconCAT strategy and selected reaction monitoring (SRM) for absolute protein quantification, we have determined copy per cell values for 49 key chaperones in Saccharomyces cerevisiae under conditions of normal growth and heat shock. This work extends a previous chemostat quantification study by including up to five Q-peptides per protein to improve confidence in protein quantification. In contrast to the global proteome profile of S. cerevisiae in response to heat shock, which remains largely unchanged as determined by label-free quantification, many of the chaperones are upregulated with an average two-fold increase in protein abundance. Interestingly, eight of the significantly upregulated chaperones are direct gene targets of heat shock transcription factor-1. By performing absolute quantification of chaperones under heat stress for the first time, we were able to evaluate the individual protein-level response. Furthermore, this SRM data was used to calibrate label-free quantification values for the proteome in absolute terms, thus improving relative quantification between the two conditions. This study significantly enhances the largely transcriptomic data available in the field and illustrates a more nuanced response at the protein level.
authors.affiliation: Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK.|Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK.
authors.forename: Rebecca J
authors.initials: RJ
authors.lastname: Mackenzie
authors.affiliation: Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK.
authors.forename: Craig
authors.initials: C
authors.lastname: Lawless
authors.affiliation: Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK.
authors.forename: Stephen W
authors.initials: SW
authors.lastname: Holman
authors.affiliation: Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK.
authors.forename: Karin
authors.initials: K
authors.lastname: Lanthaler
authors.affiliation: Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Beynon
authors.affiliation: Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK.
authors.forename: Chris M
authors.initials: CM
authors.lastname: Grant
authors.affiliation: Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK.
authors.forename: Simon J
authors.initials: SJ
authors.lastname: Hubbard
authors.affiliation: Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK.
authors.forename: Claire E
authors.initials: CE
authors.lastname: Eyers
mesh_terms: D006360:Heat-Shock Proteins / Q000032:analysis; D018869:Heat-Shock Response / Q000502:physiology*; D018832:Molecular Chaperones / Q000032:analysis; D020543:Proteome / Q000032:analysis; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis
chemical_list: D006360:Heat-Shock Proteins; D018832:Molecular Chaperones; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins
keywords: Cell Biology; Chaperone; Heat shock; Label free; QconCAT; S. cerevisiae; Selected reaction monitoring