title: Quantitative proteomics of heat-treated human cells show an across-the-board mild depletion of housekeeping proteins to massively accumulate few HSPs.
abstract: Classic semiquantitative proteomic methods have shown that all organisms respond to a mild heat shock by an apparent massive accumulation of a small set of proteins, named heat-shock proteins (HSPs) and a concomitant slowing down in the synthesis of the other proteins. Yet unexplained, the increased levels of HSP messenger RNAs (mRNAs) may exceed 100 times the ensuing relative levels of HSP proteins. We used here high-throughput quantitative proteomics and targeted mRNA quantification to estimate in human cell cultures the mass and copy numbers of the most abundant proteins that become significantly accumulated, depleted, or unchanged during and following 4 h at 41 °C, which we define as mild heat shock. This treatment caused a minor across-the-board mass loss in many housekeeping proteins, which was matched by a mass gain in a few HSPs, predominantly cytosolic HSPCs (HSP90s) and HSPA8 (HSC70). As the mRNAs of the heat-depleted proteins were not significantly degraded and less ribosomes were recruited by excess new HSP mRNAs, the mild depletion of the many housekeeping proteins during heat shock was attributed to their slower replenishment. This differential protein expression pattern was reproduced by isothermal treatments with Hsp90 inhibitors. Unexpectedly, heat-treated cells accumulated 55 times more new molecules of HSPA8 (HSC70) than of the acknowledged heat-inducible isoform HSPA1A (HSP70), implying that when expressed as net copy number differences, rather than as mere "fold change" ratios, new biologically relevant information can be extracted from quantitative proteomic data. Raw data are available via ProteomeXchange with identifier PXD001666.
authors.affiliation: Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland.
authors.forename: Andrija
authors.initials: A
authors.lastname: Finka
authors.forename: Vishal
authors.initials: V
authors.lastname: Sood
authors.forename: Manfredo
authors.initials: M
authors.lastname: Quadroni
authors.forename: Paolo De Los
authors.initials: Pde L
authors.lastname: Rios
authors.forename: Pierre
authors.initials: P
authors.lastname: Goloubinoff
mesh_terms: D016227:Benzoquinones / Q000633:toxicity; D002851:Chromatography, High Pressure Liquid; D050883:HSC70 Heat-Shock Proteins / Q000235:genetics / Q000378:metabolism; D018840:HSP70 Heat-Shock Proteins / Q000235:genetics / Q000378:metabolism; D018841:HSP90 Heat-Shock Proteins / Q000235:genetics / Q000378:metabolism; D006360:Heat-Shock Proteins / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D007553:Isotope Labeling; D019169:Jurkat Cells; D047029:Lactams, Macrocyclic / Q000633:toxicity; D013058:Mass Spectrometry; D040901:Proteomics; D012333:RNA, Messenger / Q000378:metabolism; D013696:Temperature; D059467:Transcriptome / Q000187:drug effects
chemical_list: D016227:Benzoquinones; D050883:HSC70 Heat-Shock Proteins; D018840:HSP70 Heat-Shock Proteins; D018841:HSP90 Heat-Shock Proteins; D006360:Heat-Shock Proteins; D047029:Lactams, Macrocyclic; D012333:RNA, Messenger; C001277:geldanamycin
references.citation: Nat Biotechnol. 2008 Mar;26(3):317-25
references.pmid: 18278033
references.citation: Shock. 2008 May;29(5):623-30
references.pmid: 17885648
references.citation: Traffic. 2007 Jun;8(6):640-6
references.pmid: 17488288
references.citation: Proc Natl Acad Sci U S A. 1975 Sep;72(9):3604-8
references.pmid: 810802
references.citation: Nat Chem Biol. 2014 Nov;10(11):892-901
references.pmid: 25325700
references.citation: Plant Physiol. 2008 Feb;146(2):748-61
references.pmid: 18055584
references.citation: J Proteome Res. 2009 Dec;8(12):5674-8
references.pmid: 19848406
references.citation: Science. 1986 Apr 25;232(4749):522-4
references.pmid: 3083508
references.citation: J Cell Biol. 1999 Dec 27;147(7):1431-42
references.pmid: 10613902
references.citation: J Clin Invest. 2005 Oct;115(10):2633-9
references.pmid: 16200196
references.citation: Trends Biochem Sci. 2012 Mar;37(3):118-25
references.pmid: 22236506
references.citation: Nat Cell Biol. 2000 Aug;2(8):469-75
references.pmid: 10934466
references.citation: EMBO J. 2012 Nov 5;31(21):4221-35
references.pmid: 22990239
references.citation: J Biol Chem. 2010 Dec 3;285(49):38173-82
references.pmid: 20847048
references.citation: Nat Chem Biol. 2010 Dec;6(12):914-20
references.pmid: 20953191
references.citation: Cell Mol Life Sci. 2015 Feb;72(3):401-15
references.pmid: 25283146
references.citation: Trends Biochem Sci. 2007 Aug;32(8):372-80
references.pmid: 17629485
references.citation: Neuron. 2014 Jan 22;81(2):349-65
references.pmid: 24462098
references.citation: Mol Cell. 2013 Feb 7;49(3):439-52
references.pmid: 23290915
references.citation: Cancer Res. 1987 Jul 15;47(14):3712-7
references.pmid: 3109731
references.citation: Cell Stress Chaperones. 2011 Jan;16(1):15-31
references.pmid: 20694844
references.citation: J Neurochem. 2012 Nov;123(4):542-54
references.pmid: 22909049
references.citation: Biochemistry. 1998 Jul 7;37(27):9688-94
references.pmid: 9657681
references.citation: Eur J Biochem. 1993 Dec 1;218(2):413-20
references.pmid: 8269929
references.citation: Eur J Cancer. 2013 May;49(8):2000-9
references.pmid: 23498875
references.citation: PLoS One. 2011;6(2):e14695
references.pmid: 21358815
references.citation: PLoS One. 2013;8(2):e57149
references.pmid: 23468922
references.citation: Proc Natl Acad Sci U S A. 1982 Jan;79(2):525-9
references.pmid: 6804941
references.citation: Elife. 2014;3:e02218
references.pmid: 24867638
references.citation: Cell Stress Chaperones. 1998 Jun;3(2):100-8
references.pmid: 9672245
references.citation: Adv Bioinformatics. 2008;2008:420747
references.pmid: 19956698
references.citation: Cell Mol Life Sci. 2014 Sep;71(17):3311-25
references.pmid: 24760129
references.citation: Cancers (Basel). 2011 Oct 21;3(4):3921-56
references.pmid: 24213118
references.citation: Adv Exp Med Biol. 2007;594:89-99
references.pmid: 17205678
references.citation: Cell Rep. 2014 Nov 6;9(3):1135-50
references.pmid: 25437566
references.citation: J Neurooncol. 2004 Jun;68(2):101-11
references.pmid: 15218946
references.citation: Plant Cell. 2012 Aug;24(8):3333-48
references.pmid: 22904147
references.citation: EMBO J. 2000 Aug 15;19(16):4310-22
references.pmid: 10944114
references.citation: Cell Stress Chaperones. 1999 Sep;4(3):153-61
references.pmid: 10547064
references.citation: Cell Death Differ. 2001 Apr;8(4):357-66
references.pmid: 11550087
references.citation: Nucleic Acids Res. 2004;32(18):5693-702
references.pmid: 15498926
references.citation: Nat Genet. 1999 Dec;23(4):387-8
references.pmid: 10581018
references.citation: Genetics. 2006 Feb;172(2):851-61
references.pmid: 16299395
references.citation: Nature. 2011 May 19;473(7347):337-42
references.pmid: 21593866
references.citation: Mol Cell Biol. 1987 Dec;7(12):4357-68
references.pmid: 3437893
references.citation: J Biol Chem. 1983 Jun 10;258(11):7228-35
references.pmid: 6853516
references.citation: Adv Exp Med Biol. 2010;694:138-59
references.pmid: 20886762
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6166-71
references.pmid: 16606842
references.citation: Annu Rev Biochem. 2011;80:1089-115
references.pmid: 21417720
references.citation: Bioessays. 2013 Dec;35(12):1050-5
references.pmid: 24114984
references.citation: Prog Brain Res. 2007;162:373-92
references.pmid: 17645928
references.citation: Cell Stress Chaperones. 2005 Summer;10(2):86-103
references.pmid: 16038406
references.citation: Int J Oncol. 2014 Jul;45(1):18-30
references.pmid: 24789222
references.citation: J Proteome Res. 2011 Apr 1;10(4):1794-805
references.pmid: 21254760
references.citation: Mol Cell. 2008 Jul 25;31(2):232-43
references.pmid: 18550409
references.citation: Nat Biotechnol. 2008 Dec;26(12):1367-72
references.pmid: 19029910
references.citation: Mol Cell Biol. 1982 Nov;2(11):1388-98
references.pmid: 6761581
references.citation: Cancer Res. 1992 Apr 1;52(7):1721-8
references.pmid: 1551101
references.citation: PLoS One. 2013;8(11):e80425
references.pmid: 24312219
references.citation: Mol Cell Proteomics. 2014 Dec;13(12):3497-506
references.pmid: 25225357
references.citation: Am J Physiol. 1994 Jul;267(1 Pt 1):C104-14
references.pmid: 8048473
references.citation: Cell Death Differ. 2004 Apr;11(4):390-402
references.pmid: 14752510
references.citation: Proteins. 2011 Jun;79(6):1991-8
references.pmid: 21488102
references.citation: Ann N Y Acad Sci. 2005 Dec;1066:222-42
references.pmid: 16533928
references.citation: FEBS Lett. 1997 Apr 28;407(2):215-9
references.pmid: 9166902
references.citation: Nat Cell Biol. 2001 Sep;3(9):839-43
references.pmid: 11533664
references.citation: Mol Cell. 2013 Feb 7;49(3):453-63
references.pmid: 23290916
references.citation: Cancers (Basel). 2011 Sep 30;3(4):3799-823
references.pmid: 24213112
references.citation: Technol Cancer Res Treat. 2010 Apr;9(2):149-59
references.pmid: 20218737
references.citation: Crit Care Med. 2007 Sep;35(9):2128-38
references.pmid: 17855826
references.citation: Bioinformatics. 2010 Sep 1;26(17):2176-82
references.pmid: 20610611
references.citation: Plant Cell. 2009 Sep;21(9):2829-43
references.pmid: 19773386
references.citation: J Cell Biol. 2010 Apr 5;189(1):57-68
references.pmid: 20368618
references.citation: PLoS One. 2011;6(11):e26956
references.pmid: 22132083
references.citation: Toxicol Pathol. 2007 Jun;35(4):495-516
references.pmid: 17562483
references.citation: Ageing Res Rev. 2005 Nov;4(4):548-63
references.pmid: 16243590
references.citation: Mol Cell Proteomics. 2012 Mar;11(3):M111.014050
references.pmid: 22278370
references.citation: Mol Cell Biol. 1997 Apr;17(4):2107-15
references.pmid: 9121459
references.citation: Proc Natl Acad Sci U S A. 1982 Oct;79(20):6181-5
references.pmid: 6815647
references.citation: Cell Stress Chaperones. 2014 Jan;19(1):83-90
references.pmid: 23666745
references.citation: J Biol Chem. 2003 Aug 1;278(31):28490-500
references.pmid: 12750378
references.citation: Annu Rev Biochem. 2013;82:323-55
references.pmid: 23746257
references.citation: Cell Stress Chaperones. 2013 Sep;18(5):591-605
references.pmid: 23430704
references.citation: J Biol Chem. 2013 Jul 19;288(29):21399-411
references.pmid: 23737532
references.citation: Mol Cell Biochem. 2000 Jan;204(1-2):169-78
references.pmid: 10718636
references.citation: PLoS Genet. 2012;8(2):e1002527
references.pmid: 22383896
references.citation: Mol Cell Proteomics. 2012 Jun;11(6):M111.016675
references.pmid: 22337586
references.citation: Mol Cell Proteomics. 2012 Mar;11(3):M111.014654
references.pmid: 22167270
references.citation: J Mol Biol. 1974 Apr 15;84(3):389-98
references.pmid: 4219221
references.citation: J Biol Chem. 1997 Aug 22;272(34):21213-20
references.pmid: 9261129
references.citation: Proc Natl Acad Sci U S A. 2013 Apr 30;110(18):7199-204
references.pmid: 23584019
references.citation: Cell. 1977 May;11(1):201-12
references.pmid: 326416
references.citation: Semin Reprod Med. 2006 Nov;24(5):330-9
references.pmid: 17123228
references.citation: J Mol Neurosci. 2006;30(3):249-65
references.pmid: 17401151
references.citation: Cell Mol Life Sci. 2000 Mar;57(3):450-63
references.pmid: 10823246
references.citation: Nucleic Acids Res. 2014 Jan;42(Database issue):D191-8
references.pmid: 24253303
references.citation: Int J Mol Sci. 2013;14(9):19169-85
references.pmid: 24051401