title: A chemostat array enables the spatio-temporal analysis of the yeast proteome.
abstract: Observing cellular responses to perturbations is central to generating and testing hypotheses in biology. We developed a massively parallel microchemostat array capable of growing and observing 1,152 yeast-GFP strains on the single-cell level with 20 min time resolution. We measured protein abundance and localization changes in 4,085 GFP-tagged strains in response to methyl methanesulfonate and analyzed 576 GFP strains in five additional conditions for a total of more than 10,000 unique experiments, providing a systematic view of the yeast proteome in flux. We observed that processing bodies formed rapidly and synchronously in response to UV irradiation, and in conjunction with 506 deletion-GFP strains, identified four gene disruptions leading to abnormal ribonucleotide-diphosphate reductase (Rnr4) localization. Our microchemostat platform enables the large-scale interrogation of proteomes in flux and permits the concurrent observation of protein abundance, localization, cell size, and growth parameters on the single-cell level for thousands of microbial cultures in one experiment.
authors.affiliation: Institute of Bioengineering, School of Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Dénervaud
authors.forename: Johannes
authors.initials: J
authors.lastname: Becker
authors.forename: Ricard
authors.initials: R
authors.lastname: Delgado-Gonzalo
authors.forename: Pascal
authors.initials: P
authors.lastname: Damay
authors.forename: Arun S
authors.initials: AS
authors.lastname: Rajkumar
authors.forename: Michael
authors.initials: M
authors.lastname: Unser
authors.forename: David
authors.initials: D
authors.lastname: Shore
authors.forename: Felix
authors.initials: F
authors.lastname: Naef
authors.forename: Sebastian J
authors.initials: SJ
authors.lastname: Maerkl
mesh_terms: D017353:Gene Deletion; D049452:Green Fluorescent Proteins / Q000378:metabolism; D008741:Methyl Methanesulfonate / Q000494:pharmacology; D044085:Microfluidics / Q000295:instrumentation* / Q000379:methods*; D010641:Phenotype; D020543:Proteome / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000254:growth & development / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D062211:Spatio-Temporal Analysis
chemical_list: D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D049452:Green Fluorescent Proteins; D008741:Methyl Methanesulfonate
keywords: DNA damage response; cell arrays; high-content imaging; microfluidics; yeast proteomics
references.citation: Radiat Res. 2008 Oct;170(4):411-21
references.pmid: 19024647
references.citation: Science. 1988 Jul 15;241(4863):317-22
references.pmid: 3291120
references.citation: Fungal Genet Biol. 2011 Dec;48(12):1116-23
references.pmid: 22056521
references.citation: Science. 2006 Apr 14;312(5771):217-24
references.pmid: 16614209
references.citation: Science. 2003 May 2;300(5620):805-8
references.pmid: 12730603
references.citation: Mol Biol Cell. 2001 Oct;12(10):2987-3003
references.pmid: 11598186
references.citation: Nat Genet. 2006 Jun;38(6):636-43
references.pmid: 16715097
references.citation: EMBO Rep. 2008 Oct;9(10):1034-40
references.pmid: 18704118
references.citation: Biochemistry. 2004 Jun 22;43(24):7736-42
references.pmid: 15196016
references.citation: Nature. 2006 Jun 15;441(7095):840-6
references.pmid: 16699522
references.citation: J Cell Biol. 2013 Mar 18;200(6):839-50
references.pmid: 23509072
references.citation: Proc Natl Acad Sci U S A. 2003 May 27;100(11):6628-33
references.pmid: 12732713
references.citation: PLoS Genet. 2009 Oct;5(10):e1000697
references.pmid: 19851444
references.citation: Nat Cell Biol. 2012 Sep;14(9):966-76
references.pmid: 22842922
references.citation: Genes Dev. 2009 Apr 15;23(8):963-74
references.pmid: 19390089
references.citation: Nature. 2011 Dec 18;481(7379):39-44
references.pmid: 22178928
references.citation: Nature. 2003 Oct 16;425(6959):686-91
references.pmid: 14562095
references.citation: Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3758-63
references.pmid: 19223588
references.citation: Nature. 2008 Aug 28;454(7208):1119-22
references.pmid: 18668041
references.citation: Science. 2008 Dec 5;322(5907):1511-6
references.pmid: 19023046
references.citation: Genetics. 2012 Jul;191(3):671-702
references.pmid: 22785621
references.citation: Cell. 2009 Aug 21;138(4):795-806
references.pmid: 19664813
references.citation: Proc Natl Acad Sci U S A. 2009 Jun 23;106(25):10147-52
references.pmid: 19502427
references.citation: Nature. 2003 Oct 16;425(6959):737-41
references.pmid: 14562106
references.citation: Science. 2010 Jul 30;329(5991):533-8
references.pmid: 20671182
references.citation: Proc Natl Acad Sci U S A. 2007 Jan 23;104(4):1183-8
references.pmid: 17227840
references.citation: Nature. 2010 Apr 1;464(7289):721-7
references.pmid: 20360735
references.citation: Genes Dev. 2006 Feb 1;20(3):334-44
references.pmid: 16452505
references.citation: Mol Cell. 2007 Mar 9;25(5):635-46
references.pmid: 17349952
references.citation: Mol Syst Biol. 2011 Jul 19;7:514
references.pmid: 21772262
references.citation: Mol Biol Cell. 2008 Nov;19(11):4980-92
references.pmid: 18768757
references.citation: Genetics. 2004 May;167(1):21-33
references.pmid: 15166134
references.citation: Nat Rev Genet. 2009 Sep;10(9):628-38
references.pmid: 19668248