title: Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans.
abstract: Natural genetic variation is the raw material of evolution and influences disease development and progression. An important question is how this genetic variation translates into variation in protein abundance. To analyze the effects of the genetic background on gene and protein expression in the nematode Caenorhabditis elegans, we quantitatively compared the two genetically highly divergent wild-type strains N2 and CB4856. Gene expression was analyzed by microarray assays, and proteins were quantified using stable isotope labeling by amino acids in cell culture. Among all transcribed genes, we found 1,532 genes to be differentially transcribed between the two wild types. Of the total 3,238 quantified proteins, 129 proteins were significantly differentially expressed between N2 and CB4856. The differentially expressed proteins were enriched for genes that function in insulin-signaling and stress-response pathways, underlining strong divergence of these pathways in nematodes. The protein abundance of the two wild-type strains correlates more strongly than protein abundance versus transcript abundance within each wild type. Our findings indicate that in C. elegans only a fraction of the changes in protein abundance can be explained by the changes in mRNA abundance. These findings corroborate with the observations made across species.
authors.affiliation: From the ‡Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; §Ph.D. Program in Molecular Life Sciences Zurich, 8057 Zurich, Switzerland;
authors.forename: Polina
authors.initials: P
authors.lastname: Kamkina
authors.affiliation: ‖Laboratory of Nematology, Wageningen University, Wageningen 6708 PB, The Netherlands;
authors.forename: L Basten
authors.initials: LB
authors.lastname: Snoek
authors.affiliation: **Functional Genomics Center Zurich, University of Zurich and Swiss Federal Institute of Technology Zurich, 8057 Zurich, Switzerland.
authors.forename: Jonas
authors.initials: J
authors.lastname: Grossmann
authors.affiliation: ‖Laboratory of Nematology, Wageningen University, Wageningen 6708 PB, The Netherlands;
authors.forename: Rita J M
authors.initials: RJ
authors.lastname: Volkers
authors.affiliation: ‖Laboratory of Nematology, Wageningen University, Wageningen 6708 PB, The Netherlands;
authors.forename: Mark G
authors.initials: MG
authors.lastname: Sterken
authors.affiliation: From the ‡Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland;
authors.forename: Michael
authors.initials: M
authors.lastname: Daube
authors.affiliation: **Functional Genomics Center Zurich, University of Zurich and Swiss Federal Institute of Technology Zurich, 8057 Zurich, Switzerland.
authors.forename: Bernd
authors.initials: B
authors.lastname: Roschitzki
authors.affiliation: **Functional Genomics Center Zurich, University of Zurich and Swiss Federal Institute of Technology Zurich, 8057 Zurich, Switzerland.
authors.forename: Claudia
authors.initials: C
authors.lastname: Fortes
authors.affiliation: **Functional Genomics Center Zurich, University of Zurich and Swiss Federal Institute of Technology Zurich, 8057 Zurich, Switzerland.
authors.forename: Ralph
authors.initials: R
authors.lastname: Schlapbach
authors.affiliation: From the ‡Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland;
authors.forename: Alexander
authors.initials: A
authors.lastname: Roth
authors.affiliation: From the ‡Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland;
authors.forename: Christian
authors.initials: C
authors.lastname: von Mering
authors.affiliation: From the ‡Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland;
authors.forename: Michael O
authors.initials: MO
authors.lastname: Hengartner
authors.affiliation: From the ‡Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; jan.kammenga@wur.nl sabine.schrimpf@imls.uzh.ch.
authors.forename: Sabine P
authors.initials: SP
authors.lastname: Schrimpf
authors.affiliation: ‖Laboratory of Nematology, Wageningen University, Wageningen 6708 PB, The Netherlands; jan.kammenga@wur.nl sabine.schrimpf@imls.uzh.ch.
authors.forename: Jan E
authors.initials: JE
authors.lastname: Kammenga
mesh_terms: D000818:Animals; D005075:Biological Evolution; D017173:Caenorhabditis elegans / Q000145:classification / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D014644:Genetic Variation; D007553:Isotope Labeling / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D040901:Proteomics / Q000379:methods*
chemical_list: D029742:Caenorhabditis elegans Proteins