Natural genetic variation differentially affects the proteome and transcriptome in C. elegans

Polina Kamkina, Basten Snoek, Jonas Grossmann, Rita J M Volkers, Mark G Sterken, Michael Daube, Bernd Roschitzki, Claudia Fortes, Ralph Schlapbach, Alexander Roth, Christian von Mering, Michael O Hengartner, Sabine P Schrimpf, Jan E Kammenga

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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 (C. 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 SILAC labeling. Among all transcribed genes, we found 1,532 genes to be differentially transcribed between the two wild types. Of in 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.

Original languageEnglish
JournalMolecular and Cellular Proteomics
DOIs
Publication statusPublished - 04 Mar 2016
Externally publishedYes

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    Kamkina, P., Snoek, B., Grossmann, J., Volkers, R. J. M., Sterken, M. G., Daube, M., Roschitzki, B., Fortes, C., Schlapbach, R., Roth, A., von Mering, C., Hengartner, M. O., Schrimpf, S. P., & Kammenga, J. E. (2016). Natural genetic variation differentially affects the proteome and transcriptome in C. elegans. Molecular and Cellular Proteomics. https://doi.org/10.1074/mcp.M115.052548