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.
Highlights
Natural genetic variation in gene expression shapes the diversity in phenotypic traits and is the raw material for evolutionary processes [1]
The genomes of these two wild-type strains, as well as polymorphisms between them, have been characterized extensively [33,34,35,36,37,38,39,40]. These genetic polymorphisms often lead to gene expression differences, which are playing a role in a whole range of phenotypic differences between N2 and CB4856, such as life history traits [4, 41,42,43,44], behavior [40, 45,46,47,48,49], and life span [9, 41, 50]
Transcriptome Comparison—As the strongest mRNA expression differences between N2 and CB4856 were observed at stage larval stage 4 (L4) (3, 4, 30 –32), we measured the genome-wide transcription levels of three biological replicates of L4 stage synchronized larvae using microarrays
Summary
C. elegans Strains and Culture Conditions—The two C. elegans wild-type strains N2 (Bristol) and CB4856 (Hawaii) were grown at 20 °C on 9-cm NGM agar plates without peptone (3 g/liter NaCl, 20 g/liter bacto-agar, 5 mg/liter cholesterol, 25 mM K2PO4, 1 mM MgSO4, 1 mM CaCl2) and with a lawn of Escherichia coli (OP50 strain) bacteria. 40 raw data files were generated for every biological replicate and combined for database searching with the match between runs set to 2 min. The protein group log H/L median ratios were calculated separately for each biological replicate; median was normalized to 1 and used for further analysis (supplemental Table 2). Proline corrected heavy and light peptide intensities correlated well between the replicates (r Ն0.74, see supplemental Fig. 2). To identify proteins that are differentially expressed between N2 and CB4856, SILAC data were filtered for proteins that were quantified at least twice with at least a 1.3-fold difference in abundance (the biological significance of the 1.3-fold change cutoff has been shown by Ref. 56, and a p value Ͻ 0.000457 (z-test, permutation determined threshold with the FDR cutoff of 0.05)). The MS proteomics data have been deposited to the ProteomeXchange Consortium [64] via the PRIDE partner repository with the dataset identifier PXD002010
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