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Organismal responses to stressful environments are influenced by numerous transcript- and protein-level mechanisms, and the relationships between expression changes at these levels are not always straightforward. Here, we used paired transcriptomic and proteomic datasets from two previous studies from gill of the California mussel, Mytilus californianus, to explore how simultaneous transcript and protein abundance patterns may diverge under different environmental scenarios. Field-acclimatized mussels were sampled from two disparate intertidal sites; individuals from one site were subjected to three further treatments (common garden, low-intertidal or high-intertidal outplant) that vary in temperature and feeding time. Assessing 1519 genes shared between the two datasets revealed that both transcript and protein expression patterns differentiated the treatments at a global level, despite numerous underlying discrepancies. There were far more instances of differential expression between treatments in transcript only (1451) or protein only (226) than of the two levels shifting expression concordantly (68 instances). Upregulated expression of cilium-associated transcripts (likely related to feeding) was associated with relatively benign field treatments. In the most stressful treatment, transcripts, but not proteins, for several molecular chaperones (including heat shock proteins and endoplasmic reticulum chaperones) were more abundant, consistent with a threshold model for induction of translation of constitutively available mRNAs. Overall, these results suggest that the relative importance of transcript- and protein-level regulation (translation and/or turnover) differs among cellular functions and across specific microhabitats or environmental contexts. Furthermore, the degree of concordance between transcript and protein expression can vary across benign versus acutely stressful environmental conditions.


This article was originally published in Journal of Experimental Biology, volume 226, issue 22, in 2023.

jeb245962supp.pdf (760 kB)
Supplementary information

tables1.xlsx (156 kB)
Table S1. The contig identity and Gene Ontology (GO) category or categories of all genes with a significant correlation between their normalized expression values and Dimension 1 or 2 of the transcript and protein PCAs in Fig. 1.- xlsx file

tables2.xlsx (17 kB)
Table S2. Overrepresented Gene Ontology (GO) functions and corresponding normalized expression values in each treatment (average±b 1 SEM) for differentially expressed transcripts in the (i) PCG v. POL, (ii) PCG vs. POH, and (iii) POL vs. POH treatment comparisons. No overrepresented functions were identified for the EFA vs. PFA and PFA vs. PCG comparisons and thus no genes from those comparisons are presented here. The treatment group written first in each comparison is the reference, and asterisks on individual gene names indicate transcripts that showed significantly higher expression (indicated by FDR values from EdgeR) in the reference group.- xlsx file

tables3.xlsx (137 kB)
Table S3. List of gene names and associated Gene Ontology (GO) terms for those contigs that were 1) differentially expressed (DE) at both the RNA and protein level and share the same direction of expression change (aka match); 2) those that are DE at both levels but change expression in opposite directions (aka mismatch); 3) those that are DE at the transcript but not the protein level; 4) those that are DE at the protein but not the transcript level; and 5) stably expressed at both the RNA and protein level (no DE) in each of the five treatment groups. The treatment group written first in each comparison is the reference. Upregulated = higher expression in the reference group; downregulated = lower expression in the reference group- xlsx file

tables4.xlsx (158 kB)
Table S4. Contigs in WGCNA transcript and protein modules that are significantly correlated with catalase enzyme activity at the transcript (TR2 and TR9) or protein level (PR6), with anti-peroxyl radical capacity at the RNA transcript (TR1 and TR4) or protein level (PR5 and PR8), and with anti-hydroxyl radical capacity at the protein level (PR11). Annotation information, gene significance with each respective physiological metric, and module membership values are provided for each contig.- xlsx file


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