Transcriptional counterbalance of parental acclimation in TGP
Transcriptional studies show that when WGP and TGP co-exist, these plastic responses tend to follow different trajectories and are influenced by different sets of genes and molecular functions (Shama et al., 2016; Bell and Stein, 2017; Hales et al., 2017; Webster et al., 2018; Bernal et al., 2022). However, this question has rarely been considered when both plastic responses are adaptive. We address this question in D. mojavensis (Diaz et al., 2020) , where we have previously analyzed the level of parent-to-offspring environmental predictability linked to TGP when comparing life stages. As expected from previous thermal tolerance data, transcriptional TGP was only detected in larva stages. Our results also support the hypothesis of diverging transcriptional trajectories between plastic responses within and across generations. However, in contrast to previous findings in other organisms (Bell and Stein, 2017; Hales et al., 2017), we found that such diverging trajectories involve many of the same genes normally expressed in WGP. Approximately 56 % of DE genes associated with TGP overlapped with WGP. Interestingly, most genes significantly associated with TGP are up-regulated, as opposed to transcriptional WGP, where many more genes are down-regulated in response to acclimation in the offspring.
We suggest that this up-regulation caused by the parental acclimation in TGP represents a transcriptional counterbalance of gene expression that helps explain the molecular bases of the adaptive component previously detected from heat tolerance data in TGP (Diaz et al., 2020). Thus, the offspring might benefit from parental acclimation by restoring the expression of genes that will be down-regulated by the heat-shock response when they are themselves acclimated. To understand their role in thermal tolerance, we identify different types of these genes triggered by parental acclimation, which can be classified into two groups. First, parental acclimation activates some genes clearly associated with the heat shock response, such as proteolysis, and only two Hsp genes (Sørensen et al., 2005; Mahat et al., 2016). One of these, Hsp83, is down-regulated in WGP, suggesting a transcriptional constraint in the activation of this gene in the larva stage, which is compensated by parental acclimation. Interestingly, this gene has been associated with maternal transfer to early embryos in D. melanogaster (Ding et al., 1993), being expressed during oogenesis and embryogenesis.
We also identified genes activated by parental acclimation that might be associated with heat tolerance but are not part of the heat-shock response. Genes associated with GO categories of collagen modifications are particularly interesting, such as procollagen-proline 4-dioxygenase activity and peptidyl-proline hydroxylation to 4-hydroxyl-L-proline. We identified four such genes, which encode enzymes that catalyze the formation of hydroxyproline (Myllyharju, 2008; Gorres and Raines, 2010). Collagens are extracellular matrix proteins that contribute to tissue structure and remodeling (Myllyharju and Kivirikko, 2004). This hydroxylation increases the melting temperature of helical collagen, which allows these proteins to be stable at body temperatures in mammals (Rappu et al., 2019). In addition, the down-regulation of these enzymes has been previously associated with thermal sensitivity in low-tolerantD. melanogaster lines (Vermeulen et al., 2014). As a major connective tissue, more thermally stable hydroxylated collagen in the offspring larvae of acclimated parents might allow them to tolerate the direct effect of heat stress without necessarily accessing the energetically expensive heat-shock response (Vermeulen et al., 2014). The fact that these pathways are not directly activated during WGP suggests that such genes are constrained or negatively affected by the massive up-regulation of chaperones during the heat-shock response in WGP acclimation.
We provide compelling evidence demonstrating substantial and distinct differences between adaptive WGP and TGP that contribute to explaining how selection shapes their transcriptional evolution. The first difference is evidenced in the role played by the mechanisms of alternative splicing in transcriptional plasticity, which is linked to acclimation within generations but not to parental acclimation. Moreover, our results demonstrate the importance of exploring alternative splicing in plasticity studies, as these mechanisms involve distinct genes and functions from those detected in differential expression analyses. The second difference between WGP and TGP was detected in the direction of gene expression. Most differentially expressed genes in response to thermal acclimation are common to both types of plasticity but are primarily down-regulated in WGP and up-regulated in TGP. We propose that this pattern might be a transcriptional counterbalance, where parental acclimation compensates for the negative effects of thermal stress on the expression level of some genes despite their potential role in thermal tolerance. Instead of enhancing the expression of the more energetically expensive molecular chaperones that characterize acclimation in WGP, parental acclimation counteracts the negative effects of the heat-shock response. How much of this pattern can be extended to other organisms or traits remains to be seen. However, we believe our findings help understand the molecular bases of adaptive TGP and how the offspring benefit from parental acclimation to increase their fitness compared to unacclimated parents.