Adaptive mechanisms for high temperature
In the ST population, different mechanisms were involved in the biological response to high temperature. Cells increase the baseline of some proteins to adapt to high water temperature. RAB6A andDDX52 were found under high selection pressures in the ST population. These genes are responsible for intracellular protein transport, retrograde vesicle-mediated transport of Golgi apparatus to endoplasmic reticulum, and ATP-dependent RNA helicase activity, a response that reflects the protein turnover stimulated by heat shock (Saadeldin et al., 2020).
Chronic thermal stress causes damaging effects on the cytoskeleton, catalytic activities of enzymes, single- and double-stranded DNA breaks and mutations, and inhibition of the DNA repair pathway, leading to apoptosis and necrosis (Saadeldin et al., 2020). Genome-wide selective sweep analysis of the ST population revealed that numerous genes embedded in selected genome regions belonged predominantly to functional categories related to paracellular permeability, including cell junction (GO: 0030054), bicellular tight junction (GO: 0005923), apical junction complex (GO: 0043296), cell–cell junction (GO: 0005911), and occluding junction (GO: 0070160) (Supplementary Table S8), as well as tight junction pathway (KEGG: 04512), cell adhesion molecule pathway (KEGG:04514), and its downstream pathway leukocyte transendothelial migration (KEGG:04670). We identified several essential genes, includingLRAD4 , PAK3 , BCAS3 , MINK1 , PDLI4 ,RTN4RL1 , CLAUDIN (CLDN3 , CLDN4 , and CLDN6 ),CDH4 , NLGN3 , and JAM1 , within the genome regions under selective sweeps. When exposed to heat stress, cells respond by dramatically reorganizing various cytoskeletal networks, such as microtubules, intermediate filaments, and actin microfilaments. TheLRDA4 gene serves as a negative regulator of TGF-beta signaling. The TGF-beta signaling pathway is related to cytoskeleton organization and involved in morphological changes associated with cellular responses to chronic heat (Saadeldin et al., 2020). Therefore, LRAD4prohibits the expression of the TGF-beta signaling pathway to maintain cell morphology during heat stress. The PAK3 , BCAS3 ,MINK1 , PDLI4 , and RTN4RL1 genes play an important role in cytoskeleton regulation to ensure cytoskeletal integrity under chronic heat shock. PAK3 plays a role in various signaling pathways, including cytoskeleton regulation, cell migration, and cell cycle regulation (Boda et al., 2004).
Cadherin, Claudin, and Jam1 are the key components of the tight junctions of KEGG pathways. The tight junction maintains the integrity of the epithelial cell layer that protects multicellular organisms under external stress and stimuli (Anderson & Itallie, 2009). The tight junction also serves as a physical barrier to prevent solutes and water from passing freely through the paracellular space between epithelial and endothelial cell sheets. Cell dehydration is an important cause of high-temperature injury. Claudin4 , a member of the Claudin family, was located in two significant GO terms (establishment of the skin barrier, GO: 0061436; regulation of water loss via skin, GO: 0033561) that are related to water homeostasis.
Moreover, aside from negatively affecting the cytoskeleton and cytomembrane integrity, high-temperature stress usually causes DNA damage and apoptosis. We found that ATRX , RFC3 ,Npas2 , and RFA1 were under higher selection pressures in the ST population than in the ZS and RS populations. These genes are involved in DNA repair or cellular response to DNA damage stimulus (Juhász, Elbakry, Mathes, & Löbrich, 2018; Xia, Xiao, Gannon, & Li, 2010; Lisby, Barlow, Burgess, & Rothstein, 2004). Four genes, namely, BNIP1 ,AIFM1 , AIFM3 , and Taok1 , were in the GO term execution phase of apoptosis (GO: 0097194). Cells die as the execution phase is completed. AIFM1 and AIFM3 , which are apoptosis-inducing factors, trigger chromatin condensation and DNA fragmentation in cells to induce programmed cell death.
Heat stress usually changes membrane permeability, thereby increasing intracellular Na+ and Ca2+ (Park, Han, Oh, & Kang, 2005). The TRPC4 channel is involved in various physiological and pathophysiological processes, such as vascular smooth muscles, endothelial functions, adiponectin regulation, and oxidative stress. TRPC4 has an important role in regulating cytosolic calcium ion concentration in mice and interferes with actin expression (Yang et al., 2005). High temperature causes endoplasmic reticulum physiological dysfunction and calcium homeostasis imbalance. High temperature also induces unfolded and misfolded proteins to accumulate in the endoplasmic reticulum in excess, thereby triggering the endoplasmic reticulum stress response. Four genes, namely,DNAJB14 , AIFM1 , CREBRF , and Stc2 , are part of the endoplasmic reticulum stress response. ER stress responses include unfolded protein response, which is initially aimed at compensating for damage but can eventually trigger cell death if endoplasmic reticulum dysfunction is severe or prolonged. DNAJB14acts as a co-chaperone of HSPA8/Hsc70 in promoting protein folding and trafficking, as well as in promoting unfolded proteins to the endoplasmic reticulum-associated degradation pathway. AIFM1functions as an NADH oxidoreductase and a regulator of apoptosis. It interacts with EIF3G , thereby inhibiting the EIF3 machinery and protein synthesis. Moreover, it activates caspase-7 to amplify apoptosis. Furthermore, DNAJB14 , CCT6 , CCT8 , andDNAJB13 are important molecular chaperones that assist in the folding of proteins upon ATP hydrolysis, thereby preventing or correcting misfolding caused by high temperature.
Thus, natural selection has substantially changed genetic variations in a vast number of genes in the ST population related to the regulation of the cytoskeleton, cell morphogenesis, ion transmembrane transport, DNA repair, protein folding, and apoptosis. These processes may maintain the integrity of cells and homeostasis, allowing the fitness of S. japonica to increase under high-temperature stress.