In times of global warming, food shortages and growing populations, deciphering how phototrophic organisms cope with heat stress (HS) is essential for securing future crop yields. Thus, the present study uses the genetically trackable unicellular red alga Cyanidioschyzon merolae to study principles of basal and acquired thermotolerance in a simplified model phototroph. Basal thermotolerance is defined as the innate ability to withstand an initial heat shock. Acquired thermotolerance arises after a priming exposure to a sublethal HS and a subsequent recovery phase, during which a transcriptomic memory is established that enhances the organism’s resilience to a second HS exposure. Through genome‐wide RNA sequencing, the present study identifies three classes of genes in C. merolae: heat shock-responsive genes, that are differentially expressed upon primary HS exposition, type I memory genes that maintain elevated expression or repression during the recovery phase, and type II memory genes that are hyperinduced upon secondary HS exposure. Strikingly, nearly half of the chloroplast‐encoded genes fall into the type II memory gene category. They encode subunits of the photosynthetic electron transport chain, whose enhanced expression likely counters heat‐induced oxidative damage, and components of the chloroplast transcription and translation machinery, which may form a self‐reinforcing circuit to perpetuate thermomemory. Moreover, the alga’s serine/arginine rich splicing factor 2 (SRSF2) homolog is identified as a master regulator of the transcriptomic heat shock response and transcriptomic thermomemory, as both are severely impaired in the srsf2 loss-of-function mutant. Additionally, srsf2 is found to be severely impaired in the establishment of acquired thermotolerance, demonstrating the t importance of CmSRSF2-dependend transcriptomic memory for the establishment of enhanced HS resilience. This reveals a novel role for SRSF2, that is likely independent of its canonical splicing function. Further, it is shown here that although small heat shock proteins (sHSPs) are among the most strongly induced HSPs after priming, they are not required for basal thermotolerance. In contrast, CmsHSP2 is essential for thermomemory, as the loss-of-function mutant is impaired in acquired thermotolerance. Moreover, the C. merolae homolog of the serine/arginine-rich protein (SRP) kinase cell division control (CDC2)-like kinase (CLK) is found to be implicated in both basal and acquired thermotolerance, and a link between CmCLK, CmSRSF2 and CmsHSP expression is proposed. Altogether, these findings identify CmSRSF2 as a master regulator of a conserved thermomemory mechanism in phototrophs and provide a framework for engineering enhanced heat resilience in crops.
