The Adaptive Landscape of Genetic Interaction Network Has No Impact on Yeast Adaptive Evolution

Abstract

In both data sets, we identified over-representation of genes involved directly or indirectly in genome stability and ploidy maintenance: CIN8, \u200bCSM3, \u200bEAP1, ISW1, KIP1, MEI5 \u200b(this was unexpected because this gene encodes a meiosis-specific protein), PAN2, PAT1, PDE2, RIM15, RSC30, RFC1 (although the significant 2/3 truncation of the latter should be lethal), SRB8, TEL1, UBX6, \u200band \u200bYNG2\u200b. This can be easily explained because genome instability usually leads to changes in ploidy which in yeast are evolutionarily beneficial. Another over-represented group of genes comprised those linked to metabolism or nutrient-sensing: HXK2, HXT13, IRA1 ART5, PBP1, YOR1, CAT8, COX6, \u200band COX4\u200b. We assume that the inactivation of these genes could be linked to reducing unnecessary processes in the given environmental conditions. It has to be noticed that some nonsense mutations identified by Echenique \u200bet al\u200b. (2019) were compensated for by mutations in other genes. For instance, a mutation in \u200bADE2 was compensated by \u200bade6\u200b. The accumulation of the red pigment in \u200bade2 \u200bcells is likely to cause an impaired growth. However, \u200bade6 \u200bis epistatic to \u200bade2 and blocks adenine biosynthesis before the accumulation of the red pigment, resulting in a white cell phenotype (Roman (1956, 1957)). Some truncations studied by Echenique \u200bet al\u200b., (2019) e.g., \u200bPEP8, VPS29, ERG3, SOK2, and again \u200bADE2 were compensated for by mutations in the \u200bSTE4, STE5, STE7, STE11, or \u200bSTE50 genes linked to stress response, MAP kinases signaling, and pheromone response and mating pathways. It cannot be excluded that the compensatory mutations in these genes led to a mating-type switch and in consequence allowed diploidization. Truncation/nonsense Frameshift Szamecz \u200bet al\u200b., (2014) ARP3, ART5, CAT8, DNM1, GEA1, HXT13, IRA1, KIP1, PAT1, PBP1, PUF4, RFC1, RIM15, RSC30, SRB8, UBX6, WHI2, YOR1, YCR025C, YMR010W CSM3, MNC1, PEX6, SUN4, TMN3, TEL1, YKR040C