bioRxiv2023
The SAM1 and SAM2 genes encode for S-AdenosylMethionine (AdoMet) synthetase enzymes, with AdoMet serving as the main methyl donor. We have previously shown that independent deletion of these genes alters chromosome stability and AdoMet concentrations in opposite ways in S. cerevisiae. To characterize other changes occurring in these mutants, we grew wildtype, sam1{Delta}/sam1{Delta}, and sam2{Delta}/sam2{Delta} strains in 15 different Phenotypic Microarray plates with different components, equal to 1440 wells, and measured for growth variations. RNA-Sequencing was also carried out on these strains and differential gene expression determined for each mutant. In this study, we explore how the phenotypic growth differences are linked to the altered gene expression, and thereby predict the mechanisms by which loss of the SAM genes and subsequent AdoMet level changes, impact S. cerevisiae pathways and processes. We present six stories, discussing changes in sensitivity or resistance to azoles, cisplatin, oxidative stress, arginine biosynthesis perturbations, DNA synthesis inhibitors, and tamoxifen, to demonstrate the power of this novel methodology to broadly profile changes due to gene mutations. The large number of conditions that result in altered growth, as well as the large number of differentially expressed genes with wide-ranging functionality, speaks to the broad array of impacts that altering methyl donor abundance can impart, even when the conditions tested were not specifically selected as targeting known methyl involving pathways. Our findings demonstrate that some cellular changes are directly related to AdoMet-dependent methyltransferases and AdoMet availability, some are directly linked to the methyl cycle and its role is production of several important cellular components, and others reveal impacts of SAM gene mutations on previously unconnected pathways. AUTHOR SUMMARYS-AdenosylMethionine, or AdoMet, is the main methyl donor in all cells. Methylation reactions are used broadly and impact numerous processes and pathways. The SAM1 and SAM2 genes of Saccharomyces cerevisiae are responsible for producing the enzymes called S-Adenosylmethionine synthetases, which make AdoMet from methionine and ATP. Our previous research showed that when these genes are deleted independently, they have opposite effects on AdoMet levels and chromosome stability. To advance our understanding of the wide array of changes going on in cells with these gene deletions we characterized our mutants phenotypically, growing in various different conditions to look for growth changes, and for their different gene expression profiles. In this study, we investigated how the differences in growth patterns are connected to the altered gene expression, and thereby were able to predict the mechanisms through which the loss of the SAM genes affects different pathways. Our investigations have uncovered novel mechanisms of sensitivity or resistance to many conditions and shown linkages to AdoMet availability, AdoMet-dependent methyltransferases, methyl cycle compounds, or new connections to sam1 and sam2 gene deletions.