The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast

The experimental evolution of laboratory populations of microbes provides an opportunity to observe the evolutionary dynamics of adaptation in real time. Until very recently, however, such studies have been limited by our inability to systematically find mutations in evolved organisms. We overcome this limitation by using a variety of DNA microarray-based techniques to characterize genetic changes—including point mutations, structural changes, and insertion variation—that resulted from the experimental adaptation of 24 haploid and diploid cultures of Saccharomyces cerevisiae to growth in either glucose, sulfate, or phosphate-limited chemostats for ∼200 generations. We identified frequent genomic amplifications and rearrangements as well as novel retrotransposition events associated with adaptation. Global nucleotide variation detection in ten clonal isolates identified 32 point mutations. On the basis of mutation frequencies, we infer that these mutations and the subsequent dynamics of adaptation are determined by the batch phase of growth prior to initiation of the continuous phase in the chemostat. We relate these genotypic changes to phenotypic outcomes, namely global patterns of gene expression, and to increases in fitness by 5–50%. We found that the spectrum of available mutations in glucose- or phosphate-limited environments combined with the batch phase population dynamics early in our experiments allowed several distinct genotypic and phenotypic evolutionary pathways in response to these nutrient limitations. By contrast, sulfate-limited populations were much more constrained in both genotypic and phenotypic outcomes. Thus, the reproducibility of evolution varies with specific selective pressures, reflecting the constraints inherent in the system-level organization of metabolic processes in the cell. We were able to relate some of the observed adaptive mutations (e.g., transporter gene amplifications) to known features of the relevant metabolic pathways, but many of the mutations pointed to genes not previously associated with the relevant physiology. Thus, in addition to answering basic mechanistic questions about evolutionary mechanisms, our work suggests that experimental evolution can also shed light on the function and regulation of individual metabolic pathways

Protein kinase CK2: Systematic relationships with other posttranslational modifications

© Springer International Publishing Switzerland 2015. A wealth of biochemical and genetic evidence has demonstrated that protein kinase CK2 has critical roles in the regulation and execution of numerous biological processes. Large-scale proteomic and phosphoproteomics studies have further reinforced the widespread impact of CK2 on cellular events through interactions with many cellular proteins or protein complexes and through phosphorylation of a vast number of cellular proteins. Given its global participation in many fundamental processes, it is not surprising that CK2 has been implicated in numerous human diseases, a factor that has spurred interest in CK2 as a candidate for molecular- targeted therapy. Despite this growing profile, many questions regarding its precise mechanisms of regulation remain. In fact, several lines of evidence suggest that CK2 is constitutively active, leading to a speculation that CK2 is an unregulated enzyme. Accordingly, there is an apparent paradox that leads to the question of how an unregulated enzyme such as CK2 can be a participant in regulatory processes. In an effort to resolve this paradox, studies in our lab and others have focused on an investigation of the relationships between CK2 and other cellular pathways. Using a combination of computational predictions and database mining together with proteomic strategies and biochemical assays, we have been elucidating systematic relationships between CK2 and regulatory pathways where CK2 phosphorylation sites overlap other posttranslational modifications. Overall, these studies suggest intriguing mechanisms by which CK2 can participate in regulatory events and also how alterations in CK2 levels that accompany disease may promote pathological rewiring of regulatory pathways