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Abstract
Adaptive laboratory evolution (ALE) is a method used to select for microbes with increased fitness during cultivation under experimentally imposed conditions for extended periods of time. This allows organisms with desirable phenotypes to evolve naturally through sequential propagation, relying on the inherent capacity of the organism to introduce adaptive mutations. The conditions can be gradually changed as the organism adapts, leading to selection for more extreme traits. Here, adaptive laboratory evolution was used to push the boundaries of life by adapting extremophilic archaea to even more extreme conditions. The metal-resistant lithoautotroph Metallosphaera sedula was adapted to become significantly more resistant to both copper and arsenic, while thermoacidophile Sulfolobus solfataricus was adapted to growth under much more acidic conditions. Analysis of the acid-adapted cell lines of S. solfataricus showed evidence that suggests the presence of epigenetic mechanisms in archaea, with chromatin proteins playing a role in regulating gene expression. Some of these chromatin proteins also showed lineage-specific alterations to the post-translational modification (PTM) state of the Cren7 and Sso7d chromatin proteins, similar to the heritable changes in histone PTM state that are known to affect gene expression in eukaryotes. Further analysis of these chromatin proteins was done to characterize their genome-wide DNA-binding patterns in vivo, and revealed distinct functions for these two proteins despite their highly similar structures.
