Methylation deficiency of chromatin proteins is a non-mutational and epigenetic-like trait in evolved lines of the archaeon Sulfolobus solfataricus

Abstract

Edited by John M. Denu Archaea are a distinct and deeply rooted lineage that harbor eukaryotic-like mechanisms, including several that manage chromosome function. In previous work, the thermoacidophilic crenarchaeon, Sulfolobus solfataricus, was subjected to adaptive laboratory evolution to produce three strains, called SARC, with a new heritable trait of super acid resistance. These strains acquired heritable conserved transcriptomes, yet one strain contained no mutations. Homologous recombination without allele replacement at SARC acid resistance genes caused changes in both phenotype and expression of the targeted gene. As recombination displaces chromatin proteins, their involvement was predicted in the SARC trait. Native chromatin proteins are basic and highly abundant and undergo post-translational modification through lysine monomethylation. In this work, their modification states were investigated. In all SARC lines, two chromatin proteins, Cren7 and Sso7d, were consistently undermethylated, whereas other chromatin proteins were unaltered. This pattern was heritable in the absence of selection and independent of transient exposure to acid stress. The bulk of Sso7d was undermethylated at three contiguous N-terminal lysine residues but not at central or C-terminal regions. The N-terminal region formed a solvent-exposed patch located on the opposite side of the binding domain associated with the DNA minor groove. By analogy to eukaryotic histones, this patch could interact with other chromosomal proteins and be modulated by differential post-translational modification. Previous work established an epigenetic-like mechanism of adaptation and inheritance in S. solfataricus. The identification of heritable epigenetic marks in this work further supports the occurrence of an epigenetic process in archaea.

Conservation of an Ancient Oxidation Response That Controls Archaeal Epigenetic Traits Through Chromatin Protein Networks

“…Prior work indicated that heritable hypomethylation of chromatin proteins and their binding to particular genes may mediate the SARC traits (10,12). However, these proteins bind the minor groove and their methylated residues are on solvent-facing surfaces (10) that do not appear to alter DNA-binding affinity (17,32). Therefore, it was predicted that the location and binding affinity of these proteins was invariant between wild type and SARC strains.…”

“…In eukaryotic histones, methylation changes on the solvent facing surfaces of histone cores do not alter DNA-binding affinity but can dramatically alter transcription and DNA repair through protein-protein interactions (23,37). Johnson et al found Cren7 and Sso7D were modified at solvent facing residues and not at DNA-contacting sites (10). Furthermore, methylation state does not alter DNA-binding affinity (17,32).…”

“…Although the euryarchaeotal phylum use histone homologs (8) to package DNA, they are not post translationally modified (9) and lack epigenetic activity. However, recent work indicates epigenetic mechanisms are operative in the crenarchaeotal phylum (4,10–12).…”

“…The crenarchaeote and thermoacidophile, Sulfolobus solfataricus , was used in adaptive laboratory evolution experiments to improve acid resistance (11). Surprisingly, this and additional evolved traits appeared to arise through an epigenetic mechanism (4,10,12). Triplicate trials involving serial passage at sequentially lower pH values produced independent cell lines named super-acid-resistant Crenarchaeota (SARC) (11).…”

“…As DNA methylation in archaea is bacterial-like, the eukaryotic epigenetic mechanism of CpG site methylation is unlikely to occur in Sulfolobus (15). However, because chromatin proteins Sso7D (16) and Cren7 (17) are heritably hypomethylated (10), the SARC traits may instead be mediated by Cren7 and Sso7D and their modification state in a process analogous to that of undermodified eukaryotic histones.…”