Nonmutational mechanism of inheritance in the Archaeon
            <i>Sulfolobus solfataricus</i>

Payne, Sophie; McCarthy, Samuel; Johnson, Tyler B.; North, Erica M; Blum, Paul H.

doi:10.1073/pnas.1808221115

Cited by 12 publications

(32 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In assessing the impact of adaptive evolution on Cren7 and Sso7d lysine methylation, it was found that these proteins were under‐methylated, relative to cells not exposed to the adaptive regime . As the decreased methylation of Cren7 and Sso7d was not due to mutations of the encoding genes in the evolved strains and was, moreover, found to be a hereditable trait, such hypomethylation was deemed to reflect the epigenetic system recently described in this organism that was assigned responsibility for adaption to enhanced temperature and acidity . Moreover, hypomethylation in Cren7 was N ‐terminal‐specific, occurring at lysines 5, 7, and 40 but not at lysine residues found in the central or C‐terminal regions of the protein.…”

Section: Changing the Ptms That Decorate Archaeal Proteins As A Functmentioning

confidence: 99%

Modifying Post‐Translational Modifications: A Strategy Used by Archaea for Adapting to Changing Environments?

Eichler

2020

BioEssays

View full text Add to dashboard Cite

In concert with the selective pressures affecting protein folding and function in the extreme environments in which they can exist, proteins in Archaea have evolved to present permanent molecular adaptations at the amino acid sequence level. Such adaptations may not, however, suffice when Archaea encounter transient changes in their surroundings. Post‐translational modifications offer a rapid and reversible layer of adaptation for proteins to cope with such situations. Here, it is proposed that Archaea further augment their ability to survive changing growth conditions by modifying the extent, position, and, where relevant, the composition of different post‐translational modifications, as a function of the environment. Support for this hypothesis comes from recent reports describing how patterns of protein glycosylation, methylation, and other post‐translational modifications of archaeal proteins are altered in response to environmental change. Indeed, adjusting post‐translational modifications as a means to cope with environmental variability may also hold true beyond the Archaea.

show abstract

Section: Changing the Ptms That Decorate Archaeal Proteins As A Functmentioning

confidence: 99%

Modifying Post‐Translational Modifications: A Strategy Used by Archaea for Adapting to Changing Environments?

Eichler

2020

BioEssays

View full text Add to dashboard Cite

show abstract

“…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).…”

Section: Introductionmentioning

confidence: 99%

“…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).…”

Section: Introductionmentioning

confidence: 99%

“…All SARC had a 100-fold increase in acidophily and 10-fold increase in resistance to the common oxidative microbicide sulfite, supporting the link between pH and oxidative stress (11–14). These traits were accompanied by a conserved and heritable transcriptome of “SARC genes” related to acid tolerance that was retained after passage without selection (11,12). In addition, SARC had increased genome integrity manifested as reduced mutation and transposition rates relative to a control strain passaged without selection.…”

Section: Introductionmentioning

confidence: 99%

“…In addition, SARC had increased genome integrity manifested as reduced mutation and transposition rates relative to a control strain passaged without selection. Although mutations that explained the SARC traits were predicted, the genome of one of the SARC lines (SARC-I), had no mutations, transpositions or rearrangements relative to its parent (SULG) after extensive PCR, resequencing and bioinformatic analysis (12). Therefore, an epigenetic mechanism was proposed to explain the evolved traits (12).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Payne

Facciotti

Cott

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

21Epigenetic variants of the archaeon Sulfolobus solfataricus called SARC have evolved heritable traits 22 including extreme acid resistance, enhanced genome integrity and a conserved "SARC" transcriptome 23 related to acid resistance. These traits appear to result from altered chromatin protein function related 24 to the heritable hypomethylation of chromatin proteins Cren7 and Sso7D. To clarify how this might 25 occur, ChIPseq and Affinity Purification Mass Spectrometry (AP-MS) were used to compare Cren7 and 26 Sso7D genome binding sites and protein networks between lineages (wild type and SARC) and culture 27 pH (pH 1 and 3). All SARC transcriptome loci were bound by these chromatin proteins but with invariant 28 patterns indicating binding alone was insufficient to mediate the SARC traits. In contrast, chromosome 29 association varied at other loci. Quantitative AP-MS was then used to identify protein interaction 30 networks and these included transcription and DNA repair proteins implicated in the evolved heritable 31 traits that varied in abundance between SARC and wild type strains. Protein networks included most of 32 the S-adenosylmethionine (SAM) synthesis pathway including serine hydroxymethyltransferase (SHMT), 33 whose abundance varied widely with culture pH. Because epigenetic marks are coupled to SAM pools 34 and oxidative stress in eukaryotes, occurrence of a similar process was investigated here. Archaeal SAM 35 pools were depleted by treatment with SAM pathway inhibitors, acid or oxidative stress and, like 36 eukaryotes, levels were raised by vitamin B12 and methionine supplementation. We propose that in 37 archaea, oxidation-induced SAM pool depletion acting through an SHMT sensor, drove chromatin 38 protein hypomethylation and thereby protein network changes that established the evolved SARC 39 epigenetic traits. 40 Significance Statement 41Archaea and eukaryotes share many molecular processes, including chromatin-mediated epigenetic 42 inheritance of traits. As with eukaryotes, archaeal protein complexes were formed between trait-related 43 proteins and chromatin proteins, subject to chromatin protein methylation state. Oxidation-induced 44 depletion of S-adenosylmethionine (SAM) pools likely resulted in chromatin protein hypomethylation. 45 Subsequent chromatin enrichment of serine hydroxymethyltransferase as a response to oxidative stress 46 could modulate methylation at specific genomic loci. The interplay between archaeal metabolism and 47 chromatin appear consistent with patterns observed in eukaryotes and indicate the existence of an 48 ancient oxidation signal transduction pathway controlling epigenetics. 49 50 Immunoprecipitation for ChIP-Seq. Triplicate crosslinked cell pellets were sonicated and subjected to 105 chromatin immunoprecipitation using polyclonal antibody serum for Cren7 or Sso7D as described 106 previously (30) with alterations described in and SI Appendix, Supplemental Methods. 107ChIP-Seq and data analysis. DNA samples were blunt ended, A-tailed, ligated to barcoded a...

show abstract