Abundant Lysine Methylation and N-Terminal Acetylation in Sulfolobus islandicus Revealed by Bottom-Up and Top-Down Proteomics

Vorontsov, Egor; Rensen, Elena; Prangishvili, David; Krupovìč, Mart; Chamot‐Rooke, Julia

doi:10.1074/mcp.m116.058073

Cited by 39 publications

(36 citation statements)

References 69 publications

(71 reference statements)

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“…Apart from methylation at K16, additional PTMs were also detected. Nt‐acetylation occurred extensively (97% of the spectra for N‐terminal peptides) on the penultimate amino acid serine, as reported previously (Mackay et al ., ; Vorontsov et al ., ). Other PTMs included methylation at lysine residues other than K16 (i.e., K40, K64 and K97), aspartate residues (i.e., D51 and D81) and a glutamine residue (Q75), acetylation at lysine residues (i.e., K48, K64 and K68) and deamidation at asparagine residues (i.e., N31 and N58) and a glutamine residue (i.e., Q32).…”

Section: Resultsmentioning

confidence: 97%

Insights into the post‐translational modifications of archaeal Sis10b (Alba): lysine‐16 is methylated, not acetylated, and this does not regulate transcription or growth

Cao

Wang

Liu

et al. 2018

Molecular Microbiology

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Nucleic acid-binding proteins of the Sac10b family, also referred to as Alba (for acetylation lowers binding affinity), are highly conserved in Archaea. It was reported that Sso10b, a Sac10b homologue from Sulfolobus solfataricus, was acetylated at the ɛ-amino group of K16 and the α-amino group of the N-terminal residue. Notably, acetylation of K16 reduced the affinity of Sso10b for DNA and de-repressed transcription in vitro. Here, we show that Sis10b, a Sac10b homologue from Sulfolobus islandicus, underwent a range of post-translational modifications (PTMs). K16 in Sis10b as well as Sso10b was not acetylated. Substitution of K16 for R16, which resulted in the loss of the PTMs at the site, showed little effect on the growth of the cell and resulted in only a slight change in the expression of a very small fraction of the genes. The N-terminus of Sis10b was nearly completely N -acetylated. The reduction or loss of the terminal acetylation led to a significant increase in the cellular concentration of Sis10b, suggesting the involvement of the modification in the control of the turnover of the protein. These results have clarified the PTMs of Sac10b homologues and shed light on the proposed roles of acetylation of the protein.

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Section: Resultsmentioning

confidence: 97%

Insights into the post‐translational modifications of archaeal Sis10b (Alba): lysine‐16 is methylated, not acetylated, and this does not regulate transcription or growth

Cao

Wang

Liu

et al. 2018

Molecular Microbiology

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“…New evidence in eukaryotes suggest that histones store methyl groups and that histone undermethylation is a controlled process (26). In S. solfataricus , the calculated protein-bound methyl pool (27) is two orders of magnitude greater than the soluble SAM pool per cell (28), supporting this idea. The studies described here were undertaken to identify factors controlling archaeal chromatin protein methylation that might link epigenetics, oxidative stress and metabolism.…”

Section: Introductionmentioning

confidence: 84%

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

Payne

Facciotti

Cott

et al. 2019

Preprint

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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...

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“…Given the pace at which proteomics technology is advancing, it is reasonable to expect that we will soon be able to readily assess differences in the extent, positions, and contents of different PTMs decorating a protein in response to any cell‐level change, and not just in extremophilic Archaea. Indeed, the growth phase‐dependent methylation seen in the archaeon S. islandicus , the growth phase‐dependent pupylation seen in the bacterium Mycobacterium smegmatis , and the differentiation stage‐dependent glycosylation and distinct outcomes associated with differential protein ubiquitination in Eukarya all hint that this may be the case …”

Section: Discussionmentioning

confidence: 99%

“…Indeed, the growth phasedependent methylation seen in the archaeon S. islandicus, the growth phase-dependent pupylation seen in the bacterium Mycobacterium smegmatis, and the differentiation stage-dependent glycosylation and distinct outcomes associated with differential protein ubiquitination in Eukarya all hint that this may be the case. [74,101,104,105]…”

Section: Discussionmentioning

confidence: 99%

“…These complementary approaches have been successfully combined to accurately address changes in methylation and acetylation in the Sulfolobus islandicus proteome. [101] Such combined mass spectrometry analysis using ever increasingly sensitive machines, along with the use of improved peptide labeling protocols and PTM affinity-enrichment techniques, will allow for better and more routine qualitative and quantitative analysis of PTMs. [102] Accordingly, future studies aimed at assessing the role of modulated post-translational modifications in allowing Archaea and their proteins to adapt to environmental change could exploit a combination of the strategies described above on samples taken from cells exposed to a range of surroundings.…”

Section: What's Next?mentioning

confidence: 99%

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

Eichler

2020

BioEssays

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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.

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Abundant Lysine Methylation and N-Terminal Acetylation in Sulfolobus islandicus Revealed by Bottom-Up and Top-Down Proteomics

Cited by 39 publications

References 69 publications

Insights into the post‐translational modifications of archaeal Sis10b (Alba): lysine‐16 is methylated, not acetylated, and this does not regulate transcription or growth

Insights into the post‐translational modifications of archaeal Sis10b (Alba): lysine‐16 is methylated, not acetylated, and this does not regulate transcription or growth

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

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

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