A Prototypic Lysine Methyltransferase 4 from Archaea with Degenerate Sequence Specificity Methylates Chromatin Proteins Sul7d and Cren7 in Different Patterns

Niu, Yanling; Xia, Yisui; Wang, Sishuo; Li, Jiani; Niu, Caoyuan; Li, Xiao; Zhao, Yuehui; Xiong, Huiyang; Li, Zhen; Lou, Huiqiang; Cao, Qinhong

doi:10.1074/jbc.m113.452979

Cited by 29 publications

(43 citation statements)

References 54 publications

(95 reference statements)

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“…In any case, the presence of multiple methylation states in proteins may serve a regulatory role that remains to be understood. No apparent sequence preference by aKMT was detected through the analysis of sequences flanking methylated lysine residues, in agreement with the previous finding that the enzyme exhibits broad substrate specificity (35,36). Given the observation that ϳ21% of the total lysine residues in cellular proteins were methylated and the report that lysine residues undergoing methylation were often found on the surface of a protein (6), most, if not all, lysine residues accessible to methyltransferases are presumably potential targets of posttranslational modification by protein methyltransferases in the cell.…”

Section: Discussionsupporting

confidence: 77%

“…S2). This finding agrees with the observation that the intracellular level of aKMT, as determined by immunoblotting using anti-aKMT antibodies, was nearly constant throughout the growth phase (data not shown; (35,36)) as well as at various temperatures within a tested range. Therefore, we subjected samples containing the same number of either the parental or the mutant cells (OD 600 ϭ ϳ1.0) to electrophoresis on a SDS-PAGE gel, followed by in-gel trypsin digestion and mass spectrometry.…”

Section: S Islandicus Defective In Akmt Is Viable But Shows Asupporting

confidence: 81%

“…Recently, we identified the first crenarchaeal protein lysine methyltransferase, designated as aKMT, from S. islandicus (35). This protein resembles methyltransferases of the eukaryotic Dot1 family (36). Notably, aKMT is capable of methylating several tested recombinant Sulfolobus proteins overproduced in Escherichia coli, exhibiting broad substrate specificity in vitro (35).…”

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confidence: 99%

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aKMT Catalyzes Extensive Protein Lysine Methylation in the Hyperthermophilic Archaeon Sulfolobus islandicus but is Dispensable for the Growth of the Organism

Chu

Zhu

Chen

et al. 2016

Molecular & Cellular Proteomics

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Protein methylation is believed to occur extensively in creanarchaea. Recently, aKMT, a highly conserved crenarchaeal protein lysine methyltransferase, was identified and shown to exhibit broad substrate specificity in vitro. Here, we have constructed an aKMT deletion mutant of the hyperthermophilic crenarchaeon Sulfolobus islandicus. The mutant was viable but showed a moderately slower growth rate than the parental strain under nonoptimal growth conditions. Consistent with the moderate effect of the lack of aKMT on the growth of the cell, expression of a small number of genes, which encode putative functions in substrate transportation, energy metabolism, transcriptional regulation, stress response proteins, etc, was differentially regulated by more than twofold in the mutant strain, as compared with that in the parental strain. Analysis of the methylation of total cellular protein by mass spectrometry revealed that methylated proteins accounted for ϳ2/3 (1,158/1,751) and ϳ1/3 (591/ 1,757) of the identified proteins in the parental and the mutant strains, respectively, indicating that there is extensive protein methylation in S. islandicus and that aKMT is a major protein methyltransferase in this organism. No significant sequence preference was detected at the sites of methylation by aKMT. Methylated lysine residues, when visible in the structure, are all located on the surface of the proteins. The crystal structure of aKMT in complex with S-adenosyl-L-methionine (SAM) or S-adenosyl homocysteine (SAH) reveals that the protein consists of four ␣ helices and seven ␤ sheets, lacking a substrate recognition domain found in PrmA, a bacterial homolog of aKMT, in agreement with the broad substrate specificity of aKMT. Our results suggest that aKMT may serve a role in maintaining the methylation status of cellular proteins required for the efficient growth of the organism under certain non-optimal conditions. Molecular & Cellular

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Section: Discussionsupporting

confidence: 77%

Section: S Islandicus Defective In Akmt Is Viable But Shows Asupporting

confidence: 81%

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confidence: 99%

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aKMT Catalyzes Extensive Protein Lysine Methylation in the Hyperthermophilic Archaeon Sulfolobus islandicus but is Dispensable for the Growth of the Organism

Chu

Zhu

Chen

et al. 2016

Molecular & Cellular Proteomics

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“…Top-down and bottom-up approaches are therefore complementary in this case, because top-down provides the exact number of simultaneously methylated lysine residues and the preferential modification locations, whereas bottom-up reveals minor methylation locations. This is in accordance with a previous report (51) showing that Cren7 is methylated on many residues, however the top-down analysis allows us to suggest that the N-terminal part is methylated preferentially.…”

Section: Label-free Relative Quantitation Of Protein Expression Betwesupporting

confidence: 81%

“…Alba1 is found to be acetylated at the N-terminal serine and occasionally oxidized on Met-20. The previous report states that Alba1 is not methylated in vivo and even in vitro under action of the promiscuous Sulfolobus protein methyltransferase aKMT4, which is known to methylate other chromatin proteins (51). However, our results unequivocally show that Alba1 is methylated at K-16.…”

Section: Fig 4 Summary Of the Top-down Lc-ms/ms Analysis Of The Saxcontrasting

confidence: 54%

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

Vorontsov

Rensen

Prangishvili

et al. 2016

Molecular & Cellular Proteomics

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Protein post-translational methylation has been reported to occur in archaea, including members of the genus Sulfolobus, but has never been characterized on a proteome-wide scale. Among important Sulfolobus proteins carrying such modification are the chromatin proteins that have been described to be methylated on lysine side chains, resembling eukaryotic histones in that aspect. To get more insight into the extent of this modification and its dynamics during the different growth steps of the thermoacidophylic archaeon S. islandicus LAL14/1, we performed a global and deep proteomic analysis using a combination of high-throughput bottom-up and top-down approaches on a single high-resolution mass spectrometer. 1,931 methylation sites on 751 proteins were found by the bottom-up analysis, with methylation sites on 526 proteins monitored throughout three cell culture growth stages: early-exponential, mid-exponential, and stationary. The top-down analysis revealed 3,978 proteoforms arising from 681 proteins, including 292 methylated proteoforms, 85 of which were comprehensively characterized. Methylated proteoforms of the five chromatin proteins (Alba1, Alba2, Cren7, Sul7d1, Sul7d2) were fully characterized by a combination of bottom-up and topdown data. The top-down analysis also revealed an increase of methylation during cell growth for two chromatin proteins, which had not been evidenced by bottom-up. These results shed new light on the ubiquitous lysine methylation throughout the S. islandicus proteome. Furthermore, we found that S. islandicus proteins are frequently acetylated at the N terminus, following the removal of the N-terminal methionine. This study highlights the great value of combining bottom-up and top-down proteomics for obtaining an unprecedented level of accuracy in detecting differentially modified intact proteoforms. The data have been deposited to the ProteomeXchange with identifiers PXD003074

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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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A Prototypic Lysine Methyltransferase 4 from Archaea with Degenerate Sequence Specificity Methylates Chromatin Proteins Sul7d and Cren7 in Different Patterns

Cited by 29 publications

References 54 publications

aKMT Catalyzes Extensive Protein Lysine Methylation in the Hyperthermophilic Archaeon Sulfolobus islandicus but is Dispensable for the Growth of the Organism

aKMT Catalyzes Extensive Protein Lysine Methylation in the Hyperthermophilic Archaeon Sulfolobus islandicus but is Dispensable for the Growth of the Organism

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

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

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