Methylation, a new epigenetic mark for protein stability

Yang, Xiaodong; Lamb, Acacia; Chen, Lin Feng

doi:10.4161/epi.4.7.9787

Cited by 43 publications

(36 citation statements)

References 23 publications

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“…Supporting this, the acetylation of lysine 310 is specifically recognized by the bromodomains of Brd4, enhancing transactivation by NF-B (16). Similarly, methylated lysines 314 and 315 are likely recognized by some domain-containing E3 ligase for the ubiquitination and degradation of NF-B (40,41). Therefore, modifications of RelA by methylation or acetylation at specific sites could, in fact, dictate specific biological responses, reflecting the gain or loss of selective cofactors whose association with RelA is regulated by its state of modifications.…”

Section: Discussionmentioning

confidence: 90%

Functional Interplay between Acetylation and Methylation of the RelA Subunit of NF-κB

Yang¹,

Tajkhorshid

Chen

2010

Molecular and Cellular Biology

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104

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Posttranslational modifications of the RelA subunit of NF-B, including acetylation and methylation, play a key role in controlling the strength and duration of its nuclear activity. Whether these modifications are functionally linked is largely unknown. Here, we show that the acetylation of lysine 310 of RelA impairs the Set9-mediated methylation of lysines 314 and 315, which is important for the ubiquitination and degradation of chromatin-associated RelA. Abolishing the acetylation of lysine 310 either by the deacetylase SIRT1 or by mutating lysine 310 to arginine enhances methylation. Conversely, enhancing the acetylation of lysine 310 by depleting SIRT1 or by replacing lysine 310 with acetyl-mimetic glutamine inhibits methylation, thereby decreasing ubiquitination, prolonging the stability of chromatin-associated RelA, and enhancing the transcriptional activity of NF-B. The acetylation of lysine 310 of RelA interferes with its interaction with Set9. Based on structural modeling of the SET domain of Set9 with RelA, we propose that the positive charge of lysine 310 is critical for the binding of RelA to a negatively charged "exosite" within the SET domain of Set9.Together, these findings demonstrate for the first time an interplay between RelA acetylation and methylation and also provide a novel mechanism for the regulation of lysine methylation by acetylation.In several cases an interplay between different posttranslational modifications has been identified for histone and nonhistone proteins, with one modification either enhancing or inhibiting another modification (11,37,42). For example, the phosphorylation of serine 10 of histone H3 interferes with the methylation of lysine 9 and stimulates the acetylation of lysine 14 (4,5,23,24). The methylation of lysine 372 of p53 promotes its acetylation (19,21). These effects can be direct, in which one modification alters the conformation of the protein, thereby influencing the second modification, or can be indirect, in which the first modification results in the recruitment of an effector, which alters the other modification. The interplays between these modifications together with the distinct combinations of covalent modifications form the basis of the "histone code" and, probably, the "protein code" hypotheses (20,35).The inducible transcription factor NF-B plays an important role in regulating inflammatory responses, apoptosis, cell proliferation and differentiation, and tumorigenesis (12). The prototypical NF-B complex, a heterodimer of p50 and RelA, is sequestered in the cytoplasm by its assembly with the inhibitor IB␣. Upon stimulation, the IB kinase (IKK) complex is activated, leading to the phosphorylation and degradation of IB␣, the nuclear translocation of NF-B, and the activation of its target genes (12). Once in the nucleus, the RelA subunit of NF-B undergoes a series of stimulus-coupled posttranslational modifications, including phosphorylation, acetylation, and methylation. These modifications impose various effects on nuclear NF-B, regulating both ...

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Section: Discussionmentioning

confidence: 90%

Functional Interplay between Acetylation and Methylation of the RelA Subunit of NF-κB

Yang¹,

Tajkhorshid

Chen

2010

Molecular and Cellular Biology

Self Cite

119

104

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“…has been suggested to increase the stability of proteins from Eukarya and Archaea (12,26,62,63). Because proteins are extensively methylated in S. islandicus, and aKMT is responsible for much of the protein lysine methylation in this organism, we were interested in learning if cellular proteins from the mutant differed from those from the parental strain in thermal stability.…”

Section: Cellular Proteins From the Parental And The Akmt Deletion Mumentioning

confidence: 99%

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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“…SET domain enzymes represent a family of S-adenosylmethionine (AdoMet) 3 -dependent methyltransferases that catalyze the site-specific methylation of protein lysyl residues in a host of proteins, including histones, transcription factors, chromatin-modifying enzymes, ribosomal subunits, and other substrates (1)(2)(3). In many instances, these modifications serve to recruit effector proteins that recognize methyl-lysyl residues in a sequence-dependent fashion (4).…”

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confidence: 99%

SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation

Rizzo

Couture

Dirk

et al. 2010

Journal of Biological Chemistry

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SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine ⑀-amino group. To elucidate the molecular mechanism underlying this specificity, we have characterized the Y245A and Y305F mutants of the human KMT SET7/9 (also known as KMT7) that alter its product specificity from a monomethyltransferase to a di-and a trimethyltransferase, respectively. Crystal structures of these mutants in complex with peptides bearing unmodified, mono-, di-, and trimethylated lysines illustrate the roles of active site water molecules in aligning the lysine ⑀-amino group for methyl transfer with S-adenosylmethionine. Displacement or dissociation of these solvent molecules enlarges the diameter of the active site, accommodating the increasing size of the methylated ⑀-amino group during successive methyl transfer reactions. Together, these results furnish new insights into the roles of active site water molecules in modulating lysine multiple methylation by SET domain KMTs and provide the first molecular snapshots of the mono-, di-, and trimethyl transfer reactions catalyzed by these enzymes.SET domain enzymes represent a family of S-adenosylmethionine (AdoMet) 3 -dependent methyltransferases that catalyze the site-specific methylation of protein lysyl residues in a host of proteins, including histones, transcription factors, chromatin-modifying enzymes, ribosomal subunits, and other substrates (1-3). In many instances, these modifications serve to recruit effector proteins that recognize methyl-lysyl residues in a sequence-dependent fashion (4). In addition, SET domain KMTs exhibit product specificity, defined as their ability to catalyze mono-, di-, or trimethylation of the lysine ⑀-amino group. This specificity is biologically relevant because many methyllysine-binding proteins can discriminate among different degrees of lysine methylation (4). Thus, both the site and degree of lysine methylation are critical to recognition by effector proteins.Structural and functional studies have identified a Phe/Tyr switch in the active site of SET domain KMTs that governs their respective product specificities (5, 6). According to this model, KMTs that possess a tyrosine in the Phe/Tyr switch site are limited to catalyzing lysine monomethylation, whereas enzymes that possess a phenylalanine or another hydrophobic residue in this position display di-or trimethyltransferase activity. Mutational analysis of various SET domain KMTs, including DIM-5 (KMT1) (6), SET7/9 (6), G9A (KMT1C) (5), and SET8 (also known as PR-SET7 and KMT5A) (7,8), has demonstrated that substitutions in the Phe/Tyr switch result in predictable changes in product specificity. Several models have been proposed to explain the mechanism by which the Phe/Tyr switch site governs this specificity, including variations in the diameter of the active site due to the size of Phe/Tyr switch residue and steric hindrance by t...

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Methylation, a new epigenetic mark for protein stability

Cited by 43 publications

References 23 publications

Functional Interplay between Acetylation and Methylation of the RelA Subunit of NF-κB

Functional Interplay between Acetylation and Methylation of the RelA Subunit of NF-κB

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

SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation

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