The emerging field of dynamic lysine methylation of non-histone proteins

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Post-translational modifications (PTMs) regulate protein structure and function. Lysine methylation abundantly decorates histone proteins and has recently been detected on non-histone proteins. In particular, the tumor suppressor and transcription factor p53 has provided a model for lysine methylation on a non-histone protein. As found for histones, lysine methylation is dynamic and can be reversed by demethylation. Lysine methylation regulates function via several distinct mechanisms. Methyl lysine provides docking sites for binding of effector proteins. Methylation can serve to inhibit alternate PTMs on the same lysine residue. In addition, lysine can be monomethylated, dimethylated, or trimethylated, and these levels of methylation correlate with distinct genomic locations and functions. Taking into account combinatorial activity with numerous other PTMs, lysine methylation provides enormous functional diversity and regulatory complexity.

Introduction

Post-translational modifications (PTMs) regulate protein structure and function. While protein phosphorylation of serine/threonine and tyrosine are the most intensively studied modifications, lysine has emerged over the past decade as a crucial amino acid residue. Lysines can be modified by small chemical changes, such as acetylation, and by large ‘peptide’ modifications, such as ubiquitylation and sumoylation. Modification of lysine both reduces its positive charge and changes the structure of the side chain. Thus, lysine modifications have the potential to alter function directly via increasing negative charge, and/or to influence activity indirectly by providing a novel interface for docking of cognate proteins. In addition, the fact that alternate modifications occur on lysine provides another level of regulation, since the presence of one inhibits attachment of the other modifications.

This review focuses on the newest member of the family of lysine modifications, that is, lysine methylation. Methylation is arguably the most ‘exciting’ modification within the lysine group because many interesting layers of regulation occur for methylation, as discussed below. By far most of our understanding of lysine methylation comes from the study of histone substrates; hence, the most salient observations will be briefly discussed below. However, the study of non-histone lysine methylation is poised to explode. Indeed, a parallel can be made to lysine acetylation, whose study began to skyrocket five years preceding lysine methylation with identification of the first histone acetylation enzymes but was then further enhanced by the identification of non-histone lysine acetylation substrates [1]. Currently there are many more than 100 non-histone proteins shown to be modified by lysine acetylation, and there is little doubt that methylation will prove to be similarly common among non-histone proteins.

Section snippets

Lysine modifications on histone proteins

Although histone lysine methylation has been known for decades [2], the first enzyme responsible for lysine methylation and its cognate methylation site was discovered in 2000. The first identified enzymatic activity was found to be harbored within SUV39H1 [3••], containing an enzymatic domain that was previously recognized as conserved structurally and named SET (suppressor of variegation, enhancer of zeste and trithorax) [4]. The SET domain occurs in a large family of evolutionarily conserved

p53 provides a model for lysine modification

p53 is an important tumor suppressor, and is mutated in greater than 50% of all human cancers [22]. One important function of p53 is as a DNA binding protein and classical transcriptional activator [22]. Phosphorylation of p53 has been intensively investigated because of its obvious role as the end product of signal transduction in the nucleus, leading to stimulation of p53 DNA binding and ability to activate transcription [23]. More recently, p53 has been shown to be regulated by lysine

p53 is regulated by lysine methylation

Recently, lysine methylation has emerged as a novel modification of p53 and three methylation sites have been identified: K370, K372, and K382 (Figure 2b and Table 1) [25••, 26••, 27••]. It is interesting and pertinent to function (see below) that these same p53 lysine residues are subject to acetylation/ubiquitylation/sumoylation [23]. Also fascinating is a direct parallel to mechanisms on histones exerted by these modification classes, that is, acetylation correlates only with activation of

Dam1 methylation by Set1

A genetic approach to discover new targets of Set1, the histone H3K4 methyltransferase in S. cerevisiae, revealed a novel role for Set in chromosome segregation. Surprisingly the target was not histone but rather the kinetochore protein, Dam1, and the methylation was at lysine 233 (K233) (Table 1) [32••]. Methylation at K233 in Dam1 inhibits the phosphorylation of neighboring residues by Ipl Aurora kinase. Phosphorylation of Dam1 by Ip1 plays an important role during chromosome segregation.

Other non-histone proteins are lysine methylation targets

A large number of additional proteins are lysine methylated in vitro and have been characterized to varying degrees in vivo (Table 1). These may be bona fide methylation substrates; however, in these examples a clear demonstration of methylation in vivo, as well as physiological mechanisms, has been limited. This is largely because in these cases methylation site-specific antibodies have not been used to unequivocally establish the existence of methylation in vivo. Examples include

Biological functions and future studies of lysine methylation on non-histone proteins

Multiple molecular mechanisms may be affected by lysine methylation of non-histone proteins to alter their function, as exemplified in the preceding examples. One type of functional effect is direct alteration of protein function or stability. In the case of p53, K372me1 induces transcription by enhancing protein stability via blocking of K372 ubiquitylation and subsequent proteolysis [25••]. In another case, kinase activity of VEGFR1 is enhanced by Smyd3-mediated lysine 831 dimethylation

References and recommended reading

Papers of particular interest, published within the annual period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Glossary

SET
suppressor of variegation, enhancer of zeste and trithorax
SUV39H1
suppressor of variegation 3–9 homolog 1
Smyd2
SET and MYND domain containing protein 2
LSD1
lysine-specific demethylase 1
BHC110
BRAF35–HDAC complex 110
Rubisco
ribulose 1,5-bisphosphate carboxylase/oxygenase
SS
small subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase
LS
large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase
LSMT
LS lysine 14 is trimethylated (K14me3) by LS methyltransferase
Rkm1
ribosomal lysine

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