Substrate and Functional Diversity of Protein Lysine Post-translational Modifications

Abstract

Lysine post-translational modifications (PTMs) are widespread and versatile protein PTMs that are involved in diverse biological processes by regulating the fundamental functions of histone and non-histone proteins. Dysregulation of lysine PTMs is implicated in many diseases, and targeting lysine PTM regulatory factors, including writers, erasers, and readers, has become an effective strategy for disease therapy. The continuing development of mass spectrometry (MS) technologies coupled with antibody-based affinity enrichment technologies greatly promotes the discovery and decoding of PTMs. The global characterization of lysine PTMs is crucial for deciphering the regulatory networks, molecular functions, and mechanisms of action of lysine PTMs. In this review, we focus on lysine PTMs, and provide a summary of the regulatory enzymes of diverse lysine PTMs and the proteomics advances in lysine PTMs by MS technologies. We also discuss the types and biological functions of lysine PTM crosstalks on histone and non-histone proteins and current druggable targets of lysine PTM regulatory factors for disease therapy.

Keywords: Acylation; Drug target; PTM crosstalk; Protein lysine PTM; Regulatory enzyme.

Figure 1

Structures of lysine acylation

Figure 2

Writers, readers, and erasers of novel histone acylations Writers that catalyze the addition include HAT1, GNAT family, p300/CBP family, and MYST family. Readers that recognize novel acylations include bromodomain-, YEATS domain-, and DPF domain-containing proteins. Erasers that catalyze the removal include Class I and Class III HDACs. These regulators are listed with their regulated modification types and sites. Red triangles and green circles represent different histone acylations. HAT, histone acetyltransferase; GNAT, GCN5-related N-acetyltransferase; GCN5, general control non-depressible 5; PCAF, p300/CBP-associated factor; MOZ, monocytic leukemic zinc finger; MORF, MOZ-related factor; MOF, males absent on the first; HBO1, HAT binding to origin recognition complex 1; BRD, bromodomain-containing protein; BAF, BRG1/BRM-associated factor; PBAF, polybromo-associated BAF; CECR2, cat eye syndrome chromosome region candidate 2; BRDT, bromodomain testis-specific protein; Taf, transcription initiation factor TFIID subunit; AF9, ALL1-fused gene from chromosome 9 protein; GAS41, glioma-amplified sequence 41; YEATS2, YEATS domain-containing protein 2; DPF, double PHD finger; HDAC, histone deacetylase; SIRT, sirtuin.

Figure 3

Lysine methylation enrichment strategies for LC-MS/MS analysis A. Protein-level enrichment includes methyl-recognizing domain-based strategy. B.–D. Peptide-level enrichment includes pan-anti-methylation antibody-based strategy (B), SCX-based chromatography (C), and chemical proteomics approach (D). LC, liquid chromatography; MS, mass spectrometry; SCX, strong cation-exchange.

Figure 4

The catalytic process and MS-based identification strategies of ubiquitin-like modifications A. The catalytic process of ubiquitin-like modifications by E1/E2/E3 enzymes and de-modified enzymes. B.–E. The MS-based identification strategies of ubiquitination (B), neddylation (C), and sumoylation (D and E). DUB, deubiquitinating enzyme; Ub, ubiquitin; NEDD8, neural precursor cell expressed developmentally downregulated protein 8; SUMO, small ubiquitin-like modifier; WaLP, wild-type α-lytic protease.

Figure 5

Examples of lysine PTM crosstalk on histone and non-histone proteins A. Examples of lysine PTM crosstalk on histone. Left: methylation and acetylation on H3K27 compete each other, acetylation on H3K27 enhances the level of methylation on H3K4, and methylation on H3K4 promotes the acetylation on H4K16. Right: ubiquitination and acetylation on H2BK120 compete each other, and co-occurrence of ubiquitination on H2BK120 and acetylation on H4K16 enhances the methylation on H3K79. B. Examples of crosstalk between lysine ubiquitination and other lysine PTMs on non-histone proteins. Upper: methyl-dependent ubiquitination. Middle: competition between methylation and ubiquitination at the same lysine site. Lower: auto-ubiquitination of E3 ligases regulates the ubiquitination of substrates. PTM, post-translational modification.