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The diversity of modifications that a nascent peptide acquires as it is transported to its target cellular location is long established, as is the ability of tags such as phosphorylation and ubiquitylation to regulate signalling and protein turnover. But recently we have seen a renaissance of interest in the ability of additional modifications — from ubiquitin-like proteins to moieties such as sugars or methyl, acetyl and prenyl groups — to target specific sites in proteins and to coordinately exert dynamic control over protein function in diverse cell biological contexts. The articles in this series discuss new insights that have been gained into how ‘old and new’ modifications are regulated and recognized, and how they crosstalk with one another to control fundamental biological processes.
Recent studies have expanded our understanding of the mechanisms and functions of ubiquitylation. Pathogens rewrite ubiquitylation to promote infection through unconventional ubiquitylation involving lipids and sugars, and structural studies have revealed that ubiquitin functions involve elaborate multivalent interactions that regulate transcription or protein degradation.
Sumoylation regulates thousands of proteins, many of which are nuclear. Recent studies have implicated sumoylation in liquid–liquid phase separation and assembly of nuclear bodies, and have uncovered its roles in immunity and pluripotency and links to disease, thereby opening new therapeutic avenues.
During mammalian development, certain regulatory-gene promoters acquire both histone modifications associated with gene activation and with gene repression (bivalent chromatin), which is key to cell-lineage specification. Recent work has expanded our understanding of the molecular basis of bivalent chromatin and its roles in development and cancer.
Lysine acetyltransferases and lysine deacetylases regulate gene expression and protein function by controlling acetylation and deacetylation of histones and diverse non-histone proteins. The activity of lysine acetyltransferases and lysine deacetylases is regulated by cellular metabolic states, offering the potential for therapeutic modulation through dietary and pharmacological interventions.
Polycomb repressive complex 1 (PRC1) and PRC2 are important gene regulators in various physiological contexts, especially in development. Recent studies have uncovered the molecular mechanisms that enable mammalian PRC1 and PRC2 to identify their genomic target sites, modify chromatin properties and control transcription.
The histone modifiers Polycomb repressive complex 1 (PRC1) and PRC2 have important roles in development and disease, especially cancer. Recent studies have revealed the existence of various mutually exclusive PRC1 and PRC2 variants, and provided new insights into their molecular functions and physiological importance.
The mechanical and dynamic properties of microtubules are determined by their complement of subunits, known as tubulin isotypes, and the post-translational modifications found on these isotypes. This concept is known as the ‘tubulin code’. The regulation of microtubules and microtubule-associated proteins by this code is critical for the correct function of a range of tissues. Consequently, recent studies have linked perturbation of the tubulin code to disease, including neurodegenerative diseases.
The methylation of arginine residues regulates gene expression, DNA repair, growth factor signalling and liquid–liquid phase separation. Targeting this modification can thus be therapeutically relevant and inhibitors of arginine methylation are being tested in clinical trials, especially for neurodegenerative diseases and cancer.
The dynamic methylation of chromatin components — DNA, histones and RNA — is crucial in development, ageing and cancer. Therapies that target regulators of DNA and histone methylation in cancer have recently been developed. These promising therapies, which include strategies that may improve tumour immune surveillance, are already being tested in early-phase clinical trials.
Histone methylation regulates gene expression throughout animal development, governing processes as diverse as cell fate decisions, lineage specification, body patterning and organogenesis. Better understanding of the complex, context-specific roles of histone methylation in development will shed new light on the aetiology of developmental disorders.
By opposing protein ubiquitylation, deubiquitylating enzymes (DUBs) regulate various cellular processes, including protein degradation, the DNA damage response, cell signalling and autophagy. Many DUBs show high specificity for ubiquitin chain architecture and/or the protein substrate that they recognize, and have emerged as exciting therapeutic targets within the field of proteostasis.
The activity of many cell type-specific enhancers is regulated by histone deacetylase 3 (HDAC3), which acts in complex with various nuclear receptor co-repressors. HDAC3 is required for many aspects of mammalian development and physiology, including the metabolism of various organs, neuronal- and haematopoietic stem cell fate and function, lung and bone development and intestinal homeostasis.
Non-histone-lysine acetylation affects protein functions by modulating protein stability, interactions, subcellular localization and enzymatic activity and through crosstalk with other post-translational modifications. Acetylation regulates many cellular processes, such as transcription, DNA repair, signal transduction, protein folding and autophagy.
Ubiquitylation is a post-translational modification that modulates protein stability and regulates various cellular signalling pathways and cellular processes, including cell differentiation, proliferation and migration. Recent insights highlight its crucial role in development and how its deregulation is associated with several diseases.
Protein methylation was discovered over 50 years ago, but only with the advent of genomic and proteomic technologies could its mechanisms and cellular functions be studied in detail. Shi and Murn discuss the seminal discoveries in protein methylation research and highlight future directions for this field.
Many cellular proteins are reversibly modified byO-linked N-acetylglucosamine (O-GlcNAc) moieties on Ser and Thr residues. Studies on the mechanisms and functions of O-GlcNAcylation and its links to metabolism reveal the importance of this modification in the maintenance of cellular and organismal homeostasis.
In addition to acetylation, eight types of structurally and functionally different short-chain acylations have recently been identified as important histone Lys modifications: propionylation, butyrylation, 2-hydroxyisobutyrylation, succinylation, malonylation, glutarylation, crotonylation and β-hydroxybutyrylation. These modifications are regulated by enzymatic and metabolic mechanisms and have physiological functions, which include signal-dependent gene activation and metabolic stress.
Analysis of the available human small ubiquitin-like modifier (SUMO) proteomics data provided evidence for the sumoylation of thousands of proteins and residues, and clustered the sumoylated proteins into functional networks. Sumoylation is a frequent modification, occurring mostly on nuclear proteins, with functions including transcription, mRNA processing and the DNA-damage response.
Learning more about the biochemistry of protein prenylation (modification by isoprenoid lipids) and its functional effects on target CAAX proteins has provided opportunities for therapeutic intervention in a range of human diseases.
DNA methylation and H3K9 methylation are typically associated with gene silencing. Genetic, genomic, structural and biochemical data reveal functional connections between these two epigenetic marks. They also highlight how specialized protein domains that recognize the marks are essential for their establishment and maintenance at appropriate genomic loci.
Repressive histone Lys methyltransferases (KMTs) mediate gene silencing by methylating histone H3 Lys 9 (H3K9), H3K27 and H4K20. Progress has been made in our understanding of the biochemical and functional properties of KMTs, the mechanisms of their recruitment to chromatin and the interplay between them.
The year 2014 marks the 50th anniversary of the discovery of protein acetylation. In this Timeline article, Verdin and Ott discuss the identification of this modification, of its regulatory enzymes and of the roles of acetylation in transcription and other cellular processes, and provide an outlook on the future of the field.
Lys and Arg methylation on non-histone proteins regulates various signalling pathways, and its crosstalk with other post-translational modifications and with histone methylation affects cellular processes such as transcription and DNA damage repair. Advances in proteomics now allow us to decode the methylproteome and elucidate its functions.
Post-translational modification of proteins by NEDD8 has been mainly characterized in terms of the cullin–RING E3 ligase family. However, recent studies have indicated that there might be non-cullin neddylation targets that require further verification.
Recent technical advances are expanding our understanding of how lysine acetylation, as well as other metabolite-sensitive acylations, regulates various cellular processes. Emerging findings point to new functions for different acylations and deacylating enzymes, and clarify the intricate link between lysine acetylation and cellular metabolism.
Intermediate filaments (IFs) are cytoskeletal and nucleoskeletal structures that promote cell integrity and intracellular communication and contribute to subcellular and tissue-specific functions. Our understanding of how post-translational modifications of IF proteins (including nuclear lamins and cytoplasmic keratins, vimentin, desmin, neurofilaments and glial fibrillary acidic protein, among others) regulate IF function is increasing.
The function and regulation of poly(ADP-ribosyl)ation is partially understood. By contrast, little is known about intracellular mono(ADP-ribosyl)ation (MARylation) by ADP-ribosyl transferases. Recent findings indicate that MARylation regulates signalling and transcription by modifying key components in these processes, and that specific macrodomain-containing proteins 'read' and 'erase' this modification.
Sumoylation is a highly regulated process that is counteracted by specialized enzymes known as small ubiquitin-related modifier (SUMO) proteases. The recent discovery of novel SUMO proteases, together with new findings for established SUMO proteases, has led to augmented appreciation of this enzyme family.
The identification of an hydrogen sulfide (H2S)-mediated post-translational modification (protein sulfhydration) has provided novel insights into H2S signalling, which controls many cellular functions. As a result, a new research area has arisen that investigates how metabolic stress and other environmental signals influence protein function through Cys modification by H2S.
Approximately half of human proteins are glycosylated, and the resulting diverse glycan patterns encode an additional level of information. The process of protein glycosylation is mediated by numerous enzymes with dynamic localization, regulation and specificity. High-throughput techniques facilitate the study of complex protein glycans and may give further insights into their roles in protein homeostasis, cell signalling and cell adhesion.
Poly(ADP-ribosyl)ation (PARylation) is a dynamic protein modification, the control of which is important for diverse cell biological processes and normal physiology. Common mechanistic themes are being characterized by which PARylation alters the functions of target proteins, and the PAR-binding modules that mediate this.
Histone demethylases are important for both chromatin structure and transcription. The insights being gained into their regulation and target specificity have important implications for both normal development and disease.
O-GlcNAcylation is a post-translational modification that seems to regulate the function of numerous target proteins in a nutrient-sensitive manner. Recent evidence suggests an important role forO-GlcNAcylation in epigenetic regulation.
Methylation of Lys36 at histone H3 is important for transcription and has also been implicated in diverse processes, including splicing and DNA replication and repair. Understanding the dynamic control of this modification is crucial for understanding the numerous diseases that its dysfunction are linked with.
RAS proteins are monomeric GTPases that act as binary molecular switches to regulate a wide range of cellular processes. Their trafficking and activity are regulated by constitutive post-translational modifications (PTMs), including farnesylation, methylation and palmitoylation, as well as conditional PTMs, such as phosphorylation, peptidyl-proly isomerization, ubiquitylation, nitrosylation, ADP ribosylation and glucosylation.
Cells generate distinct microtubule subtypes by expressing different tubulin isotypes and through tubulin post-translational modifications, such as detyrosination, acetylation, polyglutamylation and polyglycylation. The recent discovery of enzymes responsible for many of these modifications has shown how they may regulate microtubule functions.
The ability of methylarginine sites to serve as binding motifs for Tudor proteins, and the functional significance of this, is now becoming clear. Tudor proteins are thought to interact with methylated PIWI proteins and regulate the PIWI-interacting RNA pathway in the germ line.
The regulation of apoptosis is essential for cell homeostasis and the survival of multicellular organisms, and excessive or diminished apopotosis can contribute to various diseases. The post-translational modification of apoptotic proteins by ubiquitylation is a key regulatory mechanism of cell death signalling cascades. Targeting apoptotic regulatory proteins in the ubiquitin proteasome system might afford clinical benefits.
The production of mature and export-competent messenger ribonucleoproteins (mRNPs) is a multistep process that is regulated in a spatial and temporal manner. Recent studies suggest that post-translational modifications play a part in coordinating the co-transcriptional assembly, remodelling and export of mRNP complexes through nuclear pores.