Unraveling the Dynamics of Protein Acetylation: A Comprehensive Overview
Protein acetylation stands as the most prevalent form of acylation modification. This intricate process is orchestrated by lysine acetyltransferases (KATs), responsible for transferring acetyl groups from acetyl coenzyme A to the ε-amino group of lysine residues. It's crucial to note that lysine acetylation represents a dynamic post-translational modification, known for its reversibility. Furthermore, lysine residues can undergo non-enzymatic deacetylation through acetyl coenzyme A in eukaryotes and acetyl phosphate in bacteria.
In the realm of KATs, a total of 13 have been identified, predominantly falling into three distinctive families—GCN5, p300, and MYST19. The counterpart to acetylation, deacetylation, is facilitated by NAD+-dependent sirtuins (deacetylases) and Zn2+-dependent deacetylases (KDAC/HDACs). Remarkably, the human genome hosts a repertoire of 18 KDACs, emphasizing the intricate regulatory network governing protein acetylation dynamics.
Acetylation Plays a Crucial Role in Diverse Biological Processes
Nε-lysine acetylation, an age-old post-translational modification initially recognized in histones, has garnered extensive attention for its role in transcriptional regulation. In the last decade, proteomic investigations have unveiled the pervasive acetylation of non-histone proteins, emerging as a predominant element within the mammalian cellular acetylome. Notably, non-histone acetylation orchestrates pivotal cellular phenomena integral to both physiological and pathological states, encompassing gene transcription, DNA damage repair, cell division, signal transduction, protein folding, autophagy, and metabolism.
The impact of acetylation on protein function is orchestrated through diverse mechanisms. These include the nuanced regulation of protein stability, modulation of enzyme activity, determination of subcellular localization, intricate crosstalk with other post-translational modifications, and precise control of protein-protein and protein-DNA interactions.
Exploring Key Molecular Regulations in Acetylation
Enzyme Regulation via Acetylation
Modulation of Enzyme Activity: Acetyl-CoA synthetase 1 (ACSS1) and Acetyl-CoA synthetase 2 (ACSS2) are strategically positioned in the cytoplasm and mitochondria, respectively. The acetylation process functions as a regulatory mechanism, exerting inhibitory effects on the activities of both ACSS1 and ACSS2.
Acetylation Modulating Enzyme Activity
Augmenting Enzyme Activity: Autoacetylation is a phenomenon observed in acetyltransferases (KATs), contributing to an elevation in the activity levels of acetylation enzymes.
Acetylation enhances enzyme activity
Modifying Enzyme-Substrate Specificity: P300 acetylates lysine residues at positions 182 and 185 of MDM2, promoting its interaction with the deacetylase USP7. This molecular interaction subsequently triggers the ubiquitination of MDM2's substrate, p53.
Acetylation changes enzyme-substrate specificity
Acetylation-Mediated Control of Protein Interactions and Subcellular Localization:
Acetylation of non-histone proteins exhibits a dual role in either augmenting or impeding protein-protein interactions. Notably, the acetylation of specific residues at the N-terminus of the transcription factor C-ets-1 (ETS1) enhances its binding with BRD4, thereby facilitating the release of RNA polymerase II (PolII). Moreover, acetylation of the transcriptional regulator TWIST (also recognized as TWIST1) amplifies its interaction with the second bromodomain of BRD4. Concurrently, the first bromodomain of BRD4 engages with acetylated histone H4, fostering the assembly of a complex comprising TWIST, BRD4, and PolII.
Acetylation Facilitates Protein-Protein Interactions
Acetylation Orchestrates the Subcellular Localization of Diverse Non-Histone Proteins: Virus infection initiates the p300-mediated acetylation of the nuclear localization signal (NLS) within the gamma-interferon-inducible protein 16 (IFI16), inducing its translocation to the cytoplasm. Conversely, acetylation of the transcription factor SOX2 promotes its interaction with the nuclear export machinery, leading to its redistribution to the cytoplasm. Following this relocation, SOX2 undergoes degradation through the ubiquitin-proteasome pathway.
Acetylation regulates the localization of many non-histone proteins
Crosstalk Between Acetylation and Other Modifications
In most mammalian proteins, multiple post-translational modifications (PTMs) occur, and they can influence each other, a phenomenon referred to as PTM crosstalk. PTM crosstalk serves as an integrative hub for diverse cellular signals. Due to the amino group of lysine being amenable to various modifications, including acetylation, methylation, ubiquitination, and sumoylation, competitive PTM crosstalk may arise where different PTMs vie for the same lysine residue.
Proteomic studies reveal that a substantial portion of acetylated lysine residues is also subjected to other PTMs, such as ubiquitination and succinylation. The tumor suppressor protein p53 exemplifies non-histone PTM crosstalk. Acetylation at its lysine residues directly competes with ubiquitination, thereby inhibiting ubiquitin-proteasome-dependent degradation. Acetylation of p53 is augmented through methylation catalyzed by proteins containing SET domains. This process is facilitated by proteins that promote the recruitment of TIP60, enhancing acetylation at Lys120 of p53.
Acetylation Profiling of the Proteome: Methodological Insights
The exploration of acetylation in the proteome poses challenges inherent to all proteomic experiments: complexity, dynamic range, and temporal dynamics. The temporal dynamics of protein acetylation, orchestrating rapid activation and deactivation of cellular signaling networks, add an additional layer of complexity to the analysis of acetylated proteomes. Mass spectrometry stands as a pivotal tool for identifying acetylation sites and quantifying changes in acetylation. The intricacy of mass spectrometric analysis of protein acetylation lies in factors such as low abundance of modified proteins and suboptimal ionization efficiency.
Successful analysis of acetylated peptides via mass spectrometry critically hinges on effective enrichment methods. Presently, antibody-based approaches serve as the primary means for the enrichment of acetylated peptide segments.
Technical route to acetylated proteomics
Cases of Applications of Acetylated Proteomics
A proteogenomic portrait of lung squamous cell carcinoma
Proteomic Insights into Lung Squamous Cell Carcinoma: Unraveling Novel Therapeutic Targets
Lung squamous cell carcinoma (LSCC), also known as lung squamous cell cancer, is a prevalent form of lung cancer, accounting for approximately 40% to 51% of primary lung cancers. In this study, the authors conducted a protein genomics analysis on tumor tissues from 108 untreated cases of primary LSCC and their corresponding adjacent tissues. The analysis encompassed the study of phosphorylation, acetylation, and ubiquitination post-translational modifications.
The comprehensive exploration of the proteomic landscape of LSCC unveiled distinctive features, shedding light on the intricate molecular makeup of this type of lung cancer. Furthermore, the study identified several novel targets for precise therapeutic interventions in LSCC, offering crucial insights with significant clinical implications.
Multi-omics technology routes
Acetylation modification site analysis
References
- Leonie G.Graf, Robert Vogt, Anna-Theresa Blasl,et al. Assays to Study Enzymatic and Non-Enzymatic Protein Lysine Acetylation In Vitro. Curr Protoc 2021 Nov;1(11).
- Takeo Narita, Brian T.Weinert and Chunaram Choudhary. Functions and mechanisms of non-histone protein acetylation. Nat Rev Mol Cell Biol 2019 03;20(3).
- Birgit Schilling,Jesse G.Meyer,et al.High-Resolution Mass Spectrometry to Identify and Quantify Acetylation Protein Targets. Methods Mol Biol 2019;1983.
- Shankha Satpathy,Karsten Krug,Pierre M.Jean Beltranr,et al. A proteogenomic portrait of lung squamous cell carcinoma. Cell 2021 08 05;184(16)
