Enzymes Involved in Acetylation and Deacetylation Processes
The acetylation modification of proteins plays a crucial role in cellular physiology, exerting significant effects on chromosome structure and activation of nuclear transcriptional regulatory factors. It extensively participates in various physiological processes, including transcriptional regulation, signaling pathway modulation, protein stability control, cellular metabolism, and regulation of pathogenic microbial infections.
Over 100 proteins, including nuclear proteins, cytoplasmic proteins, membrane receptor proteins, cytoskeletal proteins, and mitochondrial enzyme proteins, undergo reversible acetylation modification post-translation. This reversible acetylation occurs exclusively on lysine residues and is catalyzed by lysine acetyltransferases (KAT) and lysine deacetylases (KDAC). Due to the initial confirmation of lysine acetylation and deacetylation modifications in histones, KAT and KDAC are also referred to as histone acetyltransferases (HAT) and histone deacetylases (HDAC), respectively. As research progresses, it has been discovered that non-histone proteins also undergo acetylation and deacetylation modifications.
- Lysine Acetyltransferases (HAT): HAT enzymes can be classified into three major classes: GNAT (Gcn5-related N-acetyltransferase), P300/CBP (E1A-associated protein of 300kDa/CREB-binding protein), and MYST (MOZ, Ybf2/Sas2, and Tip60).
- Lysine Deacetylases (HDAC): Based on functionality and DNA sequence similarity, HDACs can be categorized into four classes. Class I HDACs, with activity inhibited by trichostatin A (TSA), are homologous to Rpd3 (reduce potassium dependency 3) in yeast. Class II HDACs are homologous to Hda1 (Histone deacetylase 1) in yeast. Class III HDACs' activity depends on NAD+ and is not inhibited by TSA; they are homologous to Sir2 (silent information regulator) in yeast. Class IV HDACs, considered non-classical, often form multiprotein complexes, whether functioning as acetyltransferases or deacetylases. Both acetylation and deacetylation enzymes are present not only in the cell nucleus but also in the cytoplasm, allowing both nuclear and non-nuclear proteins to undergo acetylation and deacetylation processes.
Function of Acetylation
Acetylation is a process involving the addition of an acetyl functional group to organic compounds, modifying them by binding with another molecule. For example, in proteins, acetylation modification of lysine residues can regulate various protein properties, including DNA-protein interactions, protein stability, subcellular localization, and transcriptional activity.
Acetylation modifications are mainly categorized into three classes: N-terminal alpha-amino acetylation, lysine ε-amino acetylation, and serine/threonine acetylation. This process commonly occurs on histones, catalyzed by histone acetyltransferases (HAT), with deacetylation catalyzed by histone deacetylases (HDAC). The N-terminal of histones is rich in lysine, carrying a positive charge under physiological conditions. Interaction with negatively charged DNA or adjacent nucleosomes leads to compact nucleosome conformation and highly folded chromatin.
Acetylation weakens the interaction between histones and DNA, further loosening chromatin conformation, facilitating the approach of transcriptional regulatory factors, and promoting gene transcription. Conversely, deacetylation plays an inhibitory role in gene transcription.
Research suggests that acetylation modifications play a role in the regulation of cellular autophagy, involving histone acetylation and deacetylation enzymes. Dynamic regulation of the autophagic process is achieved by modulating the acetylation levels of key proteins. Additionally, acetylation modifications may occur at phosphorylation sites, competitively interfering with host cell signaling pathways.
Acetylation modifications not only impact chromosomal structure and activation of nuclear transcriptional regulatory factors but also play a role in non-nuclear proteins. In some bacteria, central metabolic enzymes undergo reversible acetylation under different carbon source conditions, ensuring flexible cellular responses to environmental changes as cells grow and metabolic flux varies.
Beyond biological functions, lysine acetylation is associated with aging and various diseases such as cancer, cardiovascular diseases, and neurodegenerative disorders. Some studies have also found that acetylation modifications of serine and threonine in eukaryotes compete with phosphorylation modifications of these amino acids, intricately regulating cellular signaling pathways.
Acetylation Modification of Transcription Factors
Transcription factors play a crucial role in the regulation of gene expression by binding to specific DNA sequences. Acetylation modification is one of the post-translational modifications that can occur on transcription factors, influencing their activity and function.
Acetylation involves the addition of an acetyl group (-COCH3) to the lysine residues of transcription factors. This modification is dynamically regulated by the opposing actions of histone acetyltransferases (HATs) and histone deacetylases (HDACs). HATs catalyze the transfer of acetyl groups to lysine residues, leading to increased transcriptional activity by creating a more open chromatin structure. On the other hand, HDACs remove acetyl groups, resulting in a more condensed chromatin structure and decreased transcriptional activity.
The acetylation of transcription factors can have several functional consequences. First, acetylation may directly affect the DNA-binding ability of transcription factors, influencing their affinity for target gene promoters or enhancers. Second, acetylation can serve as a signal for recruitment of co-activators or co-repressors, modulating the overall transcriptional activity of the target genes. Third, acetylation can impact protein stability, subcellular localization, and interactions with other cellular components.
Studies have shown that dysregulation of transcription factor acetylation is implicated in various diseases, including cancer and neurodegenerative disorders. Understanding the intricate mechanisms of transcription factor acetylation provides insights into the fine-tuned control of gene expression and opens avenues for therapeutic interventions targeting these modifications.
Factor acetylation regulates transcription (Bannister et al., 2000).
Acetylation Modification in the Interferon Signaling Pathway
In antiviral responses, the signaling cascade initiated by the cytokine interferon (IFN) plays a pivotal role. Beyond the well-known phosphorylation cascade in IFN-α signal transduction, acetylation modifications are also present among various signaling components. Upon IFN-α binding to the receptor IFN-αR2, phosphorylation occurs at serine residues 364, 384, and 400 within the cytoplasmic tyrosine-rich domain. Subsequently, CBP induces acetylation modification at lysine 399 within the receptor, and deacetylation of the receptor may occur under the action of HDAC6. The acetylated lysine 399 and phosphorylated serine 400 residues in IFN-αR2 together form an anchor point, recruiting the IFN regulatory factor IRF9. Under the influence of p300, acetylation of IRF9 takes place, promoting dimerization and DNA-binding affinity of IRF9. STAT, with a dual role in signal transduction and gene expression in cytokine signaling pathways, undergoes acetylation modification in the IFN-α-IFN-αR2-STAT pathway. This modification facilitates heterodimerization, nuclear translocation, and trimer formation with acetylated IRF9, ultimately enhancing gene expression. The cascade of acetylation reactions induced by IFN is analogous to the phosphorylation cascade. The prevalence and regulatory pathways of acetylation cascade reactions in cellular transmission, as well as the reversibility of acetylation-based modifications, warrant further in-depth investigation.
Research Methods for Acetylation and Deacetylation of Proteins
Proteomic Separation: Researchers leverage advanced proteomic techniques to isolate proteins from complex mixtures. This involves methods such as gel electrophoresis or liquid chromatography, followed by mass spectrometry for the precise identification of proteins. This approach enables the discovery of novel acetylated proteins within cellular systems.
Mass Spectrometry Analysis for Acetylation Sites: In the case of already known acetylated proteins, scientists employ sophisticated mass spectrometry technologies to systematically analyze and map the precise locations of acetyl groups on the protein structure. This detailed mapping provides insights into the specific residues undergoing acetylation.
Molecular Biology and Genetics Approaches: To unravel the functional implications of acetylated proteins or specific acetylation sites, researchers turn to molecular biology and genetic tools. By manipulating the genes associated with these proteins or modification sites, scientists can study the resulting changes in cellular function. This approach allows for a deeper understanding of the functional role played by acetylated proteins in biological processes.
Small Molecule Deacetylase Inhibitors: Employing small molecules as deacetylase inhibitors is a key strategy in studying deacetylation processes. Compounds like Trichostatin A (TSA) and short-chain fatty acids such as sodium butyrate serve as potent inhibitors of deacetylase enzymes. TSA, in particular, is widely utilized to investigate the activities of Class I and II HDACs both in controlled in vitro experiments and in more complex in vivo conditions.
Reference
- Bannister*, A. J., and E. A. Miska. "Regulation of gene expression by transcription factor acetylation." Cellular and Molecular Life Sciences CMLS 57 (2000): 1184-1192.
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