Organisms use post-translational modifications to selectively alter the structure of proteins and elicit functional changes. Lysine acetylation is a common, reversible post-translational modification that is implicated in a variety of cellular activities. Using proteomics strategies, Lundby et al. (2012) created a searchable, comprehensive map of lysine acetylation sites that extended previous data by four-fold and doubled the available acetylated proteins data.1
To accomplish this, the researchers digested protein extracts derived from rat tissues, immunoprecipitated the resultant lysine-acetylated peptides, and subjected those to micro-scale chromatography followed by tandem mass spectrometry on an LTQ Orbitrap Velos (Thermo Scientific). They identified 265,034 peptide–spectrum matches with a false discovery rate below 0.01. Of these matches, 40% were lysine-acetylated peptides. The data represent 19,965 lysine-acetylated peptides and 15,474 lysine acetylation sites derived from 4,541 proteins.
Overall, Lundby et al. observed that lysine acetylation is differentially accomplished, tissue-specific, and comparable to phosphorylation in terms of its role as a commonly occurring post-translational modification. The large data set also enabled researchers to demonstrate sequence motifs and tissue specificity within the subcellular compartment. Within the compartment, acetylated proteins can be found as follows: cytoplasm (30%), nucleus (30%), mitochondria (15%), plasma membrane (15%), endoplasmic reticulum (ER)/Golgi apparatus (5%) and extracellular space (5%). In general, mitochondrial proteins possess the highest densities of acetylation sites. This is particularly true within the high energy-demand tissues such as muscle, heart, and brown fat.
The research team identified pathways with previously known regulation by lysine acetylation, such as gene expression, protein metabolism, the citric acid cycle, and apoptosis. They also noted pathways whose relationships to lysine acetylation were previously unknown. Examples of the latter include the finding that nearly all proteins contributing to the contraction of striated muscle are lysine acetylated. The researchers also evaluated the role that lysine acetylation plays in regulating glucose metabolism and enzymatic activity. They hypothesize that while phosphorylation acts as an on-switch for enzymes, acetylation may function as an enzyme deactivator.
Lundby et al. also evaluated the 12 residues on either side of each identified lysine acetylation site for sequence motifs. They found that acetylation generally occurs in lysine-rich regions and that the most common flanking residues were glycine at position 1, proline/phenylalanine/tyrosine at position +1, and valine/isoleucine at position +2. Within the subcellular compartments, the preference for lysine-rich regions is conserved. Cytoplasmic proteins demonstrated a preference for flanking glutamate residues. Mitochondrial proteins showed preference for flanking negatively charged residues and hydrophobic residues at position +2. ER/Golgi proteins preferred negative neighboring residues with hydrophobic residues at positions 1 and 2. Nuclear proteins favored glycine residues at position 1 and proline residues at position +1.
The researchers assert that this comprehensive mapping of lysine acetylation sites may have clinical significance and allow clinicians to interrogate for aberrant acetylation patterns that may occur with diseased and/or cancerous tissues.
1. Lundby, A. et al. (2012) “Proteomic Analysis of Lysine Acetylation Sites in Rat Tissues Reveals Organ Speciﬁcity and Subcellular Patterns,” Cell Reports, 2 (pp. 419–31).
Post Author: Melissa J. Mayer. Melissa is a freelance writer who specializes in science journalism. She possesses passion for and experience in the fields of proteomics, cellular/molecular biology, microbiology, biochemistry, and immunology. Melissa is also bilingual (Spanish) and holds a teaching certificate with a biology endorsement.