Figure 1.
Lysine acetylation sites were collected from three sources; PhosphositePlus, Uniprot, and from the work of Choudhary, et al. BLAST-P was used to map each acetylation site to the corresponding IPI protein. The data were condensed to remove redundant sites. Subsequent analyses included conservation studies, subcellular localization, pathway analysis, domain analysis, secondary structure prediction, and crosstalk prediction. Details and methods are outlined in the text.
Figure 2.
Subcellular localization of acetylated lysine residues.
The gene ontology annotations for identified IPI genes were obtained from the GOA database. Of the 2384 lysine acetylation genes identified, 488 (20.4%) are exclusively nuclear, 182 (7.6%) are mitochondrial only, and 499 (20.9%) are only found in the cytoplasm. 570 proteins (23.9%) were not assigned to any compartment.
Figure 3.
Using the Kyoto Encyclopedia of Genes and Genomes (KEGG), we identified pathways enriched for the acetylated proteins identified. False discovery rate control was used to correct for multiple hypothesis testing, the KEGG pathways with a corrected p-value<0.01 were considered significant. A diverse array of cellular pathways and functions were identified including those involved in cellular processes (light green), genetic information processing (red), human diseases (indigo), metabolism (yellow).
Figure 4.
Proteins with acetylated lysines were aligned to the distribution of domains in the NCBI Conserved Domain Database using PRS-BLAST. Correction for multiple hypothesis testing was carried out using standard false discovery rate control methods, and domains with a corrected p-value<0.01 were considered significant. Domains with more than the number expected K-Ac sites were considered “overrepresented.”
Figure 5.
Secondary structure prediction.
The secondary structure of acetylated proteins was derived from Uniprot and the Dictionary of Protein Secondary Structure (DSSP). There was significant enrichment of acetylated lysine sites in alpha helices and beta-sheets only.
Figure 6.
Top: (A) The influence of acetylated lysine on neighboring phosphorylation sites was predicted by substituting a leucine for a lysine at all predicted K-Ac sites and then predicting potential phosphorylation sites using NetPhosK 1.0. (B) In all, 51% of nearby phosphorylation sites were affected, and these were classified as Type I (gain of a phosphorylation site, 10%), Type II (loss of a phosphorylation site, 35%), Type III (retention of a phosphorylation site with gain of kinase binding site, 16%), Type IV (retention of a phosphorylation site with loss of kinase binding site, 29%), and Type V (loss of an endogenous kinase binding site with concomitant gain of a new one, 10%). This analysis was repeated by substituting glutamine for lysine (Panels C and D). This analysis was repeated for methylation using BPB-PPMS (middle) and ubiquitination using UbPred (bottom). For further details, see text.