Fig 1.
Overview of the number of methylation, acetylation and ubiquitination sites and the coincidence of different MAU types at the same residue in ordered and disordered regions.
(A) total number of MAU sites in ordered and disordered regions of 7160 human proteins showing that the higher number of MAU sites in disordered regions than in ordered regions and ubiquitination sites show preference for ordered regions. (B) Venn diagram illustrates the co-incidence of MAU (i.e., how many can have two or three different MAU at the same residue) in ordered and disordered regions.
Fig 2.
Percentage distribution of MAU and phosphorylation sites in ordered and disordered regions of human proteins.
Percentages of MAU and phosphorylation sites (out of the total number of residues of the same type) in ordered and disordered regions of the human proteins analysed. The total number of each site present in ordered (olive green) and disordered (peach) regions are given in the centre of the bar. The hypergeometric distribution is used to identify the enrichment of MAU-modified residues in (dis)ordered regions in all lysines/arginines present in both ordered and disordered regions, with the total set of MAU sites as background population, and the diamond symbol on top of the bar indicates the corrected P-value (0.0071) for significant enrichment of PTMs in ordered and disordered regions, and NS represents non-significant enrichment.
Fig 3.
Distribution of PTM sites in ordered and disordered regions of human proteins for various subsets of the data.
(A) Distribution of MAU and phosphorylation sites in folding on binding (FB) regions and the percentage distribution of sites in FB non-FB/unclassified regions. Enrichment analysis is performed for the FB set as a sample of total ordered or disordered regions. Due to the limited experimental data, other PTM sites were detected only at very low levels or were not present: nitrosylated cysteines 2 sites, O-linked glycosylation (serine, 1 site and threonine, 5 sites), prenylated cysteine (2 sites), sulfated tyrosine (2 sites) and sumoylated lysines (24 sites), whereas carboxylation, myristoylation, palmitoylation sites are not present in the FB regions. We used hypergeometric probability tests to perform the enrichment/depletion analyses of PTM sites in FB regions. The critical P-value to test the significance is P<0.0014 (to correct for multiple hypotheses). (B) Distribution of MAU and phosphorylation sites in homopeptides. The enrichment and depletion analyses are calculated for homopeptides present in the ordered (olive green) and disordered (peach) regions. The statistical test and critical P-value is as for part (A). (C) Distribution of MAU and phosphorylation sites in Human prion-like proteins (grey). Enrichment analysis is performed for lysines or arginines in the prion-like protein set as a sample of total lysines or arginines in the disordered set, as appropriate. The statistical test and critical P-value is as for part (B).
Fig 4.
Organismal phylogeny and pipeline.
(A) Organismal phylogenetic tree of eukaryotes separated into eleven clades and the total number of organisms for each is given in brackets. (B) Pipeline for the conservation analysis. MAU sites conserved in ordered and disordered regions are considered as two separate datasets.
Fig 5.
Example of a protein with methylation, acetylation and ubiquitination sites in ordered and disordered regions.
Multiple sequence alignment of human chromobox protein homolog 3 and its primate orthologs, depicted using JalView [88], showing methylation, acetylation (purple) and ubiquitination (yellow) sites in ordered (green) and disordered (peach) regions. The sites with both acetylation and methylation sites are highlighted in brown, sites with both acetylation and ubiquitination sites are highlighted in cyan and the sites with acetylation, methylation and ubiquitination sites are highlighted in red.
Fig 6.
Summary of significantly enriched conserved MAU sites in ordered and disordered regions at 11 evolutionary clades.
Evolutionary levels with significant enrichment (after correction for multiple hypotheses) are labelled with four different shapes: lysine methylation (square), arginine methylation (circle), lysine acetylation (star) and ubiquitination (triangle) sites. The ordered and disordered regions with enriched MAU sites are labelled in olive green and peach respectively and the sites with significant enrichment in both disordered and ordered regions are coloured blue. Where there are conservation signals for newly emerged MAU sites in ordered and disordered regions the symbols are marked with black and red borders respectively. The results are depicted in more detail (with P-values, specific thresholds and total numbers of sites) in S1 File. Table A in S1 File is for the total data set, and Table B in S1 File is for histones.
Table 1.
Percentages of human MAU-site residues in ordered and disordered regions that are conserved across all eukaryotes.
Fig 7.
The trends in enrichments for conserved PTM-site lysines and arginines that are maintained at each level (parts A and B) and newly-emerged (‘new sites’, parts C and D). The eleven evolutionary levels examined are on the horizontal axis. The P-values for enrichment are on the logarithmic vertical axis. Panels (A) and (C) are for Ordered regions, and (B) and (D) for Disordered regions.