A study of bias and increasing organismal complexity from their post-translational modifications and reaction site interplays

Abstract

Post-translational modifications (PTMs) are important steps in the biosynthesis of proteins. Aside from their integral contributions to protein development, i.e. perform specialized proteolytic cleavage of regulatory subunits, the covalent addition of functional groups of proteins or the degradation of entire proteins, PTMs are also involved in enabling proteins to withstand and recover from temporary environmental stresses (heat shock, microgravity and many others). The literature supports evidence of thousands of recently discovered PTMs, many of which may likely contribute similarly (perhaps, even, interchangeably) to protein stress response. Although there are many PTM actors on the biological stage, our study determines that these PTMs are generally cast into organism-specific, preferential roles. In this work, we study the PTM compositions across the mitochondrial (Mt) and non-Mt proteomes of 11 diverse organisms to illustrate that each organism appears to have a unique list of PTMs, and an equally unique list of PTM-associated residue reaction sites (RSs), where PTMs interact with protein.Despite the present limitation of available PTM data across different species, we apply existing and current protein data to illustrate particular organismal biases. We explore the relative frequencies of observed PTMs, the RSs and general amino-acid compositions of Mt and non-Mt proteomes. We apply these data to create networks and heatmaps to illustrate the evidence of bias. We show that the number of PTMs and RSs appears to grow along with organismal complexity, which may imply that environmental stress could play a role in this bias.

Peptide binding landscapes: Specificity and homophilicity across sequence space in a lattice model

“…within a sequence [26,27]. For example, the sequence HPPPH has three two-words, HP (25% frequency), PP (50%), and PH (25%).…”

Donepezil down‐regulates propionylation, 2‐hydroxyisobutyrylation, butyrylation, succinylation, and crotonylation in the brain of bilateral common carotid artery occlusion‐induced vascular dementia rats

“…Post‐translational modifications (PTMs) have been shown to increase the functional diversity of the proteome by covalent addition of functional groups, proteolytic cleavage of regulatory subunits, or selective degradation of entire proteins 4 . These modifications include phosphorylation, glycosylation, ubiquitination, methylation, acetylation among other modifications.…”