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

Oliver Bonham-Carter, Ishwor Thapa, Steven From, Dhundy Raj Bastola

Research output: Contribution to journalArticle

Abstract

Post-translationalmodifications (PTMs) are important steps in the biosynthesis of proteins. Aside from their integral contributions to protein development, i.e. performspecialized 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 andmany others). The literature supports evidence of thousands of recently discovered PTMs,many of whichmay likely contribute similarly (perhaps, even, interchangeably) to protein stress response. Although there aremany 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 organismappears 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 ofMt 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, whichmay imply that environmental stress could play a role in this bias.

Original languageEnglish (US)
Pages (from-to)69-84
Number of pages16
JournalBriefings in bioinformatics
Volume18
Issue number1
DOIs
StatePublished - Jan 1 2017

Fingerprint

Post Translational Protein Processing
Proteins
Proteome
Weightlessness
Protein Biosynthesis
Heat-Shock Proteins
Proteolysis
Shock
Hot Temperature
Amino Acids
Biosynthesis
Microgravity
Chemical analysis
Functional groups
Amino acids
Degradation

Keywords

  • Amino acid bias
  • Organismcomplexity
  • PTM bias
  • Reaction site bias

ASJC Scopus subject areas

  • Information Systems
  • Molecular Biology

Cite this

A study of bias and increasing organismal complexity from their post-translational modifications and reaction site interplays. / Bonham-Carter, Oliver; Thapa, Ishwor; From, Steven; Bastola, Dhundy Raj.

In: Briefings in bioinformatics, Vol. 18, No. 1, 01.01.2017, p. 69-84.

Research output: Contribution to journalArticle

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