Classification of Complete Proteomes of Different Organisms and Protein Sets Based on Their Protein Distributions in Terms of Some Key Attributes of Proteins

Abstract

The existence of complete genome sequences makes it important to develop different approaches for classification of large-scale data sets and to make extraction of biological insights easier. Here, we propose an approach for classification of complete proteomes/protein sets based on protein distributions on some basic attributes. We demonstrate the usefulness of this approach by determining protein distributions in terms of two attributes: protein lengths and protein intrinsic disorder contents (ID). The protein distributions based on L and ID are surveyed for representative proteome organisms and protein sets from the three domains of life. The two-dimensional maps (designated as fingerprints here) from the protein distribution densities in the LD space defined by ln(L) and ID are then constructed. The fingerprints for different organisms and protein sets are found to be distinct with each other, and they can therefore be used for comparative studies. As a test case, phylogenetic trees have been constructed based on the protein distribution densities in the fingerprints of proteomes of organisms without performing any protein sequence comparison and alignments. The phylogenetic trees generated are biologically meaningful, demonstrating that the protein distributions in the LD space may serve as unique phylogenetic signals of the organisms at the proteome level.

A Suggestion of Converting Protein Intrinsic Disorder to Structural Entropy Using Shannon’s Information Theory

“…This trend is also expected from the ΣH: ΣI ratios. However, similar to our previous study [ 37 ], for all prokaryotes, the phylogeny failed to separate bacteria from archaea without introducing other attributes. Further investigations, such as considering the domain components in the proteins [ 39 ], will be required to understand the evolution of the protein entropy.…”

“…Previously, by using the protein length L (structural capacity C ) and the disorder content D , distributions of proteins in the space with attributes L and D have been used to reconstruct a phylogenetic tree that indicates intriguing evolutionary dynamics associated with the variations of L and D in the proteomes [ 37 ]. A similar approach is used here to study protein distributions in the HI- space.…”

The Importance of Protein Phosphorylation for Signaling and Metabolism in Response to Diel Light Cycling and Nutrient Availability in a Marine Diatom

“…Current estimates suggest that the fraction of proteins regulated by phosphorylation range between 10 to 60%, depending on organism [ 23 , 24 , 25 , 26 , 27 ]. In commonly studied model eukaryotic organisms such as the yeast, Saccharomyces cerevisiae , and the vascular plant, Arabidopsis thaliana , ~44% and ~18% of the proteome has been shown to be subject to regulation by phosphorylated respectively [ 27 , 28 ]. In the unicellular photosynthetic eukaryotic green algae, Chlamydomonas reinhardtii , 23% of the proteome was found to be subject to phosphorylation [ 29 ].…”