Protein Family Expansions and Biological Complexity

Introduction

Scope: We analyse domain superfamily expansions across a variety of eukaryotic genomes.

Summary:
During the course of evolution, new proteins are produced very largely as the result of gene duplication, divergence and, in many cases, combination. This means that proteins, or protein domains belong to families or, in the cases where their relationships can only be recognised on the basis of structure, superfamilies whose members are descended from a common ancestor. The size of superfamilies can vary greatly. Also, during the course of evolution organisms of increasing complexity has arisen. In this paper we determine the identity of those superfamilies whose relative sizes in different organisms is highly correlated to the different complexity of the organisms
As a measure of the complexity of 38 uni- and multicellular eukaryotes we took the number of different cell types of which they are composed. Of 1219 different superfamilies, there are 194 whose sizes in the 38 organisms have a high correlation with the number of cell types in the organisms. We give outline descriptions of these superfamilies. Half are involved in extra-cellular processes or regulation and smaller proportions in other types of activity. Half of all superfamilies have no significant correlation with complexity. We also determined whether the expansions of large superfamilies correlate with each other. We found three large clusters of correlated expansions: one involves vertebrate and plant superfamilies, one those in vertebrates and one those in plants.

Analysis of 38 eukaryotic genomes

Data files

• List of 38 eukaryotic genomes and two-letter abbreviations
• Phylogenetic relationship of the 38 genomes as taken from NCBI
• List of domain superfamilies, their five-digit identifiers, position in SCOP hierarchy and name -- note that the analysis focusses on SCOP classes a to g
• Raw abundance counts for each superfamily in each genome
• Mapping of 'small' function categories to 'large' function categories, used for domain function annotation
• The function annotation of SCOP superfamilies is available upon request from the authors.

Files

• abundance >=1; R-value >=0.7
• abundance >=1; R-value >=0.8
• abundance >=1; R-value >=0.9
• abundance >=1; no R-value cutoff


• abundance >=25; R-value >=0.7
• abundance >=25; R-value >=0.8
• abundance >=25; R-value >=0.9
• abundance >=25; no R-value cutoff

Files from the publication:

• Main text, uncorrected proofs
• Main paper, figures only
• Supporting Material, Dataset S1 -- genome and superfamily information
• Supporting Material, Protocol S1 -- description of additional procedures
• Supporting Material, Table S1
• Supporting Material, Table S2
• Supporting Material, Figure S1 -- distributions of domain function
• Supporting Material, Figure S2 -- expansion profiles of all 1,219 superfamilies
• Supporting Material, Figure S3 -- correlations of number of different cell types

Links

• SCOP -- Structural Classifications of Proteins database.
• SUPERFAMILY -- SCOP domain prediction server.
• Other papers on protein domain duplication and recombination(by the same authors)