The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes

John W Whitaker,David R Westhead,Glenn A Mcconkey

doi:10.1186/gb-2009-10-4-r36

Abstract

Metabolic network analysis in multiple eukaryotes identifies how horizontal and endosymbiotic gene transfer of metabolic enzyme-encoding genes leads to functional gene gain during evolution.

Highlights

Metabolic networks are responsible for many essential cellular processes, and exhibit a high level of evolutionary conservation from bacteria to eukaryotes
Methods of detecting Horizontal gene transfer (HGT) from sequence data can be split into four categories: codon-based approaches that identify genes with a codon usage differing from the other genes in the genome [19,20]; BLAST-based approaches that identify sequences with high-scoring similarities to sequences from taxonomically distant species [21]; gene distribution-based approaches that compare the species that posses a gene to the accepted species phylogeny, allowing unusual patterns of gene possession that could be explained by HGT to be identified [6]; and phylogenetic approaches that construct phylogenetic trees and identify clades that differ from the expected organismal phylogeny [22,23]
To investigate the extent of the horizontal transfer of genes that encode metabolic enzymes in unicellular eukaryotes, the metabolic evolution resource metaTIGER [32] was used. metaTIGER is suited to this task because it contains 2,257 maximum-likelihood phylogenetic trees, each including sequences from up to 121 eukaryotes and 404 prokaryotes predicted to code for enzymes with specific Enzyme Commission (EC) numbers and located within reference metabolic networks

Summary

Introduction

Metabolic networks are responsible for many essential cellular processes, and exhibit a high level of evolutionary conservation from bacteria to eukaryotes. In addition to core metabolic processes, peripheral processes allow species to adapt to different environments - for example, metabolism of a rare sugar This adaptation can be driven by the gain of genes encoding enzymes through horizontal gene transfer (HGT) [6], and this process has for some time been seen as an important aspect of prokaryotic evolution [7,8,9]. HGT that accompanies endosymbiosis, termed endosymbiotic gene transfer (EGT), was important in establishing the eukaryotic organelles: the mitochondria and plastids. An important example is the event, or events, that gave rise to the chromalveolates, in which a heterotrophic eukaryote gained a plastid through endocytosis of a plastid-containing red alga [13] This brought together five genomes in one cell - two nuclear, two mitochondrial and one plastid - and with them came the opportunity for large scale EGT [14,15]. A further potential source of EGT in eukaryotes is from Chlamydia and may have occurred during the establishment of the primary plastid [16,17]

Methods

Results

Conclusion