Testing the Domino Theory of Gene Loss in Buchnera aphidicola: The Relevance of Epistatic Interactions.

David Martínez-Cano,Luis Delaye,Gil Bor,Andrés Moya

doi:10.3390/life8020017

Abstract

The domino theory of gene loss states that when some particular gene loses its function and cripples a cellular function, selection will relax in all functionally related genes, which may allow for the non-functionalization and loss of these genes. Here we study the role of epistasis in determining the pattern of gene losses in a set of genes participating in cell envelope biogenesis in the endosymbiotic bacteria Buchnera aphidicola. We provide statistical evidence indicating pairs of genes in B. aphidicola showing correlated gene loss tend to have orthologs in Escherichia coli known to have alleviating epistasis. In contrast, pairs of genes in B. aphidicola not showing correlated gene loss tend to have orthologs in E. coli known to have aggravating epistasis. These results suggest that during the process of genome reduction in B. aphidicola by gene loss, positive or alleviating epistasis facilitates correlated gene losses while negative or aggravating epistasis impairs correlated gene losses. We interpret this as evidence that the reduced proteome of B. aphidicola contains less pathway redundancy and more compensatory interactions, mimicking the situation of E. coli when grown under environmental constrains.

Highlights

Mutualistic endosymbiotic bacteria from insects show the most reduced genomes of all cells [1].The genomes of these bacteria are the outcome of an evolutionary process driven by the symbiotic interaction with its host [2]
We study the role of epistasis in determining the pattern of gene losses in a set of genes participating in cell envelope biogenesis in the endosymbiotic bacteria Buchnera aphidicola
We find the same result if we relax our false discovery rate to FDR < 0.45, this to include all p-values from BayesTratisV2 analysis smaller than 0.05

Summary

Introduction

Mutualistic endosymbiotic bacteria from insects show the most reduced genomes of all cells [1].The genomes of these bacteria are the outcome of an evolutionary process driven by the symbiotic interaction with its host [2]. One of the best studied cases of genome reduction among these prokaryotes is that of Buchnera aphidicola, the endosymbiotic bacteria from aphids [3]. The basis of this mutualistic interaction is nutritional. B. aphidicola provides essential amino acids lacking in the diet of its host [4,5,6,7,8,9]. Genome reduction in these bacteria is a complex process that is only partially understood

Methods

Discussion

Conclusion