Analysis of coevolving gene families using mutually exclusive orthologous modules

Abstract

Coevolutionary networks can encapsulate information about the dynamics of presence and absence of gene families in organisms. Analysis of such networks should reveal fundamental principles underlying the evolution of cellular systems and the functionality of sets of genes. In this study, we describe a new approach for analyzing coevolutionary networks. Our method detects Mutually Exclusive Orthologous Modules (MEOMs). A MEOM is composed of two sets of gene families, each including gene families that tend to appear in the same organisms, such that the two sets tend to mutually exclude each other (if one set appears in a certain organism the second set does not). Thus, a MEOM reflects the evolutionary replacement of one set of genes by another due to reasons such as lineage/environmental specificity, incompatibility, or functional redundancy. We use our method to analyze a coevolutionary network that is based on 383 microorganisms from the three domains of life. As we demonstrate, our method is useful for detecting meaningful evolutionary clades of organisms as well as sets of proteins that interact with each other. Among our results, we report that: 1) MEOMs tend to include gene families whose cellular functions involve transport, energy production, metabolism, and translation, suggesting that changes in the metabolic environments that require adaptation to new sources of energy are central triggers of complex/pathway replacement in evolution. 2) Many MEOMs are related to outer membrane proteins, such proteins are involved in interaction with the environment and could thus be replaced as a result of adaptation. 3) MEOMs tend to separate organisms with large phylogenetic distance but they also separate organisms that live in different ecological niches. 4) Strikingly, although many MEOMs can be identified, there are much fewer cases where the two cliques in the MEOM completely mutually exclude each other, demonstrating the flexibility of protein evolution. 5) CO dehydrogenase and thymidylate synthase and the glycine cleavage genes mutually exclude each other in archaea; this may represent an alternative route for generation of methyl donors for thymidine synthesis.

FIG. 1.—

Finding MEOMs in coevolutionary networks: a flow diagram. (A) A coevolutionary network is reconstructed based on biological (e.g., physical interaction, coexpression, etc.) and statistical evidence. (B) In a coevolutionary network, each node corresponds to a gene family; green edges denote co-occurrence of the two nodes in the same organisms; red edges denote mutually exclusive occurrence (i.e., occurrence in different organisms). (C) The optimization score of a MEOM was based on Kelley and Ideker (2005). (D) Each MEOM is composed of two green (close to) cliques that are connected by a red (close to) bi-clique; in practice, the green (red) cliques (bi-cliques) may not be perfect (i.e., some of the edges may be missing; Materials and Methods). (E) Projection of a MEOM on a (gene family) × (organism) table; black denotes a case where there is a gene from the gene family in the organism; white denote cases where no gene from the gene family appears in the organism. (F) The approach can be implemented iteratively on subtaxonomic/phylogenetic groups.

FIG. 2.—

The most striking MEOM detected in data set of 95 organisms. (A) The coevolutionary edges between the gene families that are part of the MEOM. (B) The solution splits the analyzed organisms to the three domains of life (bacteria, archaea, and eukarya).

FIG. 3.—

General properties of MEOMS. (A) The subgroups that were analyzed from a data set of 383 organisms, the number of organisms in each subgroup (blue) and the number of MEOMs that were detected in each subgroup (red). (B) Number of incomplete mutually exclusions in each of the analyzed group of organisms (out of the total number of MEOMs detected). (C–E) MEOMs reflect both lineage specificity and environmental changes. (C) Mean MEOMs' separation increases with phylogenetic distance (Materials and Methods) for pair of organisms that are not in the same environment (Spearman correlation r = 0.96; P = 2.4 × 10⁻¹⁰). (D) Mean MEOM separation increases with phylogenetic distance for pair of organisms that are in the same environment (Spearman correlation r = 0.96; P = 3.3 × 10⁻⁹). (E) For every phylogenetic distance, pairs of organisms that are in the same community (Materials and Methods) have lower mean MEOM separation than pairs of organisms that are in different communities (Wilcoxon test: P = 0.0005).

FIG. 4.—

One of the MEOMs found in the entire data set (383 organisms): the “archaeal/vacuolar-type H+-ATPase” versus “F0/F1-type ATP synthase.” The COGs related to these two pathways are marked.