TY - JOUR
T1 - Analysis of coevolving gene families using Mutually Exclusive Orthologous Modules
AU - Zhang, Xiuwei
AU - Kupiec, Martin
AU - Gophna, Uri
AU - Tuller, Tamir
N1 - Israel Science Foundation; McDonnell Foundation; Israeli Ministry of HealthWe would like to thank Dr Igor Ulitsky, Prof Elchanan Mossel, and Prof Yitzhak Pilpel for very helpful discussions. T.T. is a Koshland Scholar at Weizmann Institute of Science. M.K.'s research was supported by grants from the Israel Science Foundation and the McDonnell Foundation. U.G. is supported by the McDonnell Foundation and the Israeli Ministry of Health.
PY - 2011
Y1 - 2011
N2 - 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, aMEOMreflects 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 thatinteract 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 tonew sources of energy are central triggers of complex/pathway replacement in evolution. 2) ManyMEOMs 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)MEOMstend 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.
AB - 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, aMEOMreflects 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 thatinteract 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 tonew sources of energy are central triggers of complex/pathway replacement in evolution. 2) ManyMEOMs 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)MEOMstend 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.
UR - http://www.scopus.com/inward/record.url?scp=79960098811&partnerID=8YFLogxK
U2 - https://doi.org/10.1093/gbe/evr030
DO - https://doi.org/10.1093/gbe/evr030
M3 - مقالة
SN - 1759-6653
VL - 3
SP - 413
EP - 423
JO - Genome Biology and Evolution
JF - Genome Biology and Evolution
IS - 1
ER -