Modularity of stress response evolution

@article{singh08, abstract = {Responses to extracellular stress directly confer survival fitness by means of complex regulatory networks. Despite their complexity, the networks must be evolvable because of changing ecological and environmental pressures. Although the regulatory networks underlying stress responses are characterized extensively, their mechanism of evolution remains poorly understood. Here, we examine the evolution of three candidate stress response networks (chemotaxis, competence for DNA uptake, and endospore formation) by analyzing their phylogenetic distribution across several hundred diverse bacterial and archaeal lineages. We report that genes in the chemotaxis and sporulation networks group into well defined evolutionary modules with distinct functions, phenotypes, and substitution rates as compared with control sets of randomly chosen genes. The evolutionary modules vary in both number and cohesiveness among the three pathways. Chemotaxis has five coherent modules whose distribution among species shows a clear pattern of interdependence and rewiring. Sporulation, by contrast, is nearly monolithic and seems to be inherited vertically, with three weak modules constituting early and late stages of the pathway. Competence does not seem to exhibit well defined modules either at or below the pathway level. Many of the detected modules are better understood in engineering terms than in protein functional terms, as we demonstrate using a control-based ontology that classifies gene function according to roles such as "sensor," "regulator," and "actuator." Moreover, we show that combinations of the modules predict phenotype, yet surprisingly do not necessarily correlate with phylogenetic inheritance. The architectures of these three pathways are therefore emblematic of different modes and constraints on evolution. 10.1073/pnas.0709764105}, author = {Singh, Amoolya H. and Wolf, Denise M. and Wang, Peggy and Arkin, Adam P. }, citeulike-article-id = {2857451}, doi = {10.1073/pnas.0709764105}, journal = {Proceedings of the National Academy of Sciences}, keywords = {modularity, network\_evolution}, month = {May}, number = {21}, pages = {7500--7505}, posted-at = {2008-06-05 03:40:14}, priority = {4}, title = {Modularity of stress response evolution}, url = {http://dx.doi.org/10.1073/pnas.0709764105}, volume = {105}, year = {2008} }

TY - JOUR ID - singh08 L3 - citeulike-article-id:2857451 TI - Modularity of stress response evolution JF - Proceedings of the National Academy of Sciences VL - 105 IS - 21 SP - 7500 EP - 7505 N2 - Responses to extracellular stress directly confer survival fitness by means of complex regulatory networks. Despite their complexity, the networks must be evolvable because of changing ecological and environmental pressures. Although the regulatory networks underlying stress responses are characterized extensively, their mechanism of evolution remains poorly understood. Here, we examine the evolution of three candidate stress response networks (chemotaxis, competence for DNA uptake, and endospore formation) by analyzing their phylogenetic distribution across several hundred diverse bacterial and archaeal lineages. We report that genes in the chemotaxis and sporulation networks group into well defined evolutionary modules with distinct functions, phenotypes, and substitution rates as compared with control sets of randomly chosen genes. The evolutionary modules vary in both number and cohesiveness among the three pathways. Chemotaxis has five coherent modules whose distribution among species shows a clear pattern of interdependence and rewiring. Sporulation, by contrast, is nearly monolithic and seems to be inherited vertically, with three weak modules constituting early and late stages of the pathway. Competence does not seem to exhibit well defined modules either at or below the pathway level. Many of the detected modules are better understood in engineering terms than in protein functional terms, as we demonstrate using a control-based ontology that classifies gene function according to roles such as "sensor," "regulator," and "actuator." Moreover, we show that combinations of the modules predict phenotype, yet surprisingly do not necessarily correlate with phylogenetic inheritance. The architectures of these three pathways are therefore emblematic of different modes and constraints on evolution. 10.1073/pnas.0709764105 KW - modularity KW - network_evolution AU - Singh, Amoolya AU - Wolf, Denise AU - Wang, Peggy AU - Arkin, Adam PY - 2008/05/27/ UR - http://dx.doi.org/10.1073/pnas.0709764105 ER -