ArticleProceedings of the National Academy of Sciences of the United States of America2008
Modularity of stress response evolution.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 59 citations in OpenAlex.
- Unravelling the temporal dynamics of community functions in protists induced by treated wastewater exposure using metatranscriptomics.Scientific reports · 2025Article
- Network architecture of transcriptomic stress responses in zebrafish embryos.PLoS computational biology · 2025Article
- Evolution of biological cooperation: an algorithmic approach.Scientific reports · 2024Article
- Deciphering Macromolecular Interactions Involved in Abiotic Stress Signaling: A Review of Bioinformatics Analysis.Methods in molecular biology (Clifton, N.J.) · 2023Review
- Interplay of Methodology and Conceptualization in Plant Abiotic Stress Signaling.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Survival ofMicroorganisms · 2022Article
- Rapid evolution of trait correlation networks during bacterial adaptation to the rhizosphere.Evolution; international journal of organic evolution · 2021Article
- Significance of DopEcR, a G-protein coupled dopamine/ecdysteroid receptor, in physiological and behavioral response to stressors.Journal of neurogenetics · 2020Review
- The landscape of microbial phenotypic traits and associated genes.Nucleic acids research · 2016Article
- Identification of key player genes in gene regulatory networks.BMC systems biology · 2016Article
- A Glimpse to Background and Characteristics of Major Molecular Biological Networks.BioMed research international · 2015Review
- Spatiotemporal positioning of multipotent modules in diverse biological networks.Cellular and molecular life sciences : CMLS · 2014Review
- Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis.Nucleic acids research · 2012Article
- SPICE: discovery of phenotype-determining component interplays.BMC systems biology · 2012Article
- Pulsed feedback defers cellular differentiation.PLoS biology · 2012Article
- Integrated inference and analysis of regulatory networks from multi-level measurements.Methods in cell biology · 2012Review
- Article
- The emergence of modularity in biological systems.Physics of life reviews · 2011Review
- The population dynamics of bacteria in physically structured habitats and the adaptive virtue of random motility.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- The evolutionary rate variation among genes of HOG-signaling pathway in yeast genomes.Biology direct · 2010Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.