ArticlePLoS genetics2008
Expression profiles reveal parallel evolution of epistatic interactions involving the CRP regulon in Escherichia coli.
Article in PLoS genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed, 69 citations in OpenAlex.
- Escherichia coli adaptation under prolonged resource exhaustion is characterized by extreme parallelism and frequent historical contingency.PLoS genetics · 2024Article
- Manipulating multi-level selection in a fungal entomopathogen reveals social conflicts and a method for improving biocontrol traits.PLoS pathogens · 2024Article
- Diversity inmBio · 2019Article
- Adapting the engine to the fuel: mutator populations can reduce the mutational load by reorganizing their genome structure.BMC evolutionary biology · 2019Article
- Genetics of Adaptation of the Ascomycetous Fungus Podospora anserina to Submerged Cultivation.Genome biology and evolution · 2019Article
- Article
- Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism.Nature communications · 2018Article
- The Fructose-Specific Phosphotransferase System of Klebsiella pneumoniae Is Regulated by Global Regulator CRP and Linked to Virulence and Growth.Infection and immunity · 2018Article
- The Transcriptional Regulators of the CRP Family Regulate Different Essential Bacterial Functions and Can Be Inherited Vertically and Horizontally.Frontiers in microbiology · 2017Review
- Evolution after introduction of a novel metabolic pathway consistently leads to restoration of wild-type physiology.PLoS genetics · 2013Article
- Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks.Genome biology and evolution · 2013Article
- Culture history and population heterogeneity as determinants of bacterial adaptation: the adaptomics of a single environmental transition.Microbiology and molecular biology reviews : MMBR · 2012Review
- New insights into bacterial adaptation through in vivo and in silico experimental evolution.Nature reviews. Microbiology · 2012Review
- Signal correlations in ecological niches can shape the organization and evolution of bacterial gene regulatory networks.Advances in microbial physiology · 2012Review
- Robust detection of hierarchical communities from Escherichia coli gene expression data.PLoS computational biology · 2012Article
- Functional and metabolic effects of adaptive glycerol kinase (GLPK) mutants in Escherichia coli.The Journal of biological chemistry · 2011Article
- Second-order selection for evolvability in a large Escherichia coli population.Science (New York, N.Y.) · 2011Article
- Altered regulation of the OmpF porin by Fis in Escherichia coli during an evolution experiment and between B and K-12 strains.Journal of bacteriology · 2011Article
- Advantages and limitations of current network inference methods.Nature reviews. Microbiology · 2010Review
- Divergence involving global regulatory gene mutations in an Escherichia coli population evolving under phosphate limitation.Genome biology and evolution · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The extent and nature of epistatic interactions between mutations are issues of fundamental importance in evolutionary biology. However, they are difficult to study and their influence on adaptation remains poorly understood. Here, we use a systems-level approach to examine epistatic interactions that arose during the evolution of Escherichia coli in a defined environment. We used expression arrays to compare the effect on global patterns of gene expression of deleting a central regulatory gene, crp. Effects were measured in two lineages that had independently evolved for 20,000 generations and in their common ancestor. We found that deleting crp had a much more dramatic effect on the expression profile of the two evolved lines than on the ancestor. Because the sequence of the crp gene was unchanged during evolution, these differences indicate epistatic interactions between crp and mutations at other loci that accumulated during evolution. Moreover, a striking degree of parallelism was observed between the two independently evolved lines; 115 genes that were not crp-dependent in the ancestor became dependent on crp in both evolved lines. An analysis of changes in crp dependence of well-characterized regulons identified a number of regulatory genes as candidates for harboring beneficial mutations that could account for these parallel expression changes. Mutations within three of these genes have previously been found and shown to contribute to fitness. Overall, these findings indicate that epistasis has been important in the adaptive evolution of these lines, and they provide new insight into the types of genetic changes through which epistasis can evolve. More generally, we demonstrate that expression profiles can be profitably used to investigate epistatic interactions.
Indexed as
Identifiers
What OpenQuestion holds
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.