Genome-wide analysis of a long-term evolution experiment with Drosophila

Nature ◽  
2010 ◽  
Vol 467 (7315) ◽  
pp. 587-590 ◽  
Author(s):  
Molly K. Burke ◽  
Joseph P. Dunham ◽  
Parvin Shahrestani ◽  
Kevin R. Thornton ◽  
Michael R. Rose ◽  
...  
Keyword(s):  
Long Term Evolution ◽  
Genome Wide Analysis ◽  
Term Evolution ◽  
Genome Wide ◽  
Evolution Experiment

scholarly journals Universal constraints on protein evolution in the long-term evolution experiment with Escherichia coli

2020 ◽  
Author(s):  
Rohan Maddamsetti
Keyword(s):  
Protein Evolution ◽  
Long Term Evolution ◽  
Protein Abundance ◽  
Interacting Proteins ◽  
Protein Thermostability ◽  
Protein Protein Interaction ◽  
Term Evolution ◽  
Evolution Experiment ◽  
Positive Correlations

AbstractAlthough it is well known that highly expressed and highly interacting proteins evolve slowly across the tree of life, there is little consensus for why this is true. Here, I report that highly abundant and highly interacting proteins evolve slowly in the hypermutator populations of Lenski’s long-term evolution experiment with E. coli (LTEE). Specifically, the density of observed mutations per gene, as measured in metagenomic time series covering 60,000 generations of the LTEE, strongly anti-correlates with mRNA abundance, protein abundance, and degree of protein-protein interaction. Weaker positive correlations between protein thermostability and mutation density are observed in the hypermutator populations, counterbalanced by negative correlations between protein thermostability and mRNA and protein abundance. These results show that universal constraints on protein evolution are visible in data spanning three decades of experimental evolution. Therefore, it should be possible to design experiments to answer why highly expressed and highly interacting proteins evolve slowly.

scholarly journals Evolution and coexistence in response to a key innovation in a long-term evolution experiment withEscherichia coli

2015 ◽  
Author(s):  
Caroline B. Turner ◽  
Zachary D. Blount ◽  
Daniel H. Mitchell ◽  
Richard E. Lenski
Keyword(s):  
Environmental Changes ◽  
Carbon Sources ◽  
Dicarboxylic Acids ◽  
Long Term Evolution ◽  
E Coli ◽  
Term Evolution ◽  
Key Innovation ◽  
Evolution Experiment ◽  
Evolutionary Trajectories

Evolution of a novel function can greatly alter the effects of an organism on its environment. These environmental changes can, in turn, affect the further evolution of that organism and any coexisting organisms. We examine these effects and feedbacks following evolution of a novel function in the long-term evolution experiment (LTEE) withEscherichia coli. A characteristic feature ofE. coliis its inability to consume citrate aerobically. However, that ability evolved in one of the LTEE populations. In this population, citrate-utilizing bacteria (Cit+) coexisted stably with another clade of bacteria that lacked the capacity to utilize citrate (Cit−). This coexistence was shaped by the evolution of a cross-feeding relationship in which Cit+cells released the dicarboxylic acids succinate, fumarate, and malate into the medium, and Cit−cells evolved improved growth on these carbon sources, as did the Cit+cells. Thus, the evolution of citrate consumption led to a flask-based ecosystem that went from a single limiting resource, glucose, to one with five resources either shared or partitioned between two coexisting clades. Our findings show how evolutionary novelties can change environmental conditions, thereby facilitating diversity and altering both the structure of an ecosystem and the evolutionary trajectories of coexisting organisms.

scholarly journals Evolution with private resources reverses some changes from long-term evolution with public resources

2021 ◽  
Author(s):  
Katrina van Raay ◽  
Sergey Stolyar ◽  
Jordana Sevigny ◽  
Jeremy Draghi ◽  
Richard E. Lenski ◽  
...  
Keyword(s):  
Long Term Evolution ◽  
Phosphotransferase System ◽  
Shared Resources ◽  
Term Evolution ◽  
Public Resources ◽  
Concomitant Reduction ◽  
Evolution Experiment ◽  
Oil Emulsions ◽  
Open Question

A population under selection to improve one trait may evolve a sub-optimal state for another trait due to tradeoffs and other evolutionary constraints. How this evolution affects the capacity of a population to adapt when conditions change to favor the second trait is an open question. We investigated this question using isolates from a lineage spanning 60,000 generations of the Long-Term Evolution Experiment (LTEE) with Escherichia coli, where cells have access to a shared pool of resources, and have evolved increased competitive ability and a concomitant reduction in numerical yield. Using media-in oil emulsions we shifted the focus of selection to numerical yield, where cells grew in isolated patches with private resources. We found that the time spent evolving under shared resources did not affect the ability to re-evolve toward higher numerical yield. The evolution of numerical yield commonly occurred through mutations in the phosphoenolpyruvate phosphotransferase system. These mutants exhibit slower uptake of glucose, making them poorer competitors for public resources, and produce smaller cells that release less carbon as overflow metabolites. Our results demonstrate that mutations that were not part of adaptation under one selective regime may enable access to ancestral phenotypes when selection changes to favor evolutionary reversion.

scholarly journals Selection maintains protein interactome resilience in the long-term evolution experiment with Escherichia coli

2021 ◽  
Author(s):  
Rohan Maddamsetti
Keyword(s):  
Experimental Evolution ◽  
Long Term Evolution ◽  
Rate Of Change ◽  
Network Resilience ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Term Evolution ◽  
Protein Interactome ◽  
Evolution Experiment

AbstractMost cellular functions are carried out by a dynamic network of interacting proteins. An open question is whether the network properties of protein interactomes represent phenotypes under natural selection. One proposal is that protein interactomes have evolved to be resilient, such that they tend to maintain connectivity when proteins are removed from the network. This hypothesis predicts that interactome resilience should be maintained during long-term experimental evolution. I tested this prediction by modeling the evolution of protein-protein interaction (PPI) networks in Lenski’s long-term evolution experiment with Escherichia coli (LTEE). In this test, I removed proteins affected by nonsense, insertion, deletion, and transposon mutations in evolved LTEE strains, and measured the resilience of the resulting networks. I compared the rate of change of network resilience in each LTEE population to the rate of change of network resilience for corresponding randomized networks. The evolved PPI networks are significantly more resilient than networks in which random proteins have been deleted. Moreover, the evolved networks are generally more resilient than networks in which the random deletion of proteins was restricted to those disrupted in LTEE. These results suggest that evolution in the LTEE has favored PPI networks that are, on average, more resilient than expected from the genetic variation across the evolved populations. My findings therefore support the hypothesis that selection maintains protein interactome resilience over evolutionary time.Significance StatementUnderstanding how protein-protein interaction (PPI) networks evolve is a central goal of evolutionary systems biology. One property that has been hypothesized to be important for PPI network evolution is resilience, which means that networks tend to maintain connectivity even after many nodes (proteins in this case) have been removed. This hypothesis predicts that PPI network resilience should be maintained during long-term experimental evolution. Consistent with this prediction, I found that the PPI networks that evolved over 50,000 generations of Lenski’s long-term evolution experiment with E. coli are more resilient than expected by chance.

scholarly journals Integration of Foreign Genetic Material Provokes Local Mutagenesis in the Recipient Genome

2016 ◽  
Vol 11 (2) ◽  
pp. 394-405 ◽  
Author(s):  
О.А. Глазунова ◽  
О.А. Glazunova
Keyword(s):  
Genetic Material ◽  
Long Term Evolution ◽  
Bacterial Cells ◽  
New Host ◽  
Term Evolution ◽  
Evolution Experiment ◽  
Foreign Genes ◽  
Genomic Regions ◽  
And Control

An exchange with genetic information is one of the key factors driving bacterial evolution. However, the mechanisms for integration of horizontally transferred genes into the regulatory network of a new host remain almost unexplored so far. The present work aimed to investigate this adaptive process, specifically, involvement of the transcription machinery of bacterial cells. Two foreign genes in the genome of Escherichia coli K12 MG1655 were substituted with their copies from the genomes of predicted donors, and a long-term evolution experiment was initiated for both mutant and control cultures. After 2000 (for the sfmA gene) and 4000 (for the ydhZ gene) generations, modified and native genomic regions were amplified and used for population sequencing. Spontaneous mutations were analyzed, and it was found that substitutions of G/C- to A/T-pairs occurred more frequently in the modified regions as compared to non-modified, whereas A/T → G/C substitutions occurred more rarely. That means that the host genome responds to integration of foreign genetic material with an adaptive reaction aimed to enrich the modified region with A/T-pairs. In the course of long-term evolution, it may result either in “silencing” of an unfavourable gene with a specific suppressor of foreign genes, H-NS, or in creation of a promoter acceptable for adequate expression as a part of promoter island.

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