scholarly journals Regulating General Mutation Rates: Examination of the Hypermutable State Model for Cairnsian Adaptive Mutation

Genetics ◽  
2003 ◽  
Vol 163 (4) ◽  
pp. 1483-1496 ◽  
Author(s):  
John R Roth ◽  
Eric Kofoid ◽  
Frederick P Roth ◽  
Otto G Berg ◽  
Jon Seger ◽  
...  
Keyword(s):  
Fold Increase ◽  
Genetic System ◽  
Selective Advantage ◽  
State Model ◽  
Adaptive Mutation ◽  
E Coli ◽  
Term Evolution ◽  
Mutation System ◽  
Response To Stress

Abstract In the lac adaptive mutation system of Cairns, selected mutant colonies but not unselected mutant types appear to arise from a nongrowing population of Escherichia coli. The general mutagenesis suffered by the selected mutants has been interpreted as support for the idea that E. coli possesses an evolved (and therefore beneficial) mechanism that increases the mutation rate in response to stress (the hypermutable state model, HSM). This mechanism is proposed to allow faster genetic adaptation to stressful conditions and to explain why mutations appear directed to useful sites. Analysis of the HSM reveals that it requires implausibly intense mutagenesis (105 times the unselected rate) and even then cannot account for the behavior of the Cairns system. The assumptions of the HSM predict that selected revertants will carry an average of eight deleterious null mutations and thus seem unlikely to be successful in long-term evolution. The experimentally observed 35-fold increase in the level of general mutagenesis cannot account for even one Lac+ revertant from a mutagenized subpopulation of 105 cells (the number proposed to enter the hypermutable state). We conclude that temporary general mutagenesis during stress is unlikely to provide a long-term selective advantage in this or any similar genetic system.

Evidence That Selected Amplification of a Bacterial lac Frameshift Allele Stimulates Lac+ Reversion (Adaptive Mutation) With or Without General Hypermutability

Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 945-956 ◽  
Author(s):  
E Susan Slechta ◽  
Jing Liu ◽  
Dan I Andersson ◽  
John R Roth
Keyword(s):  
Model Selection ◽  
Direct Effect ◽  
Mutation Rate ◽  
Side Effect ◽  
Copy Number ◽  
Fold Increase ◽  
Genetic System ◽  
Adaptive Mutation ◽  
E Coli ◽  
Frameshift Mutant

Abstract In the genetic system of Cairns and Foster, a nongrowing population of an E. coli lac frameshift mutant appears to specifically accumulate Lac+ revertants when starved on medium including lactose (adaptive mutation). This behavior has been attributed to stress-induced general mutagenesis in a subpopulation of starved cells (the hypermutable state model). We have suggested that, on the contrary, stress has no direct effect on mutability but favors only growth of cells that amplify their leaky mutant lac region (the amplification mutagenesis model). Selection enhances reversion primarily by increasing the mutant lac copy number within each developing clone on the selection plate. The observed general mutagenesis is attributed to a side effect of growth with an amplification—induction of SOS by DNA fragments released from a tandem array of lac copies. Here we show that the S. enterica version of the Cairns system shows SOS-dependent general mutagenesis and behaves in every way like the original E. coli system. In both systems, lac revertants are mutagenized during selection. Eliminating the 35-fold increase in mutation rate reduces revertant number only 2- to 4-fold. This discrepancy is due to continued growth of amplification cells until some clones manage to revert without mutagenesis solely by increasing their lac copy number. Reversion in the absence of mutagenesis is still dependent on RecA function, as expected if it depends on lac amplification (a recombination-dependent process). These observations support the amplification mutagenesis model.

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 Efficient anaerobic consumption of D-xylose by E. coli BL21(DE3) via xylR adaptive mutation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jung Min Heo ◽  
Hyun Ju Kim ◽  
Sang Jun Lee
Keyword(s):  
Consumption Rate ◽  
Xylose Isomerase ◽  
Fold Increase ◽  
Adaptive Mutation ◽  
Growth Media ◽  
Missense Mutations ◽  
Xylose Consumption ◽  
E Coli ◽  
Fermentation Technology ◽  
Xylose Transporter

Abstract Background Microorganisms can prioritize the uptake of different sugars depending on their metabolic needs and preferences. When both D-glucose and D-xylose are present in growth media, E. coli cells typically consume D-glucose first and then D-xylose. Similarly, when E. coli BL21(DE3) is provided with both D-glucose and D-xylose under anaerobic conditions, glucose is consumed first, whereas D-xylose is consumed very slowly. Results When BL21(DE3) was adaptively evolved via subculture, the consumption rate of D-xylose increased gradually. Strains JH001 and JH019, whose D-xylose consumption rate was faster, were isolated after subculture. Genome analysis of the JH001 and JH019 strains revealed that C91A (Q31K) and C740T (A247V) missense mutations in the xylR gene (which encodes the XylR transcriptional activator), respectively, controlled the expression of the xyl operon. RT-qPCR analyses demonstrated that the XylR mutation caused a 10.9-fold and 3.5-fold increase in the expression of the xylA (xylose isomerase) and xylF (xylose transporter) genes, respectively, in the adaptively evolved JH001 and JH019 strains. A C91A adaptive mutation was introduced into a new BL21(DE3) background via single-base genome editing, resulting in immediate and efficient D-xylose consumption. Conclusions Anaerobically-adapted BL21(DE3) cells were obtained through short-term adaptive evolution and xylR mutations responsible for faster D-xylose consumption were identified, which may aid in the improvement of microbial fermentation technology.

scholarly journals Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli

2016 ◽  
Author(s):  
Rohan Maddamsetti ◽  
Philip J. Hatcher ◽  
Anna G. Green ◽  
Barry L. Williams ◽  
Debora S. Marks ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Positive Selection ◽  
Long Term Evolution ◽  
Fine Tuning ◽  
Adaptive Mutations ◽  
E Coli ◽  
Term Evolution ◽  
Evolution Experiment ◽  
Core Genes

AbstractBacteria can evolve rapidly under positive selection owing to their vast numbers, allowing their genes to diversify by adapting to different environments. We asked whether the same genes that are fast evolving in the long-term evolution experiment with Escherichia coli (LTEE) have also diversified extensively in nature. We identified ~2000 core genes shared among 60 E. coli strains. During the LTEE, core genes accumulated significantly more nonsynonymous mutations than flexible (i.e., noncore) genes. Furthermore, core genes under positive selection in the LTEE are more conserved in nature than the average core gene. In some cases, adaptive mutations appear to fine-tune protein functions, rather than merely knocking them out. The LTEE conditions are novel for E. coli, at least in relation to the long sweep of its evolution in nature. The constancy and simplicity of the environment likely favor the complete loss of some unused functions and the fine-tuning of others.Competing Interests StatementWe, the authors, declare that we have no conflicts of interest.

scholarly journals The landscape of transcriptional and translational changes over 22 years of bacterial adaptation

2021 ◽  
Author(s):  
John S. Favate ◽  
Shun Liang ◽  
Srujana S. Yadavalli ◽  
Premal Shah
Keyword(s):  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Transcriptional Level ◽  
Genomic Changes ◽  
E Coli ◽  
Fitness Effects ◽  
Term Evolution ◽  
Evolution Experiment ◽  
Genetic Level

AbstractOrganisms can adapt to an environment by taking multiple mutational paths. This redundancy at the genetic level, where many mutations have similar phenotypic and fitness effects, can make untangling the molecular mechanisms of complex adaptations difficult. Here we use the E. coli long-term evolution experiment (LTEE) as a model to address this challenge. To bridge the gap between disparate genomic changes and parallel fitness gains, we characterize the landscape of transcriptional and translational changes across 11 replicate populations evolving in parallel for 50,000 generations. By quantifying absolute changes in mRNA abundances, we show that not only do all evolved lines have more mRNAs but that this increase in mRNA abundance scales with cell size. We also find that despite few shared mutations at the genetic level, clones from replicate populations in the LTEE are remarkably similar to each other in their gene expression patterns at both the transcriptional and translational levels. Furthermore, we show that the bulk of the expression changes are due to changes at the transcriptional level with very few translational changes. Finally, we show how mutations in transcriptional regulators lead to consistent and parallel changes in the expression levels of downstream genes, thereby linking genomic changes to parallel fitness gains in the LTEE. These results deepen our understanding of the molecular mechanisms underlying complex adaptations and provide insights into the repeatability of evolution.

scholarly journals Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations

2020 ◽  
Author(s):  
Milo S. Johnson ◽  
Shreyas Gopalakrishnan ◽  
Juhee Goyal ◽  
Megan E. Dillingham ◽  
Christopher W. Bakerlee ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Evolutionary Dynamics ◽  
Evolutionary Process ◽  
Mutation Rates ◽  
Historical Contingency ◽  
E Coli ◽  
Term Evolution ◽  
Changes Over Time ◽  
Over Time

AbstractLaboratory experimental evolution provides a window into the details of the evolutionary process. To investigate the consequences of long-term adaptation, we evolved 205 S. cerevisiae populations (124 haploid and 81 diploid) for ∼10,000 generations in three environments. We measured the dynamics of fitness changes over time, finding repeatable patterns of declining adaptability. Sequencing revealed that this phenotypic adaptation is coupled with a steady accumulation of mutations, widespread genetic parallelism, and historical contingency. In contrast to long-term evolution in E. coli, we do not observe long-term coexistence or populations with highly elevated mutation rates. We find that evolution in diploid populations involves both fixation of heterozygous mutations and frequent loss-of-heterozygosity events. Together, these results help distinguish aspects of evolutionary dynamics that are likely to be general features of adaptation across many systems from those that are specific to individual organisms and environmental conditions.

scholarly journals Efficient Anaerobic Consumption of D-xylose by E. coli BL21(DE3) via xylR Adaptive Mutation

2021 ◽  
Author(s):  
Jung Min Heo ◽  
Hyun Ju Kim ◽  
Sang Jun Lee
Keyword(s):  
Consumption Rate ◽  
Xylose Isomerase ◽  
Fold Increase ◽  
Adaptive Mutation ◽  
Growth Media ◽  
Missense Mutations ◽  
Xylose Consumption ◽  
E Coli ◽  
Fermentation Technology ◽  
Xylose Transporter

Abstract Background: Microorganisms can prioritize the uptake of different sugars depending on their metabolic needs and preferences. When both D-glucose and D-xylose are present in growth media, E. coli cells typically consume D-glucose first and then D-xylose. Similarly, when E. coli BL21(DE3) is provided with both glucose and xylose under anaerobic conditions, glucose is consumed first, whereas xylose is consumed very slowly.Results: When BL21(DE3) was adaptively evolved via subculture, the consumption rate of D-xylose increased gradually. Strains JH001 and JH019, whose D-xylose consumption rate was faster, were isolated after subculture. Genome analysis of the JH001 and JH019 strains revealed that C91A (Q31K) and C740T (A247V) missense mutations in the xylR gene (which encodes the XylR transcriptional activator), respectively, controlled the expression of the xyl operon. RT-qPCR analyses demonstrated that the XylR mutation caused a 10.9-fold and 3.5-fold increase in the expression of the xylA (xylose isomerase) and xylF (xylose transporter) genes, respectively, in the adaptively evolved JH001 and JH019 strains. A C91A adaptive mutation was introduced into a new BL21(DE3) background via single-base genome editing, resulting in immediate and efficient D-xylose consumption. Conclusions: We obtained anaerobically-adapted BL21(DE3) cells through short-term adaptive evolution and identified xylR mutations responsible for faster xylose consumption, which may facilitate the improvement of microbial fermentation technology.

scholarly journals Highly expressed genes evolve under strong epistasis from a proteome-wide scan in E. coli

2017 ◽  
Author(s):  
Eric Girard ◽  
Pouria Dasmeh ◽  
Adrian W.R. Serohijos
Keyword(s):  
Protein Evolution ◽  
Protein Unfolding ◽  
Long Term Evolution ◽  
Fitness Cost ◽  
Sequence Evolution ◽  
E Coli ◽  
Term Evolution ◽  
Highly Expressed Genes

ABSTRACTEpistasis or the non-additivity of mutational effects is a major force in protein evolution, but it has not been systematically quantified at the level of a proteome. Here, we estimated the extent of epistasis for 2,382 genes in E. coli using several hundreds of orthologs for each gene within the class Gammaproteobacteria. We found that the average epistasis is ~41% across genes in the proteome and that epistasis is stronger among highly expressed genes. This trend is quantitatively explained by the prevailing model of sequence evolution based on minimizing the fitness cost of protein unfolding and aggregation. Our results highlight the coupling between selection and epistasis in the long-term evolution of a proteome.

scholarly journals Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Milo S Johnson ◽  
Shreyas Gopalakrishnan ◽  
Juhee Goyal ◽  
Megan E Dillingham ◽  
Christopher W Bakerlee ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Evolutionary Dynamics ◽  
Evolutionary Process ◽  
Mutation Rates ◽  
Historical Contingency ◽  
E Coli ◽  
Term Evolution ◽  
Changes Over Time ◽  
Over Time

Laboratory experimental evolution provides a window into the details of the evolutionary process. To investigate the consequences of long-term adaptation, we evolved 205 Saccharomyces cerevisiae populations (124 haploid and 81 diploid) for ~10,000 generations in three environments. We measured the dynamics of fitness changes over time, finding repeatable patterns of declining adaptability. Sequencing revealed that this phenotypic adaptation is coupled with a steady accumulation of mutations, widespread genetic parallelism, and historical contingency. In contrast to long-term evolution in E. coli, we do not observe long-term coexistence or populations with highly elevated mutation rates. We find that evolution in diploid populations involves both fixation of heterozygous mutations and frequent loss-of-heterozygosity events. Together, these results help distinguish aspects of evolutionary dynamics that are likely to be general features of adaptation across many systems from those that are specific to individual organisms and environmental conditions.

Sign in / Sign up

Export Citation Format

Share Document