scholarly journals Evolutionary forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas

2018 ◽  
Author(s):  
Peter A. Lind
Keyword(s):  
Experimental Evolution ◽  
Negative Regulation ◽  
Mutation Rates ◽  
Short Term ◽  
Promoter Regions ◽  
Regulatory Pathways ◽  
Term Evolution ◽  
Upstream Promoter ◽  
Successful Prediction ◽  
Underlying Causes

AbstractExperimental evolution is often highly repeatable, but the underlying causes are generally unknown, which prevents extension of evolutionary forecasts to related species. Data on adaptive phenotypes, mutation rates and targets from the Pseudomonas fluorescens SBW25 Wrinkly Spreader system combined with mathematical models of the genotype-to-phenotype map allowed evolutionary forecasts to be made for several related Pseudomonas species. Predicted outcomes of experimental evolution in terms of phenotype, types of mutations, relative rates of pathways and mutational targets were then tested in Pseudomonas protegens Pf-5. As predicted, most mutations were found in three specific regulatory pathways resulting in increased production of Pel exopolysaccharide. Mutations were, as predicted, mainly found to disrupt negative regulation with a smaller number in upstream promoter regions. Mutated regions in proteins could also be predicted, but most mutations were not identical to those previously found. This study demonstrates the potential of short-term evolutionary forecasting in experimental populations.Impact statementConservation of genotype-to-phenotype maps allows successful prediction of short-term evolution in P. protegens Pf-5 and lays the foundation for evolutionary forecasting in other Pseudomonas.

scholarly journals Predicting mutational routes to new adaptive phenotypes

2018 ◽  
Author(s):  
Peter A. Lind ◽  
Eric Libby ◽  
Jenny Herzog ◽  
Paul B. Rainey
Keyword(s):  
Mathematical Modelling ◽  
Adaptive Evolution ◽  
Experimental Evolution ◽  
Additional Data ◽  
Mutation Rates ◽  
Mechanistic Models ◽  
Short Term ◽  
Regulatory Pathways ◽  
Fitness Effects ◽  
Mutational Hotspots

AbstractPredicting evolutionary change poses numerous challenges. Here we take advantage of the model bacterium Pseudomonas fluorescens in which the genotype-to-phenotype map determining evolution of the adaptive “wrinkly spreader” (WS) type is known. We present mathematical descriptions of three necessary regulatory pathways and use these to predict both the rate at which each mutational route is used and the expected mutational targets. To test predictions, mutation rates and targets were determined for each pathway. Unanticipated mutational hotspots caused experimental observations to depart from predictions but additional data led to refined models. A mismatch was observed between the spectra of WS-causing mutations obtained with and without selection due to low fitness of previously undetected WS-causing mutations. Our findings contribute toward the development of mechanistic models for forecasting evolution, highlight current limitations, and draw attention to challenges in predicting locus-specific mutational biases and fitness effects.Impact statementA combination of genetics, experimental evolution and mathematical modelling defines information necessary to predict the outcome of short-term adaptive evolution.

scholarly journals Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens

PLoS Genetics ◽  
2021 ◽  
Vol 17 (8) ◽  
pp. e1009722
Author(s):  
Jennifer T. Pentz ◽  
Peter A. Lind
Keyword(s):  
Experimental Evolution ◽  
Hot Spot ◽  
Sequence Divergence ◽  
Structural Basis ◽  
Extended Model ◽  
Short Term ◽  
Promoter Regions ◽  
Experimental Conditions ◽  
Diguanylate Cyclases ◽  
Air Liquid Interface

Experimental evolution with microbes is often highly repeatable under identical conditions, suggesting the possibility to predict short-term evolution. However, it is not clear to what degree evolutionary forecasts can be extended to related species in non-identical environments, which would allow testing of general predictive models and fundamental biological assumptions. To develop an extended model system for evolutionary forecasting, we used previous data and models of the genotype-to-phenotype map from the wrinkly spreader system in Pseudomonas fluorescens SBW25 to make predictions of evolutionary outcomes on different biological levels for Pseudomonas protegens Pf-5. In addition to sequence divergence (78% amino acid and 81% nucleotide identity) for the genes targeted by mutations, these species also differ in the inability of Pf-5 to make cellulose, which is the main structural basis for the adaptive phenotype in SBW25. The experimental conditions were changed compared to the SBW25 system to test if forecasts were extendable to a non-identical environment. Forty-three mutants with increased ability to colonize the air-liquid interface were isolated, and the majority had reduced motility and was partly dependent on the pel exopolysaccharide as a structural component. Most (38/43) mutations are expected to disrupt negative regulation of the same three diguanylate cyclases as in SBW25, with a smaller number of mutations in promoter regions, including an uncharacterized polysaccharide synthase operon. A mathematical model developed for SBW25 predicted the order of the three main pathways and the genes targeted by mutations, but differences in fitness between mutants and mutational biases also appear to influence outcomes. Mutated regions in proteins could be predicted in most cases (16/22), but parallelism at the nucleotide level was low and mutational hot spot sites were not conserved. This study demonstrates the potential of short-term evolutionary forecasting in experimental populations and provides testable predictions for evolutionary outcomes in other Pseudomonas species.

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 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.

ZFARED: A Database of the Antioxidant Response Elements in Zebrafish

2020 ◽  
Vol 15 (5) ◽  
pp. 415-419
Author(s):  
Azhwar Raghunath ◽  
Raju Nagarajan ◽  
Ekambaram Perumal
Keyword(s):  
Target Genes ◽  
Antioxidant Response ◽  
Zebrafish Genome ◽  
Promoter Regions ◽  
Protein Coding ◽  
Response Elements ◽  
Toxic Agents ◽  
Upstream Promoter ◽  
Its Gene ◽  
Antioxidant Response Elements

Background: Antioxidant Response Elements (ARE) play a key role in the expression of Nrf2 target genes by regulating the Keap1-Nrf2-ARE pathway, which offers protection against toxic agents and oxidative stress-induced diseases. Objective: To develop a database of putative AREs for all the genes in the zebrafish genome. This database will be helpful for researchers to investigate Nrf2 regulatory mechanisms in detail. Methods: To facilitate researchers functionally characterize zebrafish AREs, we have developed a database of AREs, Zebrafish Antioxidant Response Element Database (ZFARED), for all the protein-coding genes including antioxidant and mitochondrial genes in the zebrafish genome. The front end of the database was developed using HTML, JavaScript, and CSS and tested in different browsers. The back end of the database was developed using Perl scripts and Perl-CGI and Perl- DBI modules. Results: ZFARED is the first database on the AREs in zebrafish, which facilitates fast and efficient searching of AREs. AREs were identified using the in-house developed Perl algorithms and the database was developed using HTML, JavaScript, and Perl-CGI scripts. From this database, researchers can access the AREs based on chromosome number (1 to 25 and M for mitochondria), strand (positive or negative), ARE pattern and keywords. Users can also specify the size of the upstream/promoter regions (5 to 30 kb) from transcription start site to access the AREs located in those specific regions. Conclusion: ZFARED will be useful in the investigation of the Keap1-Nrf2-ARE pathway and its gene regulation. ZFARED is freely available at http://zfared.buc.edu.in/.

SHORT-TERM EVOLUTION OF FLOW & MORPHOLOGY IN AN ERODIBLE MEANDERING CHANNEL WITH & WITHOUT GROYNES

2018 ◽  
Vol 74 (4) ◽  
pp. I_1147-I_1152
Author(s):  
Saroj KARKI ◽  
Yuji HASEGAWA ◽  
Masakazu HASHIMOTO ◽  
Hajime NAKAGAWA ◽  
Kenji KAWAIKE
Keyword(s):  
Short Term ◽  
Meandering Channel ◽  
Term Evolution ◽  
Flow Morphology

Effects of Dipyridamole on the Short-Term Evolution of Glomerulonephritis

Nephron ◽  
1991 ◽  
Vol 58 (1) ◽  
pp. 13-16 ◽  
Author(s):  
S. Camara ◽  
J.P. de la Cruz ◽  
M.A. Frutos ◽  
P. Sanchez ◽  
Lopez de Novales ◽  
...  
Keyword(s):  
Short Term ◽  
Term Evolution

scholarly journals Sequence-specific activation of transcription by adenovirus EIa products is observed in HeLa cells but not in 293 cells.

1986 ◽  
Vol 6 (1) ◽  
pp. 201-208 ◽  
Author(s):  
T Leff ◽  
P Chambon
Keyword(s):  
Hela Cells ◽  
Upstream Region ◽  
Gene Products ◽  
Promoter Regions ◽  
Chimeric Promoter ◽  
293 Cells ◽  
Activation Of Transcription ◽  
Upstream Promoter ◽  
Sequence Elements ◽  
Responsive Element

The adenovirus EIa gene products activate transcription from the viral EIII and EIIaE promoters. We studied the mechanism of this stimulation by constructing a series of chimeric promoter recombinants containing the upstream regions of the EIII and EIIaE promoters linked to the TATA box-start-site regions of the viral major late and EIIa late promoters. By introducing these recombinants into HeLa cells together with recombinants producing the EIa gene products, we demonstrated that the induction of EIII and EIIaE transcription by EIa 13S and 12S mRNA products is dependent on sequences located in the upstream region (approximately -40 to -250) of these promoters. In addition, we showed that the major late and EIIa late upstream promoter regions do not contain such EIa-responsive sequence elements. In contrast, after transfection of these chimeric promoter recombinants into 293 cells (which constitutively express the EIa proteins), we found that their relative levels of transcription are similar and markedly different from those observed when they are cotransfected into HeLa cells with EIa protein-producing recombinants. We conclude that the efficiency of transcription from a given promoter in 293 cells is not necessarily related to the presence of a specific EIa-responsive element.

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