scholarly journals Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
DeElegant Robinson ◽  
Mike Place ◽  
James Hose ◽  
Adam Jochem ◽  
Audrey P Gasch
Keyword(s):  
Genetic Background ◽  
Natural Variation ◽  
Gene Overexpression ◽  
Fitness Costs ◽  
Resource Limitations ◽  
Specific Effects ◽  
Term Evolution ◽  
Number Variation ◽  
Evolutionary Trajectories

Copy number variation (CNV) through gene or chromosome amplification provides a route for rapid phenotypic variation and supports long-term evolution of gene functions. Although the evolutionary importance of CNV is known, little is understood about how genetic background influences CNV tolerance. Here, we measured fitness costs of over 4,000 over-expressed genes in 15 Saccharomyces cerevisiae strains representing different lineages, to explore natural variation in tolerating gene overexpression (OE). Strain-specific effects dominated the fitness costs of gene OE. We report global differences in the consequences of gene OE, independent of the amplified gene, as well as gene-specific effects that were dependent on the genetic background. Natural variation in the response to gene OE could be explained by several models, including strain-specific physiological differences, resource limitations, and regulatory sensitivities. This work provides new insight on how genetic background influences tolerance to gene amplification and the evolutionary trajectories accessible to different backgrounds.

scholarly journals Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories

2021 ◽  
Author(s):  
DeElegant Robinson ◽  
Michael Place ◽  
James Hose ◽  
Adam Jochem ◽  
Audrey P Gasch
Keyword(s):  
Genetic Background ◽  
Natural Variation ◽  
Gene Overexpression ◽  
Fitness Costs ◽  
Resource Limitations ◽  
Specific Effects ◽  
Term Evolution ◽  
Number Variation ◽  
Evolutionary Trajectories

Copy number variation (CNV) through gene or chromosome amplification provides a route for rapid phenotypic variation and supports long-term evolution of gene functions. Although the evolutionary importance of CNV is known, little is understood about how genetic background influences CNV tolerance. Here, we measured fitness costs of over 4,000 over-expressed genes in 15 Saccharomyces cerevisiae strains representing different lineages, to explore natural variation in tolerating gene overexpression (OE). Strain-specific effects dominated the fitness costs of gene OE. We report global differences in the consequences of gene OE, independent of the amplified gene, as well as gene-specific effects that were dependent on the genetic background. Natural variation in the response to gene OE could be explained by several models, including strain-specific physiological differences, resource limitations, and regulatory sensitivities. This work provides new insight on how genetic background influences tolerance to gene amplification and the evolutionary trajectories accessible to different backgrounds.

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 Leveraging Genetic-Background Effects in Saccharomyces cerevisiae To Improve Lignocellulosic Hydrolysate Tolerance

2016 ◽  
Vol 82 (19) ◽  
pp. 5838-5849 ◽  
Author(s):  
Maria Sardi ◽  
Nikolay Rovinskiy ◽  
Yaoping Zhang ◽  
Audrey P. Gasch
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Stress Tolerance ◽  
Genetic Background ◽  
Biofuel Production ◽  
Gene Overexpression ◽  
Lignocellulosic Hydrolysate ◽  
Content Type ◽  
Cellular Targets ◽  
Specific Effects ◽  
New Genes

ABSTRACTA major obstacle to sustainable lignocellulosic biofuel production is microbe inhibition by the combinatorial stresses in pretreated plant hydrolysate. Chemical biomass pretreatment releases a suite of toxins that interact with other stressors, including high osmolarity and temperature, which together can have poorly understood synergistic effects on cells. Improving tolerance in industrial strains has been hindered, in part because the mechanisms of tolerance reported in the literature often fail to recapitulate in other strain backgrounds. Here, we explored and then exploited variations in stress tolerance, toxin-induced transcriptomic responses, and fitness effects of gene overexpression in differentSaccharomyces cerevisiae(yeast) strains to identify genes and processes linked to tolerance of hydrolysate stressors. Using six differentS. cerevisiaestrains that together maximized phenotypic and genetic diversity, first we explored transcriptomic differences between resistant and sensitive strains to identify common and strain-specific responses. This comparative analysis implicated primary cellular targets of hydrolysate toxins, secondary effects of defective defense strategies, and mechanisms of tolerance. Dissecting the responses to individual hydrolysate components across strains pointed to synergistic interactions between osmolarity, pH, hydrolysate toxins, and nutrient composition. By characterizing the effects of high-copy gene overexpression in three different strains, we revealed the breadth of the background-specific effects of gene fitness contributions in synthetic hydrolysate. Our approach identified new genes for engineering improved stress tolerance in diverse strains while illuminating the effects of genetic background on molecular mechanisms.IMPORTANCERecent studies on natural variation withinSaccharomyces cerevisiaehave uncovered substantial phenotypic diversity. Here, we took advantage of this diversity, using it as a tool to infer the effects of combinatorial stress found in lignocellulosic hydrolysate. By comparing sensitive and tolerant strains, we implicated primary cellular targets of hydrolysate toxins and elucidated the physiological states of cells when exposed to this stress. We also explored the strain-specific effects of gene overexpression to further identify strain-specific responses to hydrolysate stresses and to identify genes that improve hydrolysate tolerance independent of strain background. This study underscores the importance of studying multiple strains to understand the effects of hydrolysate stress and provides a method to find genes that improve tolerance across strain backgrounds.

scholarly journals Genetic variation in aneuploidy prevalence and tolerance across Saccharomyces cerevisiae lineages

Genetics ◽  
2021 ◽  
Vol 217 (4) ◽  
Author(s):  
Eduardo F C Scopel ◽  
James Hose ◽  
Douda Bensasson ◽  
Audrey P Gasch
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Variation ◽  
Genetic Background ◽  
Species Variation ◽  
Unanswered Question ◽  
Fitness Costs ◽  
Chromosome Gain ◽  
Evolutionary Trajectories ◽  
Ecological Associations ◽  
Genetic Makeup

Abstract Individuals carrying an aberrant number of chromosomes can vary widely in their expression of aneuploidy phenotypes. A major unanswered question is the degree to which an individual’s genetic makeup influences its tolerance of karyotypic imbalance. Here we investigated within-species variation in aneuploidy prevalence and tolerance, using Saccharomyces cerevisiae as a model for eukaryotic biology. We analyzed genotypic and phenotypic variation recently published for over 1,000 S. cerevisiae strains spanning dozens of genetically defined clades and ecological associations. Our results show that the prevalence of chromosome gain and loss varies by clade and can be better explained by differences in genetic background than ecology. The relationships between lineages with high aneuploidy frequencies suggest that increased aneuploidy prevalence emerged multiple times in S. cerevisiae evolution. Separate from aneuploidy prevalence, analyzing growth phenotypes revealed that some genetic backgrounds—such as the European Wine lineage—show fitness costs in aneuploids compared to euploids, whereas other clades with high aneuploidy frequencies show little evidence of major deleterious effects. Our analysis confirms that chromosome gain can produce phenotypic benefits, which could influence evolutionary trajectories. These results have important implications for understanding genetic variation in aneuploidy prevalence in health, disease, and evolution.

scholarly journals Genetic variation in aneuploidy prevalence and tolerance across the Saccharomyces cerevisiae phylogeny

2020 ◽  
Author(s):  
Eduardo FC Scopel ◽  
James Hose ◽  
Douda Bensasson ◽  
Audrey Gasch
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Variation ◽  
Genetic Background ◽  
Unanswered Question ◽  
Fitness Costs ◽  
Chromosome Duplication ◽  
Evolutionary Trajectories ◽  
Selective Forces ◽  
Ecological Associations ◽  
Genetic Makeup

Individuals carrying an aberrant number of chromosomes can vary widely in their expression of aneuploidy phenotypes. A major unanswered question is the degree to which an individual's genetic makeup influences its tolerance of karyotypic imbalance. Here we took a population genetics perspective to investigate the selective forces influencing aneuploidy prevalence in Saccharomyces cerevisiae populations as a model for eukaryotic biology. We analyzed genotypic and phenotypic variation recently published for over 1,000 S. cerevisiae strains spanning dozens of genetically defined clades and ecological associations. Our results show that the prevalence of chromosome gain and loss varies by clade and can be better explained by differences in genetic background than ecology. The phylogenetic context of lineages showing high aneuploidy rates suggests that increased aneuploidy frequency arose multiple times in S. cerevisiae evolution. Separate from aneuploidy frequency, analyzing growth phenotypes reveals that some backgrounds – such as European Wine strains – show fitness costs upon chromosome duplication, whereas other clades with high aneuploidy rates show little evidence of major deleterious effects. Our analysis confirms that chromosome amplification can produce phenotypic benefits that can influence evolutionary trajectories. These results have important implications for understanding genetic variation in aneuploidy prevalence in health, disease, and evolution.

Link-Level Simulator for Wireless local Area Network

2018 ◽  
Vol 6 (7) ◽  
pp. 314
Author(s):  
Chaithra. H. U ◽  
Vani H.R
Keyword(s):  
Wireless Local Area Network ◽  
Local Area Network ◽  
Local Area Networks ◽  
Local Area ◽  
Long Term Evolution ◽  
Wireless Local Area Networks ◽  
Area Network ◽  
Network Simulator ◽  
Term Evolution

Now a days in Wireless Local Area Networks (WLANs) used in different fields because its well-suited simulator and higher flexibility. The concept of WLAN  with  advanced 5th Generation technologies, related to a Internet-of-Thing (IOT). In this project, representing the Network Simulator (NS-2) used linked-level simulators for Wireless Local Area Networks and still utilized IEEE 802.11g/n/ac with advanced IEEE 802.11ah/af technology. Realization of the whole Wireless Local Area Networking linked-level simulators inspired by the recognized Vienna Long Term Evolution- simulators. As a outcome, this is achieved to link together that simulator to detailed performances of Wireless Local Area Networking with Long Term Evolution, operated in the similar RF bands. From the advanced 5th Generation support cellular networking, such explore is main because different coexistences scenario can arise linking wireless communicating system to the ISM and UHF bands.

Sign in / Sign up

Export Citation Format

Share Document