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Visualizing evolution in real-time method for strain engineering.

Reyes LH, Winkler J, Kao KC - Front Microbiol (2012)

Bottom Line: The adaptive landscape for an industrially relevant phenotype is determined by the effects of the genetic determinants on the fitness of the microbial system.Identifying the underlying adaptive landscape for a particular phenotype of interest will greatly enhance our abilities to engineer more robust microbial strains.Visualizing evolution in real-time (VERT) is a recently developed method based on in vitro adaptive evolution that facilitates the identification of fitter mutants throughout the course of evolution.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical Engineering, Texas A&M University, College Station, TX, USA.

ABSTRACT
The adaptive landscape for an industrially relevant phenotype is determined by the effects of the genetic determinants on the fitness of the microbial system. Identifying the underlying adaptive landscape for a particular phenotype of interest will greatly enhance our abilities to engineer more robust microbial strains. Visualizing evolution in real-time (VERT) is a recently developed method based on in vitro adaptive evolution that facilitates the identification of fitter mutants throughout the course of evolution. Combined with high-throughput genomic tools, VERT can greatly enhance the mapping of adaptive landscapes of industrially relevant phenotypes in microbial systems, thereby expanding our knowledge on the parameters that can be used for strain engineering.

No MeSH data available.


Related in: MedlinePlus

Example population dynamics from a three-colored VERT system (adapted from Kao and Sherlock, 2008). The colored bars represent the relative proportions of each colored subpopulation. An increase in the relative proportion of a colored subpopulation is indicative of the occurrence and expansion of an adaptive mutation in that subpopulation, and is defined as an adaptive event. Under the assumption that the adaptive mutant responsible for the specific adaptive event is at its’ highest proportion at the end of the sustained expansion, the adaptive mutants are isolated from the expanding subpopulation from the generation at the end of each expansion. The generation and colored subpopulation from which adaptive mutants were isolated are numbered 1–5.
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Figure 3: Example population dynamics from a three-colored VERT system (adapted from Kao and Sherlock, 2008). The colored bars represent the relative proportions of each colored subpopulation. An increase in the relative proportion of a colored subpopulation is indicative of the occurrence and expansion of an adaptive mutation in that subpopulation, and is defined as an adaptive event. Under the assumption that the adaptive mutant responsible for the specific adaptive event is at its’ highest proportion at the end of the sustained expansion, the adaptive mutants are isolated from the expanding subpopulation from the generation at the end of each expansion. The generation and colored subpopulation from which adaptive mutants were isolated are numbered 1–5.

Mentions: The original development of VERT used the yeast Saccharomyces cerevisiae evolving under glucose-limited conditions; a three-colored VERT system was used to seed eight parallel populations (Kao and Sherlock, 2008). The VERT data from one of the populations is shown in Figure 3; generations and subpopulations from which adaptive mutants were isolated from are indicated. Detailed genotypic and transcriptomics analyses of the isolated adaptive mutants showed convergence in the perturbation of the protein kinase A regulatory network in independent lineages (Kao and Sherlock, 2008). Subsequent development and application of a two-colored VERT system in E. coli for n-butanol tolerance revealed previously undiscovered resistance mechanisms (Reyes et al., 2012).


Visualizing evolution in real-time method for strain engineering.

Reyes LH, Winkler J, Kao KC - Front Microbiol (2012)

Example population dynamics from a three-colored VERT system (adapted from Kao and Sherlock, 2008). The colored bars represent the relative proportions of each colored subpopulation. An increase in the relative proportion of a colored subpopulation is indicative of the occurrence and expansion of an adaptive mutation in that subpopulation, and is defined as an adaptive event. Under the assumption that the adaptive mutant responsible for the specific adaptive event is at its’ highest proportion at the end of the sustained expansion, the adaptive mutants are isolated from the expanding subpopulation from the generation at the end of each expansion. The generation and colored subpopulation from which adaptive mutants were isolated are numbered 1–5.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3362087&req=5

Figure 3: Example population dynamics from a three-colored VERT system (adapted from Kao and Sherlock, 2008). The colored bars represent the relative proportions of each colored subpopulation. An increase in the relative proportion of a colored subpopulation is indicative of the occurrence and expansion of an adaptive mutation in that subpopulation, and is defined as an adaptive event. Under the assumption that the adaptive mutant responsible for the specific adaptive event is at its’ highest proportion at the end of the sustained expansion, the adaptive mutants are isolated from the expanding subpopulation from the generation at the end of each expansion. The generation and colored subpopulation from which adaptive mutants were isolated are numbered 1–5.
Mentions: The original development of VERT used the yeast Saccharomyces cerevisiae evolving under glucose-limited conditions; a three-colored VERT system was used to seed eight parallel populations (Kao and Sherlock, 2008). The VERT data from one of the populations is shown in Figure 3; generations and subpopulations from which adaptive mutants were isolated from are indicated. Detailed genotypic and transcriptomics analyses of the isolated adaptive mutants showed convergence in the perturbation of the protein kinase A regulatory network in independent lineages (Kao and Sherlock, 2008). Subsequent development and application of a two-colored VERT system in E. coli for n-butanol tolerance revealed previously undiscovered resistance mechanisms (Reyes et al., 2012).

Bottom Line: The adaptive landscape for an industrially relevant phenotype is determined by the effects of the genetic determinants on the fitness of the microbial system.Identifying the underlying adaptive landscape for a particular phenotype of interest will greatly enhance our abilities to engineer more robust microbial strains.Visualizing evolution in real-time (VERT) is a recently developed method based on in vitro adaptive evolution that facilitates the identification of fitter mutants throughout the course of evolution.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical Engineering, Texas A&M University, College Station, TX, USA.

ABSTRACT
The adaptive landscape for an industrially relevant phenotype is determined by the effects of the genetic determinants on the fitness of the microbial system. Identifying the underlying adaptive landscape for a particular phenotype of interest will greatly enhance our abilities to engineer more robust microbial strains. Visualizing evolution in real-time (VERT) is a recently developed method based on in vitro adaptive evolution that facilitates the identification of fitter mutants throughout the course of evolution. Combined with high-throughput genomic tools, VERT can greatly enhance the mapping of adaptive landscapes of industrially relevant phenotypes in microbial systems, thereby expanding our knowledge on the parameters that can be used for strain engineering.

No MeSH data available.


Related in: MedlinePlus