Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens.

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 t...

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Autores principales:	Jennifer T Pentz, Peter A Lind
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Genetics QH426-470
Acceso en línea:	https://doaj.org/article/5c0c6ecde8b944828352ead80825b32f
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spelling	oai:doaj.org-article:5c0c6ecde8b944828352ead80825b32f2021-12-02T20:02:53ZForecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens.1553-73901553-740410.1371/journal.pgen.1009722https://doaj.org/article/5c0c6ecde8b944828352ead80825b32f2021-08-01T00:00:00Zhttps://doi.org/10.1371/journal.pgen.1009722https://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404Experimental 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.Jennifer T PentzPeter A LindPublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 17, Iss 8, p e1009722 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Genetics QH426-470
spellingShingle	Genetics QH426-470 Jennifer T Pentz Peter A Lind Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens.
description	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.
format	article
author	Jennifer T Pentz Peter A Lind
author_facet	Jennifer T Pentz Peter A Lind
author_sort	Jennifer T Pentz
title	Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens.
title_short	Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens.
title_full	Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens.
title_fullStr	Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens.
title_full_unstemmed	Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens.
title_sort	forecasting of phenotypic and genetic outcomes of experimental evolution in pseudomonas protegens.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/5c0c6ecde8b944828352ead80825b32f
work_keys_str_mv	AT jennifertpentz forecastingofphenotypicandgeneticoutcomesofexperimentalevolutioninpseudomonasprotegens AT peteralind forecastingofphenotypicandgeneticoutcomesofexperimentalevolutioninpseudomonasprotegens
_version_	1718375661456850944

Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens.

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