A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes

James S. Horton; Louise M. Flanagan; Robert W. Jackson; Nicholas K. Priest; Tiffany B. Taylor

doi:10.1038/s41467-021-26286-9

A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes

James S. Horton, Louise M. Flanagan, Robert W. Jackson, Nicholas K. Priest, Tiffany B. Taylor

University of Birmingham

Research output: Contribution to journal › Article › peer-review

19 Citations (SciVal)

64 Downloads (Pure)

Abstract

Mutational hotspots can determine evolutionary outcomes and make evolution repeatable. Hotspots are products of multiple evolutionary forces including mutation rate heterogeneity, but this variable is often hard to identify. In this work, we reveal that a near-deterministic genetic hotspot can be built and broken by a handful of silent mutations. We observe this when studying homologous immotile variants of the bacteria Pseudomonas fluorescens, AR2 and Pf0-2x. AR2 resurrects motility through highly repeatable de novo mutation of the same nucleotide in >95% lines in minimal media (ntrB A289C). Pf0-2x, however, evolves via a number of mutations meaning the two strains diverge significantly during adaptation. We determine that this evolutionary disparity is owed to just 6 synonymous variations within the ntrB locus, which we demonstrate by swapping the sites and observing that we are able to both break (>95% to 0%) and build (0% to 80%) a deterministic mutational hotspot. Our work reveals a key role for silent genetic variation in determining adaptive outcomes.

Original language	English
Article number	6092
Number of pages	10
Journal	Nature Communications
Volume	12
Issue number	1
DOIs	https://doi.org/10.1038/s41467-021-26286-9
Publication status	Published - 19 Oct 2021

Bibliographical note

Funding Information:
We thank Laurence Hurst for comments on earlier versions of this manuscript. In addition, we thank member of the Taylor lab Matthew Shepherd for insightful comments and discussion, and Mark Silby for contributing the ancestral P. fluorescens Pf0-2x strain used in the study. This work was supported by the University of Bath University Research Studentship Account (URSA) awarded to TBT and NKP; a Royal Society Dorothy Hodgkin Research Fellowship awarded to TBT (DH150169); and the JABBS Foundation for RWJ. Bioinformatics analysis of the paper was carried out using the Medical Research Council’s (MRC) Cloud Infrastructure for Microbial Bioinformatics (CLIMB), and Illumina Whole-Genome Sequencing by the Milner Genomics Centre, Bath, UK and MicrobesNG, Birmingham, UK.

Data availability
Data used for the generation of this manuscript is publicly available and can be accessed
[https://doi.org/10.17605/OSF.IO/VUYWP]68. Source data for Figs. 1, 2, 3, 4, 5, and
supplementary figs. 1 and 3 are provided with the paper. Partial sequences in the form of
individual loci with mutations can be found on the data repository, and a wiki page that
details the filetypes and nomenclature of these partial sequences can be found on the
repository homepage. Publicly accessible Pseudomonas sequences were accessed via the
Pseudomonas Genome Database (https://www.pseudomonas.com/) and the SBW25
genome assembly was accessed via NCBI (NCBI Assembly: ASM922v1, GenBank
sequence: AM181176.4). Whole genomes have been deposited onto GenBank with
accession codes: JAIOKC000000000, JAIOKD000000000, JAIOKE000000000,
JAIOKF000000000, JAIOKG000000000, JAIOKH000000000, JAIOKN000000000,
JAIOKO000000000, JAIOKW000000000. Source data are provided with this paper.

Keywords

Experimental evolution
Mutation bias
Molecular microbiology
Predicting evolution
Pseudomonas fluorescens

ASJC Scopus subject areas

General Chemistry
General Biochemistry,Genetics and Molecular Biology
General Physics and Astronomy

Access to Document

10.1038/s41467-021-26286-9Licence: CC BY

A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Final published version, 977 KBLicence: CC BY

Cite this

@article{387fe6f0db2a4f40b885e3bda2e46edf,

title = "A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes",

abstract = "Mutational hotspots can determine evolutionary outcomes and make evolution repeatable. Hotspots are products of multiple evolutionary forces including mutation rate heterogeneity, but this variable is often hard to identify. In this work, we reveal that a near-deterministic genetic hotspot can be built and broken by a handful of silent mutations. We observe this when studying homologous immotile variants of the bacteria Pseudomonas fluorescens, AR2 and Pf0-2x. AR2 resurrects motility through highly repeatable de novo mutation of the same nucleotide in >95% lines in minimal media (ntrB A289C). Pf0-2x, however, evolves via a number of mutations meaning the two strains diverge significantly during adaptation. We determine that this evolutionary disparity is owed to just 6 synonymous variations within the ntrB locus, which we demonstrate by swapping the sites and observing that we are able to both break (>95% to 0%) and build (0% to 80%) a deterministic mutational hotspot. Our work reveals a key role for silent genetic variation in determining adaptive outcomes.",

keywords = "Experimental evolution, Mutation bias, Molecular microbiology, Predicting evolution, Pseudomonas fluorescens",

author = "Horton, {James S.} and Flanagan, {Louise M.} and Jackson, {Robert W.} and Priest, {Nicholas K.} and Taylor, {Tiffany B.}",

note = "Funding Information: We thank Laurence Hurst for comments on earlier versions of this manuscript. In addition, we thank member of the Taylor lab Matthew Shepherd for insightful comments and discussion, and Mark Silby for contributing the ancestral P. fluorescens Pf0-2x strain used in the study. This work was supported by the University of Bath University Research Studentship Account (URSA) awarded to TBT and NKP; a Royal Society Dorothy Hodgkin Research Fellowship awarded to TBT (DH150169); and the JABBS Foundation for RWJ. Bioinformatics analysis of the paper was carried out using the Medical Research Council{\textquoteright}s (MRC) Cloud Infrastructure for Microbial Bioinformatics (CLIMB), and Illumina Whole-Genome Sequencing by the Milner Genomics Centre, Bath, UK and MicrobesNG, Birmingham, UK. Data availability Data used for the generation of this manuscript is publicly available and can be accessed [https://doi.org/10.17605/OSF.IO/VUYWP]68. Source data for Figs. 1, 2, 3, 4, 5, and supplementary figs. 1 and 3 are provided with the paper. Partial sequences in the form of individual loci with mutations can be found on the data repository, and a wiki page that details the filetypes and nomenclature of these partial sequences can be found on the repository homepage. Publicly accessible Pseudomonas sequences were accessed via the Pseudomonas Genome Database (https://www.pseudomonas.com/) and the SBW25 genome assembly was accessed via NCBI (NCBI Assembly: ASM922v1, GenBank sequence: AM181176.4). Whole genomes have been deposited onto GenBank with accession codes: JAIOKC000000000, JAIOKD000000000, JAIOKE000000000, JAIOKF000000000, JAIOKG000000000, JAIOKH000000000, JAIOKN000000000, JAIOKO000000000, JAIOKW000000000. Source data are provided with this paper.",

year = "2021",

month = oct,

day = "19",

doi = "10.1038/s41467-021-26286-9",

language = "English",

volume = "12",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

number = "1",

}

TY - JOUR

T1 - A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes

AU - Horton, James S.

AU - Flanagan, Louise M.

AU - Jackson, Robert W.

AU - Priest, Nicholas K.

AU - Taylor, Tiffany B.

N1 - Funding Information: We thank Laurence Hurst for comments on earlier versions of this manuscript. In addition, we thank member of the Taylor lab Matthew Shepherd for insightful comments and discussion, and Mark Silby for contributing the ancestral P. fluorescens Pf0-2x strain used in the study. This work was supported by the University of Bath University Research Studentship Account (URSA) awarded to TBT and NKP; a Royal Society Dorothy Hodgkin Research Fellowship awarded to TBT (DH150169); and the JABBS Foundation for RWJ. Bioinformatics analysis of the paper was carried out using the Medical Research Council’s (MRC) Cloud Infrastructure for Microbial Bioinformatics (CLIMB), and Illumina Whole-Genome Sequencing by the Milner Genomics Centre, Bath, UK and MicrobesNG, Birmingham, UK. Data availability Data used for the generation of this manuscript is publicly available and can be accessed [https://doi.org/10.17605/OSF.IO/VUYWP]68. Source data for Figs. 1, 2, 3, 4, 5, and supplementary figs. 1 and 3 are provided with the paper. Partial sequences in the form of individual loci with mutations can be found on the data repository, and a wiki page that details the filetypes and nomenclature of these partial sequences can be found on the repository homepage. Publicly accessible Pseudomonas sequences were accessed via the Pseudomonas Genome Database (https://www.pseudomonas.com/) and the SBW25 genome assembly was accessed via NCBI (NCBI Assembly: ASM922v1, GenBank sequence: AM181176.4). Whole genomes have been deposited onto GenBank with accession codes: JAIOKC000000000, JAIOKD000000000, JAIOKE000000000, JAIOKF000000000, JAIOKG000000000, JAIOKH000000000, JAIOKN000000000, JAIOKO000000000, JAIOKW000000000. Source data are provided with this paper.

PY - 2021/10/19

Y1 - 2021/10/19

N2 - Mutational hotspots can determine evolutionary outcomes and make evolution repeatable. Hotspots are products of multiple evolutionary forces including mutation rate heterogeneity, but this variable is often hard to identify. In this work, we reveal that a near-deterministic genetic hotspot can be built and broken by a handful of silent mutations. We observe this when studying homologous immotile variants of the bacteria Pseudomonas fluorescens, AR2 and Pf0-2x. AR2 resurrects motility through highly repeatable de novo mutation of the same nucleotide in >95% lines in minimal media (ntrB A289C). Pf0-2x, however, evolves via a number of mutations meaning the two strains diverge significantly during adaptation. We determine that this evolutionary disparity is owed to just 6 synonymous variations within the ntrB locus, which we demonstrate by swapping the sites and observing that we are able to both break (>95% to 0%) and build (0% to 80%) a deterministic mutational hotspot. Our work reveals a key role for silent genetic variation in determining adaptive outcomes.

AB - Mutational hotspots can determine evolutionary outcomes and make evolution repeatable. Hotspots are products of multiple evolutionary forces including mutation rate heterogeneity, but this variable is often hard to identify. In this work, we reveal that a near-deterministic genetic hotspot can be built and broken by a handful of silent mutations. We observe this when studying homologous immotile variants of the bacteria Pseudomonas fluorescens, AR2 and Pf0-2x. AR2 resurrects motility through highly repeatable de novo mutation of the same nucleotide in >95% lines in minimal media (ntrB A289C). Pf0-2x, however, evolves via a number of mutations meaning the two strains diverge significantly during adaptation. We determine that this evolutionary disparity is owed to just 6 synonymous variations within the ntrB locus, which we demonstrate by swapping the sites and observing that we are able to both break (>95% to 0%) and build (0% to 80%) a deterministic mutational hotspot. Our work reveals a key role for silent genetic variation in determining adaptive outcomes.

KW - Experimental evolution

KW - Mutation bias

KW - Molecular microbiology

KW - Predicting evolution

KW - Pseudomonas fluorescens

UR - http://www.scopus.com/inward/record.url?scp=85117694589&partnerID=8YFLogxK

U2 - 10.1038/s41467-021-26286-9

DO - 10.1038/s41467-021-26286-9

M3 - Article

C2 - 34667151

AN - SCOPUS:85117694589

SN - 2041-1723

VL - 12

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 6092

ER -

A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this