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Experimental Evolution: and Fitness Effects of Mutations
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. (Dan I Andersson)
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Bacteria have small, streamlined genomes and evolve rapidly. Their large population sizes allow selection to be the main driver of evolution. With advances in sequencing technologies and precise methods for genetic engineering, many bacteria are excellent models for studying elementary questions in evolutionary biology. The work in this thesis has broadly been devoted to adaptive evolution and fitness effects of different types of mutations.

In Paper I we experimentally tested the fitness constrains of horizontal gene transfer (HGT), which could be used to predict how the fixation of HGT events are affected by selection and fitness effects. We found that the majority of the examined HGT inserts were indistinguishable from neutral, implying that extra DNA transferred by HGT, even though it does not confer an immediate selective advantage, could be maintained at transfer-selection balance and serve as a reservoir for the evolution of novel beneficial functions.

Paper II examined why four synonymous mutations in rpsT (encoding ribosomal protein S20) reduced fitness, and how this cost could be genetically compensated. We found that the cause for the fitness reduction was low S20 levels and that this lead to a defective subpopulation of 30S subunits lacking S20. In an adaptive evolution experiment, these impairments were compensated by up-regulation of S20 though various types of mutations.

In Paper III we continued the studies of how the deleterious rpsT mutations could be compensated. The mutations either down-regulated the global regulator Fis or altered a subunit of the RNA polymerase (rpoA). We found that the decreased S20 levels in the cells causes an assembly defect of the 30S particles and that the fis and rpoA mutations restored the skewed S20:ribosome ratio by both increasing S20 levels and decreasing other ribosomal components.

Paper IV examined adaptation of two bacterial species to different growth media. A total of 142 different adaptive mutations were identified and 112 mutants were characterized in terms of fitness. We found that the experimental variation in fitness measurements could be reduced 10-fold by introducing some adaptive mutations prior to the experiment, allowing measurements of fitness differences as small as 0.04%.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2016. , 72 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1276
Keyword [en]
Experimental evolution, Fitness effects, mutations, S20, fis, ribosome, horizontal gene transfer, adaptation, synonymous mutations
National Category
Evolutionary Biology Genetics Microbiology
Research subject
Microbiology
Identifiers
URN: urn:nbn:se:uu:diva-306592ISBN: 978-91-554-9749-1OAI: oai:DiVA.org:uu-306592DiVA: diva2:1040866
Public defence
2016-12-19, B21, BMC, Husargatan 3, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2016-11-28 Created: 2016-10-29 Last updated: 2016-11-28
List of papers
1. Minor Fitness Costs in an Experimental Model of Horizontal Gene Transfer in Bacteria
Open this publication in new window or tab >>Minor Fitness Costs in an Experimental Model of Horizontal Gene Transfer in Bacteria
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2014 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 31, no 5, 1220-1227 p.Article in journal (Refereed) Published
Abstract [en]

Genes introduced by horizontal gene transfer (HGT) from other species constitute a significant portion of many bacterial genomes, and the evolutionary dynamics of HGTs are important for understanding the spread of antibiotic resistance and the emergence of new pathogenic strains of bacteria. The fitness effects of the transferred genes largely determine the fixation rates and the amount of neutral diversity of newly acquired genes in bacterial populations. Comparative analysis of bacterial genomes provides insight into what genes are commonly transferred, but direct experimental tests of the fitness constraints on HGT are scarce. Here, we address this paucity of experimental studies by introducing 98 random DNA fragments varying in size from 0.45 to 5 kb from Bacteroides, Proteus, and human intestinal phage into a defined position in the Salmonella chromosome and measuring the effects on fitness. Using highly sensitive competition assays, we found that eight inserts were deleterious with selection coefficients (s) ranging from a parts per thousand -0.007 to -0.02 and 90 did not have significant fitness effects. When inducing transcription from a P-BAD promoter located at one end of the insert, 16 transfers were deleterious and 82 were not significantly different from the control. In conclusion, a major fraction of the inserts had minor effects on fitness implying that extra DNA transferred by HGT, even though it does not confer an immediate selective advantage, could be maintained at selection-transfer balance and serve as raw material for the evolution of novel beneficial functions.

Keyword
bacterial evolution, horizontal gene transfer, lateral gene transfer, fitness effects
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-227191 (URN)10.1093/molbev/msu076 (DOI)000335914400014 ()
Available from: 2014-06-26 Created: 2014-06-24 Last updated: 2016-11-30
2. Compensating the fitness costs of synonymous mutations
Open this publication in new window or tab >>Compensating the fitness costs of synonymous mutations
2016 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, no 6, 1461-1477 p.Article in journal (Refereed) Published
Abstract [en]

Synonymous mutations do not change the sequence of the polypeptide but they may still influence fitness. We investigated in Salmonella enterica how four synonymous mutations in the rpsT gene (encoding ribosomal protein S20) reduce fitness (i.e. growth rate) and the mechanisms by which this cost can be genetically compensated. The reduced growth rates of the synonymous mutants were correlated with reduced levels of the rpsT transcript and S20 protein. In an adaptive evolution experiment these fitness impairments could be compensated by mutations that either caused up-regulation of S20 through increased gene dosage (due to duplications), increased transcription of the rpsT gene (due to an rpoD mutation or mutations in rpsT), or increased translation from the rpsT transcript (due to rpsT mutations). We suggest that the reduced levels of S20 in the synonymous mutants result in production of a defective subpopulation of 30S subunits lacking S20 that reduce protein synthesis and bacterial growth and that the compensatory mutations restore S20 levels and the number of functional ribosomes. Our results demonstrate how specific synonymous mutations can cause substantial fitness reductions and that many different types of intra- and extragenic compensatory mutations can efficiently restore fitness. Furthermore, our study highlights that also synonymous sites can be under strong selection, which may have implications for the use of dN/dS ratios as signature for selection.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-277280 (URN)10.1093/molbev/msw028 (DOI)000376170300006 ()26882986 (PubMedID)
Funder
Swedish Research Council
Available from: 2016-02-18 Created: 2016-02-18 Last updated: 2016-10-29Bibliographically approved
3. Synonymous mutations that reduce S20 levels can be compensated by mutations in fis and rpoA 
Open this publication in new window or tab >>Synonymous mutations that reduce S20 levels can be compensated by mutations in fis and rpoA 
(English)Manuscript (preprint) (Other academic)
National Category
Genetics
Research subject
Microbiology
Identifiers
urn:nbn:se:uu:diva-306590 (URN)
Available from: 2016-10-29 Created: 2016-10-29 Last updated: 2016-11-30
4. Genetic adaptations to growth under laboratory conditions in Escherichia coli and Salmonella enterica
Open this publication in new window or tab >>Genetic adaptations to growth under laboratory conditions in Escherichia coli and Salmonella enterica
Show others...
(English)Manuscript (preprint) (Other academic)
National Category
Evolutionary Biology
Research subject
Microbiology
Identifiers
urn:nbn:se:uu:diva-306591 (URN)
Available from: 2016-10-29 Created: 2016-10-29 Last updated: 2016-11-30

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