uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Experimental Determination and Prediction of the Fitness Effects of Random Point Mutations in the Biosynthetic Enzyme HisA
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.ORCID iD: 0000-0001-8354-2398
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.ORCID iD: 0000-0002-6831-3105
Show others and affiliations
2018 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 35, no 3, p. 704-718Article in journal (Refereed) Published
Abstract [en]

The distribution of fitness effects of mutations is a factor of fundamental importance in evolutionary biology. We determined the distribution of fitness effects of 510 mutants that each carried between 1 and 10 mutations (synonymous and nonsynonymous) in the hisA gene, encoding an essential enzyme in the L-histidine biosynthesis pathway of Salmonella enterica. For the full set of mutants, the distribution was bimodal with many apparently neutral mutations and many lethal mutations. For a subset of 81 single, nonsynonymous mutants most mutations appeared neutral at high expression levels, whereas at low expression levels only a few mutations were neutral. Furthermore, we examined how the magnitude of the observed fitness effects was correlated to several measures of biophysical properties and phylogenetic conservation.We conclude that for HisA: (i) The effect of mutations can be masked by high expression levels, such that mutations that are deleterious to the function of the protein can still be neutral with regard to organism fitness if the protein is expressed at a sufficiently high level; (ii) the shape of the fitness distribution is dependent on the extent to which the protein is rate-limiting for growth; (iii) negative epistatic interactions, on an average, amplified the combined effect of nonsynonymous mutations; and (iv) no single sequence-based predictor could confidently predict the fitness effects of mutations in HisA, but a combination of multiple predictors could predict the effect with a SD of 0.04 resulting in 80% of the mutations predicted within 12% of their observed selection coefficients.

Place, publisher, year, edition, pages
2018. Vol. 35, no 3, p. 704-718
Keywords [en]
mutation, fitness, Salmonella enterica, HisA protein
National Category
Evolutionary Biology Microbiology
Research subject
Biology with specialization in Microbiology; Biology with specialization in Molecular Evolution
Identifiers
URN: urn:nbn:se:uu:diva-339126DOI: 10.1093/molbev/msx325ISI: 000427260700017PubMedID: 29294020OAI: oai:DiVA.org:uu-339126DiVA, id: diva2:1174817
Funder
Swedish Research CouncilAvailable from: 2018-01-16 Created: 2018-01-16 Last updated: 2018-10-02Bibliographically approved
In thesis
1. Evolution of New Genes and Functions
Open this publication in new window or tab >>Evolution of New Genes and Functions
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

To answer major evolutionary questions, we need a better understanding of the effects of mutations on specific functions and organism fitness. The aim of this thesis was to elucidate how new functions evolve and potential trade-offs with the original function.

Paper I identified a bimodal distribution of fitness effects of mutations in Salmonella enterica HisA protein. Most mutations negatively affected protein function but the effect was masked at high gene expression. Expression levels and the extent to which the studied protein limited growth were important in determining the fitness effects of mutations. No fitness prediction tool was satisfactorily alone but in combination predictions were improved.

In Paper II, S. enterica HisA was evolved to acquire TrpF activity. Numerous pathways towards improved TrpF activity were examined and several improvement mechanisms were identified. Improved TrpF activity extensively reduced the original activity, generalist enzymes were rare and restoring original activity after an initial loss was difficult. Furthermore, expression levels had a major impact on the shape of the trade-off curve.

In Paper III, adaptation during serial passage of Escherichia coli and S. enterica under laboratory conditions were examined. Adaptive mutations were identified in four different laboratory media and their fitness effects were determined. Little overlap in mutation spectra was found in the different media and species suggesting that adaptation was media-specific. Furthermore, media adaptation mutations reduced the accuracy of fitness assays and the use of pre-adapted strains improved the sensitivity of fitness assays 10-fold.

Paper IV examined evolution of novel metabolic capabilities in S. enterica by analyzing growth on 124 non-native carbon sources. Growth was observed on 25 compounds and for five of these, the causative mutation was identified. Increased gene expression of cryptic genes was a major mechanism for acquiring the novel phenotypes.

In conclusion, my results show that in most cases many types of mutations can improve a function and allow adaptive evolution but this often is associated with a trade-off and loss in other abilities. Increased gene expression was a major mechanism by which bacteria could compensate for loss of an activity as well as acquire new metabolic capabilities.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2018. p. 72
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1502
National Category
Microbiology
Research subject
Biology with specialization in Microbiology
Identifiers
urn:nbn:se:uu:diva-362157 (URN)978-91-513-0463-2 (ISBN)
Public defence
2018-11-23, B42, BMC, Husargatan 3, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2018-10-31 Created: 2018-10-02 Last updated: 2018-11-19

Open Access in DiVA

fulltext(1391 kB)15 downloads
File information
File name FULLTEXT01.pdfFile size 1391 kBChecksum SHA-512
1b279a8bf71f94ebbd60919d5666cb6763284bea96bf95a17f5e4cfaa2df8a84a8d9e8acc133b9a48ad0b2bbaff28bde25acd160dda980b62d6527d0a8657be0
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Authority records BETA

Lundin, ErikTang, Po-ChengGuy, LionelAndersson, Dan I

Search in DiVA

By author/editor
Lundin, ErikTang, Po-ChengGuy, LionelNäsvall, JoakimAndersson, Dan I
By organisation
Department of Medical Biochemistry and Microbiology
In the same journal
Molecular biology and evolution
Evolutionary BiologyMicrobiology

Search outside of DiVA

GoogleGoogle Scholar
Total: 15 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 49 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf