Journal article
Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms
- Abstract:
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Background: Genomes are composed of long strings of nucleotide monomers (A, C, G, and T) that are either scavenged from the organism’s environment or built from metabolic precursors. The biosynthesis of each nucleotide differs in atomic requirements with different nucleotides requiring different quantities of nitrogen atoms. However the impact of the relative availability of dietary nitrogen on genome composition and codon bias is poorly understood.
Results: Here we show that differential nitrogen availability, due to differences in environment and dietary inputs, is a major determinant of genome nucleotide composition and synonymous codon use in both bacterial and eukaryotic microorganisms. Specifically low nitrogen availability species use nucleotides that require fewer nitrogen atoms to encode the same genes when compared to high nitrogen availability species. Furthermore we provide a novel selection-mutation framework for the evaluation of the impact of metabolism on gene sequence evolution and show that it is possible to predict the metabolic inputs of related organisms from an analysis of the raw nucleotide sequence of their genes.
Conclusions: Taken together, these results reveal a previously hidden relationship between cellular metabolism and genome evolution and provide new insight into how genome sequence evolution can be influenced by adaptation to different diets and environment.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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- Files:
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(Preview, Version of record, pdf, 1.1MB, Terms of use)
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- Publisher copy:
- 10.1186/s13059-016-1087-9
Authors
- Funding agency for:
- Kelly, S
- Grant:
- University Research Fellow
- Funding agency for:
- Seward, E
- Grant:
- BB/J014427/1
- Publisher:
- BioMed Central
- Journal:
- Genome Biology More from this journal
- Volume:
- 17
- Pages:
- 226
- Publication date:
- 2016-11-01
- Acceptance date:
- 2016-10-03
- DOI:
- ISSN:
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1465-6906
- Keywords:
- Pubs id:
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pubs:652540
- UUID:
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uuid:602d9e3d-cb8c-4e62-a656-884d117ad647
- Local pid:
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pubs:652540
- Source identifiers:
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652540
- Deposit date:
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2016-10-14
Terms of use
- Copyright holder:
- Seward and Kelly
- Copyright date:
- 2016
- Notes:
- © The Author(s). 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
- Licence:
- CC Attribution (CC BY)
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