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Gradients in nucleotide and codon usage along Escherichia coli genes
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
2000 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 28, no 18, 3517-3523 p.Article in journal (Refereed) Published
Abstract [en]

The usage of codons and nucleotide combinations varies along genes and systematic variation causes gradients in usage. We have studied such gradients of nucleotides and nucleotide combinations and their immediate context in Escherichia coli. To distinguish mutational and selectional effects, the genes were subdivided into three groups with different codon usage bias and the gradients of nucleotide usage were studied in each group. Some combinations that can be associated with a propensity for processivity errors show strong negative gradients that become weaker in genes with low codon bias, consistent with a selection on translational efficiency. One of the strongest gradients is for third position G, which shows a pervasive positive gradient in usage in most contexts of surrounding bases.

Place, publisher, year, edition, pages
2000. Vol. 28, no 18, 3517-3523 p.
National Category
Natural Sciences
URN: urn:nbn:se:uu:diva-90104DOI: 10.1093/nar/28.18.3517PubMedID: 110745OAI: oai:DiVA.org:uu-90104DiVA: diva2:162309
Available from: 2003-01-29 Created: 2003-01-29 Last updated: 2013-06-12Bibliographically approved
In thesis
1. Dynamics of Microbial Genome Evolution
Open this publication in new window or tab >>Dynamics of Microbial Genome Evolution
2003 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The success of microbial life on Earth can be attributed not only to environmental factors, but also to the surprising hardiness, adaptability and flexibility of the microbes themselves. They are able to quickly adapt to new niches or circumstances through gene evolution and also by sheer strength of numbers, where statistics favor otherwise rare events.

An integral part of adaptation is the plasticity of the genome; losing and acquiring genes depending on whether they are needed or not. Genomes can also be the birthplace of new gene functions, by duplicating and modifying existing genes. Genes can also be acquired from outside, transcending species boundaries. In this work, the focus is set primarily on duplication, deletion and import (lateral transfer) of genes – three factors contributing to the versatility and success of microbial life throughout the biosphere.

We have developed a compositional method of identifying genes that have been imported into a genome, and the rate of import/deletion turnover has been appreciated in a number of organisms. Furthermore, we propose a model of genome evolution by duplication, where through the principle of gene amplification, novel gene functions are discovered within genes with weak- or secondary protein functions. Subsequently, the novel function is maintained by selection and eventually optimized. Finally, we discuss a possible synergic link between lateral transfer and duplicative processes in gene innovation.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2003. 45 p.
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1104-232X ; 796
Bioinformatics, Bioinformatik
National Category
Bioinformatics and Systems Biology
Research subject
Molecular Biology
urn:nbn:se:uu:diva-3283 (URN)91-554-5510-7 (ISBN)
Public defence
2003-02-21, Linddahlssalen, EBC, Uppsala, 13:00
Available from: 2003-01-29 Created: 2003-01-29Bibliographically approved

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