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Protein evolutionary rates correlate with expression independently of synonymous substitutions in Helicobacter pylori
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
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2006 (English)In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 62, no 5, 600-614 p.Article in journal (Refereed) Published
Abstract [en]

In free-living microorganisms, such as Escherichia coli and Saccharomyces cerevisiae, both synonymous and nonsynonymous substitution frequencies correlate with expression levels. Here, we have tested the hypothesis that the correlation between amino acid substitution rates and expression is a by-product of selection for codon bias and translational efficiency in highly expressed genes. To this end, we have examined the correlation between protein evolutionary rates and expression in the human gastric pathogen Helicobacter pylori, where the absence of selection on synonymous sites enables the two types of substitutions to be uncoupled. The results revealed a statistically significant negative correlation between expression levels and nonsynonymous substitutions in both H. pylori and E. coli. We also found that neighboring genes located on the same, but not on opposite strands, evolve at significantly more similar rates than random gene pairs, as expected by co-expression of genes located in the same operon. However, the two species differ in that synonymous substitutions show a strand-specific pattern in E. coli, whereas the weak similarity in synonymous substitutions for neighbors in H. pylori is independent of gene orientation. These results suggest a direct influence of expression levels on nonsynonymous substitution frequencies independent of codon bias and selective constraints on synonymous sites.

Place, publisher, year, edition, pages
2006. Vol. 62, no 5, 600-614 p.
Keyword [en]
Amino Acid Substitution/*genetics, Bacterial Proteins/chemistry/*genetics, Chromosomes; Bacterial/genetics, Codon/genetics, Evolution; Molecular, Gene Expression Regulation; Bacterial, Genes; Bacterial/genetics, Helicobacter pylori/chemistry/*genetics, RNA; Messenger/genetics/metabolism, Variation (Genetics)
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-23093DOI: 10.1007/ss00239-005-0104-5PubMedID: 16586017OAI: oai:DiVA.org:uu-23093DiVA: diva2:50866
Available from: 2007-01-24 Created: 2007-01-24 Last updated: 2011-02-18Bibliographically approved
In thesis
1. Evolutionary Processes and Genome Dynamics in Host-Adapted Bacteria
Open this publication in new window or tab >>Evolutionary Processes and Genome Dynamics in Host-Adapted Bacteria
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Many bacteria live in close association with other organisms such as plants and animals, with important implications for both health and disease. This thesis investigates bacteria that are well adapted to live inside an animal host, and describes the molecular evolutionary processes underlying host-adaptation, based on bacterial genome comparisons.

Insect-transmitted bacteria of the genus Bartonella infect the red blood cells of mammals, and we investigate host adaptation and genome evolution in this genus. In Bartonella, many host-interaction systems are encoded in a highly variable chromosomal segment previously shown to be amplified and packaged into bacteriophage particles. Among all genes imported into the Bartonella ancestor, we identify the short gene cluster encoding these phage particles as the most evolutionary conserved, indicating a strong selective advantage and a role in niche adaptation. We also provide an overview of the remarkable evolutionary dynamics of type IV and type V secretion systems, including a detailed analysis of the type IV secretion system trw. Our results highlight the importance of recombination and gene conversion in the evolution of host-adaptation systems, and reveal how these mutational mechanisms result in strikingly different outcomes depending on the selective constraints.

In the insect endosymbionts Buchnera and Blochmannia, we show that genes frameshifted at poly(A) tracts can remain functional due to transcriptional slippage. Selection against poly(A) tracts is very inefficient in these genomes compared to other bacteria, and we discuss why this can lead to increased rates of gene loss. Using the human pathogen Helicobacter pylori as a model, we provide a deeper understanding of why highly expressed genes evolve slowly.

This thesis emphasizes the power of using complete genome sequences to study evolutionary processes. In particular, we argue that knowledge about the complex evolution of duplicated gene segments is crucial to understand host adaptation in bacteria.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2009. 64 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 668
molecular evolution, pathogen, secretion system, Bartonella, Buchnera, Blochmannia, Helicobacter
National Category
Bioinformatics and Systems Biology
Research subject
Evolutionary Genetics
urn:nbn:se:uu:diva-107720 (URN)978-91-554-7596-3 (ISBN)
Public defence
2009-10-09, Lindahlsalen, EBC, Norbyvägen 18, Uppsala, 09:15 (English)
Available from: 2009-09-18 Created: 2009-08-24 Last updated: 2009-09-22

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