Evolution of codon usage in bacteria
Initially, this thesis investigates patterns of intragenomic codon usage within the genome of the Delta Proteobacterium Bdellovibrio bacteriovorus. Correspondence analyses revealed the primary factor influencing codon usage within this genome to be related to translational selection. The relationshi...
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| Format: | Thesis (University of Nottingham only) |
| Language: | English |
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2007
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| Online Access: | https://eprints.nottingham.ac.uk/10694/ |
| _version_ | 1848791116826017792 |
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| author | Henry, Ian |
| author_facet | Henry, Ian |
| author_sort | Henry, Ian |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | Initially, this thesis investigates patterns of intragenomic codon usage within the genome of the Delta Proteobacterium Bdellovibrio bacteriovorus. Correspondence analyses revealed the primary factor influencing codon usage within this genome to be related to translational selection. The relationship between the degree of codon
usage adaptation (as given by the ‘frequency of optimal codons’ statistic) and putative gene expression level was used to look for genes with unusually high or low expression levels in B. bacteriovorus, in comparison to Escherichia coli, in order to gain further insight into the unusual lifestyle of this Delta Proteobacterium.
The scope was then broadened to explore intergenomic patterns of codon usage and initially extend a study measuring the strength of selected codon usage bias across bacterial genomes (Sharp et al. 2005). A dataset of 160 fully sequenced bacterial genomes was used and the strength of selected codon usage bias was seen to vary greatly between species. A correlation was observed between (log of) generation time and the strength of selected codon usage bias with fast growing bacteria showing a higher degree of selected codon usage bias than slow growing bacteria.
In bacterial species exhibiting significant levels of selected codon usage bias optimal codon choice was examined. It was observed that optimal codon choice is not always conserved across all bacterial genomes under selection but broad trends in optimal codon choice were seen to be associated with particular bacterial clades. In general, optimal codon choice was seen to be linked with differences in mutational biases among the clades, as seen by a correlation between optimal codon choice in particular clades and the G+C content of their genomes. Clades that were A+U rich (Firmicutes, Gamma Proteobacteria main clade) were seen to largely prefer codons of the form NNA/U whilst G+C rich clades (Alpha Proteobacteria, Actinobacteria and Xanthomonas species) showed preference for codons of the form NNG/C in their highly expressed genes.
Finally the relationship between optimal codon usage and tRNA abundances was explored. Changes in tRNA abundances were seen to coincide with switches in optimal codon usage. Therefore, switches in codon usage and tRNA abundance are thought to be influenced by changing mutational bias within the genome as reflected by the correlation between optimal codon choice, tRNA gene complements and genomic G+C content. |
| first_indexed | 2025-11-14T18:23:24Z |
| format | Thesis (University of Nottingham only) |
| id | nottingham-10694 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-14T18:23:24Z |
| publishDate | 2007 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-106942025-02-28T11:09:14Z https://eprints.nottingham.ac.uk/10694/ Evolution of codon usage in bacteria Henry, Ian Initially, this thesis investigates patterns of intragenomic codon usage within the genome of the Delta Proteobacterium Bdellovibrio bacteriovorus. Correspondence analyses revealed the primary factor influencing codon usage within this genome to be related to translational selection. The relationship between the degree of codon usage adaptation (as given by the ‘frequency of optimal codons’ statistic) and putative gene expression level was used to look for genes with unusually high or low expression levels in B. bacteriovorus, in comparison to Escherichia coli, in order to gain further insight into the unusual lifestyle of this Delta Proteobacterium. The scope was then broadened to explore intergenomic patterns of codon usage and initially extend a study measuring the strength of selected codon usage bias across bacterial genomes (Sharp et al. 2005). A dataset of 160 fully sequenced bacterial genomes was used and the strength of selected codon usage bias was seen to vary greatly between species. A correlation was observed between (log of) generation time and the strength of selected codon usage bias with fast growing bacteria showing a higher degree of selected codon usage bias than slow growing bacteria. In bacterial species exhibiting significant levels of selected codon usage bias optimal codon choice was examined. It was observed that optimal codon choice is not always conserved across all bacterial genomes under selection but broad trends in optimal codon choice were seen to be associated with particular bacterial clades. In general, optimal codon choice was seen to be linked with differences in mutational biases among the clades, as seen by a correlation between optimal codon choice in particular clades and the G+C content of their genomes. Clades that were A+U rich (Firmicutes, Gamma Proteobacteria main clade) were seen to largely prefer codons of the form NNA/U whilst G+C rich clades (Alpha Proteobacteria, Actinobacteria and Xanthomonas species) showed preference for codons of the form NNG/C in their highly expressed genes. Finally the relationship between optimal codon usage and tRNA abundances was explored. Changes in tRNA abundances were seen to coincide with switches in optimal codon usage. Therefore, switches in codon usage and tRNA abundance are thought to be influenced by changing mutational bias within the genome as reflected by the correlation between optimal codon choice, tRNA gene complements and genomic G+C content. 2007-12-12 Thesis (University of Nottingham only) NonPeerReviewed application/pdf en arr https://eprints.nottingham.ac.uk/10694/1/Thesis_IanHenry.pdf Henry, Ian (2007) Evolution of codon usage in bacteria. PhD thesis, University of Nottingham. Codon Usage Bacteria Genome |
| spellingShingle | Codon Usage Bacteria Genome Henry, Ian Evolution of codon usage in bacteria |
| title | Evolution of codon usage in bacteria |
| title_full | Evolution of codon usage in bacteria |
| title_fullStr | Evolution of codon usage in bacteria |
| title_full_unstemmed | Evolution of codon usage in bacteria |
| title_short | Evolution of codon usage in bacteria |
| title_sort | evolution of codon usage in bacteria |
| topic | Codon Usage Bacteria Genome |
| url | https://eprints.nottingham.ac.uk/10694/ |