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Comprehensive analysis of stop codon usage in bacteria and its correlation with release factor abundance
Gürkan Korkmaz1, Mikael Holm1, Tobias Wiens1
1Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, Uppsala S-75124, Sweden.
The Journal of Biological Chemistry
|September 14, 2014
Summary
Bacterial stop codon usage varies with genomic GC content, with TAA decreasing and TGA increasing. Highly expressed genes favor TAA for efficient termination, while TAG usage correlates with release factor 1 levels.
Area of Science:
- Microbiology
- Genomics
- Molecular Biology
Background:
- Stop codons (TAA, TAG, TGA) terminate protein synthesis in bacteria.
- The usage and frequency of these codons can vary across bacterial species.
- Release factors (RF1 and RF2) recognize specific stop codons.
Purpose of the Study:
- To comprehensively analyze stop codon usage patterns across a large bacterial dataset.
- To investigate the relationship between genomic GC content and stop codon frequency.
- To explore the correlation between gene expression, stop codon usage, and release factor abundance.
Main Methods:
- Analysis of over eight million bacterial coding sequences from 4684 species.
- Development and application of a "stop codon counter" program.
- Correlation analysis of codon frequencies with genomic GC content and gene expression data.
Main Results:
- Genomic GC content inversely correlates with TAA frequency and directly with TGA frequency.
- TAG codon frequency remains relatively stable (~20%) across varying GC content.
- Highly expressed genes predominantly use TAA, while TAG and TGA frequencies correlate with RF1 and RF2 levels, respectively.
Conclusions:
- Bacterial stop codon usage is influenced by genomic GC content and gene expression levels.
- The abundance of release factors RF1 and RF2 is linked to the usage of their cognate stop codons (TAG and TGA).
- TAA is favored in highly expressed genes for robust termination, ensuring efficient protein synthesis.
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