The influence of codon content on gene expression in mycobacteriaPublic
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Tuberculosis (TB) is a deadly infectious disease caused by Mycobacterium tuberculosis (Mtb). It primarily affects the lungs and has a 50% survival rate if left untreated. Treatment is difficult, costly, and can last up to six months, and drug resistance is a growing concern. The bacterium enters the body through inhalation and survives in the lungs inside a granuloma. In this environment, M. tuberculosis can slow its growth, become drug tolerant, and develop drug resistance. Altered gene expression is a key part of this slowed growth, but little is known about the mechanisms involved. Synonymous codon usage and adjacent codon context have emerged as important factors influencing gene expression. The focus of this study was to determine whether codon content and context have a causal effect on mRNA degradation rate and translation efficiency in the model mycobacterium Mycolicibacterium smegmatis. Through machine learning analysis, the arginine CGC (ArgCGC) codon was associated with decreased transcript stability in M. smegmatis. To investigate this relationship further, the ArgCGC codon, synonymous arginine codons, and frameshift codons with the same nucleotide content were each integrated into the Mycolicibacterium smegmatis chromosome in a series of four, as translational fusions to a gene encoding yellow fluorescent protein (YFP). Quantitative PCR (qPCR) was conducted on the various strains to determine the codon inserts’ impact on mRNA abundance, and flow cytometry was used to determine the impact on protein abundance. Translation efficiency of the ArgCGC codon appears to be dependent on codon position relative to translation initiation and codon context. Overall, codons show a strong effect on translation efficiency in mycobacteria.
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