Professor Mark Carrington, Department of Biochemistry, University of Cambridge
Wednesday 24th June, 4.00 p.m., Stacey Lecture Theatre 2
In trypanosomes, most or all protein coding genes are constitutively transcribed and there is little evidence for selective regulation of expression by RNA polymerase II. Thus, regulation of mRNA levels is largely post-transcriptional. We have developed a novel codon usage metric called the ‘gene expression codon adaptation index’ (geCAI) that is predictive of both relative protein abundance and relative mRNA abundance with a coefficient of determination of 0.84 and 0.55 respectively. The predictive capacity of this novel scoring metric was tested using GFP reporter gene expression. 22 synonymous GFP mRNAs were expressed in procyclic cell lines. Protein expression and mRNA levels were modifiable over a ~40-fold range. The range and expression levels were similar to the measured mRNAs per haploid gene copy for the transcriptome and thus geCAI score is sufficient to account for 50% of the variation observed in mRNA copy number. GFP mRNAs with low geCAI scores decayed more rapidly than those with high scores suggesting translational efficiency is the mechanism that produces the differences in mRNA steady state levels. The translational efficiency model was tested by selectively blocking translation of individual GFP mRNAs by insertion of a hairpin in the 5’UTR, this equalized steady state levels to that of high geCAI score GFP mRNAs. In contrast, inclusion of a short upstream open reading frame in the 5’UTR greatly decreased translation of GFP and decreased steady state mRNA levels to that of a very low geCAI score GFP mRNA. Thus, geCAI is a good predictor of mRNA levels and efficiency of translation is a major determinant of mRNA levels.