Translation elongation mediated quality control of integral membrane protein synthesis

Saccharomyces cerevisiae has been engineered to utilize cellobiose, which are prevalent in plant cell wall, by introducing a cellodextrin transporter gene (cdt-1) and an intracellular β-glucosidase gene (codon-optimized gh1-1) from Neurospora crassa. We previously found that codon-optimization of GH1-1 improved fermentation rates under aerobic and anaerobic conditions. However, we found that the codon-optimized version of the CDT-1 transporter (here denoted OPT for the mRNA) resulted in reduced cellobiose uptake and slower growth in cellobiose by S. cerevisiae relative to the transporter with Neurospora-derived coding sequence (hereafter NC for the mRNA). We performed ribosome profiling and RNA deep sequencing of cells expressing NC and OPT grown at mid-exponential phases, respectively. Differences in ribosome occupancy on NC and OPT transcripts suggested increased rates of translation elongation of the N-terminal sequence of OPT in contrast to NC, which may be responsible for the slow-growth phenotype of cells expressing OPT. Examine ribosome footprints and mRNA abundance in biological replicates of S. cerevisiae strains expressing a cellodextrin transporter gene (cdt-1) and the codon-optimized version of cdt-1, respecitively