Fig. 5: The Tma proteins recycle 40S subunits at stop codons in vivo.
a Average 40S (top) and 80S (bottom) ribosome footprint occupancy from all genes aligned by their stop codons reveals increased 40S footprints on stop codons and 80S footprints positioned further upstream in the tma∆∆ strains. Footprints plotted by 5′ ends. 80S data have been previously published10. The schematic shows a model of the recycling defect in the tma∆∆ strains where a 40S subunit is stalled at the stop codon and an 80S ribosome is queued behind it. b Correlation analysis of 40S stop codon peak heights (total count of footprints at the stop codon) between WT strain and tma∆∆ strains. The plot reveals that the peaks on stop codons are broadly higher across the transcriptome in the tma∆∆ strains (data points shifted above the diagonal). Each point represents the data for one gene. Footprint reads were quantitated by shifting them by 14 nt and then counting reads around the stop codon. c Average ratio of 40S stop codon peaks (tma64∆tma20∆ vs WT) are plotted against their significance (p value) as determined by bootstrapping (see Methods) for penultimate codons with at least ten occurrences. Significant codons (DNA sequences) are indicated (red) at the 99th confidence interval. Dotted line indicates average increase across the entire transcriptome of 23.4-fold. d Average ratio of 40S stop codon peaks (tma64∆tma20∆ vs WT) were computed for subsets of particular codons near the end of the ORF. Significant codons are indicated (red) at the 99th confidence interval (dotted line). The penultimate codon (−1) position has far more codons that significantly change between tma64∆tma20∆ and WT than other positions. e Average 40S ribosome occupancy in a window surrounding 3′UTR AUG codons. f Average 40S ribosome occupancy in a window surrounding 3′UTR stop codons. Note that loss of the Tma proteins increases this peak, showing their activity in recycling 40S subunits in the 3′UTR. nt nucleotide, rpm reads per million. Source data are provided as a Source Data file. See also Supplementary Fig. 4.
