Analysing environmentally induced genome-wide frameshift in S. cerevisiae and bacteria  using 5PSeq
In this study, we examine the impact of poor nutrient conditions on -1 ribosome frameshifting and its effect on mRNA degradation.To explore this process, we utilized HT-5PSeq (Zhang & Pelechano, 2021, PMID:35474692) to measure the ribosome footprint of co-translationally degraded mRNAs in S.cerevisiae under different stresses in YPD and CSM (poor nutrients).  To show the mechanism is conserved in bacteria, we performed HT-5PSeq in  B.subtilis upon starvation .Our goal with HT-5PSeq is to identify gene- and codon-specific features that contribute to genome-wide frameshifting events. Overall design: HT5P-seq was carried out on S. cerevisiae and B. subtilis 168 (trpC2) under various environmental conditions (3 replicates). Stress-induced S. cerevisiae cells were subjected to heat shock , oxidative stress, and amino acid deprivation. S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium.  For B. subtilis,  cells were grown in both LB and minimal media.