Figure S6.

Effects of Amino Acid Starvation on Protein Production, Number of Free Ribosomes, Overall Elongation Rates, and Ribosomal Stalling, Related to Figure 7

All quantities are shown relative to a wild-type cell without any amino acid starvation. We simulated starvation of a particular amino acid by reducing the abundance of all its (charged) cognate tRNAs by either two-, five-, or ten-fold. The rate of protein production decreases under stress, and it can decrease extensively when starvation is severe. Starvation of different amino acids has radically different effects on protein production.

(A–D) Decreased protein synthesis upon starvation is caused primarily by a corresponding decrease in the pool of free ribosomes (comparing panel A to panel B). Starving a cell of amino acids reduces the number of free ribosomes, and this in turn leads to fewer free tRNAs. The combined effects of these two processes lead to an overall decrease in (C) total elongation rates across all mRNAs. Starving a cell of amino acids leads to higher densities of ribosomes bound to mRNAs (D). As a result, greater proportions of bound ribosomes are stalled - that is, they are obstructed from further elongation due to a neighboring ribosome bound 10 codons ahead on the same mRNA.