  Deprivation of essential nutrients can have stark consequences for many
processes in a cell. We consider amino acid starvation, which can result in
bottlenecks in mRNA translation when ribosomes stall due to lack of resources,
i.e. tRNAs charged with the missing amino acid. Recent experiments also show
less obvious effects such as increased charging of other (non-starved) tRNA
species and selective charging of isoaccepting tRNAs. We present a mechanism
which accounts for these observations, and shows that production of some
proteins can actually increase under starvation. One might assume that such
responses could only be a result of sophisticated control pathways, but here we
show that these effects can occur naturally due to changes in the supply and
demand for different resources, and that control can be accomplished through
selective use of rare codons. We develop a model for translation which includes
the dynamics of the charging and use of aa-tRNAs, explicitly taking into
account the effect of specific codon sequences. This constitutes a new control
mechanism in gene regulation which emerges at the community level, i.e., via
resources used by all ribosomes.
