Polyamines are Required for tRNA Anticodon Modification in Escherichia coli

Biogenic polyamines are natural aliphatic polycations formed from amino acids by biochemical pathways that are highly conserved from bacteria to humans. Their cellular concentrations are carefully regulated and dysregulation causes severe cell growth defects. Polyamines have high affinity for nucleic acids and are known to interact with mRNA, tRNA and rRNA to stimulate the translational machinery, but the exact molecular mechanism(s) for this stimulus is still unknown. Here we exploit that Escherichia coli is viable in the absence of polyamines, including the universally conserved putrescine and spermidine. Using global macromolecule labelling approaches we find that ribosome efficiency is reduced by 50-70% in the absence of polyamines and this reduction is caused by slow translation elongation speed. The low efficiency causes rRNA and multiple tRNA species to be overproduced in the absence of polyamines, suggesting an impact on the feedback regulation of stable RNA transcription. Importantly, we find that polyamine deficiency affects both tRNA levels and tRNA modification patterns. Specifically, a large fraction of tRNA(his), tRNA(tyr) and tRNA(asn) lack the queuosine modification in the anticodon wobble base, which can be reversed by addition of polyamines to the growth medium. In conclusion, we demonstrate that polyamines are needed for modification of specific tRNA, possibly by facilitating the interaction with modification enzymes. (C) 2021 The Author(s). Published by Elsevier Ltd.

Automated summary

Biogenic polyamines are essential for cell growth, as their deficiency can lead to reduced ribosome efficiency, overproduction of rRNA and multiple tRNA species, and impact on feedback regulation of stable RNA transcription. In addition, polyamine deficiency affects tRNA levels and modification patterns, particularly the lack of queuosine modification in specific tRNA species.