TY - JOUR

T1 - Polyamines are Required for tRNA Anticodon Modification in Escherichia coli

AU - Winther, Kristoffer Skovbo

AU - Sørensen, Michael Askvad

AU - Svenningsen, Sine Lo

N1 - Funding Information: The authors thank Caroline Schou Nielsen for her contribution during the initiation of the project. We acknowledge funding by the Independent Research Fund Denmark (8049-00071B and 8021-00280A). Publisher Copyright: © 2021 The Author(s)

PY - 2021

Y1 - 2021

N2 - 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 tRNAhis, tRNAtyr and tRNAasn 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.

AB - 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 tRNAhis, tRNAtyr and tRNAasn 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.

KW - anticodon

KW - polyamine

KW - queuosine

KW - spermidine

KW - tRNA

U2 - 10.1016/j.jmb.2021.167073

DO - 10.1016/j.jmb.2021.167073

M3 - Journal article

C2 - 34058151

AN - SCOPUS:85107689723

VL - 433

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 15

M1 - 167073

ER -