TY - JOUR

T1 - Fast Translation within the First 45 Codons Decreases mRNA Stability and Increases Premature Transcription Termination in E. coli

AU - Pedersen, Steen

AU - Terkelsen, Thilde Bagger

AU - Eriksen, Mette

AU - Hauge, Magnus Krarup

AU - Lund, Casper Carstens

AU - Sneppen, Kim

AU - Mitarai, Namiko

PY - 2019

Y1 - 2019

N2 - We show here that the specific use of fast or slowly translated codons in the early coding region of a gene may influence both the mRNA stability and premature transcription termination. We first inserted a pair of nearly identical 42-base-pair (bp)-long sequences into codon 3 of the Escherichia coli lacZ gene. The only difference between the two inserts was that the first base in one was moved to become the last base in the other, providing a difference in the reading frame, one of which had the biased codons typical for ribosomal protein genes and which previously was shown to be faster translated than average. This insert reduced the mRNA stability and increased premature transcription termination and together resulted in a hundred-fold difference in lacZ expression. We next generated lacZ variants with 7, 14 or 21 fast translated, ribosomal-type codons inserted into codon 13 of lacZ. This gave progressively more unstable mRNAs and also progressively increased transcription termination up to 90%. By modeling, based on estimates of the translation rate of individual codons, we can explain these observations by an increased susceptibility of the mRNA to degradation, determined by the length and degree of the early mRNA being uncovered by ribosomes. Thus, we suggest that the translation rate differences among the synonymous codons early in a gene enable a “velocity code” within the amino acid coding ability, where the translation rate differences encode the mRNA stability and the premature termination of the RNA polymerase.

AB - We show here that the specific use of fast or slowly translated codons in the early coding region of a gene may influence both the mRNA stability and premature transcription termination. We first inserted a pair of nearly identical 42-base-pair (bp)-long sequences into codon 3 of the Escherichia coli lacZ gene. The only difference between the two inserts was that the first base in one was moved to become the last base in the other, providing a difference in the reading frame, one of which had the biased codons typical for ribosomal protein genes and which previously was shown to be faster translated than average. This insert reduced the mRNA stability and increased premature transcription termination and together resulted in a hundred-fold difference in lacZ expression. We next generated lacZ variants with 7, 14 or 21 fast translated, ribosomal-type codons inserted into codon 13 of lacZ. This gave progressively more unstable mRNAs and also progressively increased transcription termination up to 90%. By modeling, based on estimates of the translation rate of individual codons, we can explain these observations by an increased susceptibility of the mRNA to degradation, determined by the length and degree of the early mRNA being uncovered by ribosomes. Thus, we suggest that the translation rate differences among the synonymous codons early in a gene enable a “velocity code” within the amino acid coding ability, where the translation rate differences encode the mRNA stability and the premature termination of the RNA polymerase.

KW - mRNA half-life

KW - premature transcription termination

KW - synonymous codons

KW - translation velocity

U2 - 10.1016/j.jmb.2019.01.026

DO - 10.1016/j.jmb.2019.01.026

M3 - Journal article

C2 - 30690030

AN - SCOPUS:85061621524

VL - 431

SP - 1088

EP - 1097

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 6

ER -