An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria

Scientific Reports
Yulong WeiX Xia

Abstract

The degree to which codon usage can be explained by tRNA abundance in bacterial species is often inadequate, partly because differential tRNA abundance is often approximated by tRNA copy numbers. To better understand the coevolution between tRNA abundance and codon usage, we provide a better estimate of tRNA abundance by profiling tRNA mapped reads (tRNA tpm) using publicly available RNA Sequencing data. To emphasize the feasibility of our approach, we demonstrate that tRNA tpm is consistent with tRNA abundances derived from RNA fingerprinting experiments in Escherichia coli, Bacillus subtilis, and Salmonella enterica. Furthermore, we do not observe an appreciable reduction in tRNA sequencing efficiency due to post-transcriptional methylations in the seven bacteria studied. To determine optimal codons, we calculate codon usage in highly and lowly expressed genes determined by protein per transcript. We found that tRNA tpm is sensitive to identify more translationally optimal codons than gene copy number and early tRNA fingerprinting abundances. Additionally, tRNA tpm improves the predictive power of tRNA adaptation index over codon preference. Our results suggest that dependence of codon usage on tRNA availability is not always...Continue Reading

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Citations

Jan 19, 2021·Mitochondrial DNA. Part B, Resources·Zhiwen ChenCorrinne E Grover
Oct 8, 2021·ACS Nano·Niki K ThomasRobin L Abu-Shumays
Jan 23, 2022·Genome Research·Yanqun WangXin Jin

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Datasets Mentioned

BETA
SRX860738
SRX669653
SRX405952
SRX4374910
SRX1258668
SRX4145044
SRX515181
SRX2804667

Methods Mentioned

BETA
RNA-Seq
electrophoresis

Software Mentioned

DAMBE
tAI R
MINLEN
ARSDA
SAMtools
kallisto
Trimmomatic
tpm
PaxDb
CutAdapt

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