Soman et al. 2021 (PRJNA637044)

General Details

Title Translatome analysis of Mycobacterium tuberculosis
Organism
Number of Samples 5
Release Date 2020/06/03 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP265811
ENA SRP265811
GEO GSE151718
BioProject PRJNA637044

Publication

Title
Authors Soman S, Chattopadhyay S, Ram S, Nandicoori VK, Arimbasseri GA
Journal Scientific reports
Publication Date 2023 Jan 9
Abstract Mycobacterium tuberculosis (Mtb) is a slow-growing, intracellular pathogen that exhibits a high GC-rich genome. Several factors, including the GC content of the genome, influence the evolution of specific codon usage biases in genomes. As a result, the Mtb genome exhibits strong biases for amino acid usage and codon usage. Codon usage of mRNAs affects several aspects of translation, including accuracy, efficiency, and protein folding. Here we address the effect of codon usage biases in determining the translation efficiency of mRNAs in Mtb. Unlike most commonly studied organisms, Mtb carries a single copy of each tRNA gene. However, we show that the relative levels of tRNAs in the Mtb tRNA pool vary by an order of magnitude. Our results show that the codons decoded by the abundant tRNAs indeed show higher adaptability. Moreover, there is a general positive correlation between genomic codon usage and the tRNA adaptability of codons (TAc). We further estimated the optimality of the codon and mRNAs by considering both the TAc and the tRNA demand. These measures did not show any correlation with mRNA abundance and translation efficiency. There was no correlation between tRNA adaptability and ribosome pausing as well. Taken together, we conclude that the translation machinery, and the tRNA pool of an organism, co-evolve with the codon usage to optimize the translation efficiency of an organism. Thus the deleterious effect of maladapted codons is not pronounced. © 2023. The Author(s).
PMC PMC9829911
PMID 36624167
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR11917594 PRJNA637044 Mycobacterium tuberculosis 0.0 Ribo-Seq 0.0
SRR11917595 PRJNA637044 Mycobacterium tuberculosis 0.0 Ribo-Seq 0.0
SRR11917596 PRJNA637044 Mycobacterium tuberculosis 0.0 Ribo-Seq 0.0
SRR11917597 PRJNA637044 Mycobacterium tuberculosis 0.0 Ribo-Seq 0.0
SRR11917598 PRJNA637044 Mycobacterium tuberculosis 0.0 Ribo-Seq 0.0
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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