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

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 estimat...

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Autores principales: Wei, Yulong, Silke, Jordan R., Xia, Xuhua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6395768/
https://www.ncbi.nlm.nih.gov/pubmed/30816249
http://dx.doi.org/10.1038/s41598-019-39369-x
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author Wei, Yulong
Silke, Jordan R.
Xia, Xuhua
author_facet Wei, Yulong
Silke, Jordan R.
Xia, Xuhua
author_sort Wei, Yulong
collection PubMed
description 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 associated with species growth-rate. Conversely, tRNA availability is better optimized to codon usage in fast-growing than slow-growing species.
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spelling pubmed-63957682019-03-04 An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria Wei, Yulong Silke, Jordan R. Xia, Xuhua Sci Rep Article 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 associated with species growth-rate. Conversely, tRNA availability is better optimized to codon usage in fast-growing than slow-growing species. Nature Publishing Group UK 2019-02-28 /pmc/articles/PMC6395768/ /pubmed/30816249 http://dx.doi.org/10.1038/s41598-019-39369-x Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Wei, Yulong
Silke, Jordan R.
Xia, Xuhua
An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria
title An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria
title_full An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria
title_fullStr An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria
title_full_unstemmed An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria
title_short An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria
title_sort improved estimation of trna expression to better elucidate the coevolution between trna abundance and codon usage in bacteria
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6395768/
https://www.ncbi.nlm.nih.gov/pubmed/30816249
http://dx.doi.org/10.1038/s41598-019-39369-x
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