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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
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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. |
format | Online Article Text |
id | pubmed-6395768 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
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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