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Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability
Protein translation is a central step in gene expression and affected by many factors such as codon usage bias, mRNA folding energy and tRNA abundance. Despite intensive previous studies, how metabolic amino acid supply correlates with protein translation efficiency remains unknown. In this work, we...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460870/ https://www.ncbi.nlm.nih.gov/pubmed/26056817 http://dx.doi.org/10.1038/srep11113 |
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author | Hu, Xiao-Pan Yang, Yi Ma, Bin-Guang |
author_facet | Hu, Xiao-Pan Yang, Yi Ma, Bin-Guang |
author_sort | Hu, Xiao-Pan |
collection | PubMed |
description | Protein translation is a central step in gene expression and affected by many factors such as codon usage bias, mRNA folding energy and tRNA abundance. Despite intensive previous studies, how metabolic amino acid supply correlates with protein translation efficiency remains unknown. In this work, we estimated the amino acid flux from metabolic network for each protein in Escherichia coli and Saccharomyces cerevisiae by using Flux Balance Analysis. Integrated with the mRNA expression level, protein abundance and ribosome profiling data, we provided a detailed description of the role of amino acid supply in protein translation. Our results showed that amino acid supply positively correlates with translation efficiency and ribosome density. Moreover, with the rank-based regression model, we found that metabolic amino acid supply facilitates ribosome utilization. Based on the fact that the ribosome density change of well-amino-acid-supplied genes is smaller than poorly-amino-acid-supply genes under amino acid starvation, we reached the conclusion that amino acid supply may buffer ribosome density change against amino acid starvation and benefit maintaining a relatively stable translation environment. Our work provided new insights into the connection between metabolic amino acid supply and protein translation process by revealing a new regulation strategy that is dependent on resource availability. |
format | Online Article Text |
id | pubmed-4460870 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-44608702015-06-18 Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability Hu, Xiao-Pan Yang, Yi Ma, Bin-Guang Sci Rep Article Protein translation is a central step in gene expression and affected by many factors such as codon usage bias, mRNA folding energy and tRNA abundance. Despite intensive previous studies, how metabolic amino acid supply correlates with protein translation efficiency remains unknown. In this work, we estimated the amino acid flux from metabolic network for each protein in Escherichia coli and Saccharomyces cerevisiae by using Flux Balance Analysis. Integrated with the mRNA expression level, protein abundance and ribosome profiling data, we provided a detailed description of the role of amino acid supply in protein translation. Our results showed that amino acid supply positively correlates with translation efficiency and ribosome density. Moreover, with the rank-based regression model, we found that metabolic amino acid supply facilitates ribosome utilization. Based on the fact that the ribosome density change of well-amino-acid-supplied genes is smaller than poorly-amino-acid-supply genes under amino acid starvation, we reached the conclusion that amino acid supply may buffer ribosome density change against amino acid starvation and benefit maintaining a relatively stable translation environment. Our work provided new insights into the connection between metabolic amino acid supply and protein translation process by revealing a new regulation strategy that is dependent on resource availability. Nature Publishing Group 2015-06-09 /pmc/articles/PMC4460870/ /pubmed/26056817 http://dx.doi.org/10.1038/srep11113 Text en Copyright © 2015, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Hu, Xiao-Pan Yang, Yi Ma, Bin-Guang Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability |
title | Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability |
title_full | Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability |
title_fullStr | Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability |
title_full_unstemmed | Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability |
title_short | Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability |
title_sort | amino acid flux from metabolic network benefits protein translation: the role of resource availability |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460870/ https://www.ncbi.nlm.nih.gov/pubmed/26056817 http://dx.doi.org/10.1038/srep11113 |
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