Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Hu, Xiao-Pan, Yang, Yi, Ma, Bin-Guang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2015
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
_version_ 1782375450580877312
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
work_keys_str_mv AT huxiaopan aminoacidfluxfrommetabolicnetworkbenefitsproteintranslationtheroleofresourceavailability
AT yangyi aminoacidfluxfrommetabolicnetworkbenefitsproteintranslationtheroleofresourceavailability
AT mabinguang aminoacidfluxfrommetabolicnetworkbenefitsproteintranslationtheroleofresourceavailability