Genome-scale analysis of translation elongation with a ribosome flow model.

We describe the first large scale analysis of gene translation that is based on a model that takes into account the physical and dynamical nature of this process. The Ribosomal Flow Model (RFM) predicts fundamental features of the translation process, including translation rates, protein abundance l...

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Autores principales:	Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/c7bba5c4181a407d947b76b5c7749371
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spelling	oai:doaj.org-article:c7bba5c4181a407d947b76b5c77493712021-11-18T05:50:20ZGenome-scale analysis of translation elongation with a ribosome flow model.1553-734X1553-735810.1371/journal.pcbi.1002127https://doaj.org/article/c7bba5c4181a407d947b76b5c77493712011-09-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21909250/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358We describe the first large scale analysis of gene translation that is based on a model that takes into account the physical and dynamical nature of this process. The Ribosomal Flow Model (RFM) predicts fundamental features of the translation process, including translation rates, protein abundance levels, ribosomal densities and the relation between all these variables, better than alternative ('non-physical') approaches. In addition, we show that the RFM can be used for accurate inference of various other quantities including genes' initiation rates and translation costs. These quantities could not be inferred by previous predictors. We find that increasing the number of available ribosomes (or equivalently the initiation rate) increases the genomic translation rate and the mean ribosome density only up to a certain point, beyond which both saturate. Strikingly, assuming that the translation system is tuned to work at the pre-saturation point maximizes the predictive power of the model with respect to experimental data. This result suggests that in all organisms that were analyzed (from bacteria to Human), the global initiation rate is optimized to attain the pre-saturation point. The fact that similar results were not observed for heterologous genes indicates that this feature is under selection. Remarkably, the gap between the performance of the RFM and alternative predictors is strikingly large in the case of heterologous genes, testifying to the model's promising biotechnological value in predicting the abundance of heterologous proteins before expressing them in the desired host.Shlomi ReuveniIsaac MeilijsonMartin KupiecEytan RuppinTamir TullerPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 7, Iss 9, p e1002127 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Shlomi Reuveni Isaac Meilijson Martin Kupiec Eytan Ruppin Tamir Tuller Genome-scale analysis of translation elongation with a ribosome flow model.
description	We describe the first large scale analysis of gene translation that is based on a model that takes into account the physical and dynamical nature of this process. The Ribosomal Flow Model (RFM) predicts fundamental features of the translation process, including translation rates, protein abundance levels, ribosomal densities and the relation between all these variables, better than alternative ('non-physical') approaches. In addition, we show that the RFM can be used for accurate inference of various other quantities including genes' initiation rates and translation costs. These quantities could not be inferred by previous predictors. We find that increasing the number of available ribosomes (or equivalently the initiation rate) increases the genomic translation rate and the mean ribosome density only up to a certain point, beyond which both saturate. Strikingly, assuming that the translation system is tuned to work at the pre-saturation point maximizes the predictive power of the model with respect to experimental data. This result suggests that in all organisms that were analyzed (from bacteria to Human), the global initiation rate is optimized to attain the pre-saturation point. The fact that similar results were not observed for heterologous genes indicates that this feature is under selection. Remarkably, the gap between the performance of the RFM and alternative predictors is strikingly large in the case of heterologous genes, testifying to the model's promising biotechnological value in predicting the abundance of heterologous proteins before expressing them in the desired host.
format	article
author	Shlomi Reuveni Isaac Meilijson Martin Kupiec Eytan Ruppin Tamir Tuller
author_facet	Shlomi Reuveni Isaac Meilijson Martin Kupiec Eytan Ruppin Tamir Tuller
author_sort	Shlomi Reuveni
title	Genome-scale analysis of translation elongation with a ribosome flow model.
title_short	Genome-scale analysis of translation elongation with a ribosome flow model.
title_full	Genome-scale analysis of translation elongation with a ribosome flow model.
title_fullStr	Genome-scale analysis of translation elongation with a ribosome flow model.
title_full_unstemmed	Genome-scale analysis of translation elongation with a ribosome flow model.
title_sort	genome-scale analysis of translation elongation with a ribosome flow model.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/c7bba5c4181a407d947b76b5c7749371
work_keys_str_mv	AT shlomireuveni genomescaleanalysisoftranslationelongationwitharibosomeflowmodel AT isaacmeilijson genomescaleanalysisoftranslationelongationwitharibosomeflowmodel AT martinkupiec genomescaleanalysisoftranslationelongationwitharibosomeflowmodel AT eytanruppin genomescaleanalysisoftranslationelongationwitharibosomeflowmodel AT tamirtuller genomescaleanalysisoftranslationelongationwitharibosomeflowmodel
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Genome-scale analysis of translation elongation with a ribosome flow model.

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