A genome-scale integration and analysis of Lactococcus lactis translation data.

Protein synthesis is a template polymerization process composed by three main steps: initiation, elongation, and termination. During translation, ribosomes are engaged into polysomes whose size is used for the quantitative characterization of translatome. However, simultaneous transcription and tran...

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Autores principales:	Julien Racle, Flora Picard, Laurence Girbal, Muriel Cocaign-Bousquet, Vassily Hatzimanikatis
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/2d32b91674024964be5458c69736b837
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spelling	oai:doaj.org-article:2d32b91674024964be5458c69736b8372021-11-18T05:53:32ZA genome-scale integration and analysis of Lactococcus lactis translation data.1553-734X1553-735810.1371/journal.pcbi.1003240https://doaj.org/article/2d32b91674024964be5458c69736b8372013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24130467/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Protein synthesis is a template polymerization process composed by three main steps: initiation, elongation, and termination. During translation, ribosomes are engaged into polysomes whose size is used for the quantitative characterization of translatome. However, simultaneous transcription and translation in the bacterial cytosol complicates the analysis of translatome data. We established a procedure for robust estimation of the ribosomal density in hundreds of genes from Lactococcus lactis polysome size measurements. We used a mechanistic model of translation to integrate the information about the ribosomal density and for the first time we estimated the protein synthesis rate for each gene and identified the rate limiting steps. Contrary to conventional considerations, we find significant number of genes to be elongation limited. This number increases during stress conditions compared to optimal growth and proteins synthesized at maximum rate are predominantly elongation limited. Consistent with bacterial physiology, we found proteins with similar rate and control characteristics belonging to the same functional categories. Under stress conditions, we found that synthesis rate of regulatory proteins is becoming comparable to proteins favored under optimal growth. These findings suggest that the coupling of metabolic states and protein synthesis is more important than previously thought.Julien RacleFlora PicardLaurence GirbalMuriel Cocaign-BousquetVassily HatzimanikatisPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 10, p e1003240 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Julien Racle Flora Picard Laurence Girbal Muriel Cocaign-Bousquet Vassily Hatzimanikatis A genome-scale integration and analysis of Lactococcus lactis translation data.
description	Protein synthesis is a template polymerization process composed by three main steps: initiation, elongation, and termination. During translation, ribosomes are engaged into polysomes whose size is used for the quantitative characterization of translatome. However, simultaneous transcription and translation in the bacterial cytosol complicates the analysis of translatome data. We established a procedure for robust estimation of the ribosomal density in hundreds of genes from Lactococcus lactis polysome size measurements. We used a mechanistic model of translation to integrate the information about the ribosomal density and for the first time we estimated the protein synthesis rate for each gene and identified the rate limiting steps. Contrary to conventional considerations, we find significant number of genes to be elongation limited. This number increases during stress conditions compared to optimal growth and proteins synthesized at maximum rate are predominantly elongation limited. Consistent with bacterial physiology, we found proteins with similar rate and control characteristics belonging to the same functional categories. Under stress conditions, we found that synthesis rate of regulatory proteins is becoming comparable to proteins favored under optimal growth. These findings suggest that the coupling of metabolic states and protein synthesis is more important than previously thought.
format	article
author	Julien Racle Flora Picard Laurence Girbal Muriel Cocaign-Bousquet Vassily Hatzimanikatis
author_facet	Julien Racle Flora Picard Laurence Girbal Muriel Cocaign-Bousquet Vassily Hatzimanikatis
author_sort	Julien Racle
title	A genome-scale integration and analysis of Lactococcus lactis translation data.
title_short	A genome-scale integration and analysis of Lactococcus lactis translation data.
title_full	A genome-scale integration and analysis of Lactococcus lactis translation data.
title_fullStr	A genome-scale integration and analysis of Lactococcus lactis translation data.
title_full_unstemmed	A genome-scale integration and analysis of Lactococcus lactis translation data.
title_sort	genome-scale integration and analysis of lactococcus lactis translation data.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/2d32b91674024964be5458c69736b837
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A genome-scale integration and analysis of Lactococcus lactis translation data.

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