Title:
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A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants
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Author:
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Yus, Eva; Yang, Jae-Seong; Sogues, Adrià; Serrano Pubull, Luis, 1982-
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Abstract:
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Quantitative analysis of the sequence determinants of transcription and translation regulation is relevant for systems and synthetic biology. To identify these determinants, researchers have developed different methods of screening random libraries using fluorescent reporters or antibiotic resistance genes. Here, we have implemented a generic approach called ELM-seq (expression level monitoring by DNA methylation) that overcomes the technical limitations of such classic reporters. ELM-seq uses DamID (Escherichia coli DNA adenine methylase as a reporter coupled with methylation-sensitive restriction enzyme digestion and high-throughput sequencing) to enable in vivo quantitative analyses of upstream regulatory sequences. Using the genome-reduced bacterium Mycoplasma pneumoniae, we show that ELM-seq has a large dynamic range and causes minimal toxicity. We use ELM-seq to determine key sequences (known and putatively novel) of promoter and untranslated regions that influence transcription and translation efficiency. Applying ELM-seq to other organisms will help us to further understand gene expression and guide synthetic biology.Quantitative analysis of how DNA sequence determines transcription and translation regulation is of interest to systems and synthetic biologists. Here the authors present ELM-seq, which uses Dam activity as reporter for high-throughput analysis of promoter and 5'-UTR regions. |
Abstract:
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We thank the CRG/UPF Proteomics Unit that is part of the Plataforma de Recursos Biomoleculares y Bioinformáticos (Instituto de Salud Carlos III), supported by grant PT13/0001. The project was supported by funds from the Fundación Marcelino Botin and the Spanish Ministerio de Economía y Competitividad (BIO2007-61762). This project was financed by Instituto de Salud Carlos III and co-financed by Federación Española de Enfermedades Raras under grant agreement PI10/01702 and the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program, under grant agreement Nos 634942 (MycoSynVac) and 670216 (MYCOCHASSIS). We acknowledge support from the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo Ochoa 2013-2017 and the support given by Juan de la Cierva-Incorporación Program (IJCI‐2014‐22070) to J.S.Y. We also acknowledge the support of the CERCA Program/Generalitat de Catalunya. |
Subject(s):
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-Bacterial transcription -Systems analysis -Transcription -Translation |
Rights:
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© The Author(s) 2017. 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/.
http://creativecommons.org/licenses/by/4.0/ |
Document type:
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Article Article - Published version |
Published by:
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Nature Publishing Group
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