1. Measurement and modeling of intrinsic transcription terminators
- Author
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Joao C. Guimaraes, Quynh-Anh Mai, Guillaume Cambray, James M. Carothers, Drew Endy, Colin Lam, Vivek K. Mutalik, Adam P. Arkin, Tim Thimmaiah, Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), California Institute for Quantitative Biosciences [Berkeley] (QB3-Berkeley), University of California [Berkeley], University of California-University of California, St Vincents Hosp, Biofab3D, Melbourne, Vic, Australia, Department of Bioengineering, Nagaoka University of Technology, Physical Biosciences Division [LBNL Berkeley], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Chercheur indépendant, BIOFAB International Open Facility Advancing Biotechnology (BIOFAB), Beihang University (BUAA), Department of Informatics, Computer Science and Technology Center, and University of Minho
- Subjects
RNA Folding ,[SDV.BIO]Life Sciences [q-bio]/Biotechnology ,Gene Organization ,terminator ,Computational biology ,Biotechnologies ,Biology ,ENCODE ,03 medical and health sciences ,0302 clinical medicine ,Genetic ,Transcription (biology) ,Bacterial transcription ,Models ,Information and Computing Sciences ,Genetics ,Escherichia coli ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,030304 developmental biology ,Terminator Regions, Genetic ,0303 health sciences ,Models, Genetic ,030302 biochemistry & molecular biology ,Genetic systems ,Biological Sciences ,Terminator Regions ,Terminator (genetics) ,Transcription Termination, Genetic ,Synthetic Biology and Chemistry ,Forward engineering ,Rna folding ,synthetic biology ,Corrigendum ,Environmental Sciences ,030217 neurology & neurosurgery ,Transcription Termination ,Developmental Biology - Abstract
The reliable forward engineering of genetic systems remains limited by the ad hoc reuse of many types of basic genetic elements. Although a few intrinsic prokaryotic transcription terminators are used routinely, termination efficiencies have not been studied systematically. Here, we developed and validated a genetic architecture that enables reliable measurement of termination efficiencies. We then assembled a collection of 61 natural and synthetic terminators that collectively encode termination efficiencies across an ∼800-fold dynamic range within Escherichia coli . We simulated co-transcriptional RNA folding dynamics to identify competing secondary structures that might interfere with terminator folding kinetics or impact termination activity. We found that structures extending beyond the core terminator stem are likely to increase terminator activity. By excluding terminators encoding such context-confounding elements, we were able to develop a linear sequence-function model that can be used to estimate termination efficiencies ( r = 0.9, n = 31) better than models trained on all terminators ( r = 0.67, n = 54). The resulting systematically measured collection of terminators should improve the engineering of synthetic genetic systems and also advance quantitative modeling of transcription termination.
- Published
- 2013
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