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He Z, Duan Y, Zhai W, Zhang X, Shi J, Zhang X, Xu Z. Evaluating Terminator Strength Based on Differentiating Effects on Transcription and Translation. Chembiochem 2020; 21:2067-2072. [PMID: 32180310 DOI: 10.1002/cbic.202000068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/27/2020] [Indexed: 11/05/2022]
Abstract
Transcription terminators play a role in terminating the progress of gene transcription, and are thus essential elements in the gene circuit. Terminators have two main functions: terminating gene transcription and improving the stability of gene transcripts during translation. We therefore considered the detailed characteristics of terminators in relation to their different roles in gene transcription and translation, including transcription shut-down degree (α) and upstream mRNA protection capacity (β), and apparent termination efficiency (η) reflecting the overall regulatory effect of the terminator. Based on a dual-reporter gene system, we constructed three terminator-probe plasmids to investigate each characteristic in Escherichia coli. According to multiple regression analysis, the transcription shut-down degree and the upstream mRNA protection capacity contributed almost equally to the apparent termination efficiency. Sequence analysis of 12 terminators demonstrated that the terminator sequence was dominated by GC bases, and that a high ratio of GC bases in the stem structure of terminators might be associated with a high degree of transcription shut-down. This comprehensive characterization of terminators furthers our understanding of the role of terminators in gene expression and provides a guide for synthetic terminator design.
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Affiliation(s)
- Zhiyun He
- The Key Laboratory of Industrial Biotechnology of Ministry of Education School of Biotechnology, Jiangnan University, 1800, Lihu Avenue, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800, Lihu Avenue, Wuxi, 214122, China
| | - Yanting Duan
- The Key Laboratory of Industrial Biotechnology of Ministry of Education School of Biotechnology, Jiangnan University, 1800, Lihu Avenue, Wuxi, 214122, China
| | - Weiji Zhai
- The Key Laboratory of Industrial Biotechnology of Ministry of Education School of Biotechnology, Jiangnan University, 1800, Lihu Avenue, Wuxi, 214122, China
| | - Xiaomei Zhang
- Jiangsu Engineering Research Center for Bioactive Products Processing Technology, Jiangnan University, No. 1800, Lihu Avenue, Wuxi, 214122, China.,School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, China
| | - Jinsong Shi
- Jiangsu Engineering Research Center for Bioactive Products Processing Technology, Jiangnan University, No. 1800, Lihu Avenue, Wuxi, 214122, China.,School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, China
| | - Xiaojuan Zhang
- The Key Laboratory of Industrial Biotechnology of Ministry of Education School of Biotechnology, Jiangnan University, 1800, Lihu Avenue, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800, Lihu Avenue, Wuxi, 214122, China.,Jiangsu Engineering Research Center for Bioactive Products Processing Technology, Jiangnan University, No. 1800, Lihu Avenue, Wuxi, 214122, China
| | - Zhenghong Xu
- The Key Laboratory of Industrial Biotechnology of Ministry of Education School of Biotechnology, Jiangnan University, 1800, Lihu Avenue, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800, Lihu Avenue, Wuxi, 214122, China
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Naseri G, Koffas MAG. Application of combinatorial optimization strategies in synthetic biology. Nat Commun 2020; 11:2446. [PMID: 32415065 PMCID: PMC7229011 DOI: 10.1038/s41467-020-16175-y] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 04/15/2020] [Indexed: 12/26/2022] Open
Abstract
In the first wave of synthetic biology, genetic elements, combined into simple circuits, are used to control individual cellular functions. In the second wave of synthetic biology, the simple circuits, combined into complex circuits, form systems-level functions. However, efforts to construct complex circuits are often impeded by our limited knowledge of the optimal combination of individual circuits. For example, a fundamental question in most metabolic engineering projects is the optimal level of enzymes for maximizing the output. To address this point, combinatorial optimization approaches have been established, allowing automatic optimization without prior knowledge of the best combination of expression levels of individual genes. This review focuses on current combinatorial optimization methods and emerging technologies facilitating their applications.
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Affiliation(s)
- Gita Naseri
- Institut für Chemie, Humboldt Universität zu Berlin, 12489, Berlin, Germany.
| | - Mattheos A G Koffas
- Center for Biotechnology, Rensselaer Polytechnic Institute, Troy, NY, USA.
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA.
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA.
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Peng R, Wang H, Lyu Y, Xu L, Liu H, Kuai H, Liu Q, Tan W. Facile Assembly/Disassembly of DNA Nanostructures Anchored on Cell-Mimicking Giant Vesicles. J Am Chem Soc 2017; 139:12410-12413. [PMID: 28841373 PMCID: PMC5877790 DOI: 10.1021/jacs.7b07485] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA nanostructures assembled on living cell membranes have become powerful research tools. Synthetic lipid membranes have been used as a membrane model to study the dynamic behavior of DNA nanostructures on fluid soft lipid bilayers, but without the inherent complexity of natural membranes. Herein, we report the assembly and disassembly of DNA nanoprisms on cell-mimicking micrometer-scale giant membrane vesicles derived from living mammalian cells. Three-dimensional DNA nanoprisms with a DNA arm and a cholesterol anchor were efficiently localized on the membrane surface. The assembly and disassembly of DNA nanoprisms were dynamically manipulated by DNA strand hybridization and toehold-mediated strand displacement. Furthermore, the heterogeneity of reversible assembly/disassembly of DNA nanoprisms was monitored by Förster resonance energy transfer. This study suggests the feasibility of DNA-mediated functional biomolecular assembly on cell membranes for biomimetics studies and delivery systems.
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Affiliation(s)
- Ruizi Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Huijing Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Liujun Xu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Hui Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Hailan Kuai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
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Ait-Bara S, Clerté C, Declerck N, Margeat E. Competitive folding of RNA structures at a termination-antitermination site. RNA (NEW YORK, N.Y.) 2017; 23:721-734. [PMID: 28235843 PMCID: PMC5393181 DOI: 10.1261/rna.060178.116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/08/2017] [Indexed: 06/06/2023]
Abstract
Antitermination is a regulatory process based on the competitive folding of terminator-antiterminator structures that can form in the leader region of nascent transcripts. In the case of the Bacillus subtilis licS gene involved in β-glucosides utilization, the binding of the antitermination protein LicT to a short RNA hairpin (RAT) prevents the formation of an overlapping terminator and thereby allows transcription to proceed. Here, we monitored in vitro the competition between termination and antitermination by combining bulk and single-molecule fluorescence-based assays using labeled RNA oligonucleotide constructs of increasing length that mimic the progressive transcription of the terminator invading the antiterminator hairpin. Although high affinity binding is abolished as soon as the antiterminator basal stem is disrupted by the invading terminator, LicT can still bind and promote closing of the partially unfolded RAT hairpin. However, binding no longer occurs once the antiterminator structure has been disrupted by the full-length terminator. Based on these findings, we propose a kinetic competition model for the sequential events taking place at the termination-antitermination site, where LicT needs to capture its RAT target before completion of the terminator to remain tightly bound during RNAP pausing, before finally dissociating irreversibly from the elongated licS transcript.
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Affiliation(s)
- Soraya Ait-Bara
- CNRS UMR5048, Centre de Biochimie Structurale, 34090 Montpellier, France
- INSERM U1054, 34090 Montpellier, France
- Université de Montpellier, 34090 Montpellier, France
| | - Caroline Clerté
- CNRS UMR5048, Centre de Biochimie Structurale, 34090 Montpellier, France
- INSERM U1054, 34090 Montpellier, France
- Université de Montpellier, 34090 Montpellier, France
| | - Nathalie Declerck
- CNRS UMR5048, Centre de Biochimie Structurale, 34090 Montpellier, France
- INSERM U1054, 34090 Montpellier, France
- Université de Montpellier, 34090 Montpellier, France
- INRA, departement MICA, 78352 Jouy-en-Josas, France
| | - Emmanuel Margeat
- CNRS UMR5048, Centre de Biochimie Structurale, 34090 Montpellier, France
- INSERM U1054, 34090 Montpellier, France
- Université de Montpellier, 34090 Montpellier, France
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