1
|
Anooja VV, Archana K, Athira PP, Anju MV, Neelima S, Muhammed Musthafa S, Dhaneesha M, Sajeevan TP, Singh ISB, Philip R. Antibacterial activity and modes of action of a novel hepcidin isoform from the shrimp scad, Alepes djedaba (Forsskål, 1775). FISH & SHELLFISH IMMUNOLOGY 2024; 146:109406. [PMID: 38278338 DOI: 10.1016/j.fsi.2024.109406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
Hepcidin, initially identified in human blood ultrafiltrate as cysteine rich Liver Expressed Antimicrobial Peptide (LEAP-1), is a core molecular conduit between iron trafficking and immune response. Though a great share of studies has been focused on the iron regulatory function of hepcidins, investigations on the antimicrobial aspects are relatively less. The present study is aimed at identification of hepcidin from a teleost fish, Alepes djedaba followed by its recombinant expression, testing antibacterial property, stability and evaluation of cytotoxicity. Modes of action on bacterial pathogens were also examined. A novel hepcidin isoform, Ad-Hep belonging to the HAMP1 (Hepcidin antimicrobial peptide 1) group of hepcidins was identified from the shrimp scad, Alepes djedaba. Ad-Hep with 2.9 kDa size was found to be a cysteine rich, cationic peptide (+4) with antiparallel beta sheet conformation, a furin cleavage site (RXXR) and 'ATCUN' motif. It was heterologously expressed in E. coli Rosettagami B(DE3)PLysS cells and the recombinant peptide, rAd-Hep was found to have significant antibacterial activity, especially against Edwardsiella tarda, Vibrio parahaemolyticus and Escherichia coli. Membrane depolarization followed by membrane permeabilization and Reactive Oxygen Species (ROS) production were found to be the modes of action of rAd-Hep on bacterial cells. Ad-Hep was found to be non-haemolytic to hRBC and non-cytotoxic in mammalian cell line. Stability of the peptide at varying temperature, pH and metal salts qualify them for applications in vivo. With significant bactericidal activity coupled with direct killing mechanisms, the rAd-Hep can be a promising drug candidate for therapeutic applications in medicine and fish culture systems.
Collapse
Affiliation(s)
- V V Anooja
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - K Archana
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - P P Athira
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - M V Anju
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - S Neelima
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - S Muhammed Musthafa
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - M Dhaneesha
- National Center for Aquatic Animal Health, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - T P Sajeevan
- National Center for Aquatic Animal Health, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - I S Bright Singh
- National Center for Aquatic Animal Health, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - Rosamma Philip
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India.
| |
Collapse
|
2
|
Xie J, Ye F, Deng X, Tang Y, Liang JY, Huang X, Sun Y, Tang H, Lei J, Zheng S, Zou Y. Circular RNA: A promising new star of vaccine. J Transl Int Med 2023; 11:372-381. [PMID: 38130633 PMCID: PMC10732498 DOI: 10.2478/jtim-2023-0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of single-stranded RNAs with covalently closed structures. Owing to their not having 3' or 5' ends, circRNAs are highly durable and insusceptible to exonuclease-mediated degradation. Moreover, some circRNAs with certain structures are translatable, making them novel vaccines. Vaccines are efficient tools for immunotherapy, such as for the prevention of infectious diseases and cancer treatment. The immune system is activated during immunotherapy to fight against abnormal allies or invaders. CircRNA vaccines represent a potential new avenue in the vaccine era. Recently, several circRNA vaccines have been synthesized and tested in vitro and in vivo. Our review briefly introduces the current understanding of the biology and function of translatable circRNAs, molecular biology, synthetic methods, delivery of circRNA, and current circRNA vaccines. We also discussed the challenges and future directions in the field by summarizing the developments in circRNA vaccines in the past few years.
Collapse
Affiliation(s)
- Jindong Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou510060, Guangdong Province, China
| | - Fengxi Ye
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou510060, Guangdong Province, China
| | - Xinpei Deng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou510060, Guangdong Province, China
| | - Yuhui Tang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou510060, Guangdong Province, China
| | - Jie-Ying Liang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou510000, Guangdong Province, China
| | - Xufeng Huang
- Department of Data Science and Visualization, Faculty of Informatics, University of Debrecen, Debrecen, Hungary
| | - Yuying Sun
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou510060, Guangdong Province, China
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou510060, Guangdong Province, China
| | - Jinsong Lei
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou510060, Guangdong Province, China
| | - Shaoquan Zheng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou510060, Guangdong Province, China
- Breast Disease Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou510000, Guangdong Province, China
| | - Yutian Zou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou510060, Guangdong Province, China
| |
Collapse
|
3
|
Ting WW, Ng IS. Tunable T7 Promoter Orthogonality on T7RNAP for cis-Aconitate Decarboxylase Evolution via Base Editor and Screening from Itaconic Acid Biosensor. ACS Synth Biol 2023; 12:3020-3029. [PMID: 37750409 PMCID: PMC10595973 DOI: 10.1021/acssynbio.3c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Indexed: 09/27/2023]
Abstract
The deaminase-fused T7 RNA polymerase (T7RNAP) presents a promising toolkit for in vivo target-specific enzyme evolution, offering the unique advantage of simultaneous DNA modification and screening. Previous studies have reported the mutation efficiency of base editors relying on different resources. In contrast, the mechanism underlying the T7RNAP/T7 system is well-understood. Therefore, this study aimed to establish a new platform, termed dT7-Muta, by tuning the binding efficiency between T7RNAP and the T7 promoter for gene mutagenesis. The strategy for proof-of-concept involves alterations in the fluorescence distribution through dT7-Muta and screening of the mutants via flow cytometry. The cis-aconitate decarboxylase from Aspergillus terreus (AtCadA) was evolved and screened via an itaconate-induced biosensor as proof-of-function of enzyme evolution. First, the degenerated codons were designed within the binding and initial region of T7 promoters (dT7s), including upstream (U), central (C), and downstream (D) regions. Three strength variants of dT7 promoter from each design, i.e., strong (S), medium (M), and weak (W), were used for evaluation. Mutation using dT7s of varying strength resulted in a broader fluorescence distribution in sfGFP mutants from the promoters CW and DS. On the other hand, broader fluorescence distribution was observed in the AtCadA mutants from the original promoter T7, UW, and DS, with the highest fluorescence and itaconic acid titer at 860 a.u. and 0.51 g/L, respectively. The present platform introduces a novel aspect of the deaminase-based mutagenesis, emphasizing the potential of altering the binding efficiency between T7RNAP and the T7 promoter for further efforts in enzyme evolution.
Collapse
Affiliation(s)
- Wan-Wen Ting
- Department of Chemical
Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - I-Son Ng
- Department of Chemical
Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| |
Collapse
|
4
|
Ye Z, Harmon J, Ni W, Li Y, Wich D, Xu Q. The mRNA Vaccine Revolution: COVID-19 Has Launched the Future of Vaccinology. ACS NANO 2023; 17:15231-15253. [PMID: 37535899 DOI: 10.1021/acsnano.2c12584] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
During the COVID-19 pandemic, mRNA (mRNA) vaccines emerged as leading vaccine candidates in a record time. Nonreplicating mRNA (NRM) and self-amplifying mRNA (SAM) technologies have been developed into high-performing and clinically viable vaccines against a range of infectious agents, notably SARS-CoV-2. mRNA vaccines demonstrate efficient in vivo delivery, long-lasting stability, and nonexistent risk of infection. The stability and translational efficiency of in vitro transcription (IVT)-mRNA can be further increased by modulating its structural elements. In this review, we present a comprehensive overview of the recent advances, key applications, and future challenges in the field of mRNA-based vaccinology.
Collapse
Affiliation(s)
- Zhongfeng Ye
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Joseph Harmon
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Wei Ni
- Department of Medical Oncology, Dana-Farber Cancer Institute at Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Yamin Li
- Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, New York 13210, United States
| | - Douglas Wich
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| |
Collapse
|
5
|
Kang DD, Li H, Dong Y. Advancements of in vitro transcribed mRNA (IVT mRNA) to enable translation into the clinics. Adv Drug Deliv Rev 2023; 199:114961. [PMID: 37321375 PMCID: PMC10264168 DOI: 10.1016/j.addr.2023.114961] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023]
Abstract
The accelerated progress and approval of two mRNA-based vaccines to address the SARS-CoV-2 virus were unprecedented. This record-setting feat was made possible through the solid foundation of research on in vitro transcribed mRNA (IVT mRNA) which could be utilized as a therapeutic modality. Through decades of thorough research to overcome barriers to implementation, mRNA-based vaccines or therapeutics offer many advantages to rapidly address a broad range of applications including infectious diseases, cancers, and gene editing. Here, we describe the advances that have supported the adoption of IVT mRNA in the clinics, including optimization of the IVT mRNA structural components, synthesis, and lastly concluding with different classes of IVT RNA. Continuing interest in driving IVT mRNA technology will enable a safer and more efficacious therapeutic modality to address emerging and existing diseases.
Collapse
Affiliation(s)
- Diana D Kang
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Haoyuan Li
- Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Yizhou Dong
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Department of Biomedical Engineering, The Center for Clinical and Translational Science, The Comprehensive Cancer Center; Dorothy M. Davis Heart & Lung Research Institute, Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, United States; Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
| |
Collapse
|
6
|
Deich C, Cash B, Sato W, Sharon J, Aufdembrink L, Gaut NJ, Heili J, Stokes K, Engelhart AE, Adamala KP. T7Max transcription system. J Biol Eng 2023; 17:4. [PMID: 36691081 PMCID: PMC9872363 DOI: 10.1186/s13036-023-00323-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 01/04/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Efficient cell-free protein expression from linear DNA templates has remained a challenge primarily due to template degradation. In addition, the yields of transcription in cell-free systems lag behind transcriptional efficiency of live cells. Most commonly used in vitro translation systems utilize T7 RNA polymerase, which is also the enzyme included in many commercial kits. RESULTS Here we present characterization of a variant of T7 RNA polymerase promoter that acts to significantly increase the yields of gene expression within in vitro systems. We have demonstrated that T7Max increases the yield of translation in many types of commonly used in vitro protein expression systems. We also demonstrated increased protein expression yields from linear templates, allowing the use of T7Max driven expression from linear templates. CONCLUSIONS The modified promoter, termed T7Max, recruits standard T7 RNA polymerase, so no protein engineering is needed to take advantage of this method. This technique could be used with any T7 RNA polymerase- based in vitro protein expression system.
Collapse
Affiliation(s)
- Christopher Deich
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Brock Cash
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Wakana Sato
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Judee Sharon
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Lauren Aufdembrink
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Nathaniel J Gaut
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Joseph Heili
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Kaitlin Stokes
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Aaron E Engelhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA.
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA.
| |
Collapse
|
7
|
Martínez-García E, Fraile S, Algar E, Aparicio T, Velázquez E, Calles B, Tas H, Blázquez B, Martín B, Prieto C, Sánchez-Sampedro L, Nørholm MH, Volke D, Wirth N, Dvořák P, Alejaldre L, Grozinger L, Crowther M, Goñi-Moreno A, Nikel P, Nogales J, de Lorenzo V. SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes. Nucleic Acids Res 2023; 51:D1558-D1567. [PMID: 36420904 PMCID: PMC9825617 DOI: 10.1093/nar/gkac1059] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 11/27/2022] Open
Abstract
The SEVA platform (https://seva-plasmids.com) was launched one decade ago, both as a database (DB) and as a physical repository of plasmid vectors for genetic analysis and engineering of Gram-negative bacteria with a structure and nomenclature that follows a strict, fixed architecture of functional DNA segments. While the current update keeps the basic features of earlier versions, the platform has been upgraded not only with many more ready-to-use plasmids but also with features that expand the range of target species, harmonize DNA assembly methods and enable new applications. In particular, SEVA 4.0 includes (i) a sub-collection of plasmids for easing the composition of multiple DNA segments with MoClo/Golden Gate technology, (ii) vectors for Gram-positive bacteria and yeast and [iii] off-the-shelf constructs with built-in functionalities. A growing collection of plasmids that capture part of the standard-but not its entirety-has been compiled also into the DB and repository as a separate corpus (SEVAsib) because of its value as a resource for constructing and deploying phenotypes of interest. Maintenance and curation of the DB were accompanied by dedicated diffusion and communication channels that make the SEVA platform a popular resource for genetic analyses, genome editing and bioengineering of a large number of microorganisms.
Collapse
Affiliation(s)
- Esteban Martínez-García
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Sofía Fraile
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Elena Algar
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Tomás Aparicio
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Elena Velázquez
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Belén Calles
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Huseyin Tas
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Blas Blázquez
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | | | | | | | - Morten H H Nørholm
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pavel Dvořák
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 62500 Czech Republic
| | - Lorea Alejaldre
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (INIA-CSIC), Pozuelo de Alarcón 28223, Spain
| | - Lewis Grozinger
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (INIA-CSIC), Pozuelo de Alarcón 28223, Spain
- School of Computing, Newcastle University, NE4 5TG, UK
| | - Matthew Crowther
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (INIA-CSIC), Pozuelo de Alarcón 28223, Spain
- School of Computing, Newcastle University, NE4 5TG, UK
| | - Angel Goñi-Moreno
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (INIA-CSIC), Pozuelo de Alarcón 28223, Spain
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Juan Nogales
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| |
Collapse
|
8
|
Wei T, Lai W, Chen Q, Zhang Y, Sun C, He X, Zhao G, Fu X, Liu C. Exploiting spatial dimensions to enable parallelized continuous directed evolution. Mol Syst Biol 2022; 18:e10934. [PMID: 36129229 PMCID: PMC9491160 DOI: 10.15252/msb.202210934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 12/03/2022] Open
Abstract
Current strategies to improve the throughput of continuous directed evolution technologies often involve complex mechanical fluid‐controlling system or robotic platforms, which limits their popularization and application in general laboratories. Inspired by our previous study on bacterial range expansion, in this study, we report a system termed SPACE for rapid and extensively parallelizable evolution of biomolecules by introducing spatial dimensions into the landmark phage‐assisted continuous evolution system. Specifically, M13 phages and chemotactic Escherichia coli cells were closely inoculated onto a semisolid agar. The phages came into contact with the expanding front of the bacterial range, and then comigrated with the bacteria. This system leverages competition over space, wherein evolutionary progress is closely associated with the production of spatial patterns, allowing the emergence of improved or new protein functions. In a prototypical problem, SPACE remarkably simplified the process and evolved the promoter recognition of T7 RNA polymerase (RNAP) to a library of 96 random sequences in parallel. These results establish SPACE as a simple, easy to implement, and massively parallelizable platform for continuous directed evolution in general laboratories.
Collapse
Affiliation(s)
- Ting Wei
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Wangsheng Lai
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qian Chen
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yi Zhang
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chenjian Sun
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xionglei He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Guoping Zhao
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,CAS Key Laboratory for Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiongfei Fu
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chenli Liu
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
9
|
de Mey W, De Schrijver P, Autaers D, Pfitzer L, Fant B, Locy H, Esprit A, Lybaert L, Bogaert C, Verdonck M, Thielemans K, Breckpot K, Franceschini L. A synthetic DNA template for fast manufacturing of versatile single epitope mRNA. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:943-954. [PMID: 36159589 PMCID: PMC9464653 DOI: 10.1016/j.omtn.2022.08.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/14/2022] [Indexed: 11/30/2022]
Abstract
A flexible, affordable, and rapid vaccine platform is necessary to unlock the potential of personalized cancer vaccines in order to achieve full clinical efficiency. mRNA cancer vaccine manufacture relies on the rigid sequence design of multiepitope constructs produced by laborious bacterial cloning and time-consuming plasmid preparation. Here, we introduce a synthetic DNA template (SDT) assembly process, which allows cost- and time-efficient manufacturing of single (neo)epitope mRNA. We benchmarked SDT-derived mRNA against mRNA derived from a plasmid DNA template (PDT), showing that monocyte-derived dendritic cells (moDCs) electroporated with SDT-mRNA or PDT-mRNA, encoding HLA-I- or HLA-II-restricted (neo)epitopes, equally activated T cells that were modified to express the cognate T cell receptors. Furthermore, we validated the SDT-mRNA platform for neoepitope immunogenicity screening using the characterized HLA-A2-restricted neoepitope DHX40B and four new candidate HLA-A2-restricted melanoma neoepitopes. Finally, we compared SDT-mRNA with PDT-mRNA for vaccine development purposes. moDCs electroporated with mRNA encoding the HLA-A2-restricted, mutated Melan-A/Mart-1 epitope together with TriMix mRNA-generated high levels of functional Melan-A/Mart-1-specific CD8+ T cells. In conclusion, SDT single epitope mRNA can be manufactured in a more flexible, cost-efficient, and time-efficient way compared with PDT-mRNA, allowing prompt neoepitope immunogenicity screening, and might be exploited for the development of personalized cancer vaccines.
Collapse
Affiliation(s)
- Wout de Mey
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Phaedra De Schrijver
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Dorien Autaers
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Lena Pfitzer
- myNEO, Ottergemsesteenweg-Zuid 808, 9000 Ghent, Belgium
| | - Bruno Fant
- myNEO, Ottergemsesteenweg-Zuid 808, 9000 Ghent, Belgium
| | - Hanne Locy
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Arthur Esprit
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Lien Lybaert
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
- myNEO, Ottergemsesteenweg-Zuid 808, 9000 Ghent, Belgium
| | | | - Magali Verdonck
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Kris Thielemans
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Karine Breckpot
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Lorenzo Franceschini
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
- Corresponding author Lorenzo Franceschini, Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium.
| |
Collapse
|
10
|
Dionisi S, Piera K, Baumschlager A, Khammash M. Implementation of a Novel Optogenetic Tool in Mammalian Cells Based on a Split T7 RNA Polymerase. ACS Synth Biol 2022; 11:2650-2661. [PMID: 35921263 PMCID: PMC9396705 DOI: 10.1021/acssynbio.2c00067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Optogenetic tools are widely used to control gene expression
dynamics
both in prokaryotic and eukaryotic cells. These tools are used in
a variety of biological applications from stem cell differentiation
to metabolic engineering. Despite some tools already available in
bacteria, no light-inducible system currently exists to control gene
expression independently from mammalian transcriptional and/or translational
machineries thus working orthogonally to endogenous regulatory mechanisms.
Such a tool would be particularly important in synthetic biology,
where orthogonality is advantageous to achieve robust activation of
synthetic networks. Here we implement, characterize, and optimize
a new optogenetic tool in mammalian cells based on a previously published
system in bacteria called Opto-T7RNAPs. The tool is orthogonal to
the cellular machinery for transcription and consists of a split T7
RNA polymerase coupled with the blue light-inducible magnets system
(mammalian OptoT7–mOptoT7). In our study we exploited the T7
polymerase’s viral origins to tune our system’s expression
level, reaching up to an almost 20-fold change activation over the
dark control. mOptoT7 is used here to generate mRNA for protein expression,
shRNA for protein inhibition, and Pepper aptamer for RNA visualization.
Moreover, we show that mOptoT7 can mitigate the gene expression burden
when compared to another optogenetic construct. These properties make
mOptoT7 a powerful new tool to use when orthogonality and viral RNA
species (that lack endogenous RNA modifications) are desired.
Collapse
Affiliation(s)
- Sara Dionisi
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Karol Piera
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Armin Baumschlager
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| |
Collapse
|
11
|
Liu X, Zhang Y, Zhou S, Dain L, Mei L, Zhu G. Circular RNA: An emerging frontier in RNA therapeutic targets, RNA therapeutics, and mRNA vaccines. J Control Release 2022; 348:84-94. [PMID: 35649485 PMCID: PMC9644292 DOI: 10.1016/j.jconrel.2022.05.043] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022]
Abstract
Circular RNAs (circRNA) is a class of natural (biogenic) or synthetic closed RNA without 5' or 3' ends. Meanwhile, their unique covalently-closed structures of circRNA prevent RNA degradation by exonucleases, thereby empowering them with high pharmaceutical stability and biostability relative to current standard-of-care linear mRNA. Natural circRNA can be non-coding RNAs as well as protein-coding RNA, the latter of which was recently discovered. The physiological functions of biogenic circRNAs, which largely remain elusive, include protein and gene sponges, cell activity modulators, and protein translation. The discovery that the circRNA levels can be correlated with some human diseases empowers circRNA with the potential as a novel type of disease biomarkers and a noncanonical class of therapeutic targets. Recently, synthetic circRNA have been engineered to explore their applications as a novel class of mRNA therapeutics and vaccines. In this review, we will discuss the current understanding of the biogenesis and physiological functions of natural circRNAs, the approaches to circRNA synthesis, and current research in the exploration of endogenous circRNAs as novel therapeutic targets and testing circRNAs as an emerging class of RNA therapeutics and vaccines.
Collapse
Affiliation(s)
- Xiang Liu
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Yu Zhang
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Shurong Zhou
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Lauren Dain
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Lei Mei
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Guizhi Zhu
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA.
| |
Collapse
|
12
|
Calvopina-Chavez DG, Gardner MA, Griffitts JS. Engineering efficient termination of bacteriophage T7 RNA polymerase transcription. G3 (BETHESDA, MD.) 2022; 12:jkac070. [PMID: 35348690 PMCID: PMC9157156 DOI: 10.1093/g3journal/jkac070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
The bacteriophage T7 expression system is one of the most prominent transcription systems used in biotechnology and molecular-level research. However, T7 RNA polymerase is prone to read-through transcription due to its high processivity. As a consequence, enforcing efficient transcriptional termination is difficult. The termination hairpin found natively in the T7 genome is adapted to be inefficient, exhibiting 62% termination efficiency in vivo and even lower efficiency in vitro. In this study, we engineered a series of sequences that outperform the efficiency of the native terminator hairpin. By embedding a previously discovered 8-nucleotide T7 polymerase pause sequence within a synthetic hairpin sequence, we observed in vivo termination efficiency of 91%; by joining 2 short sequences into a tandem 2-hairpin structure, termination efficiency was increased to 98% in vivo and 91% in vitro. This study also tests the ability of these engineered sequences to terminate transcription of the Escherichia coli RNA polymerase. Two out of 3 of the most successful T7 polymerase terminators also facilitated termination of the bacterial polymerase with around 99% efficiency.
Collapse
Affiliation(s)
- Diana G Calvopina-Chavez
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Mikaela A Gardner
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Joel S Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| |
Collapse
|
13
|
Schaffter SW, Strychalski EA. Cotranscriptionally encoded RNA strand displacement circuits. SCIENCE ADVANCES 2022; 8:eabl4354. [PMID: 35319994 PMCID: PMC8942360 DOI: 10.1126/sciadv.abl4354] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 02/01/2022] [Indexed: 05/21/2023]
Abstract
Engineered molecular circuits that process information in biological systems could address emerging human health and biomanufacturing needs. However, such circuits can be difficult to rationally design and scale. DNA-based strand displacement reactions have demonstrated the largest and most computationally powerful molecular circuits to date but are limited in biological systems due to the difficulty in genetically encoding components. Here, we develop scalable cotranscriptionally encoded RNA strand displacement (ctRSD) circuits that are rationally programmed via base pairing interactions. ctRSD circuits address the limitations of DNA-based strand displacement circuits by isothermally producing circuit components via transcription. We demonstrate circuit programmability in vitro by implementing logic and amplification elements, as well as multilayer cascades. Furthermore, we show that circuit kinetics are accurately predicted by a simple model of coupled transcription and strand displacement, enabling model-driven design. We envision ctRSD circuits will enable the rational design of powerful molecular circuits that operate in biological systems, including living cells.
Collapse
|
14
|
E C, Dai L, Yu J. Switching promotor recognition of phage RNA polymerase in silico along lab-directed evolution path. Biophys J 2022; 121:582-595. [PMID: 35031277 PMCID: PMC8874028 DOI: 10.1016/j.bpj.2022.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/01/2021] [Accepted: 01/10/2022] [Indexed: 11/16/2022] Open
Abstract
In this work, we computationally investigated how a viral RNA polymerase (RNAP) from bacteriophage T7 evolves into RNAP variants under lab-directed evolution to switch recognition from T7 promoter to T3 promoter in transcription initiation. We first constructed a closed initiation complex for the wild-type T7 RNAP and then for six mutant RNAPs discovered from phage-assisted continuous evolution experiments. All-atom molecular dynamics simulations up to 1 μs each were conducted on these RNAPs in a complex with the T7 and T3 promoters. Our simulations show notably that protein-DNA electrostatic interactions or stabilities at the RNAP-DNA promoter interface well dictate the promoter recognition preference of the RNAP and variants. Key residues and structural elements that contribute significantly to switching the promoter recognition were identified. Followed by a first point mutation N748D on the specificity loop to slightly disengage the RNAP from the promoter to hinder the original recognition, we found an auxiliary helix (206-225) that takes over switching the promoter recognition upon further mutations (E222K and E207K) by forming additional charge interactions with the promoter DNA and reorientating differently on the T7 and T3 promoters. Further mutations on the AT-rich loop and the specificity loop can fully switch the RNAP-promoter recognition to the T3 promoter. Overall, our studies reveal energetics and structural dynamics details along an exemplary directed evolutionary path of the phage RNAP variants for a rewired promoter recognition function. The findings demonstrate underlying physical mechanisms and are expected to assist knowledge and data learning or rational redesign of the protein enzyme structure function.
Collapse
Affiliation(s)
- Chao E
- Beijing Computational Science Research Center, Beijing, China
| | - Liqiang Dai
- Beijing Computational Science Research Center, Beijing, China; Shenzhen JL Computational Science and Applied Research Institute, Shenzhen, Guangdong, China
| | - Jin Yu
- Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California.
| |
Collapse
|
15
|
Obi P, Chen YG. The design and synthesis of circular RNAs. Methods 2021; 196:85-103. [PMID: 33662562 PMCID: PMC8670866 DOI: 10.1016/j.ymeth.2021.02.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel class of RNAs distinguished by their single-stranded, covalently-closed topology. Although initially perceived as rare byproducts of aberrant splicing, circRNAs are now recognized as ubiquitously expressed and functionally significant. These discoveries have led to a growing need for ways to model circRNAs in living cells to advance our understanding of their biogenesis, regulation, and function, and to adopt them as new technologies for application within research and medicine. In this review, we provide an updated summary of approaches used to produce circRNAs in vitro and in vivo, the latter of which has grown considerably in recent years. Given increased interest in the unique functions carried out by individual circRNAs, we further dedicate a section on how to customize synthesized circRNAs for specific biological roles. We focus on the most common applications, including designing circRNAs for protein delivery, to target miRNAs and proteins, to act as fluorescent reporters, and to modulate cellular immunity.
Collapse
Affiliation(s)
- Prisca Obi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Y Grace Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
| |
Collapse
|
16
|
Veedu AM, Prahaladhan AP, Vadakkeveettil AV, Krishnakumar A, Surendran N, Philip R. An Antimicrobial peptide hepcidin, St-hep from tuberculated flathead, Sorsogona tuberculata (Cuvier, 1829): Molecular and functional characterization. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00867-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
17
|
Orlov MA, Sorokin AA. DNA sequence, physics, and promoter function: Analysis of high-throughput data On T7 promoter variants activity. J Bioinform Comput Biol 2021; 18:2040001. [PMID: 32404013 DOI: 10.1142/s0219720020400016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
RNA polymerase/promoter recognition represents a basic problem of molecular biology. Decades-long efforts were made in the area, and yet certain challenges persist. The usage of certain most suitable model subjects is pivotal for the research. System of T7 bacteriophage RNA-polymerase/T7 native promoter represents an exceptional example for the purpose. Moreover, it has been studied the most and successfully applied to aims of biotechnology and bioengineering. Both structural simplicity and high specificity of this molecular duo are the reason for this. Despite highly similar sequences of distinct T7 native promoters, the T7 RNA-polymerase enzyme is capable of binding respective promoter in a highly specific and adjustable manner. One explanation here is that the process relies primarily on DNA physical properties rather than nucleotide sequence. Here, we address the issue by analyzing massive data recently published by Komura and colleagues. This initial study employed Next Generation Sequencing (NGS) in order to quantify activity of promoter variants including ones with multiple substitutions. As a result of our work substantial bias in simultaneous occurrence of single-nucleotide sequence alterations was found: the highest rate of co-occurrence was evidenced within specificity loop of binding region while the lowest - in initiation region of promoter. If both location and a kind of nucleotides involved in replacement (both initial and resulting) are taken into consideration, one can easily note that N to A substitutions are most preferred ones across the whole 19 b.p.-long sequence. At the same time, N to C are tolerated only at crucial position in recognition loop of binding region, and N to G are uniformly least tolerable. Later in this work the complete set of variants was split into groups with mutations (1) exclusively in binding region; (2) exclusively in melting region; (3) in both regions. Among these three groups second comprises extremely few variants (at triple-digit rate lesser than in two other groups, 46 versus over one and six thousand). Yet these are all promoter with substantial to high activity. This group two appeared heterogenous by primary sequence; indeed, upon further subdivision into above versus below average activity subgroups first one was found to comprise promoters with negligible conservation at -2 position of melting region; the second was hardly conserved in this region at all. This draws our attention to perfect consensus sequence of class III T7 promoter with -2 nucleotide randomized (all four are present by one to several copies in the previously published source dataset), the picture becomes even more pronounced. We therefore suggest that mutations at the position therefore do not cause significant changes in terms of promoter activity. At the same time, such modifications dramatically change DNA physical properties which were calculated in our study (namely electrostatic potential and propensity to bend). One possible suggestion here is that -2 nucleotide might function as a generic switch; if so, substitution -2A to -2T has important regulatory consequences. The fact that that -2 b.p. is the most evidently different nucleotide between class II versus class III promoters of T7 genome and that it also distinguishes the class III promoter in T7 genome versus promoters of its relative but reproductively isolated bacteriophage T3. In other words, it appears feasible that mutation at -2 nucleotide does not impede promoter activity yet alter its physical properties thus affecting differential RNA polymerase/promoter interaction.
Collapse
Affiliation(s)
- Mikhail A Orlov
- Institute of Cell Biophysics of RAS, 3 Institutskaya str., Poushchino, 142290, Russia
| | - Anatoly A Sorokin
- Institute of Cell Biophysics of RAS, 3 Institutskaya str., Poushchino, 142290, Russia
| |
Collapse
|
18
|
Woo J, Kim JH, Kim S, Park KS. Promoter engineering improves transcription efficiency in biomolecular assays. Chem Commun (Camb) 2021; 57:1619-1622. [PMID: 33458724 DOI: 10.1039/d0cc07797f] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We identified a novel 12 bp promoter that significantly increased transcription efficiency. Unlike the standard 20 bp promoter, which contains both recognition and initiation regions, the new promoter contains only a recognition region and is more suitable for diagnostic applications due to its smaller size. This promoter effectively produced different light-up RNA aptamers via transcription. Moreover, we used the promoter to analyze RNase H activity and achieved a detection limit of 0.009 U mL-1, which was significantly better than that achieved via previous methods. We propose that the new promoter may serve as a key component in various diagnostic applications.
Collapse
Affiliation(s)
- Jisu Woo
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea.
| | | | | | | |
Collapse
|
19
|
Till P. RNA Characterization in Trichoderma reesei. Methods Mol Biol 2021; 2234:191-235. [PMID: 33165790 DOI: 10.1007/978-1-0716-1048-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This chapter provides an overview on different methods for the characterization of RNAs in Trichoderma reesei. In the first section, protocols for the extraction of total RNA from fungal mycelia and the identification of 5' and 3' ends of certain RNAs of interest via rapid amplification of cDNA ends (RACE) are presented. In the next section, this knowledge on the transcriptional start and end points is used for in vitro synthesis and fluorescence labeling of the RNA of interest. The in vitro synthesized RNA can then be applied for in vitro analyses such as RNA electrophoretic mobility shift assays (RNA-EMSA) and RNA in vitro footprinting. RNA-EMSA is a method suitable for the identification and characterization of RNA-protein interactions or interactions of an RNA with other nucleic acids. RNA in vitro footprinting allows exact mapping of protein-binding sites on RNA molecules and also the determination of RNA secondary and tertiary structures at singe-nucleotide resolution. All protocols presented in this chapter are optimized for the analysis of noncoding RNAs (ncRNAs), especially long ncRNAs (lncRNAs) or other specific RNA species of more than 200 nt in length.
Collapse
Affiliation(s)
- Petra Till
- Christian Doppler laboratory for optimized expression of carbohydrate-active enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.
| |
Collapse
|
20
|
Kartje ZJ, Janis HI, Mukhopadhyay S, Gagnon KT. Revisiting T7 RNA polymerase transcription in vitro with the Broccoli RNA aptamer as a simplified real-time fluorescent reporter. J Biol Chem 2020; 296:100175. [PMID: 33303627 PMCID: PMC7948468 DOI: 10.1074/jbc.ra120.014553] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 11/06/2022] Open
Abstract
Methods for rapid and high-throughput screening of transcription in vitro to examine reaction conditions, enzyme mutants, promoter variants, and small molecule modulators can be extremely valuable tools. However, these techniques may be difficult to establish or inaccessible to many researchers. To develop a straightforward and cost-effective platform for assessing transcription in vitro, we used the "Broccoli" RNA aptamer as a direct, real-time fluorescent transcript readout. To demonstrate the utility of our approach, we screened the effect of common reaction conditions and components on bacteriophage T7 RNA polymerase (RNAP) activity using a common quantitative PCR instrument for fluorescence detection. Several essential conditions for in vitro transcription by T7 RNAP were confirmed with this assay, including the importance of enzyme and substrate concentrations, covariation of magnesium and nucleoside triphosphates, and the effects of several typical additives. When we used this method to assess all possible point mutants of a canonical T7 RNAP promoter, our results coincided well with previous reports. This approach should translate well to a broad variety of bacteriophage in vitro transcription systems and provides a platform for developing fluorescence-based readouts of more complex transcription systems in vitro.
Collapse
Affiliation(s)
- Zachary J Kartje
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Helen I Janis
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Shaoni Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois, USA
| | - Keith T Gagnon
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA; Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois, USA.
| |
Collapse
|
21
|
Passalacqua LFM, Dingilian AI, Lupták A. Single-pass transcription by T7 RNA polymerase. RNA (NEW YORK, N.Y.) 2020; 26:2062-2071. [PMID: 32958559 PMCID: PMC7668259 DOI: 10.1261/rna.076778.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/04/2020] [Indexed: 06/11/2023]
Abstract
RNA molecules can be conveniently synthesized in vitro by the T7 RNA polymerase (T7 RNAP). In some experiments, such as cotranscriptional biochemical analyses, continuous synthesis of RNA is not desired. Here, we propose a method for a single-pass transcription that yields a single transcript per template DNA molecule using the T7 RNAP system. We hypothesized that stalling the polymerase downstream from the promoter region and subsequent cleavage of the promoter by a restriction enzyme (to prevent promoter binding by another polymerase) would allow synchronized production of a single transcript per template. The single-pass transcription was verified in two different scenarios: a short self-cleaving ribozyme and a long mRNA. The results show that a controlled single-pass transcription using T7 RNAP allows precise measurement of cotranscriptional ribozyme activity, and this approach will facilitate the study of other kinetic events.
Collapse
Affiliation(s)
- Luiz F M Passalacqua
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Armine I Dingilian
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Andrej Lupták
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
- Department of Chemistry, University of California, Irvine, California 92697, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
| |
Collapse
|
22
|
Liu Q, Ke Y, Kan Y, Tang X, Li X, He Y, Wu L. Compatibility and Fidelity of Mirror-Image Thymidine in Transcription Events by T7 RNA Polymerase. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:604-613. [PMID: 32721880 PMCID: PMC7390857 DOI: 10.1016/j.omtn.2020.06.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/15/2020] [Accepted: 06/23/2020] [Indexed: 11/16/2022]
Abstract
Due to highly enzymatic d-stereoselectivity, l-nucleotides (l-2'-deoxynucleoside 5'-triphosphates [l-dNTPs]) are not natural targets of polymerases. In this study, we synthesized series of l-thymidine (l-T)-modified DNA strands and evaluated the processivity of nucleotide incorporation for transcription by T7 RNA polymerase (RNAP) with an l-T-containing template. When single l-T was introduced into the transcribed region, transcription proceeded to afford the full-length transcript with different efficiencies. However, introduction of l-T into the non-transcribed region did not exhibit a noticeable change in the transcription efficiency. Surprisingly, when two consecutive or internal l-Ts were introduced into the transcribed region, no transcripts were detected. Compared to natural template, significant lags in NTP incorporation into the template T+4/N and T+7/N (where the number corresponds to the site of l-T position, and + means downstream of the transcribed region) were detected by kinetic analysis. Furthermore, affinity of template T+4/N was almost the same with T/N, whereas affinity of T+7/N was apparently increased. Furthermore, no mismatch opposite to l-T in the template was detected in transcription reactions via gel fidelity analysis. These results demonstrate the effects of chiral l-T in DNA on the efficiency and fidelity of RNA transcription mediated by T7 RNAP, which provides important knowledge about how mirror-image thymidine perturbs the flow of genetic information during RNA transcription and development of diseases caused by gene mutation.
Collapse
Affiliation(s)
- Qingju Liu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongqi Ke
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhe Kan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiangjun Li
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yujian He
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Li Wu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| |
Collapse
|
23
|
Huang C, Guo L, Wang J, Wang N, Huo YX. Efficient long fragment editing technique enables large-scale and scarless bacterial genome engineering. Appl Microbiol Biotechnol 2020; 104:7943-7956. [PMID: 32794018 DOI: 10.1007/s00253-020-10819-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/20/2020] [Accepted: 08/05/2020] [Indexed: 11/24/2022]
Abstract
Bacteria are versatile living systems that enhance our understanding of nature and enable biosynthesis of valuable chemicals. Long fragment editing techniques are of great importance for accelerating bacterial genome engineering to obtain desirable and genetically stable strains. However, the existing genome editing methods cannot meet the needs of engineers. We herein report an efficient long fragment editing method for large-scale and scarless genome engineering in Escherichia coli. The method enabled us to insert DNA fragments up to 12 kb into the genome and to delete DNA fragments up to 186.7 kb from the genome, with positive rates over 95%. We applied this method for E. coli genome simplification, resulting in 12 individual deletion mutants and four cumulative deletion mutants. The simplest genome lost a total of 370.6 kb of DNA sequence containing 364 open reading frames. Additionally, we applied this technique to metabolic engineering and obtained a genetically stable plasmid-independent isobutanol production strain that produced 1.3 g/L isobutanol via shake-flask fermentation. These results suggest that the method is a powerful genome engineering tool, highlighting its potential to be applied in synthetic biology and metabolic engineering. KEY POINTS: • This article reports an efficient genome engineering tool for E. coli. • The tool is advantageous for the manipulations of long DNA fragments. • The tool has been successfully applied for genome simplification. • The tool has been successfully applied for metabolic engineering.
Collapse
Affiliation(s)
- Chaoyong Huang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.,SIP-UCLA Institute for Technology Advancement, Suzhou, 215123, China
| | - Liwei Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Jingge Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Ning Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China. .,SIP-UCLA Institute for Technology Advancement, Suzhou, 215123, China.
| |
Collapse
|
24
|
Acevedo-Jake A, Ball AT, Galli M, Kukwikila M, Denis M, Singleton DG, Tavassoli A, Goldup SM. AT-CuAAC Synthesis of Mechanically Interlocked Oligonucleotides. J Am Chem Soc 2020; 142:5985-5990. [PMID: 32155338 PMCID: PMC8016193 DOI: 10.1021/jacs.0c01670] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Indexed: 12/22/2022]
Abstract
We present a simple strategy for the synthesis of main chain oligonucleotide rotaxanes with precise control over the position of the macrocycle. The novel DNA-based rotaxanes were analyzed to assess the effect of the mechanical bond on their properties.
Collapse
Affiliation(s)
- Amanda Acevedo-Jake
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Andrew T. Ball
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Marzia Galli
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Mikiembo Kukwikila
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Mathieu Denis
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Daniel G. Singleton
- ATDBio
Ltd, School of Chemistry, University of
Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Ali Tavassoli
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Stephen M. Goldup
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| |
Collapse
|
25
|
Jackson NAC, Kester KE, Casimiro D, Gurunathan S, DeRosa F. The promise of mRNA vaccines: a biotech and industrial perspective. NPJ Vaccines 2020; 5:11. [PMID: 32047656 PMCID: PMC7000814 DOI: 10.1038/s41541-020-0159-8] [Citation(s) in RCA: 242] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/20/2019] [Indexed: 12/16/2022] Open
Abstract
mRNA technologies have the potential to transform areas of medicine, including the prophylaxis of infectious diseases. The advantages for vaccines range from the acceleration of immunogen discovery to rapid response and multiple disease target manufacturing. A greater understanding of quality attributes that dictate translation efficiency, as well as a comprehensive appreciation of the importance of mRNA delivery, are influencing a new era of investment in development activities. The application of translational sciences and growing early-phase clinical experience continue to inform candidate vaccine selection. Here we review the state of the art for the prevention of infectious diseases by using mRNA and pertinent topics to the biotechnology and pharmaceutical industries.
Collapse
Affiliation(s)
- Nicholas A. C. Jackson
- Coalition for Epidemic Preparedness Innovations (CEPI), Gibbs building, 215 Euston Road, Bloomsbury, London, NW1 2BE UK
| | - Kent E. Kester
- Sanofi Pasteur, 1 Discovery Dr, Swiftwater, PA 18370 USA
| | | | | | - Frank DeRosa
- Translate Bio, 29 Hartwell Ave, Lexington, MA 02421 USA
| |
Collapse
|
26
|
Théobald-Dietrich A, de Wijn R, Rollet K, Bluhm A, Rudinger-Thirion J, Paulus C, Lorber B, Thureau A, Frugier M, Sauter C. Structural Analysis of RNA by Small-Angle X-ray Scattering. Methods Mol Biol 2020; 2113:189-215. [PMID: 32006316 DOI: 10.1007/978-1-0716-0278-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Over the past two decades small-angle X-ray scattering (SAXS) has become a popular method to characterize solutions of biomolecules including ribonucleic acid (RNA). In an integrative structural approach, SAXS is complementary to crystallography, NMR, and electron microscopy and provides information about RNA architecture and dynamics. This chapter highlights the practical advantages of combining size-exclusion chromatography and SAXS at synchrotron facilities. It is illustrated by practical case studies of samples ranging from single hairpins and tRNA to a large IRES. The emphasis is also put on sample preparation which is a critical step of SAXS analysis and on optimized protocols for in vitro RNA synthesis ensuring the production of mg amount of pure and homogeneous molecules.
Collapse
Affiliation(s)
- Anne Théobald-Dietrich
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Raphaël de Wijn
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Kévin Rollet
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Alexandra Bluhm
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Joëlle Rudinger-Thirion
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Caroline Paulus
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Bernard Lorber
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | | | - Magali Frugier
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Claude Sauter
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France.
| |
Collapse
|
27
|
Gao W, Xu J, Lian G, Wang X, Gong X, Zhou D, Chang J. A novel analytical principle using AP site-mediated T7 RNA polymerase transcription regulation for sensing uracil-DNA glycosylase activity. Analyst 2020; 145:4321-4327. [DOI: 10.1039/d0an00509f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
udgactivity could regulateT7 RNApolymerase transcription ability by the heteroduplex substrates with chemical modifications.
Collapse
Affiliation(s)
- Weichen Gao
- School of Life Sciences
- Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology (Tianjin)
- Tianjin 300072
- China
| | - Jin Xu
- Tianjin Hospital
- Tianjin 300211
- China
| | - Guowei Lian
- School of Life Sciences
- Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology (Tianjin)
- Tianjin 300072
- China
| | - Xiaojun Wang
- Department of Toxicology
- Tianjin Centers for Disease Control and Prevention
- Tianjin 300011
- China
| | - Xiaoqun Gong
- School of Life Sciences
- Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology (Tianjin)
- Tianjin 300072
- China
| | - Dianming Zhou
- Department of Toxicology
- Tianjin Centers for Disease Control and Prevention
- Tianjin 300011
- China
| | - Jin Chang
- School of Life Sciences
- Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology (Tianjin)
- Tianjin 300072
- China
| |
Collapse
|
28
|
Promoter Length Affects the Initiation of T7 RNA Polymerase In Vitro: New Insights into Promoter/Polymerase Co-evolution. J Mol Evol 2019; 88:179-193. [PMID: 31863129 DOI: 10.1007/s00239-019-09922-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 11/28/2019] [Indexed: 10/25/2022]
Abstract
Polymerases are integral factors of gene expression and are essential for the maintenance and transmission of genetic information. RNA polymerases (RNAPs) differ from other polymerases in that they can bind promoter sequences and initiate transcription de novo and this promoter recognition requires the presence of specific DNA binding domains in the polymerase. Bacteriophage T7 RNA polymerase (T7RNAP) is the prototype for single subunit RNA polymerases which include bacteriophage and mitochondrial RNAPs, and the structure and mechanistic aspects of transcription by T7 RNAP are well characterized. Here, we describe experiments to determine whether the prototype T7 RNAP is able to recognize and initiate at truncated promoters similar to mitochondrial promoters. Using an in vitro oligonucleotide transcriptional system, we have assayed transcription initiation activity by T7 RNAP. These assays have not only defined the limits of conventional de novo initiation on truncated promoters, but have identified novel activities of initiation of RNA synthesis. We propose that these novel activities may be vestigial activities surviving from the transition of single subunit polymerase initiation using primers to de novo initiation using promoters.
Collapse
|
29
|
Tools and systems for evolutionary engineering of biomolecules and microorganisms. ACTA ACUST UNITED AC 2019; 46:1313-1326. [DOI: 10.1007/s10295-019-02191-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/20/2019] [Indexed: 12/28/2022]
Abstract
Abstract
Evolutionary approaches have been providing solutions to various bioengineering challenges in an efficient manner. In addition to traditional adaptive laboratory evolution and directed evolution, recent advances in synthetic biology and fluidic systems have opened a new era of evolutionary engineering. Synthetic genetic circuits have been created to control mutagenesis and enable screening of various phenotypes, particularly metabolite production. Fluidic systems can be used for high-throughput screening and multiplexed continuous cultivation of microorganisms. Moreover, continuous directed evolution has been achieved by combining all the steps of evolutionary engineering. Overall, modern tools and systems for evolutionary engineering can be used to establish the artificial equivalent to natural evolution for various research applications.
Collapse
|
30
|
An integrative approach identifies direct targets of the late viral transcription complex and an expanded promoter recognition motif in Kaposi's sarcoma-associated herpesvirus. PLoS Pathog 2019; 15:e1007774. [PMID: 31095645 PMCID: PMC6541308 DOI: 10.1371/journal.ppat.1007774] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/29/2019] [Accepted: 04/22/2019] [Indexed: 12/25/2022] Open
Abstract
The structural proteins of DNA viruses are generally encoded by late genes, whose expression relies on recruitment of the host transcriptional machinery only after the onset of viral genome replication. β and γ-herpesviruses encode a unique six-member viral pre-initiation complex (vPIC) for this purpose, although how the vPIC directs specific activation of late genes remains largely unknown. The specificity underlying late transcription is particularly notable given that late gene promoters are unusually small, with a modified TATA-box being the only recognizable element. Here, we explored the basis for this specificity using an integrative approach to evaluate vPIC-dependent gene expression combined with promoter occupancy during Kaposi's sarcoma-associated herpesvirus (KSHV) infection. This approach distinguished the direct and indirect targets of the vPIC, ultimately revealing a novel promoter motif critical for KSHV vPIC binding. Additionally, we found that the KSHV vPIC component ORF24 is required for efficient viral DNA replication and identified a ORF24 binding element in the origin of replication that is necessary for late gene promoter activation. Together, these results identify an elusive element that contributes to vPIC specificity and suggest novel links between KSHV DNA replication and late transcription.
Collapse
|
31
|
Kajsík M, Bugala J, Kadličeková V, Szemes T, Turňa J, Drahovská H. Characterization of Dev-CD-23823 and Dev-CT57, new Autographivirinae bacteriophages infecting Cronobacter spp. Arch Virol 2019; 164:1383-1391. [DOI: 10.1007/s00705-019-04202-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/09/2019] [Indexed: 02/04/2023]
|
32
|
Garry DJ, Meyer AJ, Ellefson JW, Bull JJ, Ellington AD. Predicting Evolution of the Transcription Regulatory Network in a Bacteriophage. Genome Biol Evol 2018; 10:2614-2628. [PMID: 30184065 PMCID: PMC6171733 DOI: 10.1093/gbe/evy191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2018] [Indexed: 11/13/2022] Open
Abstract
Prediction of evolutionary trajectories has been an elusive goal, requiring a deep knowledge of underlying mechanisms that relate genotype to phenotype plus understanding how phenotype impacts organismal fitness. We tested our ability to predict molecular regulatory evolution in a bacteriophage (T7) whose RNA polymerase (RNAP) was altered to recognize a heterologous promoter differing by three nucleotides from the wild-type promoter. A mutant of wild-type T7 lacking its RNAP gene was passaged on a bacterial strain providing the novel RNAP in trans. Higher fitness rapidly evolved. Predicting the evolutionary trajectory of this adaptation used measured in vitro transcription rates of the novel RNAP on the six promoter sequences capturing all possible one-step pathways between the wild-type and the heterologous promoter sequences. The predictions captured some of the regulatory evolution but failed both in explaining 1) a set of T7 promoters that consistently failed to evolve and 2) some promoter evolution that fell outside the expected one-step pathways. Had a more comprehensive set of transcription assays been undertaken initially, all promoter evolution would have fallen within predicted bounds, but the lack of evolution in some promoters is unresolved. Overall, this study points toward the increasing feasibility of predicting evolution in well-characterized, simple systems.
Collapse
Affiliation(s)
- Daniel J Garry
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin
| | - Adam J Meyer
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology
| | - Jared W Ellefson
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin
| | - James J Bull
- Center for Computational Biology and Bioinformatics, Department of Integrative Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin
| |
Collapse
|
33
|
Moore CL, Papa LJ, Shoulders MD. A Processive Protein Chimera Introduces Mutations across Defined DNA Regions In Vivo. J Am Chem Soc 2018; 140:11560-11564. [PMID: 29991261 PMCID: PMC6166643 DOI: 10.1021/jacs.8b04001] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Laboratory time scale evolution in vivo relies on the generation of large, mutationally diverse gene libraries to rapidly explore biomolecule sequence landscapes. Traditional global mutagenesis methods are problematic because they introduce many off-target mutations that are often lethal and can engender false positives. We report the development and application of the MutaT7 chimera, a potent and highly targeted in vivo mutagenesis agent. MutaT7 utilizes a DNA-damaging cytidine deaminase fused to a processive RNA polymerase to continuously direct mutations to specific, well-defined DNA regions of any relevant length. MutaT7 thus provides a mechanism for in vivo targeted mutagenesis across multi-kb DNA sequences. MutaT7 should prove useful in diverse organisms, opening the door to new types of in vivo evolution experiments.
Collapse
Affiliation(s)
- Christopher L Moore
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Louis J Papa
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Matthew D Shoulders
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| |
Collapse
|
34
|
|
35
|
Komura R, Aoki W, Motone K, Satomura A, Ueda M. High-throughput evaluation of T7 promoter variants using biased randomization and DNA barcoding. PLoS One 2018; 13:e0196905. [PMID: 29734387 PMCID: PMC5937735 DOI: 10.1371/journal.pone.0196905] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 04/23/2018] [Indexed: 01/09/2023] Open
Abstract
Cis-regulatory elements (CREs) are one of the important factors in controlling gene expression and elucidation of their roles has been attracting great interest. We have developed an improved method for analyzing a large variety of mutant CRE sequences in a simple and high-throughput manner. In our approach, mutant CREs with unique barcode sequences were obtained by biased randomization in a single PCR amplification. The original T7 promoter sequence was randomized by biased randomization, and the target number of base substitutions was set to be within the range of 0 to 5. The DNA library and subsequent transcribed RNA library were sequenced by next generation sequencers (NGS) to quantify transcriptional activity of each mutant. We succeeded in producing a randomized T7 promoter library with high coverage rate at each target number of base substitutions. In a single NGS analysis, we quantified the transcriptional activity of 7847 T7 promoter variants. We confirmed that the bases from -9 to -7 play an important role in the transcriptional activity of the T7 promoter. This information coincides with the previous researches and demonstrated the validity of our methodology. Furthermore, using an in vitro transcription/translation system, we found that transcriptional activities of these T7 variants were well correlated with the resultant protein abundance. We demonstrate that our method enables simple and high-throughput analysis of the effects of various CRE mutations on transcriptional regulation.
Collapse
Affiliation(s)
- Ryo Komura
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Keisuke Motone
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
- Japan Society for the Promotion of Science, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Atsushi Satomura
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
- Japan Society for the Promotion of Science, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| |
Collapse
|
36
|
An Evolutionary/Biochemical Connection between Promoter- and Primer-Dependent Polymerases Revealed by Systematic Evolution of Ligands by Exponential Enrichment. J Bacteriol 2018; 200:JB.00579-17. [PMID: 29339418 DOI: 10.1128/jb.00579-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/11/2018] [Indexed: 01/06/2023] Open
Abstract
DNA polymerases (DNAPs) recognize 3' recessed termini on duplex DNA and carry out nucleotide catalysis. Unlike promoter-specific RNA polymerases (RNAPs), no sequence specificity is required for binding or initiation of catalysis. Despite this, previous results indicate that viral reverse transcriptases bind much more tightly to DNA primers that mimic the polypurine tract. In the current report, primer sequences that bind with high affinity to Taq and Klenow polymerases were identified using a modified systematic evolution of ligands by exponential enrichment (SELEX) approach. Two Taq-specific primers that bound ∼10 (Taq1) and over 100 (Taq2) times more stably than controls to Taq were identified. TaqI contained 8 nucleotides (5'-CACTAAAG-3') that matched the phage T3 RNAP "core" promoter. Both primers dramatically outcompeted primers with similar binding thermodynamics in PCRs. Similarly, exonuclease- Klenow polymerase also selected a high-affinity primer that contained a related core promoter sequence from phage T7 RNAP (5'-ACTATAG-3'). For both Taq and Klenow, even small modifications to the sequence resulted in large losses in binding affinity, suggesting that binding was highly sequence specific. The results are discussed in the context of possible effects on multiprimer (multiplex) PCR assays, molecular information theory, and the evolution of RNAPs and DNAPs.IMPORTANCE This work further demonstrates that primer-dependent DNA polymerases can have strong sequence biases leading to dramatically tighter binding to specific sequences. These may be related to biological function or be a consequence of the structural architecture of the enzyme. New sequence specificity for Taq and Klenow polymerases were uncovered, and among them were sequences that contained the core promoter elements from T3 and T7 phage RNA polymerase promoters. This suggests the intriguing possibility that phage RNA polymerases exploited intrinsic binding affinities of ancestral DNA polymerases to develop their promoters. Conversely, DNA polymerases could have evolved from related RNA polymerases and retained the intrinsic binding preference despite there being no clear function for such a preference in DNA biology.
Collapse
|
37
|
Emery NJ, Majumder S, Liu AP. Synergistic and non-specific nucleic acid production by T7 RNA polymerase and Bsu DNA polymerase catalyzed by single-stranded polynucleotides. Synth Syst Biotechnol 2018; 3:130-134. [PMID: 29900426 PMCID: PMC5995454 DOI: 10.1016/j.synbio.2018.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/21/2018] [Accepted: 02/24/2018] [Indexed: 11/18/2022] Open
Abstract
Point-of-care molecular diagnostic tests show great promise for providing accurate, timely results in low-infrastructure healthcare settings and at home. The design space for these tests is limited by a variety of possible background reactions, which often originate from relatively weak promiscuous activities of the enzymes used for nucleic acid amplification. When this background signal is amplified alongside the signal of the intended biomarker, the dynamic range of the test can be severely compromised. Therefore, a detailed knowledge of potential side reactions arising from enzyme promiscuity can improve rational design of point-of-care molecular diagnostic tests. Towards this end, we report a previously unknown synergistic reaction between T7 RNA polymerase and Bsu DNA polymerase that produces nucleic acid in the presence of single-stranded DNA or RNA. This reaction occurs in the absence of any previously reported substrates for either polymerases and compromises a theoretical microRNA amplification scheme utilizing these polymerases.
Collapse
Affiliation(s)
- Nicholas J. Emery
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Sagardip Majumder
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, United States
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
- Biophysics Program, University of Michigan, Ann Arbor, MI, United States
- Corresponding author. Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, United States.
| |
Collapse
|
38
|
Synthetic biology for microbial heavy metal biosensors. Anal Bioanal Chem 2017; 410:1191-1203. [DOI: 10.1007/s00216-017-0751-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 10/23/2017] [Accepted: 11/07/2017] [Indexed: 11/26/2022]
|
39
|
Novel T7-like expression systems used for Halomonas. Metab Eng 2017; 39:128-140. [DOI: 10.1016/j.ymben.2016.11.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 10/21/2016] [Accepted: 11/21/2016] [Indexed: 12/27/2022]
|
40
|
Bohne AV, Teubner M, Liere K, Weihe A, Börner T. In vitro promoter recognition by the catalytic subunit of plant phage-type RNA polymerases. PLANT MOLECULAR BIOLOGY 2016; 92:357-369. [PMID: 27497992 PMCID: PMC5040748 DOI: 10.1007/s11103-016-0518-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 07/20/2016] [Indexed: 06/06/2023]
Abstract
We identified sequence motifs, which enhance or reduce the ability of the Arabidopsis phage-type RNA polymerases RPOTm (mitochondrial RNAP), RPOTp (plastidial RNAP), and RPOTmp (active in both organelles) to recognize their promoters in vitro with help of a 'specificity loop'. The importance of this data for the evolution and function of the organellar RNA polymerases is discussed. The single-subunit RNA polymerase (RNAP) of bacteriophage T7 is able to perform all steps of transcription without additional transcription factors. Dicotyledonous plants possess three phage-type RNAPs, RPOTm-the mitochondrial RNAP, RPOTp-the plastidial RNAP, and RPOTmp-an RNAP active in both organelles. RPOTm and RPOTp, like the T7 polymerase, are able to recognize promoters, while RPOTmp displays no significant promoter specificity in vitro. To find out which promoter motifs are crucial for recognition by the polymerases we performed in vitro transcription assays with recombinant Arabidopsis RPOTm and RPOTp enzymes. By comparing different truncated and mutagenized promoter constructs, we observed the same minimal promoter sequence supposed to be needed in vivo for transcription initiation. Moreover, we identified elements of core and flanking sequences, which are of critical importance for promoter recognition and activity in vitro. We further intended to reveal why RPOTmp does not efficiently recognize promoters in vitro and if promoter recognition is based on a structurally defined specificity loop of the plant enzymes as described for the yeast and T7 RNAPs. Interestingly, the exchange of only three amino acids within the putative specificity loop of RPOTmp enabled the enzyme for specific promoter transcription in vitro. Thus, also in plant phage-type RNAPs the specificity loop is engaged in promoter recognition. The results are discussed with respect to their relevance for transcription in organello and to the evolution of RPOT enzymes including the divergence of their functions.
Collapse
Affiliation(s)
- Alexandra-Viola Bohne
- Institute of Biology, Humboldt University, Philippstr.13, Rhoda Erdmann Haus, 10115, Berlin, Germany
- Molecular Plant Sciences, Ludwig-Maximillians-University, Grosshaderner Str. 2-4, 82152, Planegg-Martinsried, Germany
| | - Marlene Teubner
- Institute of Biology, Humboldt University, Philippstr.13, Rhoda Erdmann Haus, 10115, Berlin, Germany
| | - Karsten Liere
- Institute of Biology, Humboldt University, Philippstr.13, Rhoda Erdmann Haus, 10115, Berlin, Germany
- SMB Services in Molecular Biology GmbH, Rudolf-Breitscheidstr. 70, 15562, Rüdersdorf, Germany
| | - Andreas Weihe
- Institute of Biology, Humboldt University, Philippstr.13, Rhoda Erdmann Haus, 10115, Berlin, Germany
| | - Thomas Börner
- Institute of Biology, Humboldt University, Philippstr.13, Rhoda Erdmann Haus, 10115, Berlin, Germany.
| |
Collapse
|
41
|
Promoter and Terminator Discovery and Engineering. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:21-44. [PMID: 27277391 DOI: 10.1007/10_2016_8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Control of gene expression is crucial to optimize metabolic pathways and synthetic gene networks. Promoters and terminators are stretches of DNA upstream and downstream (respectively) of genes that control both the rate at which the gene is transcribed and the rate at which mRNA is degraded. As a result, both of these elements control net protein expression from a synthetic construct. Thus, it is highly important to discover and engineer promoters and terminators with desired characteristics. This chapter highlights various approaches taken to catalogue these important synthetic elements. Specifically, early strategies have focused largely on semi-rational techniques such as saturation mutagenesis to diversify native promoters and terminators. Next, in an effort to reduce the length of the synthetic biology design cycle, efforts in the field have turned towards the rational design of synthetic promoters and terminators. In this vein, we cover recently developed methods such as hybrid engineering, high throughput characterization, and thermodynamic modeling which allow finer control in the rational design of novel promoters and terminators. Emphasis is placed on the methodologies used and this chapter showcases the utility of these methods across multiple host organisms.
Collapse
|
42
|
Da LT, E C, Duan B, Zhang C, Zhou X, Yu J. A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation. PLoS Comput Biol 2015; 11:e1004624. [PMID: 26599007 PMCID: PMC4658072 DOI: 10.1371/journal.pcbi.1004624] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/26/2015] [Indexed: 11/18/2022] Open
Abstract
Pyrophosphate ion (PPi) release during transcription elongation is a signature step in each nucleotide addition cycle. The kinetics and energetics of the process as well as how it proceeds with substantial conformational changes of the polymerase complex determine the mechano-chemical coupling mechanism of the transcription elongation. Here we investigated detailed dynamics of the PPi release process in a single-subunit RNA polymerase (RNAP) from bacteriophage T7, implementing all-atom molecular dynamics (MD) simulations. We obtained a jump-from-cavity kinetic model of the PPi release utilizing extensive nanosecond MD simulations. We found that the PPi release in T7 RNAP is initiated by the PPi dissociation from two catalytic aspartic acids, followed by a comparatively slow jump-from-cavity activation process. Combining with a number of microsecond long MD simulations, we also found that the activation process is hindered by charged residue associations as well as by local steric and hydrogen bond interactions. On the other hand, the activation is greatly assisted by a highly flexible lysine residue Lys472 that swings its side chain to pull PPi out. The mechanism can apply in general to single subunit RNA and DNA polymerases with similar molecular structures and conserved key residues. Remarkably, the flexible lysine or arginine residue appears to be a universal module that assists the PPi release even in multi-subunit RNAPs with charge facilitated hopping mechanisms. We also noticed that the PPi release is not tightly coupled to opening motions of an O-helix on the fingers domain of T7 RNAP according to the microsecond MD simulations. Our study thus supports the Brownian ratchet scenario of the mechano-chemical coupling in the transcription elongation of the single-subunit polymerase.
Collapse
Affiliation(s)
- Lin-Tai Da
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, United States of America
| | - Chao E
- Beijing Computational Science Research Center, Beijing, China
| | - Baogen Duan
- Beijing Computational Science Research Center, Beijing, China
| | - Chuanbiao Zhang
- School of Physics, University of the Chinese Academy of Sciences, Beijing, China
| | - Xin Zhou
- School of Physics, University of the Chinese Academy of Sciences, Beijing, China
| | - Jin Yu
- Beijing Computational Science Research Center, Beijing, China
- * E-mail:
| |
Collapse
|
43
|
Meyer AJ, Ellefson JW, Ellington AD. Directed Evolution of a Panel of Orthogonal T7 RNA Polymerase Variants for in Vivo or in Vitro Synthetic Circuitry. ACS Synth Biol 2015; 4:1070-6. [PMID: 25279711 DOI: 10.1021/sb500299c] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
T7 RNA polymerase is the foundation of synthetic biological circuitry both in vivo and in vitro due to its robust and specific control of transcription from its cognate promoter. Here we present the directed evolution of a panel of orthogonal T7 RNA polymerase:promoter pairs that each specifically recognizes a synthetic promoter. These newly described pairs can be used to independently control up to six circuits in parallel.
Collapse
Affiliation(s)
- Adam J. Meyer
- Institute for Cellular and Molecular Biology, ‡Department of Chemistry and Biochemistry, and §Center for Systems & Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jared W. Ellefson
- Institute for Cellular and Molecular Biology, ‡Department of Chemistry and Biochemistry, and §Center for Systems & Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew D. Ellington
- Institute for Cellular and Molecular Biology, ‡Department of Chemistry and Biochemistry, and §Center for Systems & Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
44
|
Lenneman BR, Rothman-Denes LB. Structural and biochemical investigation of bacteriophage N4-encoded RNA polymerases. Biomolecules 2015; 5:647-67. [PMID: 25924224 PMCID: PMC4496689 DOI: 10.3390/biom5020647] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 04/01/2015] [Accepted: 04/13/2015] [Indexed: 11/16/2022] Open
Abstract
Bacteriophage N4 regulates the temporal expression of its genome through the activity of three distinct RNA polymerases (RNAP). Expression of the early genes is carried out by a phage-encoded, virion-encapsidated RNAP (vRNAP) that is injected into the host at the onset of infection and transcribes the early genes. These encode the components of new transcriptional machinery (N4 RNAPII and cofactors) responsible for the synthesis of middle RNAs. Both N4 RNAPs belong to the T7-like "single-subunit" family of polymerases. Herein, we describe their mechanisms of promoter recognition, regulation, and roles in the phage life cycle.
Collapse
Affiliation(s)
- Bryan R Lenneman
- Committee on Genetics, Genomics, and Systems Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
| | - Lucia B Rothman-Denes
- Committee on Genetics, Genomics, and Systems Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
| |
Collapse
|
45
|
Morozov YI, Parshin AV, Agaronyan K, Cheung ACM, Anikin M, Cramer P, Temiakov D. A model for transcription initiation in human mitochondria. Nucleic Acids Res 2015; 43:3726-35. [PMID: 25800739 PMCID: PMC4402542 DOI: 10.1093/nar/gkv235] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/08/2015] [Indexed: 01/10/2023] Open
Abstract
Regulation of transcription of mtDNA is thought to be crucial for maintenance of redox potential and vitality of the cell but is poorly understood at the molecular level. In this study we mapped the binding sites of the core transcription initiation factors TFAM and TFB2M on human mitochondrial RNA polymerase, and interactions of the latter with promoter DNA. This allowed us to construct a detailed structural model, which displays a remarkable level of interaction between the components of the initiation complex (IC). The architecture of the mitochondrial IC suggests mechanisms of promoter binding and recognition that are distinct from the mechanisms found in RNAPs operating in all domains of life, and illuminates strategies of transcription regulation developed at the very early stages of evolution of gene expression.
Collapse
Affiliation(s)
- Yaroslav I Morozov
- Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Dr., Stratford, NJ 08084, USA
| | - Andrey V Parshin
- Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Dr., Stratford, NJ 08084, USA
| | - Karen Agaronyan
- Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Dr., Stratford, NJ 08084, USA
| | - Alan C M Cheung
- Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Michael Anikin
- Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Dr., Stratford, NJ 08084, USA
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Gottingen, Germany
| | - Dmitry Temiakov
- Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Dr., Stratford, NJ 08084, USA
| |
Collapse
|
46
|
Jung HI, Yan J, Zhai Z, Vatamaniuk OK. Gene functional analysis using protoplast transient assays. Methods Mol Biol 2015; 1284:433-452. [PMID: 25757786 DOI: 10.1007/978-1-4939-2444-8_22] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The protoplast transient assay system has been widely used for rapid functional analyses of genes using cellular and biochemical approaches. This system has been increasingly employed for functional genetic studies using double-stranded (ds) RNA interference (RNAi). Here, we describe a modified procedure for the isolation of protoplasts from leaf mesophyll cells of 14-day-old Arabidopsis thaliana. This modification significantly simplifies and speeds up functional studies without compromising the yield and the viability of protoplasts. We also present the procedure for the isolation and transfection of protoplasts from mesophyll cells of an emerging model grass species, Brachypodium distachyon. Further, we detail procedures for RNAi-based functional studies of genes using transient expression of in vitro synthesized dsRNA in protoplasts.
Collapse
Affiliation(s)
- Ha-il Jung
- Department of Crop and Soil Sciences, Cornell University, Ithaca, NY, 14853, USA
| | | | | | | |
Collapse
|
47
|
Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution. Proc Natl Acad Sci U S A 2013; 110:9007-12. [PMID: 23674678 DOI: 10.1073/pnas.1220670110] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
To what extent are evolutionary outcomes determined by a population's recent environment, and to what extent do they depend on historical contingency and random chance? Here we apply a unique experimental system to investigate evolutionary reproducibility and path dependence at the protein level. We combined phage-assisted continuous evolution with high-throughput sequencing to analyze evolving protein populations as they adapted to divergent and then convergent selection pressures over hundreds of generations. Independent populations of T7 RNA polymerase genes were subjected to one of two selection histories ("pathways") demanding recognition of distinct intermediate promoters followed by a common final promoter. We observed distinct classes of solutions with unequal phenotypic activity and evolutionary potential evolve from the two pathways, as well as from replicate populations exposed to identical selection conditions. Mutational analysis revealed specific epistatic interactions that explained the observed path dependence and irreproducibility. Our results reveal in molecular detail how protein adaptation to different environments, as well as stochasticity among populations evolved in the same environment, can both generate evolutionary outcomes that preclude subsequent convergence.
Collapse
|
48
|
Library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants. Proc Natl Acad Sci U S A 2013; 110:5028-33. [PMID: 23479654 DOI: 10.1073/pnas.1220157110] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The construction of synthetic gene circuits relies on our ability to engineer regulatory architectures that are orthogonal to the host's native regulatory pathways. However, as synthetic gene circuits become larger and more complicated, we are limited by the small number of parts, especially transcription factors, that work well in the context of the circuit. The current repertoire of transcription factors consists of a limited selection of activators and repressors, making the implementation of transcriptional logic a complicated and component-intensive process. To address this, we modified bacteriophage T7 RNA polymerase (T7 RNAP) to create a library of transcriptional AND gates for use in Escherichia coli by first splitting the protein and then mutating the DNA recognition domain of the C-terminal fragment to alter its promoter specificity. We first demonstrate that split T7 RNAP is active in vivo and compare it with full-length enzyme. We then create a library of mutant split T7 RNAPs that have a range of activities when used in combination with a complimentary set of altered T7-specific promoters. Finally, we assay the two-input function of both wild-type and mutant split T7 RNAPs and find that regulated expression of the N- and C-terminal fragments of the split T7 RNAPs creates AND logic in each case. This work demonstrates that mutant split T7 RNAP can be used as a transcriptional AND gate and introduces a unique library of components for use in synthetic gene circuits.
Collapse
|
49
|
Stevens DC, Hari TPA, Boddy CN. The role of transcription in heterologous expression of polyketides in bacterial hosts. Nat Prod Rep 2013; 30:1391-411. [DOI: 10.1039/c3np70060g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
50
|
Paul S, Stang A, Lennartz K, Tenbusch M, Überla K. Selection of a T7 promoter mutant with enhanced in vitro activity by a novel multi-copy bead display approach for in vitro evolution. Nucleic Acids Res 2012; 41:e29. [PMID: 23074193 PMCID: PMC3592457 DOI: 10.1093/nar/gks940] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In vitro evolution of nucleic acids and proteins is a powerful strategy to optimize their biological and physical properties. To select proteins with the desired phenotype from large gene libraries, the proteins need to be linked to the gene they are encoded by. To facilitate selection of the desired phenotype and isolation of the encoding DNA, a novel bead display approach was developed, in which each member of a library of beads is first linked to multiple copies of a clonal gene variant by emulsion polymerase chain reaction. Beads are transferred to a second emulsion for an in vitro transcription-translation reaction, in which the protein encoded by each bead's amplicon covalently binds to the bead present in the same picoliter reactor. The beads then contain multiple copies of a clonal gene variant and multiple molecules of the protein encoded by the bead's gene variant and serve as the unit of selection. As a proof of concept, we screened a randomized library of the T7 promoter for high expression levels by flow cytometry and identified a T7 promoter variant with an ~10-fold higher in vitro transcriptional activity, confirming that the multi-copy bead display approach can be efficiently applied to in vitro evolution.
Collapse
Affiliation(s)
- Siddhartha Paul
- Department of Molecular and Medical Virology, Ruhr-University Bochum, D-44780 Bochum, Germany
| | | | | | | | | |
Collapse
|