1
|
Heel SV, Breuker K. Investigating the Intramolecular Competition of Different RNA Binding Motifs for Neomycin B by Native Top-Down Mass Spectrometry. Chempluschem 2024; 89:e202400178. [PMID: 38758051 DOI: 10.1002/cplu.202400178] [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: 03/06/2024] [Revised: 04/13/2024] [Indexed: 05/18/2024]
Abstract
The ongoing search for small molecule drugs that target ribonucleic acids (RNA) is complicated by a limited understanding of the principles that govern RNA-small molecule interactions. Here we have used stoichiometry-resolved native top-down mass spectrometry (MS) to study the binding of neomycin B to small model hairpin RNAs, an unstructured RNA, and a viral RNA construct. For 15-22 nt model RNAs with hairpin structure, we found that neomycin B binding to hairpin loops relies on interactions with both the nucleobases and the 2'-OH groups, and that a simple 5' or 3' overhang can introduce an additional binding motif. For a 47 nt RNA construct derived from stem IA of the human immunodeficiency virus 1 (HIV-1) rev response element (RRE) RNA, native top-down MS identified four different binding motifs, of which the purine-rich internal loop showed the highest affinity for neomycin B. Stoichiometry-resolved binding site mapping by native top-down MS allows for a new perspective on binding specificity, and has the potential to reveal unexpected principles of small molecule binding to RNA.
Collapse
Affiliation(s)
- Sarah Viola Heel
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| |
Collapse
|
2
|
Eerlings R, Gupta P, Lee XY, Nguyen T, El Kharraz S, Handle F, Smeets E, Moris L, Devlies W, Vandewinkel B, Thiry I, Ta DT, Gorkovskiy A, Voordeckers K, Henckaerts E, Pinheiro VB, Claessens F, Verstrepen KJ, Voet A, Helsen C. Rational evolution for altering the ligand preference of estrogen receptor alpha. Protein Sci 2024; 33:e4940. [PMID: 38511482 PMCID: PMC10955623 DOI: 10.1002/pro.4940] [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: 11/02/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 03/22/2024]
Abstract
Estrogen receptor α is commonly used in synthetic biology to control the activity of genome editing tools. The activating ligands, estrogens, however, interfere with various cellular processes, thereby limiting the applicability of this receptor. Altering its ligand preference to chemicals of choice solves this hurdle but requires adaptation of unspecified ligand-interacting residues. Here, we provide a solution by combining rational protein design with multi-site-directed mutagenesis and directed evolution of stably integrated variants in Saccharomyces cerevisiae. This method yielded an estrogen receptor variant, named TERRA, that lost its estrogen responsiveness and became activated by tamoxifen, an anti-estrogenic drug used for breast cancer treatment. This tamoxifen preference of TERRA was maintained in mammalian cells and mice, even when fused to Cre recombinase, expanding the mammalian synthetic biology toolbox. Not only is our platform transferable to engineer ligand preference of any steroid receptor, it can also profile drug-resistance landscapes for steroid receptor-targeted therapies.
Collapse
Affiliation(s)
- Roy Eerlings
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
- Laboratory of Systems BiologyVIB‐KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2SKU LeuvenHeverleeBelgium
| | - Purvi Gupta
- Laboratory of Biomolecular Modelling and Design, Department of ChemistryKU LeuvenHeverleeBelgium
| | - Xiao Yin Lee
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Tien Nguyen
- Laboratory of Biomolecular Modelling and Design, Department of ChemistryKU LeuvenHeverleeBelgium
| | - Sarah El Kharraz
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Florian Handle
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Elien Smeets
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Lisa Moris
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
- Department of UrologyUniversity Hospitals LeuvenLeuvenBelgium
| | - Wout Devlies
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
- Department of UrologyUniversity Hospitals LeuvenLeuvenBelgium
| | - Bram Vandewinkel
- Laboratory of Viral Cell Biology and Therapeutics, Department of Cellular and Molecular Medicine, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Irina Thiry
- Laboratory of Viral Cell Biology and Therapeutics, Department of Cellular and Molecular Medicine, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Duy Tien Ta
- Laboratory of Viral Cell Biology and Therapeutics, Department of Cellular and Molecular Medicine, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Anton Gorkovskiy
- Laboratory of Systems BiologyVIB‐KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2SKU LeuvenHeverleeBelgium
| | - Karin Voordeckers
- Laboratory of Systems BiologyVIB‐KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2SKU LeuvenHeverleeBelgium
| | - Els Henckaerts
- Laboratory of Viral Cell Biology and Therapeutics, Department of Cellular and Molecular Medicine, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Vitor B. Pinheiro
- KU Leuven, Department of Pharmaceutical and Pharmacological SciencesRega Institute for Medical ResearchLeuvenBelgium
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Kevin J. Verstrepen
- Laboratory of Systems BiologyVIB‐KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2SKU LeuvenHeverleeBelgium
| | - Arnout Voet
- Laboratory of Biomolecular Modelling and Design, Department of ChemistryKU LeuvenHeverleeBelgium
| | - Christine Helsen
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| |
Collapse
|
3
|
Eisenhut P, Marx N, Borsi G, Papež M, Ruggeri C, Baumann M, Borth N. Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control. N Biotechnol 2024; 79:1-19. [PMID: 38040288 DOI: 10.1016/j.nbt.2023.11.003] [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] [Received: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mammalian cells have developed dedicated molecular mechanisms to tightly control expression levels of their genes where the specific transcriptomic signature across all genes eventually determines the cell's phenotype. Modulating cellular phenotypes is of major interest to study their role in disease or to reprogram cells for the manufacturing of recombinant products, such as biopharmaceuticals. Cells of mammalian origin, for example Chinese hamster ovary (CHO) and Human embryonic kidney 293 (HEK293) cells, are most commonly employed to produce therapeutic proteins. Early genetic engineering approaches to alter their phenotype have often been attempted by "uncontrolled" overexpression or knock-down/-out of specific genetic factors. Many studies in the past years, however, highlight that rationally regulating and fine-tuning the strength of overexpression or knock-down to an optimum level, can adjust phenotypic traits with much more precision than such "uncontrolled" approaches. To this end, synthetic biology tools have been generated that enable (fine-)tunable and/or inducible control of gene expression. In this review, we discuss various molecular tools used in mammalian cell lines and group them by their mode of action: transcriptional, post-transcriptional, translational and post-translational regulation. We discuss the advantages and disadvantages of using these tools for each cell regulatory layer and with respect to cell line engineering approaches. This review highlights the plethora of synthetic toolboxes that could be employed, alone or in combination, to optimize cellular systems and eventually gain enhanced control over the cellular phenotype to equip mammalian cell factories with the tools required for efficient production of emerging, more difficult-to-express biologics formats.
Collapse
Affiliation(s)
- Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
| | - Giulia Borsi
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Caterina Ruggeri
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
| |
Collapse
|
4
|
Zhu J, Wang B, Zhang Y, Wei T, Gao T. Living electrochemical biosensing: Engineered electroactive bacteria for biosensor development and the emerging trends. Biosens Bioelectron 2023; 237:115480. [PMID: 37379794 DOI: 10.1016/j.bios.2023.115480] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/30/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Bioelectrical interfaces made of living electroactive bacteria (EAB) provide a unique opportunity to bridge biotic and abiotic systems, enabling the reprogramming of electrochemical biosensing. To develop these biosensors, principles from synthetic biology and electrode materials are being combined to engineer EAB as dynamic and responsive transducers with emerging, programmable functionalities. This review discusses the bioengineering of EAB to design active sensing parts and electrically connective interfaces on electrodes, which can be applied to construct smart electrochemical biosensors. In detail, by revisiting the electron transfer mechanism of electroactive microorganisms, engineering strategies of EAB cells for biotargets recognition, sensing circuit construction, and electrical signal routing, engineered EAB have demonstrated impressive capabilities in designing active sensing elements and developing electrically conductive interfaces on electrodes. Thus, integration of engineered EAB into electrochemical biosensors presents a promising avenue for advancing bioelectronics research. These hybridized systems equipped with engineered EAB can promote the field of electrochemical biosensing, with applications in environmental monitoring, health monitoring, green manufacturing, and other analytical fields. Finally, this review considers the prospects and challenges of the development of EAB-based electrochemical biosensors, identifying potential future applications.
Collapse
Affiliation(s)
- Jin Zhu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China
| | - Baoguo Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China
| | - Yixin Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China
| | - Tianxiang Wei
- School of Environment, Nanjing Normal University, Nanjing, 210023, PR China
| | - Tao Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China.
| |
Collapse
|
5
|
Wang Y, Liu Y, Wang LL, Zhang QL, Xu L. Integrating Ligands into Nucleic Acid Systems. Chembiochem 2023; 24:e202300292. [PMID: 37401635 DOI: 10.1002/cbic.202300292] [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] [Received: 04/11/2023] [Revised: 06/12/2023] [Accepted: 07/04/2023] [Indexed: 07/05/2023]
Abstract
Signal transduction from non-nucleic acid ligands (small molecules and proteins) to structural changes of nucleic acids plays a crucial role in both biomedical analysis and cellular regulations. However, how to bridge between these two types of molecules without compromising the expandable complexity and programmability of the nucleic acid nanomachines is a critical challenge. Compared with the previously most widely applied transduction strategies, we review the latest advances of a kinetically controlled approach for ligand-oligonucleotide transduction in this Concept article. This new design works through an intrinsic conformational alteration of the nucleic acid aptamer upon the ligand binding as a governing factor for nucleic acid strand displacement reactions. The functionalities and applications of this transduction system as a ligand converter on biosensing and DNA computation are described and discussed. Furthermore, we propose some potential scenarios for utilization of this ligand transduction design to regulate gene expression through synthetic RNA switches in the cellular contexts. Finally, future perspectives regarding this ligand-oligonucleotide transduction platform are also discussed.
Collapse
Affiliation(s)
- Yang Wang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging National-Regional Key Technology Engineering Laboratory for Medical Ultrasound School of Biomedical Engineering, School of Medicine, Shenzhen, 518060, China
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yan Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Liang-Liang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qiu-Long Zhang
- School of Pharmacy and Medical Technology, Putian University, Putian, 351100, Fujian, China
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| |
Collapse
|
6
|
Liu S, Yu JM, Gan YC, Qiu XZ, Gao ZC, Wang H, Chen SX, Xiong Y, Liu GH, Lin SE, McCarthy A, John JV, Wei DX, Hou HH. Biomimetic natural biomaterials for tissue engineering and regenerative medicine: new biosynthesis methods, recent advances, and emerging applications. Mil Med Res 2023; 10:16. [PMID: 36978167 PMCID: PMC10047482 DOI: 10.1186/s40779-023-00448-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 02/23/2023] [Indexed: 03/30/2023] Open
Abstract
Biomimetic materials have emerged as attractive and competitive alternatives for tissue engineering (TE) and regenerative medicine. In contrast to conventional biomaterials or synthetic materials, biomimetic scaffolds based on natural biomaterial can offer cells a broad spectrum of biochemical and biophysical cues that mimic the in vivo extracellular matrix (ECM). Additionally, such materials have mechanical adaptability, microstructure interconnectivity, and inherent bioactivity, making them ideal for the design of living implants for specific applications in TE and regenerative medicine. This paper provides an overview for recent progress of biomimetic natural biomaterials (BNBMs), including advances in their preparation, functionality, potential applications and future challenges. We highlight recent advances in the fabrication of BNBMs and outline general strategies for functionalizing and tailoring the BNBMs with various biological and physicochemical characteristics of native ECM. Moreover, we offer an overview of recent key advances in the functionalization and applications of versatile BNBMs for TE applications. Finally, we conclude by offering our perspective on open challenges and future developments in this rapidly-evolving field.
Collapse
Affiliation(s)
- Shuai Liu
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, The Fifth Affiliated Hospital, School of Basic Medical Science, Southern Medical University, Guangzhou, 510900, China
| | - Jiang-Ming Yu
- Department of Orthopedics, Tongren Hospital, Shanghai Jiao Tong University, Shanghai, 200336, China
| | - Yan-Chang Gan
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, The Fifth Affiliated Hospital, School of Basic Medical Science, Southern Medical University, Guangzhou, 510900, China
| | - Xiao-Zhong Qiu
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, The Fifth Affiliated Hospital, School of Basic Medical Science, Southern Medical University, Guangzhou, 510900, China
| | - Zhe-Chen Gao
- Department of Orthopedics, Tongren Hospital, Shanghai Jiao Tong University, Shanghai, 200336, China
| | - Huan Wang
- The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518033, Guangdong, China.
| | - Shi-Xuan Chen
- Engineering Research Center of Clinical Functional Materials and Diagnosis & Treatment Devices of Zhejiang Province, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, Zhejiang, China.
| | - Yuan Xiong
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Guo-Hui Liu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Si-En Lin
- Department of Orthopaedics and Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Alec McCarthy
- Department of Functional Materials, Terasaki Institute for Biomedical Innovation, Los Angeles, CA, 90064, USA
| | - Johnson V John
- Mary & Dick Holland Regenerative Medicine Program, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68130, USA
| | - Dai-Xu Wei
- Department of Orthopedics, Tongren Hospital, Shanghai Jiao Tong University, Shanghai, 200336, China.
- Zigong Affiliated Hospital of Southwest Medical University, Zigong Psychiatric Research Center, Zigong Institute of Brain Science, Zigong, 643002, Sichuan, China.
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Department of Life Sciences and Medicine, Northwest University, Xi'an, 710127, China.
| | - Hong-Hao Hou
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, The Fifth Affiliated Hospital, School of Basic Medical Science, Southern Medical University, Guangzhou, 510900, China.
| |
Collapse
|
7
|
Garner AL. Contemporary Progress and Opportunities in RNA-Targeted Drug Discovery. ACS Med Chem Lett 2023; 14:251-259. [PMID: 36923915 PMCID: PMC10009794 DOI: 10.1021/acsmedchemlett.3c00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
The surprising discovery that RNAs are the predominant gene products to emerge from the human genome catalyzed a renaissance in RNA biology. It is now well-understood that RNAs act as more than just a messenger and comprise a large and diverse family of ribonucleic acids of differing sizes, structures, and functions. RNAs play expansive roles in the cell, contributing to the regulation and fine-tuning of nearly all aspects of gene expression and genome architecture. In line with the significance of these functions, we have witnessed an explosion in discoveries connecting RNAs with a variety of human diseases. Consequently, the targeting of RNAs, and more broadly RNA biology, has emerged as an untapped area of drug discovery, making the search for RNA-targeted therapeutics of great interest. In this Microperspective, I highlight contemporary learnings in the field and present my views on how to catapult us toward the systematic discovery of RNA-targeted medicines.
Collapse
Affiliation(s)
- Amanda L. Garner
- Department of Medicinal Chemistry,
College of Pharmacy, University of Michigan, 1600 Huron Parkway, NCRC B520, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
8
|
Kelvin D, Suess B. Tapping the potential of synthetic riboswitches: reviewing the versatility of the tetracycline aptamer. RNA Biol 2023; 20:457-468. [PMID: 37459466 DOI: 10.1080/15476286.2023.2234732] [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] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/20/2023] Open
Abstract
Synthetic riboswitches are a versatile class of regulatory elements that are becoming increasingly established in synthetic biology applications. They are characterized by their compact size and independence from auxiliary protein factors. While naturally occurring riboswitches were mostly discovered in bacteria, synthetic riboswitches have been designed for all domains of life. Published design strategies far exceed the number of riboswitches found in nature. A core element of any riboswitch is a binding domain, called an aptamer, which is characterized by high specificity and affinity for its ligand. Aptamers can be selected de novo, allowing the design of synthetic riboswitches against a broad spectrum of targets. The tetracycline aptamer has proven to be well suited for riboswitch engineering. Since its selection, it has been used in a variety of applications and is considered to be well established and characterized. Using the tetracycline aptamer as an example, we aim to discuss a large variety of design approaches for synthetic riboswitch engineering and their application. We aim to demonstrate the versatility of riboswitches in general and the high potential of synthetic RNA devices for creating new solutions in both the scientific and medical fields.
Collapse
Affiliation(s)
- Daniel Kelvin
- Fachbereich Biologie, TU Darmstadt, Darmstadt, Germany
| | - Beatrix Suess
- Fachbereich Biologie, TU Darmstadt, Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, Darmstadt, Germany
| |
Collapse
|
9
|
Hoetzel J, Suess B. Structural changes in aptamers are essential for synthetic riboswitch engineering. J Mol Biol 2022; 434:167631. [PMID: 35595164 DOI: 10.1016/j.jmb.2022.167631] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 11/19/2022]
Abstract
Synthetic riboswitches are powerful tools in synthetic biology in which sensing and execution are consolidated in a single RNA molecule. By using SELEX to select aptamers in vitro, synthetic riboswitches can in theory be engineered against any ligand of choice. Surprisingly, very few in vitro selected aptamers have been used for the engineering of synthetic riboswitches. In-depth studies of these aptamers suggest that the key characteristics of such regulatory active RNAs are their structural switching abilities and their binding dynamics. Conventional SELEX approaches seem to be inadequate to select for these characteristics, which may explain the lack of in vitro selected aptamers suited for engineering of synthetic riboswitches. In this review, we explore the functional principles of synthetic riboswitches, identify key characteristics of regulatory active in vitro selected aptamers and integrate these findings in context with available in vitro selection methods. Based on these insights, we propose to use a combination of capture-SELEX and subsequent functional screening for a more successful in vitro selection of aptamers that can be applied for the engineering of synthetic riboswitches.
Collapse
Affiliation(s)
- Janis Hoetzel
- Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany. https://www.twitter.com/J_Hoetzel
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany; Center for Synthetic Biology, Technical University of Darmstadt, Germany.
| |
Collapse
|
10
|
Synthetic RNA-based post-transcriptional expression control methods and genetic circuits. Adv Drug Deliv Rev 2022; 184:114196. [PMID: 35288218 DOI: 10.1016/j.addr.2022.114196] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/27/2022] [Accepted: 03/08/2022] [Indexed: 12/19/2022]
Abstract
RNA-based synthetic genetic circuits provide an alternative for traditional transcription-based circuits in applications where genomic integration is to be avoided. Incorporating various post-transcriptional control methods into such circuits allows for controlling the behaviour of the circuit through the detection of certain biomolecular inputs or reconstituting defined circuit behaviours, thus manipulating cellular functions. In this review, recent developments of various types of post-transcriptional control methods in mammalian cells are discussed as well as auxiliary components that allow for the creation and development of mRNA-based switches. How such post-transcriptional switches are combined into synthetic circuits as well as their applications in biomedical and preclinical settings are also described. Finally, we examine the challenges that need to be surmounted before RNA-based synthetic circuits can be reliably deployed into clinical settings.
Collapse
|
11
|
Climent-Catala A, Ouldridge TE, Stan GBV, Bae W. Building an RNA-Based Toggle Switch Using Inhibitory RNA Aptamers. ACS Synth Biol 2022; 11:562-569. [PMID: 35133150 PMCID: PMC9007568 DOI: 10.1021/acssynbio.1c00580] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Synthetic
RNA systems offer unique advantages such as faster response,
increased specificity, and programmability compared to conventional
protein-based networks. Here, we demonstrate an in vitro RNA-based toggle switch using RNA aptamers capable of inhibiting
the transcriptional activity of T7 or SP6 RNA polymerases. The activities
of both polymerases are monitored simultaneously by using Broccoli
and malachite green light-up aptamer systems. In our toggle switch,
a T7 promoter drives the expression of SP6 inhibitory aptamers, and
an SP6 promoter expresses T7 inhibitory aptamers. We show that the
two distinct states originating from the mutual inhibition of aptamers
can be toggled by adding DNA sequences to sequester the RNA inhibitory
aptamers. Finally, we assessed our RNA-based toggle switch in degrading
conditions by introducing controlled degradation of RNAs using a mix
of RNases. Our results demonstrate that the RNA-based toggle switch
could be used as a control element for nucleic acid networks in synthetic
biology applications.
Collapse
Affiliation(s)
- Alicia Climent-Catala
- Imperial College Centre for Synthetic Biology, London, SW7 2AZ, U.K
- Department of Chemistry, Imperial College London, London, SW7 2AZ, U.K
| | - Thomas E. Ouldridge
- Imperial College Centre for Synthetic Biology, London, SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, U.K
| | - Guy-Bart V. Stan
- Imperial College Centre for Synthetic Biology, London, SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, U.K
| | - Wooli Bae
- Imperial College Centre for Synthetic Biology, London, SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, U.K
| |
Collapse
|
12
|
Lazar JT, Tabor JJ. Bacterial two-component systems as sensors for synthetic biology applications. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:100398. [PMID: 34917859 PMCID: PMC8670732 DOI: 10.1016/j.coisb.2021.100398] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Two-component systems (TCSs) are a ubiquitous family of signal transduction pathways that enable bacteria to sense and respond to diverse physical, chemical, and biological stimuli outside and inside the cell. Synthetic biologists have begun to repurpose TCSs for applications in optogenetics, materials science, gut microbiome engineering, and soil nutrient biosensing, among others. New engineering methods including genetic refactoring, DNA-binding domain swapping, detection threshold tuning, and phosphorylation cross-talk insulation are being used to increase the reliability of TCS sensor performance and tailor TCS signaling properties to the requirements of specific applications. There is now potential to combine these methods with large-scale gene synthesis and laboratory screening to discover the inputs sensed by many uncharacterized TCSs and develop a large new family of genetically-encoded sensors that respond to an unrivaled breadth of stimuli.
Collapse
Affiliation(s)
- John T Lazar
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, Houston, TX, USA
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
| |
Collapse
|
13
|
O'Neill CE, Skilton RJ, Forster J, Cleary DW, Pearson SA, Lampe DJ, Thomson NR, Clarke IN. An inducible transposon mutagenesis approach for the intracellular human pathogen Chlamydia trachomatis. Wellcome Open Res 2021; 6:312. [PMID: 35087955 PMCID: PMC8767425 DOI: 10.12688/wellcomeopenres.16068.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Chlamydia trachomatis is a prolific human pathogen that can cause serious long-term conditions if left untreated. Recent developments in Chlamydia genetics have opened the door to conducting targeted and random mutagenesis experiments to identify gene function. In the present study, an inducible transposon mutagenesis approach was developed for C. trachomatis using a self-replicating vector to deliver the transposon-transposase cassette - a significant step towards our ultimate aim of achieving saturation mutagenesis of the Chlamydia genome. Methods: The low transformation efficiency of C. trachomatis necessitated the design of a self-replicating vector carrying the transposon mutagenesis cassette (i.e. the Himar-1 transposon containing the beta lactamase gene as well as a hyperactive transposase gene under inducible control of the tet promoter system with the addition of a riboswitch). Chlamydia transformed with this vector (pSW2-RiboA-C9Q) were induced at 24 hours post-infection. Through dual control of transcription and translation, basal expression of transposase was tightly regulated to stabilise the plasmid prior to transposition. Results: Here we present the preliminary sequencing results of transposon mutant pools of both C. trachomatis biovars, using two plasmid-free representatives: urogenital strain C. trachomatis SWFP- and the lymphogranuloma venereum isolate L2(25667R). DNA sequencing libraries were generated and analysed using Oxford Nanopore Technologies' MinION technology. This enabled 'proof of concept' for the methods as an initial low-throughput screen of mutant libraries; the next step is to employ high throughput sequencing to assess saturation mutagenesis. Conclusions: This significant advance provides an efficient method for assaying C. trachomatis gene function and will enable the identification of the essential gene set of C. trachomatis. In the long-term, the methods described herein will add to the growing knowledge of chlamydial infection biology leading to the discovery of novel drug or vaccine targets.
Collapse
Affiliation(s)
- Colette E. O'Neill
- Clinical and Experimental Sciences, University of Southampton, Southampton, Hampshire, SO166YD, UK
| | - Rachel J. Skilton
- Clinical and Experimental Sciences, University of Southampton, Southampton, Hampshire, SO166YD, UK
| | - Jade Forster
- Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
| | - David W. Cleary
- Clinical and Experimental Sciences, University of Southampton, Southampton, Hampshire, SO166YD, UK
| | - Sarah A. Pearson
- Clinical and Experimental Sciences, University of Southampton, Southampton, Hampshire, SO166YD, UK
| | - David J. Lampe
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, 15116, USA
| | - Nicholas R. Thomson
- Bacterial Genomics and Evolution, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Ian N. Clarke
- Clinical and Experimental Sciences, University of Southampton, Southampton, Hampshire, SO166YD, UK
| |
Collapse
|
14
|
Tabuchi T, Yokobayashi Y. Cell-free riboswitches. RSC Chem Biol 2021; 2:1430-1440. [PMID: 34704047 PMCID: PMC8496063 DOI: 10.1039/d1cb00138h] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/26/2021] [Indexed: 12/16/2022] Open
Abstract
The emerging community of cell-free synthetic biology aspires to build complex biochemical and genetic systems with functions that mimic or even exceed those in living cells. To achieve such functions, cell-free systems must be able to sense and respond to the complex chemical signals within and outside the system. Cell-free riboswitches can detect chemical signals via RNA-ligand interaction and respond by regulating protein synthesis in cell-free protein synthesis systems. In this article, we review synthetic cell-free riboswitches that function in both prokaryotic and eukaryotic cell-free systems reported to date to provide a current perspective on the state of cell-free riboswitch technologies and their limitations.
Collapse
Affiliation(s)
- Takeshi Tabuchi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University Onna Okinawa 904-0495 Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University Onna Okinawa 904-0495 Japan
| |
Collapse
|
15
|
Finke M, Brecht D, Stifel J, Gense K, Gamerdinger M, Hartig JS. Efficient splicing-based RNA regulators for tetracycline-inducible gene expression in human cell culture and C. elegans. Nucleic Acids Res 2021; 49:e71. [PMID: 33893804 PMCID: PMC8266659 DOI: 10.1093/nar/gkab233] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/17/2021] [Accepted: 04/23/2021] [Indexed: 01/07/2023] Open
Abstract
Synthetic riboswitches gain increasing interest for controlling transgene expression in diverse applications ranging from synthetic biology, functional genomics, and pharmaceutical target validation to potential therapeutic approaches. However, existing systems often lack the pharmaceutically suited ligands and dynamic responses needed for advanced applications. Here we present a series of synthetic riboswitches for controlling gene expression through the regulation of alternative splicing. Placing the 5′-splice site into a stem structure of a tetracycline-sensing aptamer allows us to regulate the accessibility of the splice site. In the presence of tetracycline, an exon with a premature termination codon is skipped and gene expression can occur, whereas in its absence the exon is included into the coding sequence, repressing functional protein expression. We were able to identify RNA switches controlling protein expression in human cells with high dynamic ranges and different levels of protein expression. We present minimalistic versions of this system that circumvent the need to insert an additional exon. Further, we demonstrate the robustness of our approach by transferring the devices into the important research model organism Caenorhabditis elegans, where high levels of functional protein with very low background expression could be achieved.
Collapse
Affiliation(s)
- Monika Finke
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Dominik Brecht
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Julia Stifel
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Karina Gense
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.,Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Martin Gamerdinger
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.,Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| |
Collapse
|
16
|
McCarthy J. Engineering and standardization of posttranscriptional biocircuitry in Saccharomyces cerevisiae. Integr Biol (Camb) 2021; 13:210-220. [PMID: 34270725 DOI: 10.1093/intbio/zyab013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/14/2022]
Abstract
This short review considers to what extent posttranscriptional steps of gene expression can provide the basis for novel control mechanisms and procedures in synthetic biology and biotechnology. The term biocircuitry is used here to refer to functionally connected components comprising DNA, RNA or proteins. The review begins with an overview of the diversity of devices being developed and then considers the challenges presented by trying to engineer more scaled-up systems. While the engineering of RNA-based and protein-based circuitry poses new challenges, the resulting 'toolsets' of components and novel mechanisms of operation will open up multiple new opportunities for synthetic biology. However, agreed procedures for standardization will need to be placed at the heart of this expanding field if the full potential benefits are to be realized.
Collapse
Affiliation(s)
- John McCarthy
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| |
Collapse
|
17
|
Tickner ZJ, Farzan M. Riboswitches for Controlled Expression of Therapeutic Transgenes Delivered by Adeno-Associated Viral Vectors. Pharmaceuticals (Basel) 2021; 14:ph14060554. [PMID: 34200913 PMCID: PMC8230432 DOI: 10.3390/ph14060554] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/28/2021] [Accepted: 06/04/2021] [Indexed: 11/16/2022] Open
Abstract
Vectors developed from adeno-associated virus (AAV) are powerful tools for in vivo transgene delivery in both humans and animal models, and several AAV-delivered gene therapies are currently approved for clinical use. However, AAV-mediated gene therapy still faces several challenges, including limited vector packaging capacity and the need for a safe, effective method for controlling transgene expression during and after delivery. Riboswitches, RNA elements which control gene expression in response to ligand binding, are attractive candidates for regulating expression of AAV-delivered transgene therapeutics because of their small genomic footprints and non-immunogenicity compared to protein-based expression control systems. In addition, the ligand-sensing aptamer domains of many riboswitches can be exchanged in a modular fashion to allow regulation by a variety of small molecules, proteins, and oligonucleotides. Riboswitches have been used to regulate AAV-delivered transgene therapeutics in animal models, and recently developed screening and selection methods allow rapid isolation of riboswitches with novel ligands and improved performance in mammalian cells. This review discusses the advantages of riboswitches in the context of AAV-delivered gene therapy, the subsets of riboswitch mechanisms which have been shown to function in human cells and animal models, recent progress in riboswitch isolation and optimization, and several examples of AAV-delivered therapeutic systems which might be improved by riboswitch regulation.
Collapse
Affiliation(s)
- Zachary J. Tickner
- Department of Immunology and Microbiology, the Scripps Research Institute, Jupiter, FL 33458, USA;
- Correspondence:
| | - Michael Farzan
- Department of Immunology and Microbiology, the Scripps Research Institute, Jupiter, FL 33458, USA;
- Emmune, Inc., Jupiter, FL 33458, USA
| |
Collapse
|
18
|
Yu Q, Ren K, You M. Genetically encoded RNA nanodevices for cellular imaging and regulation. NANOSCALE 2021; 13:7988-8003. [PMID: 33885099 PMCID: PMC8122502 DOI: 10.1039/d0nr08301a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nucleic acid-based nanodevices have been widely used in the fields of biosensing and nanomedicine. Traditionally, the majority of these nanodevices were first constructed in vitro using synthetic DNA or RNA oligonucleotides and then delivered into cells. Nowadays, the emergence of genetically encoded RNA nanodevices has provided a promising alternative approach for intracellular analysis and regulation. These genetically encoded RNA-based nanodevices can be directly transcribed and continuously produced inside living cells. A variety of highly precise and programmable nanodevices have been constructed in this way during the last decade. In this review, we will summarize the recent advances in the design and function of these artificial genetically encoded RNA nanodevices. In particular, we will focus on their applications in regulating cellular gene expression, imaging, logic operation, structural biology, and optogenetics. We believe these versatile RNA-based nanodevices will be broadly used in the near future to probe and program cells and other biological systems.
Collapse
Affiliation(s)
- Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| |
Collapse
|
19
|
Kim J, Quijano JF, Kim J, Yeung E, Murray RM. Synthetic logic circuits using RNA aptamer against T7 RNA polymerase. Biotechnol J 2021; 17:e2000449. [PMID: 33813787 DOI: 10.1002/biot.202000449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/05/2021] [Accepted: 03/30/2021] [Indexed: 12/23/2022]
Abstract
Recent advances in nucleic acids engineering introduced several RNA-based regulatory components for synthetic gene circuits, expanding the toolsets to engineer organisms. In this work, we designed genetic circuits implementing an RNA aptamer previously described to have the capability of binding to the T7 RNA polymerase and inhibiting its activity in vitro. We first demonstrated the utility of the RNA aptamer in combination with programmable synthetic transcription networks in vitro. As a step to quickly assess the feasibility of aptamer functions in vivo, we tested the aptamer and its sequence variants in the cell-free expression system, verifying the aptamer functionality in the cell-free testbed. The expression of aptamer in E. coli demonstrated control over GFP expression driven by T7 RNA polymerase, indicating its ability to serve as building blocks for logic circuits and transcriptional cascades. This work elucidates the potential of T7 RNA polymerase aptamer as regulators for synthetic biological circuits and metabolic engineering.
Collapse
Affiliation(s)
- Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea.,Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Juan F Quijano
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Jeongwon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Enoch Yeung
- Department of Control and Dynamical Systems, California Institute of Technology, Pasadena, California, USA.,Department of Mechanical Engineering, University of California, Santa Barbara, California, USA
| | - Richard M Murray
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA.,Department of Control and Dynamical Systems, California Institute of Technology, Pasadena, California, USA
| |
Collapse
|
20
|
Spöring M, Boneberg R, Hartig JS. Aptamer-Mediated Control of Polyadenylation for Gene Expression Regulation in Mammalian Cells. ACS Synth Biol 2020; 9:3008-3018. [PMID: 33108164 DOI: 10.1021/acssynbio.0c00222] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Small aptamer-based regulatory devices can be designed to control a range of RNA-dependent cellular processes and emerged as promising tools for fine-tuning gene expression in synthetic biology. Here, we design a conceptually new riboswitch device that allows for the conditional regulation of polyadenylation. By making use of ligand-induced sequence occlusion, the system efficiently controls the accessibility of the eukaryotic polyadenylation signal. Undesirable 3'-extended read-through products are counteracted by the downstream insertion of a microRNA target site. We demonstrate the modularity of the system with regard to sensor aptamers and polyadenylation signals used and combine the newly designed riboswitch with well-known aptazymes to yield superior composite systems. In addition, we show that the switches can be used to control alternative polyadenylation. The presented genetic switches require very little coding space and can be easily optimized by rational adjustments of the thermodynamic stability. The polyadenylation riboswitch extends the repertoire of RNA-based regulators and opens new possibilities for the generation of complex synthetic circuits.
Collapse
Affiliation(s)
- Maike Spöring
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Ronja Boneberg
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Jörg S. Hartig
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| |
Collapse
|
21
|
Jain S, Kaur J, Prasad S, Roy I. Nucleic acid therapeutics: a focus on the development of aptamers. Expert Opin Drug Discov 2020; 16:255-274. [PMID: 32990095 DOI: 10.1080/17460441.2021.1829587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Aptamers provide exciting opportunities for the development of specific and targeted therapeutic approaches. AREAS COVERED In this review, the authors discuss different therapeutic options available with nucleic acids, including aptamers, focussing on similarities and differences between them. The authors concentrate on case studies with specific aptamers, which exemplify their distinct advantages. The reasons for failure, wherever available, are deliberated upon. Attempts to accelerate the in vitro selection process have been discussed. Challenges with aptamers in terms of their specificity and targeted delivery and strategies to overcome these are described. Examples of precise regulation of systemic half-life of aptamers using antidotes are discussed. EXPERT OPINION Despite their nontoxic nature, a variety of reasons limit the therapeutic potential of aptamers in the clinic. The analysis of adverse effects observed with the pegnivacogin/anivamersen pair has highlighted the need to screen for preexisting PEG antibodies in any clinical trial involving pegylated molecules. Surprisingly, and promisingly, the ability of nucleic acid therapeutics to breach the blood brain barrier seems achievable. The recognition of specific motifs, e.g. G-quadruplex in thrombin-binding aptamers, or a 'nucleation' zone while designing aptamer-antidote pairs, is likely to accelerate the discovery of therapeutically efficacious molecules.
Collapse
Affiliation(s)
- Swati Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Jaskirat Kaur
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Shivcharan Prasad
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| |
Collapse
|
22
|
Abstract
Short regulatory RNA molecules underpin gene expression and govern cellular state and physiology. To establish an alternative layer of control over these processes, we generated chimeric regulatory RNAs that interact reversibly and light-dependently with the light-oxygen-voltage photoreceptor PAL. By harnessing this interaction, the function of micro RNAs (miRs) and short hairpin (sh) RNAs in mammalian cells can be regulated in a spatiotemporally precise manner. The underlying strategy is generic and can be adapted to near-arbitrary target sequences. Owing to full genetic encodability, it establishes optoribogenetic control of cell state and physiology. The method stands to facilitate the non-invasive, reversible and spatiotemporally resolved study of regulatory RNAs and protein function in cellular and organismal environments. Short hairpin RNAs can be used to modulate and regulate gene expression. Here the authors generate chimeric RNAs that interact with the photoreceptor PAL, allowing for optoribogenetic control of cell physiology.
Collapse
|
23
|
De D, Singh A, Gupta AN. Unveiling the transition path region in the one-dimensional free energy landscape of proteins. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
24
|
Duchardt-Ferner E, Juen M, Bourgeois B, Madl T, Kreutz C, Ohlenschläger O, Wöhnert J. Structure of an RNA aptamer in complex with the fluorophore tetramethylrhodamine. Nucleic Acids Res 2020; 48:949-961. [PMID: 31754719 PMCID: PMC6954400 DOI: 10.1093/nar/gkz1113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 12/23/2022] Open
Abstract
RNA aptamers-artificially created RNAs with high affinity and selectivity for their target ligand generated from random sequence pools-are versatile tools in the fields of biotechnology and medicine. On a more fundamental level, they also further our general understanding of RNA-ligand interactions e. g. in regard to the relationship between structural complexity and ligand affinity and specificity, RNA structure and RNA folding. Detailed structural knowledge on a wide range of aptamer-ligand complexes is required to further our understanding of RNA-ligand interactions. Here, we present the atomic resolution structure of an RNA-aptamer binding to the fluorescent xanthene dye tetramethylrhodamine. The high resolution structure, solved by NMR-spectroscopy in solution, reveals binding features both common and different from the binding mode of other aptamers with affinity for ligands carrying planar aromatic ring systems such as the malachite green aptamer which binds to the tetramethylrhodamine related dye malachite green or the flavin mononucleotide aptamer.
Collapse
Affiliation(s)
- Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Goethe University, Frankfurt/M., Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt/M., Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Michael Juen
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Benjamin Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Institute of Molecular Biology & Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Institute of Molecular Biology & Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Oliver Ohlenschläger
- Leibniz-Institute on Aging - Fritz-Lipmann-Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe University, Frankfurt/M., Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt/M., Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| |
Collapse
|
25
|
Common Secondary and Tertiary Structural Features of Aptamer-Ligand Interaction Shared by RNA Aptamers with Different Primary Sequences. Molecules 2019; 24:molecules24244535. [PMID: 31835789 PMCID: PMC6943582 DOI: 10.3390/molecules24244535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/30/2019] [Accepted: 12/05/2019] [Indexed: 11/16/2022] Open
Abstract
Aptamer selection can yield many oligonucleotides with different sequences and affinities for the target molecule. Here, we have combined computational and experimental approaches to understand if aptamers with different sequences but the same molecular target share structural and dynamical features. NEO1A, with a known NMR-solved structure, displays a flexible loop that interacts differently with individual aminoglycosides, its ligand affinities and specificities are responsive to ionic strength, and it possesses an adenosine in the loop that is critical for high-affinity ligand binding. NEO2A was obtained from the same selection and, although they are only 43% identical in overall sequence, NEO1A and NEO2A share similar loop sequences. Experimental analysis by 1D NMR and 2-aminopurine reporters combined with molecular dynamics modeling revealed similar structural and dynamical characteristics in both aptamers. These results are consistent with the hypothesis that the target ligand drives aptamer structure and also selects relevant dynamical characteristics for high-affinity aptamer-ligand interaction. Furthermore, they suggest that it might be possible to “migrate” structural and dynamical features between aptamer group members with different primary sequences but with the same target ligand.
Collapse
|
26
|
Spöring M, Finke M, Hartig JS. Aptamers in RNA-based switches of gene expression. Curr Opin Biotechnol 2019; 63:34-40. [PMID: 31811992 DOI: 10.1016/j.copbio.2019.11.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/04/2019] [Accepted: 11/06/2019] [Indexed: 01/25/2023]
Abstract
The ability to control gene expression via small molecule effectors is important in basic research as well as in future gene therapy applications. Although transcription factor-based systems are widely used, they are not well suited for certain applications due to a lack of functionality, limited available coding space, and potential immunogenicity of the regulatory proteins. RNA-based switches fill this gap since they can be designed to respond to effector compounds utilizing ligand-sensing aptamers. These systems are very modular since the aptamer can be combined with a variety of different expression platforms. RNA-based switches have been constructed that allow for controlling gene expression in diverse contexts. Here we discuss latest developments and applications of aptamer-based gene expression switches in eukaryotes.
Collapse
Affiliation(s)
- Maike Spöring
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Monika Finke
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
| |
Collapse
|
27
|
Katz N, Cohen R, Solomon O, Kaufmann B, Atar O, Yakhini Z, Goldberg S, Amit R. Synthetic 5' UTRs Can Either Up- or Downregulate Expression upon RNA-Binding Protein Binding. Cell Syst 2019; 9:93-106.e8. [PMID: 31129060 DOI: 10.1016/j.cels.2019.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/07/2019] [Accepted: 04/26/2019] [Indexed: 01/08/2023]
Abstract
The construction of complex gene-regulatory networks requires both inhibitory and upregulatory modules. However, the vast majority of RNA-based regulatory "parts" are inhibitory. Using a synthetic biology approach combined with SHAPE-seq, we explored the regulatory effect of RNA-binding protein (RBP)-RNA interactions in bacterial 5' UTRs. By positioning a library of RNA hairpins upstream of a reporter gene and co-expressing them with the matching RBP, we observed a set of regulatory responses, including translational stimulation, translational repression, and cooperative behavior. Our combined approach revealed three distinct states in vivo: in the absence of RBPs, the RNA molecules can be found in either a molten state that is amenable to translation or a structured phase that inhibits translation. In the presence of RBPs, the RNA molecules are in a semi-structured phase with partial translational capacity. Our work provides new insight into RBP-based regulation and a blueprint for designing complete gene-regulatory circuits at the post-transcriptional level.
Collapse
Affiliation(s)
- Noa Katz
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 32000 Haifa, Israel
| | - Roni Cohen
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 32000 Haifa, Israel
| | - Oz Solomon
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 32000 Haifa, Israel; School of Computer Science, Interdisciplinary Center, 46150 Herzeliya, Israel
| | - Beate Kaufmann
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 32000 Haifa, Israel
| | - Orna Atar
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 32000 Haifa, Israel
| | - Zohar Yakhini
- Department of Computer Science, Technion - Israel Institute of Technology, 32000 Haifa, Israel; School of Computer Science, Interdisciplinary Center, 46150 Herzeliya, Israel
| | - Sarah Goldberg
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 32000 Haifa, Israel
| | - Roee Amit
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 32000 Haifa, Israel; Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, 32000 Haifa, Israel.
| |
Collapse
|
28
|
Matsumoto S, Caliskan N, Rodnina MV, Murata A, Nakatani K. Small synthetic molecule-stabilized RNA pseudoknot as an activator for -1 ribosomal frameshifting. Nucleic Acids Res 2019; 46:8079-8089. [PMID: 30085309 PMCID: PMC6144811 DOI: 10.1093/nar/gky689] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 07/31/2018] [Indexed: 12/02/2022] Open
Abstract
Programmed –1 ribosomal frameshifting (−1PRF) is a recoding mechanism to make alternative proteins from a single mRNA transcript. −1PRF is stimulated by cis-acting signals in mRNA, a seven-nucleotide slippery sequence and a downstream secondary structure element, which is often a pseudoknot. In this study we engineered the frameshifting pseudoknot from the mouse mammary tumor virus to respond to a rationally designed small molecule naphthyridine carbamate tetramer (NCTn). We demonstrate that NCTn can stabilize the pseudoknot structure in mRNA and activate –1PRF both in vitro and in human cells. The results illustrate how NCTn-inducible –1PRF may serve as an important component of the synthetic biology toolbox for the precise control of gene expression using small synthetic molecules.
Collapse
Affiliation(s)
- Saki Matsumoto
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research, Josef-Schneider-Str.2/D15, 97080, Würzburg, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| |
Collapse
|
29
|
Yokobayashi Y. Aptamer-based and aptazyme-based riboswitches in mammalian cells. Curr Opin Chem Biol 2019; 52:72-78. [PMID: 31238268 PMCID: PMC7108311 DOI: 10.1016/j.cbpa.2019.05.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 05/17/2019] [Accepted: 05/21/2019] [Indexed: 11/22/2022]
Abstract
Molecular recognition by RNA aptamers has been exploited to control gene expression in response to small molecules in mammalian cells. These mammalian synthetic riboswitches offer attractive features such as small genetic size and lower risk of immunological complications compared to protein-based transcriptional gene switches. The diversity of gene regulatory mechanisms that involve RNA has also inspired the development of mammalian riboswitches that harness various regulatory mechanisms. In this report, recent advances in synthetic riboswitches that function in mammalian cells are reviewed focusing on the regulatory mechanisms they exploit such as mRNA degradation, microRNA processing, and programmed ribosomal frameshifting.
Collapse
Affiliation(s)
- Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan.
| |
Collapse
|
30
|
Aptamer-enabled uptake of small molecule ligands. Sci Rep 2018; 8:15712. [PMID: 30356136 PMCID: PMC6200808 DOI: 10.1038/s41598-018-33887-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 10/03/2018] [Indexed: 11/08/2022] Open
Abstract
The relative ease of isolating aptamers with high specificity for target molecules suggests that molecular recognition may be common in the folds of natural RNAs. We show here that, when expressed in cells, aptamers can increase the intracellular concentrations of their small molecule ligands. We have named these aptamers as DRAGINs (Drug Binding Aptamers for Growing Intracellular Numbers). The DRAGIN property, assessed here by the ability to enhance the toxicity of their ligands, was found for some, but not all, aminoglycoside aptamers. One aptamer protected cells against killing by its ligand. Another aptamer promoted killing as a singlemer and protected against killing as a tandemer. Based on a mathematical model, cell protection vs. killing is proposed as governed by aptamer affinity and access to the inner surface of the cell membrane, with the latter being a critical determinant. With RNA molecules proposed as the earliest functional polymers to drive the evolution of life, we suggest that RNA aptamer-like structures present in primitive cells might have selectively concentrated precursors for polymer synthesis. Riboswitches may be the evolved forms of these ancient aptamer-like “nutrient procurers”. Aptamers with DRAGIN capability in the modern world could be applied for imaging cells, in synthetic cell constructs, or to draw drugs into cells to make “undruggable” targets accessible to small molecule inhibitors.
Collapse
|
31
|
Page K, Shaffer J, Lin S, Zhang M, Liu JM. Engineering Riboswitches in Vivo Using Dual Genetic Selection and Fluorescence-Activated Cell Sorting. ACS Synth Biol 2018; 7:2000-2006. [PMID: 30119599 DOI: 10.1021/acssynbio.8b00099] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Riboswitches, noncoding RNAs that bind a small molecule effector to control gene expression at the level of transcription or translation, are uniquely suited to meet challenges in synthetic biology. To expand the limited set of existing riboswitches, we developed a riboswitch discovery platform that couples dual genetic selection and fluorescence-activated cell sorting to identify novel riboswitches from a 108 random-sequence library in which the aptamer domain of the ThiM#2 riboswitch was replaced with an N40 sequence. In a proof-of-principle validation, we identified novel riboswitches for the small molecule theophylline. Our best riboswitch (Hit 3-5) displays 2.3-fold activation of downstream gene expression in the presence of theophylline. Random mutagenesis of Hit 3-5, coupled with selections and screens, afforded improved riboswitches displaying nearly 3-fold activation. To the best of our knowledge, this is the first report of in vivo directed evolution of an aptamer domain to generate a functional riboswitch.
Collapse
Affiliation(s)
- Katharine Page
- Department of Chemistry, Pomona College, 645 N. College Avenue, Claremont, California 91711, United States
| | - Jeremy Shaffer
- Department of Chemistry, Pomona College, 645 N. College Avenue, Claremont, California 91711, United States
| | - Samuel Lin
- Department of Chemistry, Pomona College, 645 N. College Avenue, Claremont, California 91711, United States
| | - Mark Zhang
- Department of Chemistry, Pomona College, 645 N. College Avenue, Claremont, California 91711, United States
| | - Jane M. Liu
- Department of Chemistry, Pomona College, 645 N. College Avenue, Claremont, California 91711, United States
| |
Collapse
|
32
|
Abstract
SIGNIFICANCE The emerging connections between an increasing number of long noncoding RNAs (lncRNAs) and oncogenic hallmarks provide a new twist to tumor complexity. Recent Advances: In the present review, we highlight specific lncRNAs that have been studied in relation to tumorigenesis, either as participants in the neoplastic process or as markers of pathway activity or drug response. These transcripts are typically deregulated by oncogenic or tumor-suppressing signals or respond to microenvironmental conditions such as hypoxia. CRITICAL ISSUES Among these transcripts are lncRNAs sufficiently divergent between mouse and human genomes that may contribute to biological differences between species. FUTURE DIRECTIONS From a translational standpoint, knowledge about primate-specific lncRNAs may help explain the reason behind the failure to reproduce the results from mouse cancer models in human cell-based systems. Antioxid. Redox Signal. 29, 922-935.
Collapse
Affiliation(s)
- Xue Wu
- 1 Department of Medicine, Indiana University School of Medicine , Indianapolis, Indiana.,2 Department of Microbiology and Immunology, Indiana University School of Medicine , Indianapolis, Indiana
| | - Oana M Tudoran
- 1 Department of Medicine, Indiana University School of Medicine , Indianapolis, Indiana.,3 Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. I. Chiricuta," Cluj-Napoca, Romania
| | - George A Calin
- 4 Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center , Houston, Texas.,5 Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center , Houston, Texas
| | - Mircea Ivan
- 1 Department of Medicine, Indiana University School of Medicine , Indianapolis, Indiana.,2 Department of Microbiology and Immunology, Indiana University School of Medicine , Indianapolis, Indiana
| |
Collapse
|
33
|
Liu S, Liang A, Wu K, Zeng W, Luo Q, Wang F. Binding of Organometallic Ruthenium Anticancer Complexes to DNA: Thermodynamic Base and Sequence Selectivity. Int J Mol Sci 2018; 19:ijms19072137. [PMID: 30041439 PMCID: PMC6073332 DOI: 10.3390/ijms19072137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/03/2018] [Accepted: 07/04/2018] [Indexed: 11/16/2022] Open
Abstract
Organometallic ruthenium(II) complexes [(η⁶-arene)Ru(en)Cl][PF₆] (arene = benzene (1), p-cymene (2), indane (3), and biphenyl (4); en = ethylenediamine) are promising anticancer drug candidates both in vitro and in vivo. In this paper, the interactions between ruthenium(II) complexes and 15-mer single- and double-stranded oligodeoxynucleotides (ODNs) were thermodynamically investigated using high performance liquid chromatography (HPLC) and electrospray ionization mass spectroscopy (ESI-MS). All of the complexes bind preferentially to G₈ on the single strand 5'-CTCTCTT₇G₈T₉CTTCTC-3' (I), with complex 4 containing the most hydrophobic ligand as the most reactive one. To the analogs of I (changing T₇ and/or T₉ to A and/or C), complex 4 shows a decreasing affinity to the G₈ site in the following order: -AG₈T- (K: 5.74 × 10⁴ M-1) > -CG₈C- > -TG₈A- > -AG₈A- > -AG₈C- > -TG₈T- (I) ≈ -CG₈A- (K: 2.81 × 10⁴ M-1). In the complementary strand of I, the G bases in the middle region are favored for ruthenation over guanine (G) bases in the end of oligodeoxynucleotides (ODNs). These results indicate that both the flanking bases (or base sequences) and the arene ligands play important roles in determining the binding preference, and the base- and sequence-selectivity, of ruthenium complex in binding to the ODNs.
Collapse
Affiliation(s)
- Suyan Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Aihua Liang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Kui Wu
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
| | - Wenjuan Zeng
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
34
|
Ogawa A, Murashige Y, Takahashi H. Canonical translation-modulating OFF-riboswitches with a single aptamer binding to a small molecule that function in a higher eukaryotic cell-free expression system. Bioorg Med Chem Lett 2018; 28:2353-2357. [PMID: 29941191 DOI: 10.1016/j.bmcl.2018.06.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/16/2018] [Accepted: 06/18/2018] [Indexed: 12/30/2022]
Abstract
We have found that OFF-riboswitches that ligand-dependently downregulate the canonical translation in a higher eukaryotic expression system (wheat germ extract) can be easily created by inserting a single aptamer into the 5' untranslated region (UTR) of mRNA, even if its ligand is as small as theophylline. The key is the position of the inserted aptamer: the 5' end (+0 position) is much better than other positions for inhibiting canonical translation with the aptamer-ligand complex. The data showed that ribosome loading is suppressed by a rigid structure in the 5' end, and this suppression is dependent on the structure's stability but not on its size. Although this preference of aptamer insertion point contradicts the results in a lower eukaryote, it accords with the fact that the 5'-end structural hindrance is more effective for blocking the ribosome in higher eukaryotes. Therefore, the present type of OFF-riboswitch would function in various higher eukaryotic expression systems.
Collapse
Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
| | - Yuta Murashige
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Hajime Takahashi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| |
Collapse
|
35
|
Inuzuka S, Kakizawa H, Nishimura KI, Naito T, Miyazaki K, Furuta H, Matsumura S, Ikawa Y. Recognition of cyclic-di-GMP by a riboswitch conducts translational repression through masking the ribosome-binding site distant from the aptamer domain. Genes Cells 2018; 23:435-447. [PMID: 29693296 DOI: 10.1111/gtc.12586] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 03/18/2018] [Indexed: 12/31/2022]
Abstract
The riboswitch is a class of RNA-based gene regulatory machinery that is dependent on recognition of its target ligand by RNA tertiary structures. Ligand recognition is achieved by the aptamer domain, and ligand-dependent structural changes of the expression platform then usually mediate termination of transcription or translational initiation. Ligand-dependent structural changes of the aptamer domain and expression platform have been reported for several riboswitches with short (<40 nucleotides) expression platforms. In this study, we characterized structural changes of the Vc2 c-di-GMP riboswitch that represses translation of downstream open reading frames in a ligand-dependent manner. The Vc2 riboswitch has a long (97 nucleotides) expression platform, but its structure and function are largely unknown. Through mutational analysis and chemical probing, we identified its secondary structures that are possibly responsible for switch-OFF and switch-ON states of translational initiation.
Collapse
Affiliation(s)
- Saki Inuzuka
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Hitoshi Kakizawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Kei-Ichiro Nishimura
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan
| | - Takuto Naito
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Katsushi Miyazaki
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| |
Collapse
|
36
|
Liu Y, Li J, Chen Z, Huang W, Cai Z. Synthesizing artificial devices that redirect cellular information at will. eLife 2018; 7:31936. [PMID: 29319503 PMCID: PMC5788502 DOI: 10.7554/elife.31936] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/08/2018] [Indexed: 12/31/2022] Open
Abstract
Natural signaling circuits could be rewired to reprogram cells with pre-determined procedures. However, it is difficult to link cellular signals at will. Here, we describe signal-connectors—a series of RNA devices—that connect one signal to another signal at the translational level. We use them to either repress or enhance the translation of target genes in response to signals. Application of these devices allows us to construct various logic gates and to incorporate feedback loops into gene networks. They have also been used to rewire a native signaling pathway and even to create novel pathways. Furthermore, logical AND gates based on these devices and integration of multiple signals have been used successfully for identification and redirection of the state of cancer cells. Eventually, the malignant phenotypes of cancers have been reversed by rewiring the oncogenic signaling from promoting to suppressing tumorigenesis. We provide a novel platform for redirecting cellular information. Cells respond to signals from their surrounding environment. External signals activate a sequence of events inside the cell that can change how it behaves. These events are often called signaling pathways and they typically change the cell’s behavior by changing the activity of its genes. A major objective of the field of genetic engineering is to customize or artificially create new signaling pathways to make cells behave in certain ways. The ability to control a cell’s behavior is likely to have a major impact on human health and medicine. For instance, it may be possible to reprogram signaling events in cancer cells so that they die rather than grow rapidly. Researchers are developing artificial genetic devices to manipulate signaling pathways. Molecules of ribonucleic acid (or RNA) are widely used to design such devices. In nature, RNA molecules are highly versatile: messenger RNA molecules carry genetic information in a form that can be translated into protein, while other RNA molecules fine-tune gene expression and perform a host of other roles. RNA is apt for artificial devices because it can be tailored to detect signals and convert this information into a predictable outcome, such as turning specific genes on or off. In 2016, researchers constructed an RNA device to control the expression of genes in response to particular signals. However, this device was too large to deliver efficiently inside cells. Now, Liu, Li, Chen et al. – including some of the researchers involved the 2016 study – design smaller RNA devices to overcome this limitation. Each new device consists of two RNA components: one that recognizes the signal, and another that recognizes the messenger RNA of a target gene. Together the two components trigger the desired change in gene expression in response to a specific signal. The devices were shown to have multiple uses such as making new connections in a signaling pathway and creating new signaling networks. Furthermore, Liu, Li, Chen et al. engineered one device such that it was able to specifically turn off genes in a particular signaling pathway that allows human bladder cancer cells to divide. By silencing these genes, the cancer cells were less able to grow. These newly developed RNA devices should allow other researchers to customize cellular information and may have future therapeutic applications as well.
Collapse
Affiliation(s)
- Yuchen Liu
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Jianfa Li
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhicong Chen
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Weiren Huang
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhiming Cai
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| |
Collapse
|
37
|
Studying Parasite Gene Function and Interaction Through Ribozymes and Riboswitches Design Mechanism. Synth Biol (Oxf) 2018. [DOI: 10.1007/978-981-10-8693-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
|
38
|
Resende R, Torres H, Yuahasi K, Majumder P, Ulrich H. Delivery Systems for in Vivo use of Nucleic Acid Drugs. Drug Target Insights 2017. [DOI: 10.1177/117739280700200021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- R.R. Resende
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, SP, Brazil
- Departamento de Fisiologia e Biofísica, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - H.A.M. Torres
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04023-062, SP, Brazil
| | - K.K. Yuahasi
- Departamento de Neurologia e Neurocirurgia, Universidade Federal de São Paulo, São Paulo, SP, Brazil. Present address
| | - P Majumder
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, SP, Brazil
| | - H Ulrich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, SP, Brazil
| |
Collapse
|
39
|
Ogawa A, Masuoka H, Ota T. Artificial OFF-Riboswitches That Downregulate Internal Ribosome Entry without Hybridization Switches in a Eukaryotic Cell-Free Translation System. ACS Synth Biol 2017; 6:1656-1662. [PMID: 28613837 DOI: 10.1021/acssynbio.7b00124] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We constructed novel artificial riboswitches that function in a eukaryotic translation system (wheat germ extract), by rationally implanting an in vitro-selected aptamer into the intergenic internal ribosome entry site (IRES) of Plautia stali intestine virus. These eukaryotic OFF-riboswitches (OFF-eRSs) ligand-dose-dependently downregulate IRES-mediated translation without hybridization switches, which typical riboswitches utilize for gene regulation. The hybridization-switch-free mechanism not only allows for easy design but also requires less energy for regulation, resulting in a higher switching efficiency than hybridization-switch-based OFF-eRSs provide. In addition, even a small ligand such as theophylline can induce satisfactory repression, in contrast to other types of OFF-eRSs that modulate the 5' cap-dependent canonical translation. Because our proposed hybridization-switch-free OFF-eRSs are based on a versatile IRES that functions well in many types of eukaryotic translation systems, they would be widely usable elements for synthetic gene circuits in both cell-free and cell-based synthetic biology.
Collapse
Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3
Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Hiroki Masuoka
- Proteo-Science Center, Ehime University, 3
Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Tsubasa Ota
- Proteo-Science Center, Ehime University, 3
Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| |
Collapse
|
40
|
Hirao I, Kimoto M, Lee KH. DNA aptamer generation by ExSELEX using genetic alphabet expansion with a mini-hairpin DNA stabilization method. Biochimie 2017; 145:15-21. [PMID: 28916151 DOI: 10.1016/j.biochi.2017.09.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 09/08/2017] [Indexed: 12/21/2022]
Abstract
A novel aptamer generation method to greatly augment the affinity and stability of DNA aptamers was developed by genetic alphabet expansion combined with mini-hairpin DNA technology. The genetic alphabet expansion increases the physicochemical and structural diversities of DNA aptamers by introducing extra components, unnatural bases, as a fifth base, allowing for the enhancement of DNA aptamer affinities. Furthermore, the mini-hairpin DNA technology stabilizes DNA aptamers against nuclease digestion and thermal denaturation, by introducing an extraordinarily stable mini-hairpin DNA containing a GCGAAGC sequence. This novel method provides stabilized high-affinity DNA aptamers for diagnostic and therapeutic applications.
Collapse
Affiliation(s)
- Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #09-01, Singapore, 138669, Singapore.
| | - Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #09-01, Singapore, 138669, Singapore
| | - Kyung Hyun Lee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #09-01, Singapore, 138669, Singapore
| |
Collapse
|
41
|
Zou M, Wang S. An Aptamer-based Self-Catalytic Colorimetric Assay for Carcinoembryonic Antigen. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Mingjing Zou
- Central Laboratory; Heze Medical College; Heze 274030 China
| | - Shuyu Wang
- Clinical Laboratory; Heze City Hospital; Heze 274000 China
| |
Collapse
|
42
|
Re A. Synthetic Gene Expression Circuits for Designing Precision Tools in Oncology. Front Cell Dev Biol 2017; 5:77. [PMID: 28894736 PMCID: PMC5581392 DOI: 10.3389/fcell.2017.00077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 08/16/2017] [Indexed: 01/21/2023] Open
Abstract
Precision medicine in oncology needs to enhance its capabilities to match diagnostic and therapeutic technologies to individual patients. Synthetic biology streamlines the design and construction of functionalized devices through standardization and rational engineering of basic biological elements decoupled from their natural context. Remarkable improvements have opened the prospects for the availability of synthetic devices of enhanced mechanism clarity, robustness, sensitivity, as well as scalability and portability, which might bring new capabilities in precision cancer medicine implementations. In this review, we begin by presenting a brief overview of some of the major advances in the engineering of synthetic genetic circuits aimed to the control of gene expression and operating at the transcriptional, post-transcriptional/translational, and post-translational levels. We then focus on engineering synthetic circuits as an enabling methodology for the successful establishment of precision technologies in oncology. We describe significant advancements in our capabilities to tailor synthetic genetic circuits to specific applications in tumor diagnosis, tumor cell- and gene-based therapy, and drug delivery.
Collapse
Affiliation(s)
- Angela Re
- Centre for Sustainable Future Technologies, Istituto Italiano di TecnologiaTorino, Italy
| |
Collapse
|
43
|
Domin G, Findeiß S, Wachsmuth M, Will S, Stadler PF, Mörl M. Applicability of a computational design approach for synthetic riboswitches. Nucleic Acids Res 2017; 45:4108-4119. [PMID: 27994029 PMCID: PMC5397205 DOI: 10.1093/nar/gkw1267] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/06/2016] [Indexed: 02/07/2023] Open
Abstract
Riboswitches have gained attention as tools for synthetic biology, since they enable researchers to reprogram cells to sense and respond to exogenous molecules. In vitro evolutionary approaches produced numerous RNA aptamers that bind such small ligands, but their conversion into functional riboswitches remains difficult. We previously developed a computational approach for the design of synthetic theophylline riboswitches based on secondary structure prediction. These riboswitches have been constructed to regulate ligand-dependent transcription termination in Escherichia coli. Here, we test the usability of this design strategy by applying the approach to tetracycline and streptomycin aptamers. The resulting tetracycline riboswitches exhibit robust regulatory properties in vivo. Tandem fusions of these riboswitches with theophylline riboswitches represent logic gates responding to two different input signals. In contrast, the conversion of the streptomycin aptamer into functional riboswitches appears to be difficult. Investigations of the underlying aptamer secondary structure revealed differences between in silico prediction and structure probing. We conclude that only aptamers adopting the minimal free energy (MFE) structure are suitable targets for construction of synthetic riboswitches with design approaches based on equilibrium thermodynamics of RNA structures. Further improvements in the design strategy are required to implement aptamer structures not corresponding to the calculated MFE state.
Collapse
Affiliation(s)
- Gesine Domin
- Leipzig University, Institute for Biochemistry, 04103 Leipzig, Germany
| | - Sven Findeiß
- University of Vienna, Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, A-1090 Vienna, Austria.,University of Vienna, Institute for Theoretical Chemistry, A-1090 Vienna, Austria
| | - Manja Wachsmuth
- Leipzig University, Institute for Biochemistry, 04103 Leipzig, Germany
| | - Sebastian Will
- Leipzig University, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, 04107 Leipzig, Germany
| | - Peter F Stadler
- University of Vienna, Institute for Theoretical Chemistry, A-1090 Vienna, Austria.,Leipzig University, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, 04107 Leipzig, Germany.,Max Planck Institute for Mathematics in the Science, 04103 Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.,Santa Fe Institute, Santa Fe NM 87501, USA
| | - Mario Mörl
- Leipzig University, Institute for Biochemistry, 04103 Leipzig, Germany
| |
Collapse
|
44
|
Guzmán-Trampe S, Ceapa CD, Manzo-Ruiz M, Sánchez S. Synthetic biology era: Improving antibiotic’s world. Biochem Pharmacol 2017; 134:99-113. [DOI: 10.1016/j.bcp.2017.01.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 01/26/2017] [Indexed: 12/12/2022]
|
45
|
Jones CP, Ferré-D'Amaré AR. Long-Range Interactions in Riboswitch Control of Gene Expression. Annu Rev Biophys 2017; 46:455-481. [PMID: 28375729 DOI: 10.1146/annurev-biophys-070816-034042] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Riboswitches are widespread RNA motifs that regulate gene expression in response to fluctuating metabolite concentrations. Known primarily from bacteria, riboswitches couple specific ligand binding and changes in RNA structure to mRNA expression in cis. Crystal structures of the ligand binding domains of most of the phylogenetically widespread classes of riboswitches, each specific to a particular metabolite or ion, are now available. Thus, the bound states-one end point-have been thoroughly characterized, but the unbound states have been more elusive. Consequently, it is less clear how the unbound, sensing riboswitch refolds into the ligand binding-induced output state. The ligand recognition mechanisms of riboswitches are diverse, but we find that they share a common structural strategy in positioning their binding sites at the point of the RNA three-dimensional fold where the residues farthest from one another in sequence meet. We review how riboswitch folds adhere to this fundamental strategy and propose future research directions for understanding and harnessing their ability to specifically control gene expression.
Collapse
Affiliation(s)
- Christopher P Jones
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824;
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824;
| |
Collapse
|
46
|
Velagapudi SP, Luo Y, Tran T, Haniff HS, Nakai Y, Fallahi M, Martinez GJ, Childs-Disney JL, Disney MD. Defining RNA-Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA. ACS CENTRAL SCIENCE 2017; 3:205-216. [PMID: 28386598 PMCID: PMC5364451 DOI: 10.1021/acscentsci.7b00009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Indexed: 05/03/2023]
Abstract
RNA drug targets are pervasive in cells, but methods to design small molecules that target them are sparse. Herein, we report a general approach to score the affinity and selectivity of RNA motif-small molecule interactions identified via selection. Named High Throughput Structure-Activity Relationships Through Sequencing (HiT-StARTS), HiT-StARTS is statistical in nature and compares input nucleic acid sequences to selected library members that bind a ligand via high throughput sequencing. The approach allowed facile definition of the fitness landscape of hundreds of thousands of RNA motif-small molecule binding partners. These results were mined against folded RNAs in the human transcriptome and identified an avid interaction between a small molecule and the Dicer nuclease-processing site in the oncogenic microRNA (miR)-18a hairpin precursor, which is a member of the miR-17-92 cluster. Application of the small molecule, Targapremir-18a, to prostate cancer cells inhibited production of miR-18a from the cluster, de-repressed serine/threonine protein kinase 4 protein (STK4), and triggered apoptosis. Profiling the cellular targets of Targapremir-18a via Chemical Cross-Linking and Isolation by Pull Down (Chem-CLIP), a covalent small molecule-RNA cellular profiling approach, and other studies showed specific binding of the compound to the miR-18a precursor, revealing broadly applicable factors that govern small molecule drugging of noncoding RNAs.
Collapse
Affiliation(s)
- Sai Pradeep Velagapudi
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Yiling Luo
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Tuan Tran
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Hafeez S. Haniff
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Yoshio Nakai
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Mohammad Fallahi
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Gustavo J. Martinez
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Jessica L. Childs-Disney
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Matthew D. Disney
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
- E-mail:
| |
Collapse
|
47
|
Etzel M, Mörl M. Synthetic Riboswitches: From Plug and Pray toward Plug and Play. Biochemistry 2017; 56:1181-1198. [PMID: 28206750 DOI: 10.1021/acs.biochem.6b01218] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In synthetic biology, metabolic engineering, and gene therapy, there is a strong demand for orthogonal or externally controlled regulation of gene expression. Here, RNA-based regulatory devices represent a promising emerging alternative to proteins, allowing a fast and direct control of gene expression, as no synthesis of regulatory proteins is required. Besides programmable ribozyme elements controlling mRNA stability, regulatory RNA structures in untranslated regions are highly interesting for engineering approaches. Riboswitches are especially well suited, as they show a modular composition of sensor and response elements, allowing a free combination of different modules in a plug-and-play-like mode. The sensor or aptamer domain specifically interacts with a trigger molecule as a ligand, modulating the activity of the adjacent response domain that controls the expression of the genes located downstream, in most cases at the level of transcription or translation. In this review, we discuss the recent advances and strategies for designing such synthetic riboswitches based on natural or artificial components and readout systems, from trial-and-error approaches to rational design strategies. As the past several years have shown dramatic development in this fascinating field of research, we can give only a limited overview of the basic riboswitch design principles that is far from complete, and we apologize for not being able to consider every successful and interesting approach described in the literature.
Collapse
Affiliation(s)
- Maja Etzel
- Institute for Biochemistry, Leipzig University , Brüderstrasse 34, 04103 Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University , Brüderstrasse 34, 04103 Leipzig, Germany
| |
Collapse
|
48
|
Approaches for the Discovery of Small Molecule Ligands Targeting microRNAs. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2017_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
49
|
Pandey S, Agarwala P, Maiti S. Targeting RNA G-Quadruplexes for Potential Therapeutic Applications. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2016_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
50
|
Hansen HG, Pristovšek N, Kildegaard HF, Lee GM. Improving the secretory capacity of Chinese hamster ovary cells by ectopic expression of effector genes: Lessons learned and future directions. Biotechnol Adv 2017; 35:64-76. [DOI: 10.1016/j.biotechadv.2016.11.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 11/12/2016] [Accepted: 11/28/2016] [Indexed: 12/12/2022]
|