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Sharma NK, Dwivedi P, Bhushan R, Maurya PK, Kumar A, Dakal TC. Engineering circular RNA for molecular and metabolic reprogramming. Funct Integr Genomics 2024; 24:117. [PMID: 38918231 DOI: 10.1007/s10142-024-01394-z] [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: 04/28/2024] [Revised: 06/10/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024]
Abstract
The role of messenger RNA (mRNA) in biological systems is extremely versatile. However, it's extremely short half-life poses a fundamental restriction on its application. Moreover, the translation efficiency of mRNA is also limited. On the contrary, circular RNAs, also known as circRNAs, are a common and stable form of RNA found in eukaryotic cells. These molecules are synthesized via back-splicing. Both synthetic circRNAs and certain endogenous circRNAs have the potential to encode proteins, hence suggesting the potential of circRNA as a gene expression machinery. Herein, we aim to summarize all engineering aspects that allow exogenous circular RNA (circRNA) to prolong the time that proteins are expressed from full-length RNA signals. This review presents a systematic engineering approach that have been devised to efficiently assemble circRNAs and evaluate several aspects that have an impact on protein production derived from. We have also reviewed how optimization of the key components of circRNAs, including the topology of vector, 5' and 3' untranslated sections, entrance site of the internal ribosome, and engineered aptamers could be efficiently impacting the translation machinery for molecular and metabolic reprogramming. Collectively, molecular and metabolic reprogramming present a novel way of regulating distinctive cellular features, for instance growth traits to neoplastic cells, and offer new possibilities for therapeutic inventions.
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Affiliation(s)
- Narendra Kumar Sharma
- Department of Bioscience and Biotechnology, Banasthali Vidyapith (Deemed University), P.O. Banasthali Vidyapith Distt. Tonk, Rajasthan, 304 022, India.
| | - Pragya Dwivedi
- Department of Bioscience and Biotechnology, Banasthali Vidyapith (Deemed University), P.O. Banasthali Vidyapith Distt. Tonk, Rajasthan, 304 022, India
| | - Ravi Bhushan
- Department of Zoology, M.S. College, Motihari, Bihar, India
| | - Pawan Kumar Maurya
- Department of Biochemistry, Central University of Haryana, Mahendergarh, 123031, Haryana, India
| | - Abhishek Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Tikam Chand Dakal
- Genome and Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India.
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2
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He W, Zhang X, Zou Y, Li J, Chang L, He YC, Jin Q, Ye J. Effective synthesis of circRNA via a thermostable T7 RNA polymerase variant as the catalyst. Front Bioeng Biotechnol 2024; 12:1356354. [PMID: 38655387 PMCID: PMC11035883 DOI: 10.3389/fbioe.2024.1356354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/04/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction Circular RNAs (circRNAs) are endogenous noncoding RNAs (ncRNAs) with transcriptional lengths ranging from hundreds to thousands. circRNAs have attracted attention owing to their stable structure and ability to treat complicated diseases. Our objective was to create a one-step reaction for circRNA synthesis using wild-type T7 RNA polymerase as the catalyst. However, T7 RNA polymerase is thermally unstable, and we streamlined circRNA synthesis via consensus and folding free energy calculations for hotspot selection. Because of the thermal instability, the permuted intron and exon (PIE) method for circRNA synthesis is conducted via tandem catalysis with a transcription reaction at a low temperature and linear RNA precursor cyclization at a high temperature. Methods To streamline the process, a multisite mutant T7 RNA polymerase (S430P, N433T, S633P, F849I, F880Y, and G788A) with significantly improved thermostability was constructed, and G788A was used. Results The resulting mutant exhibited stable activity at 45°C for over an hour, enabling the implementation of a one-pot transcription and cyclization reaction. The simplified circRNA production process demonstrated an efficiency comparable to that of the conventional two-step reaction, with a cyclization rate exceeding 95% and reduced production of immunostimulatory dsRNA byproducts.
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Affiliation(s)
- Wei He
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Vazyme Biotech Co., Ltd, Nanjing, China
| | | | | | - Ji Li
- Vazyme Biotech Co., Ltd, Nanjing, China
| | - Le Chang
- Vazyme Biotech Co., Ltd, Nanjing, China
| | - Yu-Cai He
- School of Pharmacy, Changzhou University, Changzhou, China
| | | | - Jianren Ye
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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Perenkov AD, Sergeeva AD, Vedunova MV, Krysko DV. In Vitro Transcribed RNA-Based Platform Vaccines: Past, Present, and Future. Vaccines (Basel) 2023; 11:1600. [PMID: 37897003 PMCID: PMC10610676 DOI: 10.3390/vaccines11101600] [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: 09/17/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
mRNA was discovered in 1961, but it was not used as a vaccine until after three decades. Recently, the development of mRNA vaccine technology gained great impetus from the pursuit of vaccines against COVID-19. To improve the properties of RNA vaccines, and primarily their circulation time, self-amplifying mRNA and trans-amplifying mRNA were developed. A separate branch of mRNA technology is circular RNA vaccines, which were developed with the discovery of the possibility of translation on their protein matrix. Circular RNA has several advantages over mRNA vaccines and is considered a fairly promising platform, as is trans-amplifying mRNA. This review presents an overview of the mRNA platform and a critical discussion of the more modern self-amplifying mRNA, trans-amplifying mRNA, and circular RNA platforms created on its basis. Finally, the main features, advantages, and disadvantages of each of the presented mRNA platforms are discussed. This discussion will facilitate the decision-making process in selecting the most appropriate platform for creating RNA vaccines against cancer or viral diseases.
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Affiliation(s)
- Alexey D Perenkov
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
| | - Alena D Sergeeva
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
| | - Maria V Vedunova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
| | - Dmitri V Krysko
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
- Cell Death Investigation and Therapy (CDIT) Laboratory, Anatomy and Embryology Unit, Department of Human Structure and Repair, Faculty of Medicine and Health Science, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent, 9000 Ghent, Belgium
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4
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Kim YS, Kim DH, An D, Lim Y, Seo YJ, Kim HK, Kang HY. The RNA ligation method using modified splint DNAs significantly improves the efficiency of circular RNA synthesis. Anim Cells Syst (Seoul) 2023; 27:208-218. [PMID: 37808549 PMCID: PMC10552601 DOI: 10.1080/19768354.2023.2265165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023] Open
Abstract
Circular RNA (circRNA) is a non-coding RNA with a covalently closed loop structure and usually more stable than messenger RNA (mRNA). However, coding sequences (CDSs) following an internal ribosome entry site (IRES) in circRNAs can be translated, and this property has been recently utilized to produce proteins as novel therapeutic tools. However, it is difficult to produce large proteins from circRNAs because of the low circularization efficiency of lengthy RNAs. In this study, we report that we successfully synthesized circRNAs with the splint DNA ligation method using RNA ligase 1 and the splint DNAs, which contain complementary sequences to both ends of precursor linear RNAs. This method results in more efficient circularization than the conventional enzymatic method that does not use the splint DNAs, easily generating circRNAs that express relatively large proteins, including IgG heavy and light chains. Longer splint DNA (42 nucleotide) is more effective in circularization. Also, the use of splint DNAs with an adenine analog, 2,6-diaminopurine (DAP), increase the circularization efficiency presumably by strengthening the interaction between the splint DNAs and the precursor RNAs. The splint DNA ligation method requires 5 times more splint DNA than the precursor RNA to efficiently produce circRNAs, but our modified splint DNA ligation method can produce circRNAs using the amount of splint DNA which is equal to that of the precursor RNA. Our modified splint DNA ligation method will help develop novel therapeutic tools using circRNAs, to treat various diseases and to develop human and veterinary vaccines.
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Affiliation(s)
- Yoon-Seob Kim
- Drug Discovery Center, NuclixBio, Seoul, Republic of Korea
| | - Do-Hyung Kim
- Drug Discovery Center, NuclixBio, Seoul, Republic of Korea
| | - Daegi An
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Younghyun Lim
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Young-Jin Seo
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hak Kyun Kim
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Ho-Young Kang
- Drug Discovery Center, NuclixBio, Seoul, Republic of Korea
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Gamper H, McCormick C, Makhamreh A, Wanunu M, Rouhanifard SH, Hou YM. Enzymatic synthesis of RNA standards for mapping and quantifying RNA modifications in sequencing analysis. Methods Enzymol 2023; 692:127-153. [PMID: 37925177 DOI: 10.1016/bs.mie.2023.04.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Synthesis of RNA standards that contain an internal site-specific modification is important for mapping and quantification of the modified nucleotide in sequencing analysis. While RNA containing a site-specific modification can be readily synthesized by solid-state coupling for less than 100-mer nucleotides, longer RNA must be synthesized by enzymatic ligation in the presence of a DNA splint. However, long RNAs have structural heterogeneity, and those generated by in vitro transcription have 3'-end sequence heterogeneity, which together substantially reduce the yield of ligation. Here we describe a method of 3-part splint ligation that joins an in vitro transcribed left-arm RNA, an in vitro transcribed right-arm RNA, and a chemically synthesized modification-containing middle RNA, with an efficiency higher than previously reported. We report that the improved efficiency is largely attributed to the inclusion of a pair of DNA disruptors proximal to the ligation sites, and to a lesser extent to the homogeneous processing of the 3'-end of the left-arm RNA. The yields of the ligated long RNA are sufficiently high to afford purification to homogeneity for practical RNA research. We also verify the sequence accuracy at each ligation junction by nanopore sequencing.
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Affiliation(s)
- Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Caroline McCormick
- Department of Bioengineering, Northeastern University, Boston, MA, United States
| | - Amr Makhamreh
- Department of Bioengineering, Northeastern University, Boston, MA, United States
| | - Meni Wanunu
- Department of Bioengineering, Northeastern University, Boston, MA, United States; Department of Physics, Northeastern University, Boston, MA, United States
| | - Sara H Rouhanifard
- Department of Bioengineering, Northeastern University, Boston, MA, United States
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, United States.
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Dantsuji S, Ohno M, Taniguchi I. The hnRNP C tetramer binds to CBC on mRNA and impedes PHAX recruitment for the classification of RNA polymerase II transcripts. Nucleic Acids Res 2023; 51:1393-1408. [PMID: 36620872 PMCID: PMC9943658 DOI: 10.1093/nar/gkac1250] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 01/10/2023] Open
Abstract
In eukaryotic cells, various classes of RNAs are exported to the cytoplasm by class-specific factors. Accumulating evidence has shown that export factors affect the fate of RNA, demonstrating the importance of proper RNA classification upon export. We previously reported that RNA polymerase II transcripts were classified after synthesis depending on their length, and identified heterogeneous nuclear ribonucleoprotein (hnRNP) C as the key classification factor. HnRNP C inhibits the recruitment of PHAX, an adapter protein for spliceosomal U snRNA export, to long transcripts, navigating these RNAs to the mRNA export pathway. However, the mechanisms by which hnRNP C inhibits PHAX recruitment to mRNA remain unknown. We showed that the cap-binding complex, a bridging factor between m7G-capped RNA and PHAX, directly interacted with hnRNP C on mRNA. Additionally, we revealed that the tetramer-forming activity of hnRNP C and its strong RNA-binding activity were crucial for the inhibition of PHAX binding to longer RNAs. These results suggest that mRNA is wrapped around the hnRNP C tetramer without a gap from the cap, thereby impeding the recruitment of PHAX. The results obtained on the mode of length-specific RNA classification by the hnRNP C tetramer will provide mechanistic insights into hnRNP C-mediated RNA biogenesis.
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Affiliation(s)
- Sayaka Dantsuji
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Kyoto 606-8507, Japan
| | - Mutsuhito Ohno
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Kyoto 606-8507, Japan
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Abstract
Methyltransferase-like protein 16 (METTL16) is one of four catalytically active, S-adenosylmethionine (SAM)-dependent m6A RNA methyltransferases in humans. Well-known methylation targets of METTL16 are U6 small nuclear RNA (U6 snRNA) and the MAT2A mRNA hairpins; however, METTL16 binds to other RNAs, including the 3' triple helix of the metastasis-associated lung adenocarcinoma transcript 1 (MALAT1). Herein, we investigated the kinetic mechanism and biochemical properties of METTL16. METTL16 is a monomer in complex with either the MALAT1 triple helix or U6 snRNA and binds to these RNAs with respective dissociation constants of 31 nM and 18 nM, whereas binding to the methylated U6 snRNA product is 1.1 μM. The MALAT1 triple helix, on the other hand, is not methylated by METTL16 under in vitro conditions. Using the U6 snRNA to study methylation steps, preincubation and isotope partitioning assays indicated an ordered-sequential mechanism, whereby METTL16 binds U6 snRNA before SAM. The apparent dissociation constant for the METTL16·U6 snRNA·SAM ternary complex is 126 μM. Steady-state kinetic assays established a kcat of 0.07 min-1, and single-turnover assays established a kchem of 0.56 min-1. Furthermore, the methyltransferase domain of METTL16 methylated U6 snRNA with an apparent dissociation constant of 736 μM and a kchem of 0.42 min-1, suggesting that the missing vertebrate conserved regions weaken the ternary complex but do not induce any rate-limiting conformational rearrangements of the U6 snRNA. This study helps us to better understand the catalytic activity of METTL16 in the context of its biological functions.
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8
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Joo S, Lee UJ, Son HY, Kim M, Huh YM, Lee TG, Lee M. Highly Selective FRET-Aided Single-Molecule Counting of MicroRNAs Labeled by Splinted Ligation. ACS Sens 2022; 7:3409-3415. [PMID: 36279317 DOI: 10.1021/acssensors.2c01526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that play an important role in regulating gene expression. Since miRNAs are abnormally expressed in various cancers, they are considered to be promising biomarkers for early cancer diagnosis. However, the short length and strong sequence similarity among miRNAs make their reliable quantification very challenging. We developed a highly selective amplification-free miRNA detection method based on Förster resonance energy transfer (FRET)-aided single-molecule counting. miRNAs were selectively labeled with FRET probes using splinted ligation. When imaged with a single-molecule FRET setup, the miRNA molecules were accurately identified by the probe's FRET. miRNA concentrations were estimated from the count of molecules. The high sensitivity of the method in finding sparse molecules enabled us to achieve a limit of detection of 31-56 amol for miR-125b, miR-100, and miR-99a. Single nucleotide mismatch could be discriminated with a very high target-to-mismatch ratio. The method accurately measured the high expression of miR-125b in gastric cancer cells, which agreed well with previous reports. The high sensitivity and accuracy of this technique demonstrated its clinical potential as a robust miRNA detection method.
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Affiliation(s)
- Sihwa Joo
- Safety Measurement Institute, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, South Korea
| | - Ui Jin Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, South Korea
| | - Hye Young Son
- Department of Radiology, College of Medicine, Yonsei University, Seoul 03722, South Korea.,Severance Biomedical Science Institute, College of Medicine, Yonsei University, Seoul 03722, South Korea
| | - Moonil Kim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, South Korea.,Department of Biotechnology, University of Science and Technology (UST), Daejeon 34113, South Korea
| | - Yong-Min Huh
- Department of Radiology, College of Medicine, Yonsei University, Seoul 03722, South Korea.,Severance Biomedical Science Institute, College of Medicine, Yonsei University, Seoul 03722, South Korea.,Department of Biochemistry and Molecular Biology, College of Medicine, Yonsei University, Seoul 03722, South Korea.,YUHS-KRIBB Medical Convergence Research Institute, Seoul 03722, South Korea
| | - Tae Geol Lee
- Safety Measurement Institute, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, South Korea.,Department of Nano Science, University of Science and Technology (UST), Daejeon 34113, South Korea
| | - Mina Lee
- Safety Measurement Institute, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, South Korea
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9
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Liu X, Zhang Y, Zhou S, Dain L, Mei L, Zhu G. Circular RNA: An emerging frontier in RNA therapeutic targets, RNA therapeutics, and mRNA vaccines. J Control Release 2022; 348:84-94. [PMID: 35649485 PMCID: PMC9644292 DOI: 10.1016/j.jconrel.2022.05.043] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022]
Abstract
Circular RNAs (circRNA) is a class of natural (biogenic) or synthetic closed RNA without 5' or 3' ends. Meanwhile, their unique covalently-closed structures of circRNA prevent RNA degradation by exonucleases, thereby empowering them with high pharmaceutical stability and biostability relative to current standard-of-care linear mRNA. Natural circRNA can be non-coding RNAs as well as protein-coding RNA, the latter of which was recently discovered. The physiological functions of biogenic circRNAs, which largely remain elusive, include protein and gene sponges, cell activity modulators, and protein translation. The discovery that the circRNA levels can be correlated with some human diseases empowers circRNA with the potential as a novel type of disease biomarkers and a noncanonical class of therapeutic targets. Recently, synthetic circRNA have been engineered to explore their applications as a novel class of mRNA therapeutics and vaccines. In this review, we will discuss the current understanding of the biogenesis and physiological functions of natural circRNAs, the approaches to circRNA synthesis, and current research in the exploration of endogenous circRNAs as novel therapeutic targets and testing circRNAs as an emerging class of RNA therapeutics and vaccines.
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Affiliation(s)
- Xiang Liu
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Yu Zhang
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Shurong Zhou
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Lauren Dain
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Lei Mei
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Guizhi Zhu
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA.
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10
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Mala P, Saraogi I. Enhanced Codon-Anticodon Interaction at In-Frame UAG Stop Codon Improves the Efficiency of Non-Natural Amino Acid Mutagenesis. ACS Chem Biol 2022; 17:1051-1060. [PMID: 35532803 DOI: 10.1021/acschembio.1c00782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The introduction of non-natural amino acids into proteins through the stop codon readthrough methodology has been used to design proteins for diverse applications. However, this method suffers from low yields of the modified protein, as the suppressor tRNA that recognizes the stop codon is unable to compete effectively with release factor 1 (RF1), which terminates translation. We reasoned that a suppressor tRNA with improved interaction with the UAG stop codon on the mRNA will be able to compete more effectively with RF1. To test this idea, we inserted two 2,6-diaminopurine (D) units in the tRNA anticodon stem loop, including one at the third position of the tRNA anticodon. The modified suppressor tRNA could potentially form additional H-bonds between the N2-exocyclic amine of D and the C2 carbonyl group of uracil, thereby enhancing mRNA-tRNA interaction and/or altering tRNA conformation. The stronger interaction at the codon-anticodon interface resulted in improved UAG decoding efficiency and a higher yield of the modified protein containing a non-natural amino acid at multiple sites. Our findings are consistent with the importance of hydrogen bonding and tRNA conformation at the tRNA-mRNA duplex interface during in-frame UAG suppression, which improves protein translation at multiple UAG stop sites. This work provides valuable inputs toward improved non-natural amino acid mutagenesis for creating designer proteins.
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Affiliation(s)
- Purnima Mala
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India
| | - Ishu Saraogi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India
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11
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Webb C, Ip S, Bathula NV, Popova P, Soriano SKV, Ly HH, Eryilmaz B, Nguyen Huu VA, Broadhead R, Rabel M, Villamagna I, Abraham S, Raeesi V, Thomas A, Clarke S, Ramsay EC, Perrie Y, Blakney AK. Current Status and Future Perspectives on MRNA Drug Manufacturing. Mol Pharm 2022; 19:1047-1058. [PMID: 35238565 PMCID: PMC8905930 DOI: 10.1021/acs.molpharmaceut.2c00010] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/20/2022]
Abstract
The coronavirus disease of 2019 (COVID-19) pandemic launched an unprecedented global effort to rapidly develop vaccines to stem the spread of the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2). Messenger ribonucleic acid (mRNA) vaccines were developed quickly by companies that were actively developing mRNA therapeutics and vaccines for other indications, leading to two mRNA vaccines being not only the first SARS-CoV-2 vaccines to be approved for emergency use but also the first mRNA drugs to gain emergency use authorization and to eventually gain full approval. This was possible partly because mRNA sequences can be altered to encode nearly any protein without significantly altering its chemical properties, allowing the drug substance to be a modular component of the drug product. Lipid nanoparticle (LNP) technology required to protect the ribonucleic acid (RNA) and mediate delivery into the cytoplasm of cells is likewise modular, as are technologies and infrastructure required to encapsulate the RNA into the LNP. This enabled the rapid adaptation of the technology to a new target. Upon the coattails of the clinical success of mRNA vaccines, this modularity will pave the way for future RNA medicines for cancer, gene therapy, and RNA engineered cell therapies. In this review, trends in the publication records and clinical trial registrations are tallied to show the sharp intensification in preclinical and clinical research for RNA medicines. Demand for the manufacturing of both the RNA drug substance (DS) and the LNP drug product (DP) has already been strained, causing shortages of the vaccine, and the rise in development and translation of other mRNA drugs in the coming years will exacerbate this strain. To estimate demand for DP manufacturing, the dosing requirements for the preclinical and clinical studies of the two approved mRNA vaccines were examined. To understand the current state of mRNA-LNP production, current methods and technologies are reviewed, as are current and announced global capacities for commercial manufacturing. Finally, a vision is rationalized for how emerging technologies such as self-amplifying mRNA, microfluidic production, and trends toward integrated and distributed manufacturing will shape the future of RNA manufacturing and unlock the potential for an RNA medicine revolution.
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Affiliation(s)
- Cameron Webb
- Strathclyde Institute of Pharmacy and
Biomedical Sciences, University of Strathclyde, 161 Cathedral Street,
Glasgow G4 0RE, United Kingdom
| | - Shell Ip
- Precision NanoSystems Inc,
655 West Kent Avenue North Unit 50, Vancouver, British Columbia V6P 6T7,
Canada
| | - Nuthan V. Bathula
- Michael Smith Laboratories & School of Biomedical
Engineering, University of British Columbia, 2185 East Mall,
Vancouver, British Columbia V6T 1Z4, Canada
| | - Petya Popova
- Michael Smith Laboratories & School of Biomedical
Engineering, University of British Columbia, 2185 East Mall,
Vancouver, British Columbia V6T 1Z4, Canada
| | - Shekinah K. V. Soriano
- Michael Smith Laboratories & School of Biomedical
Engineering, University of British Columbia, 2185 East Mall,
Vancouver, British Columbia V6T 1Z4, Canada
| | - Han Han Ly
- Michael Smith Laboratories & School of Biomedical
Engineering, University of British Columbia, 2185 East Mall,
Vancouver, British Columbia V6T 1Z4, Canada
| | - Burcu Eryilmaz
- Strathclyde Institute of Pharmacy and
Biomedical Sciences, University of Strathclyde, 161 Cathedral Street,
Glasgow G4 0RE, United Kingdom
| | - Viet Anh Nguyen Huu
- Precision NanoSystems Inc,
655 West Kent Avenue North Unit 50, Vancouver, British Columbia V6P 6T7,
Canada
| | - Richard Broadhead
- Precision NanoSystems Inc,
655 West Kent Avenue North Unit 50, Vancouver, British Columbia V6P 6T7,
Canada
| | - Martin Rabel
- Precision NanoSystems Inc,
655 West Kent Avenue North Unit 50, Vancouver, British Columbia V6P 6T7,
Canada
| | - Ian Villamagna
- Precision NanoSystems Inc,
655 West Kent Avenue North Unit 50, Vancouver, British Columbia V6P 6T7,
Canada
| | - Suraj Abraham
- Precision NanoSystems Inc,
655 West Kent Avenue North Unit 50, Vancouver, British Columbia V6P 6T7,
Canada
| | - Vahid Raeesi
- Precision NanoSystems Inc,
655 West Kent Avenue North Unit 50, Vancouver, British Columbia V6P 6T7,
Canada
| | - Anitha Thomas
- Precision NanoSystems Inc,
655 West Kent Avenue North Unit 50, Vancouver, British Columbia V6P 6T7,
Canada
| | - Samuel Clarke
- Precision NanoSystems Inc,
655 West Kent Avenue North Unit 50, Vancouver, British Columbia V6P 6T7,
Canada
| | - Euan C. Ramsay
- Precision NanoSystems Inc,
655 West Kent Avenue North Unit 50, Vancouver, British Columbia V6P 6T7,
Canada
| | - Yvonne Perrie
- Strathclyde Institute of Pharmacy and
Biomedical Sciences, University of Strathclyde, 161 Cathedral Street,
Glasgow G4 0RE, United Kingdom
| | - Anna K. Blakney
- Michael Smith Laboratories & School of Biomedical
Engineering, University of British Columbia, 2185 East Mall,
Vancouver, British Columbia V6T 1Z4, Canada
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12
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Analysis of the conformational space and dynamics of RNA helicases by single-molecule FRET in solution and on surfaces. Methods Enzymol 2022; 673:251-310. [DOI: 10.1016/bs.mie.2022.03.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Obi P, Chen YG. The design and synthesis of circular RNAs. Methods 2021; 196:85-103. [PMID: 33662562 PMCID: PMC8670866 DOI: 10.1016/j.ymeth.2021.02.020] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel class of RNAs distinguished by their single-stranded, covalently-closed topology. Although initially perceived as rare byproducts of aberrant splicing, circRNAs are now recognized as ubiquitously expressed and functionally significant. These discoveries have led to a growing need for ways to model circRNAs in living cells to advance our understanding of their biogenesis, regulation, and function, and to adopt them as new technologies for application within research and medicine. In this review, we provide an updated summary of approaches used to produce circRNAs in vitro and in vivo, the latter of which has grown considerably in recent years. Given increased interest in the unique functions carried out by individual circRNAs, we further dedicate a section on how to customize synthesized circRNAs for specific biological roles. We focus on the most common applications, including designing circRNAs for protein delivery, to target miRNAs and proteins, to act as fluorescent reporters, and to modulate cellular immunity.
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Affiliation(s)
- Prisca Obi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Y Grace Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
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14
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Ageely EA, Chilamkurthy R, Jana S, Abdullahu L, O'Reilly D, Jensik PJ, Damha MJ, Gagnon KT. Gene editing with CRISPR-Cas12a guides possessing ribose-modified pseudoknot handles. Nat Commun 2021; 12:6591. [PMID: 34782635 PMCID: PMC8593028 DOI: 10.1038/s41467-021-26989-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/01/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas12a is a leading technology for development of model organisms, therapeutics, and diagnostics. These applications could benefit from chemical modifications that stabilize or tune enzyme properties. Here we chemically modify ribonucleotides of the AsCas12a CRISPR RNA 5' handle, a pseudoknot structure that mediates binding to Cas12a. Gene editing in human cells required retention of several native RNA residues corresponding to predicted 2'-hydroxyl contacts. Replacing these RNA residues with a variety of ribose-modified nucleotides revealed 2'-hydroxyl sensitivity. Modified 5' pseudoknots with as little as six out of nineteen RNA residues, with phosphorothioate linkages at remaining RNA positions, yielded heavily modified pseudoknots with robust cell-based editing. High trans activity was usually preserved with cis activity. We show that the 5' pseudoknot can tolerate near complete modification when design is guided by structural and chemical compatibility. Rules for modification of the 5' pseudoknot should accelerate therapeutic development and be valuable for CRISPR-Cas12a diagnostics.
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Affiliation(s)
- Eman A Ageely
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL, USA
| | - Ramadevi Chilamkurthy
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, IL, USA
| | - Sunit Jana
- Department of Chemistry, McGill University, Montreal, Canada
| | | | - Daniel O'Reilly
- Department of Chemistry, McGill University, Montreal, Canada
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Philip J Jensik
- Department of Physiology, School of Medicine, Southern Illinois University, Carbondale, IL, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Canada.
| | - Keith T Gagnon
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL, USA.
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, IL, USA.
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15
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Depmeier H, Hoffmann E, Bornewasser L, Kath‐Schorr S. Strategies for Covalent Labeling of Long RNAs. Chembiochem 2021; 22:2826-2847. [PMID: 34043861 PMCID: PMC8518768 DOI: 10.1002/cbic.202100161] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/26/2021] [Indexed: 12/17/2022]
Abstract
The introduction of chemical modifications into long RNA molecules at specific positions for visualization, biophysical investigations, diagnostic and therapeutic applications still remains challenging. In this review, we present recent approaches for covalent internal labeling of long RNAs. Topics included are the assembly of large modified RNAs via enzymatic ligation of short synthetic oligonucleotides and synthetic biology approaches preparing site-specifically modified RNAs via in vitro transcription using an expanded genetic alphabet. Moreover, recent approaches to employ deoxyribozymes (DNAzymes) and ribozymes for RNA labeling and RNA methyltransferase based labeling strategies are presented. We discuss the potentials and limits of the individual methods, their applicability for RNAs with several hundred to thousands of nucleotides in length and indicate future directions in the field.
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Affiliation(s)
- Hannah Depmeier
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
| | - Eva Hoffmann
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
| | - Lisa Bornewasser
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
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16
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Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods. Methods 2020; 183:93-107. [DOI: 10.1016/j.ymeth.2020.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 11/23/2022] Open
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17
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Chandler M, Panigaj M, Rolband LA, Afonin KA. Challenges to optimizing RNA nanostructures for large scale production and controlled therapeutic properties. Nanomedicine (Lond) 2020; 15:1331-1340. [PMID: 32452262 PMCID: PMC7304434 DOI: 10.2217/nnm-2020-0034] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/16/2020] [Indexed: 02/06/2023] Open
Abstract
Nucleic acids have been utilized to construct an expansive collection of nanoarchitectures varying in design, physicochemical properties, cellular processing and biomedical applications. However, the broader therapeutic adaptation of nucleic acid nanoassemblies in general, and RNA-based nanoparticles in particular, have faced several challenges in moving towards (pre)clinical settings. For one, the large-batch synthesis of nucleic acids is still under development, with multi-stranded and chemically modified assemblies requiring greater production capacity while maintaining consistent medical-grade outputs. Furthermore, the unknown immunostimulation by these nanomaterials poses additional challenges, necessary to be overcome for optimizing future development of clinically approved RNA nanoparticles.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Martin Panigaj
- Institute of Biology & Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice, Slovak Republic
| | - Lewis A Rolband
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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18
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A systematic investigation of key factors of nucleic acid precipitation toward optimized DNA/RNA isolation. Biotechniques 2020; 68:191-199. [PMID: 32066262 DOI: 10.2144/btn-2019-0109] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Nucleic acid precipitation is important for virtually all molecular biology investigations. However, despite its crucial role, a systematic study of the influence factors of nucleic acid precipitation has not been reported. In the present work, via rational experimental design, key factors of nucleic acid precipitation, including the type of nucleic acid, temperature and time of incubation, speed and time of centrifugation, volume ratio of ethanol/isopropanol to nucleic acid solution, type of cation-containing salt solution and type of coprecipitator, were comprehensively evaluated in an attempt to maximize the efficiency of nucleic acid precipitation. Our results indicate that the optimal conditions of each influence factor of nucleic acid precipitation may vary in accordance with the chemistry, structure and length of nucleic acids.
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19
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Conn V, Conn SJ. SplintQuant: a method for accurately quantifying circular RNA transcript abundance without reverse transcription bias. RNA (NEW YORK, N.Y.) 2019; 25:1202-1210. [PMID: 31151991 PMCID: PMC6800515 DOI: 10.1261/rna.070953.119] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/29/2019] [Indexed: 05/22/2023]
Abstract
Reverse transcription of RNA is fallible, introducing biases and confounding the quantification of transcript abundance. We demonstrate that circular RNAs (circRNAs) are more subjective to overestimation of transcript abundance than cognate linear RNAs due to their covalently closed, circular form, producing multiple concatameric products from a single priming of reverse transcriptase. We developed SplintQuant, where custom DNA oligonucleotides are ligated by PBCV-1 DNA ligase only when bound to their target RNA. These circRNA-specific DNA oligonucleotides are terminally tagged with universal primers, allowing SplintQuant to accurately quantify even lowly abundant circRNAs through highly specific quantitative PCR (qPCR) in the absence of reverse transcription. SplintQuant is sensitive, specific, highly reproducible, and applicable to the quantification of canonical and noncanonical RNA transcripts including alternative splice variants, gene fusions, and offers a gold-standard approach for accurately quantifying circRNAs.
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Affiliation(s)
- Vanessa Conn
- Flinders Centre for Innovation in Cancer, Flinders University, College of Medicine and Public Health, Bedford Park, South Australia 5042, Australia
- UniSA Cancer Research Institute, University of South Australia, School of Pharmacy and Medical Sciences, Adelaide, South Australia 5000, Australia
| | - Simon J Conn
- Flinders Centre for Innovation in Cancer, Flinders University, College of Medicine and Public Health, Bedford Park, South Australia 5042, Australia
- UniSA Cancer Research Institute, University of South Australia, School of Pharmacy and Medical Sciences, Adelaide, South Australia 5000, Australia
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20
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Rossbach O. Artificial Circular RNA Sponges Targeting MicroRNAs as a Novel Tool in Molecular Biology. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 17:452-454. [PMID: 31330496 PMCID: PMC6646861 DOI: 10.1016/j.omtn.2019.06.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 05/10/2019] [Accepted: 06/24/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Oliver Rossbach
- Institute of Biochemistry, University of Giessen, Giessen, Germany.
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21
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Leitner A, Dorn G, Allain FHT. Combining Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) Spectroscopy for Integrative Structural Biology of Protein-RNA Complexes. Cold Spring Harb Perspect Biol 2019; 11:a032359. [PMID: 31262947 PMCID: PMC6601463 DOI: 10.1101/cshperspect.a032359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Deciphering complex RNA-protein interactions on a (near-)atomic level is a hurdle that hinders advancing our understanding of fundamental processes in RNA metabolism and RNA-based gene regulation. To overcome challenges associated with individual structure determination methods, structural information derived from complementary biophysical methods can be combined in integrative structural biology approaches. Here, we review recent advances in such hybrid structural approaches with a focus on combining mass spectrometric analysis of cross-linked protein-RNA complexes and nuclear magnetic resonance (NMR) spectroscopy.
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Affiliation(s)
- Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Georg Dorn
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
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22
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Hanspach G, Trucks S, Hengesbach M. Strategic labelling approaches for RNA single-molecule spectroscopy. RNA Biol 2019; 16:1119-1132. [PMID: 30874475 DOI: 10.1080/15476286.2019.1593093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Most single-molecule techniques observing RNA in vitro or in vivo require fluorescent labels that have to be connected to the RNA of interest. In recent years, a plethora of methods has been developed to achieve site-specific labelling, in many cases under near-native conditions. Here, we review chemical as well as enzymatic labelling methods that are compatible with single-molecule fluorescence spectroscopy or microscopy and show how these can be combined to offer a large variety of options to site-specifically place one or more labels in an RNA of interest. By either chemically forming a covalent bond or non-covalent hybridization, these techniques are prerequisites to perform state-of-the-art single-molecule experiments.
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Affiliation(s)
- Gerd Hanspach
- a Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology , Frankfurt , Germany
| | - Sven Trucks
- a Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology , Frankfurt , Germany
| | - Martin Hengesbach
- a Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology , Frankfurt , Germany
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23
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Al-Behadili A, Uhler JP, Berglund AK, Peter B, Doimo M, Reyes A, Wanrooij S, Zeviani M, Falkenberg M. A two-nuclease pathway involving RNase H1 is required for primer removal at human mitochondrial OriL. Nucleic Acids Res 2018; 46:9471-9483. [PMID: 30102370 PMCID: PMC6182146 DOI: 10.1093/nar/gky708] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/21/2018] [Accepted: 07/24/2018] [Indexed: 11/12/2022] Open
Abstract
The role of Ribonuclease H1 (RNase H1) during primer removal and ligation at the mitochondrial origin of light-strand DNA synthesis (OriL) is a key, yet poorly understood, step in mitochondrial DNA maintenance. Here, we reconstitute the replication cycle of L-strand synthesis in vitro using recombinant mitochondrial proteins and model OriL substrates. The process begins with initiation of DNA replication at OriL and ends with primer removal and ligation. We find that RNase H1 partially removes the primer, leaving behind the last one to three ribonucleotides. These 5'-end ribonucleotides disturb ligation, a conclusion which is supported by analysis of RNase H1-deficient patient cells. A second nuclease is therefore required to remove the last ribonucleotides and we demonstrate that Flap endonuclease 1 (FEN1) can execute this function in vitro. Removal of RNA primers at OriL thus depends on a two-nuclease model, which in addition to RNase H1 requires FEN1 or a FEN1-like activity. These findings define the role of RNase H1 at OriL and help to explain the pathogenic consequences of disease causing mutations in RNase H1.
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Affiliation(s)
- Ali Al-Behadili
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
| | - Jay P Uhler
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
| | - Anna-Karin Berglund
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
| | - Bradley Peter
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
| | - Mara Doimo
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Aurelio Reyes
- MRC-Mitochondrial Biology Unit, University of Cambridge, MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Massimo Zeviani
- MRC-Mitochondrial Biology Unit, University of Cambridge, MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
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24
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You C, Dai X, Wang Y. Position-dependent effects of regioisomeric methylated adenine and guanine ribonucleosides on translation. Nucleic Acids Res 2017; 45:9059-9067. [PMID: 28591780 PMCID: PMC5587754 DOI: 10.1093/nar/gkx515] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/05/2017] [Indexed: 01/30/2023] Open
Abstract
Reversible methylation of the N6 or N1 position of adenine in RNA has recently been shown to play significant roles in regulating the functions of RNA. RNA can also be alkylated upon exposure to endogenous and exogenous alkylating agents. Here we examined how regio-specific methylation at the hydrogen bonding edge of adenine and guanine in mRNA affects translation. When situated at the third codon position, the methylated nucleosides did not compromise the speed or accuracy of translation under most circumstances. When located at the first or second codon position, N1-methyladenosine (m1A) and m1G constituted robust blocks to both Escherichia coli and wheat germ extract translation systems, whereas N2-methylguanosine (m2G) moderately impeded translation. While m1A, m2G and N6-methyladenosine (m6A) did not perturb translational fidelity, O6-methylguanosine (m6G) at the first and second codon positions was strongly and moderately miscoding, respectively, and it was decoded as an adenosine in both systems. The effects of methylated ribonucleosides on translation could be attributed to the methylation-elicited alterations in base pairing properties of the nucleobases, and the mechanisms of ribosomal decoding contributed to the position-dependent effects. Together, our study afforded important new knowledge about the modulation of translation by methylation of purine nucleobases in mRNA.
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Affiliation(s)
- Changjun You
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA.,State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Xiaoxia Dai
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
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25
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McCarthy P, Garside E, Meschede-Krasa Y, MacMillan A, Pomeranz Krummel D. Reversibly constraining spliceosome-substrate complexes by engineering disulfide crosslinks. Methods 2017. [PMID: 28648680 DOI: 10.1016/j.ymeth.2017.06.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The spliceosome is a highly dynamic mega-Dalton enzyme, formed in part by assembly of U snRNPs onto its pre-mRNA substrate transcripts. Early steps in spliceosome assembly are challenging to study biochemically and structurally due to compositional and conformational dynamics. We detail an approach to covalently and reversibly constrain or trap non-covalent pre-mRNA/protein spliceosome complexes. This approach involves engineering a single disulfide bond between a thiol-bearing cysteine sidechain and a proximal backbone phosphate of the pre-mRNA, site-specifically modified with an N-thioalkyl moiety. When distance and angle between reactants is optimal, the sidechain will react with the single N-thioalkyl to form a crosslink upon oxidation. We provide protocols detailing how this has been applied successfully to trap an 11-subunit RNA-protein assembly, the human U1 snRNP, in complex with a pre-mRNA.
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Affiliation(s)
- Patrick McCarthy
- Department of Biochemistry, Brandeis University, Waltham, MA, USA
| | - Erin Garside
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Andrew MacMillan
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Daniel Pomeranz Krummel
- Department of Biochemistry, Brandeis University, Waltham, MA, USA; Winship Cancer Institute, Emory School of Medicine, Atlanta, GA, USA.
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26
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Conn VM, Hugouvieux V, Nayak A, Conos SA, Capovilla G, Cildir G, Jourdain A, Tergaonkar V, Schmid M, Zubieta C, Conn SJ. A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation. NATURE PLANTS 2017; 3:17053. [PMID: 28418376 DOI: 10.1038/nplants.2017.53] [Citation(s) in RCA: 397] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 03/20/2017] [Indexed: 05/03/2023]
Abstract
Circular RNAs (circRNAs) are a diverse and abundant class of hyper-stable, non-canonical RNAs that arise through a form of alternative splicing (AS) called back-splicing. These single-stranded, covalently-closed circRNA molecules have been identified in all eukaryotic kingdoms of life1, yet their functions have remained elusive. Here, we report that circRNAs can be used as bona fide biomarkers of functional, exon-skipped AS variants in Arabidopsis, including in the homeotic MADS-box transcription factor family. Furthermore, we demonstrate that circRNAs derived from exon 6 of the SEPALLATA3 (SEP3) gene increase abundance of the cognate exon-skipped AS variant (SEP3.3 which lacks exon 6), in turn driving floral homeotic phenotypes. Toward demonstrating the underlying mechanism, we show that the SEP3 exon 6 circRNA can bind strongly to its cognate DNA locus, forming an RNA:DNA hybrid, or R-loop, whereas the linear RNA equivalent bound significantly more weakly to DNA. R-loop formation results in transcriptional pausing, which has been shown to coincide with splicing factor recruitment and AS2-4. This report presents a novel mechanistic insight for how at least a subset of circRNAs probably contribute to increased splicing efficiency of their cognate exon-skipped messenger RNA and provides the first evidence of an organismal-level phenotype mediated by circRNA manipulation.
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Affiliation(s)
- Vanessa M Conn
- Laboratoire de Physiologie Cellulaire and Végétale, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, UMR 5168, Grenoble 38000, France
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA 5000, Australia
| | - Véronique Hugouvieux
- Laboratoire de Physiologie Cellulaire and Végétale, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, UMR 5168, Grenoble 38000, France
| | - Aditya Nayak
- Laboratoire de Physiologie Cellulaire and Végétale, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, UMR 5168, Grenoble 38000, France
| | - Stephanie A Conos
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA 5000, Australia
| | - Giovanna Capovilla
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Gökhan Cildir
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA 5000, Australia
| | - Agnès Jourdain
- Laboratoire de Physiologie Cellulaire and Végétale, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, UMR 5168, Grenoble 38000, France
| | - Vinay Tergaonkar
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA 5000, Australia
- Laboratory of NF-κB Signaling, Institute of Molecular and Cell Biology (IMCB), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
| | - Markus Schmid
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire and Végétale, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, UMR 5168, Grenoble 38000, France
| | - Simon J Conn
- Laboratoire de Physiologie Cellulaire and Végétale, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, UMR 5168, Grenoble 38000, France
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA 5000, Australia
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27
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Muttach F, Rentmeister A. One-pot modification of 5′-capped RNA based on methionine analogs. Methods 2016; 107:3-9. [DOI: 10.1016/j.ymeth.2016.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/12/2016] [Indexed: 12/29/2022] Open
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28
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Abstract
RNA with site-specific modification is a useful tool for RNA biology studies. However, generating kilobase (kb) -long RNA with internal modification at a site distant from RNA termini remains challenging. Here we report an enhanced splint ligation technique, proximal disruptor aided ligation (ProDAL), which allows adequate efficiency toward this purpose. The key to our approach is using multiple DNA oligonucleotides, 'proximal disruptors', to target the RNA substrate sequence next to the ligation site. The binding of disruptors helps to free the ligation site from intramolecular RNA basepairing, and consequently promotes more efficient formation of the pre-ligation complex and a higher overall ligation yield. We used naturally occurring 1.0 kb renilla and 1.9 kb firefly luciferase mRNA sequences to test the efficacy of our approach. ProDAL yielded 9-14% efficiency for the ligation between two RNA substrates, both of which were between 414 and 1313 nucleotides (nt) long. ProDAL also allowed similarly high efficiency for generating kb-long RNA with site-specific internal modification by a simple three-part ligation between two long RNA substrates and a modification-carrying RNA oligonucleotide. In comparison, classical splint ligation yielded a significantly lower efficiency of 0-2% in all cases. We expect that ProDAL will benefit studies involving kb-long RNAs, including translation, long non-coding RNAs, RNA splicing and modification, and large ribonucleoprotein complexes.
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Affiliation(s)
- Alexander Zhovmer
- a Molecular Biology Program , Memorial Sloan Kettering Cancer Center , New York , USA
| | - Xiaohui Qu
- a Molecular Biology Program , Memorial Sloan Kettering Cancer Center , New York , USA
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29
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Liu Y, Sousa R, Wang YX. Specific labeling: An effective tool to explore the RNA world. Bioessays 2015; 38:192-200. [DOI: 10.1002/bies.201500119] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yu Liu
- Protein-Nucleic Acid Interaction Section; Structural Biophysics Laboratory; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Frederick MD USA
| | - Rui Sousa
- Department of Biochemistry; University of Texas Health Science Center; San Antonio TX USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section; Structural Biophysics Laboratory; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Frederick MD USA
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Zhou J, Wan J, Gao X, Zhang X, Jaffrey SR, Qian SB. Dynamic m(6)A mRNA methylation directs translational control of heat shock response. Nature 2015; 526:591-4. [PMID: 26458103 PMCID: PMC4851248 DOI: 10.1038/nature15377] [Citation(s) in RCA: 913] [Impact Index Per Article: 101.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 07/30/2015] [Indexed: 12/28/2022]
Abstract
The most abundant mRNA post-transcriptional modification is N6-methyladenosine (m6A) that has broad roles in RNA biology1-5. In mammalian cells, the asymmetric distribution of m6A along mRNAs leaves relatively less methylation in the 5′ untranslated region (5′UTR) compared to other regions6,7. However, whether and how 5′UTR methylation is regulated is poorly understood. Despite the crucial role of the 5′UTR in translation initiation, very little is known whether m6A modification influences mRNA translation. Here we show that in response to heat shock stress, m6A is preferentially deposited to the 5′UTR of newly transcribed mRNAs. We found that the dynamic 5′UTR methylation is a result of stress-induced nuclear localization of YTHDF2, a well characterized m6A “reader”. Upon heat shock stress, the nuclear YTHDF2 preserves 5′UTR methylation of stress-induced transcripts by limiting the m6A “eraser” FTO from demethylation. Remarkably, the increased 5′UTR methylation in the form of m6A promotes cap-independent translation initiation, providing a mechanism for selective mRNA translation under heat shock stress. Using Hsp70 mRNA as an example, we demonstrate that a single site m6A modification in the 5′UTR enables translation initiation independent of the 5′ end m7G cap. The elucidation of the dynamic feature of 5′UTR methylation and its critical role in cap-independent translation not only expands the breadth of physiological roles of m6A, but also uncovers a previously unappreciated translational control mechanism in heat shock response.
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Affiliation(s)
- Jun Zhou
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
| | - Ji Wan
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
| | - Xiangwei Gao
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
| | - Xingqian Zhang
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York City, New York 10065, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
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Conn SJ, Pillman KA, Toubia J, Conn VM, Salmanidis M, Phillips CA, Roslan S, Schreiber AW, Gregory PA, Goodall GJ. The RNA binding protein quaking regulates formation of circRNAs. Cell 2015; 160:1125-34. [PMID: 25768908 DOI: 10.1016/j.cell.2015.02.014] [Citation(s) in RCA: 1486] [Impact Index Per Article: 165.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/05/2015] [Accepted: 02/03/2015] [Indexed: 12/19/2022]
Abstract
Circular RNAs (circRNAs), formed by non-sequential back-splicing of pre-mRNA transcripts, are a widespread form of non-coding RNA in animal cells. However, it is unclear whether the majority of circRNAs represent splicing by-products without function or are produced in a regulated manner to carry out specific cellular functions. We show that hundreds of circRNAs are regulated during human epithelial-mesenchymal transition (EMT) and find that the production of over one-third of abundant circRNAs is dynamically regulated by the alternative splicing factor, Quaking (QKI), which itself is regulated during EMT. Furthermore, by modulating QKI levels, we show the effect on circRNA abundance is dependent on intronic QKI binding motifs. Critically, the addition of QKI motifs is sufficient to induce de novo circRNA formation from transcripts that are normally linearly spliced. These findings demonstrate circRNAs are both purposefully synthesized and regulated by cell-type specific mechanisms, suggesting they play specific biological roles in EMT.
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Affiliation(s)
- Simon J Conn
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia; ACRF Cancer Genomics Facility, SA Pathology, Adelaide, SA 5000, Australia
| | - John Toubia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia; ACRF Cancer Genomics Facility, SA Pathology, Adelaide, SA 5000, Australia
| | - Vanessa M Conn
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Marika Salmanidis
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Caroline A Phillips
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia; School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Suraya Roslan
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Andreas W Schreiber
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia; ACRF Cancer Genomics Facility, SA Pathology, Adelaide, SA 5000, Australia; School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Philip A Gregory
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia; Department of Medicine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia; School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia; Department of Medicine, University of Adelaide, Adelaide, SA 5005, Australia.
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