1
|
Chan SH, Molé CN, Nye D, Mitchell L, Dai N, Buss J, Kneller DW, Whipple JM, Robb GB. Biochemical characterization of mRNA capping enzyme from Faustovirus. RNA (NEW YORK, N.Y.) 2023; 29:1803-1817. [PMID: 37625853 PMCID: PMC10578482 DOI: 10.1261/rna.079738.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023]
Abstract
The mammalian mRNA 5' cap structures play important roles in cellular processes such as nuclear export, efficient translation, and evading cellular innate immune surveillance and regulating 5'-mediated mRNA turnover. Hence, installation of the proper 5' cap is crucial in therapeutic applications of synthetic mRNA. The core 5' cap structure, Cap-0, is generated by three sequential enzymatic activities: RNA 5' triphosphatase, RNA guanylyltransferase, and cap N7-guanine methyltransferase. Vaccinia virus RNA capping enzyme (VCE) is a heterodimeric enzyme that has been widely used in synthetic mRNA research and manufacturing. The large subunit of VCE D1R exhibits a modular structure where each of the three structural domains possesses one of the three enzyme activities, whereas the small subunit D12L is required to activate the N7-guanine methyltransferase activity. Here, we report the characterization of a single-subunit RNA capping enzyme from an amoeba giant virus. Faustovirus RNA capping enzyme (FCE) exhibits a modular array of catalytic domains in common with VCE and is highly efficient in generating the Cap-0 structure without an activation subunit. Phylogenetic analysis suggests that FCE and VCE are descended from a common ancestral capping enzyme. We found that compared to VCE, FCE exhibits higher specific activity, higher activity toward RNA containing secondary structures and a free 5' end, and a broader temperature range, properties favorable for synthetic mRNA manufacturing workflows.
Collapse
Affiliation(s)
- S Hong Chan
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Christa N Molé
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Dillon Nye
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Lili Mitchell
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Nan Dai
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Jackson Buss
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | | | | | - G Brett Robb
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| |
Collapse
|
2
|
Warminski M, Mamot A, Depaix A, Kowalska J, Jemielity J. Chemical Modifications of mRNA Ends for Therapeutic Applications. Acc Chem Res 2023; 56:2814-2826. [PMID: 37782471 PMCID: PMC10586375 DOI: 10.1021/acs.accounts.3c00442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Indexed: 10/03/2023]
Abstract
Messenger ribonucleic acid (mRNA) is the universal cellular instruction for ribosomes to produce proteins. Proteins are responsible for most of the functions of living organisms, and their abnormal structure or activity is the cause of many diseases. mRNA, which is expressed in the cytoplasm and, unlike DNA, does not need to be delivered into the nucleus, appears to be an ideal vehicle for pursuing the idea of gene therapy in which genetic information about proteins is introduced into an organism to exert a therapeutic effect. mRNA molecules of any sequence can be synthesized using the same set of reagents in a cell-free system via a process called in vitro transcription (IVT), which is very convenient for therapeutic applications. However, this does not mean that the path from the idea to the first mRNA-based therapeutic was short and easy. It took 30 years of trial and error in the search for solutions that eventually led to the first mRNA vaccines created in record time during the SARS-CoV-2 pandemic. One of the fundamental problems in the development of RNA-based therapeutics is the legendary instability of mRNA, due to the transient nature of this macromolecule. From the chemical point of view, mRNA is a linear biopolymer composed of four types of ribonucleic subunits ranging in length from a few hundred to hundreds of thousands of nucleotides, with unique structures at its ends: a 5'-cap at the 5'-end and a poly(A) tail at the 3'-end. Both are extremely important for the regulation of translation and mRNA durability. These elements are also convenient sites for sequence-independent labeling of mRNA to create probes for enzymatic assays and tracking of the fate of mRNA in cells and living organisms. Synthetic 5'-cap analogs have played an important role in the studies of mRNA metabolism, and some of them have also been shown to significantly improve the translational properties of mRNA or affect mRNA stability and reactogenicity. The most effective of these is used in clinical trials of mRNA-based anticancer vaccines. Interestingly, thanks to the knowledge gained from the biophysical studies of cap-related processes, even relatively large modifications such as fluorescent tags can be attached to the cap structure without significant effects on the biological properties of the mRNA, if properly designed cap analogs are used. This has been exploited in the development of molecular tools (fluorescently labeled mRNAs) to track these macromolecules in complex biological systems, including organisms. These tools are extremely valuable for better understanding of the cellular mechanisms involved in mRNA metabolism but also for designing therapeutic mRNAs with superior properties. Much less is known about the usefulness/utility of poly(A) tail modifications in the therapeutic context, but it is clear that chemical modifications of poly(A) can also affect biochemical properties of mRNA. This Account is devoted to chemical modifications of both the 5'- and 3'-ends of mRNA aimed at improving the biological properties of mRNA, without interfering with its translational function, and is based on the authors' more than 20 years of experience in this field.
Collapse
Affiliation(s)
- Marcin Warminski
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Adam Mamot
- Centre
of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Anaïs Depaix
- Centre
of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna Kowalska
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre
of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| |
Collapse
|
3
|
Domashevskiy AV, Rodriguez DJ, Gunawardana D, Goss DJ. Preparation of Functional, Fluorescently Labeled mRNA Capped with Anthraniloyl-m(7)GpppG. Methods Mol Biol 2017; 1428:61-75. [PMID: 27236792 DOI: 10.1007/978-1-4939-3625-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Fluorescent mRNA molecules offer a wide range of applications for studying capping/decapping reactions, translation, and other biophysical studies. Furthermore, fluorescent tags prove invaluable for tracking RNA molecules in cells. Here, we describe an efficient synthesis of a fluorescent cap analog, anthranioyl-GTP, its purification, and in vitro cap labeling of transcribed mRNA catalyzed by the recombinant vaccinia capping enzyme to produce anthranioyl-m(7)GpppG-capped RNA.
Collapse
Affiliation(s)
- Artem V Domashevskiy
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, New York, NY, USA.
| | - David J Rodriguez
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, New York, NY, USA
| | - Dilantha Gunawardana
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.,Department of Botany, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Dixie J Goss
- Department of Chemistry, Hunter College, City University of New York, New York, NY, USA
| |
Collapse
|
4
|
Domashevskiy AV, Williams S, Kluge C, Cheng SY. Plant Translation Initiation Complex eIFiso4F Directs Pokeweed Antiviral Protein to Selectively Depurinate Uncapped Tobacco Etch Virus RNA. Biochemistry 2017; 56:5980-5990. [PMID: 29064680 DOI: 10.1021/acs.biochem.7b00598] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pokeweed antiviral protein (PAP) is a ribosome inactivating protein (RIP) that depurinates the sarcin/ricin loop (SRL) of rRNA, inhibiting protein synthesis. PAP depurinates viral RNA, and in doing so, lowers the infectivity of many plant viruses. The mechanism by which PAP accesses uncapped viral RNA is not known, impeding scientists from developing effective antiviral agents for the prevention of the diseases caused by uncapped RNA viruses. Kinetic rates of PAP interacting with tobacco etch virus (TEV) RNA, in the presence and absence of eIFiso4F, were examined, addressing how the eIF affects selective PAP targeting and depurination of the uncapped viral RNA. PAP-eIFs copurification assay and fluorescence resonance energy transfer demonstrate that PAP forms a ternary complex with the eIFiso4G and eIFiso4E, directing the depurination of uncapped viral RNA. eIFiso4F selectively targets PAP to depurinate TEV RNA by increasing PAP's specificity constant for uncapped viral RNA 12-fold, when compared to the depurination of an oligonucleotide RNA that mimics the SRL of large rRNA, and cellular capped luciferase mRNA. This explains how PAP is able to lower infectivity of pokeweed viruses, while preserving its own ribosomes and cellular RNA from depurination: PAP utilizes cellular eIFiso4F in a novel strategy to target uncapped viral RNA. It may be possible to modulate and utilize these PAP-eIFs interactions for their public health benefit; by repurposing them to selectively target PAP to depurinate uncapped viral RNA, many plant and animal diseases caused by these viruses could be alleviated.
Collapse
Affiliation(s)
- Artem V Domashevskiy
- Department of Sciences, John Jay College of Criminal Justice, the City University of New York , New York, New York 10019, United States
| | - Shawn Williams
- Department of Sciences, John Jay College of Criminal Justice, the City University of New York , New York, New York 10019, United States
| | - Christopher Kluge
- Department of Sciences, John Jay College of Criminal Justice, the City University of New York , New York, New York 10019, United States
| | - Shu-Yuan Cheng
- Department of Sciences, John Jay College of Criminal Justice, the City University of New York , New York, New York 10019, United States
| |
Collapse
|
5
|
Warminski M, Sikorski PJ, Kowalska J, Jemielity J. Applications of Phosphate Modification and Labeling to Study (m)RNA Caps. Top Curr Chem (Cham) 2017; 375:16. [PMID: 28116583 PMCID: PMC5396385 DOI: 10.1007/s41061-017-0106-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/10/2017] [Indexed: 02/07/2023]
Abstract
The cap is a natural modification present at the 5' ends of eukaryotic messenger RNA (mRNA), which because of its unique structural features, mediates essential biological functions during the process of gene expression. The core structural feature of the mRNA cap is an N7-methylguanosine moiety linked by a 5'-5' triphosphate chain to the first transcribed nucleotide. Interestingly, other RNA 5' end modifications structurally and functionally resembling the m7G cap have been discovered in different RNA types and in different organisms. All these structures contain the 'inverted' 5'-5' oligophosphate bridge, which is necessary for interaction with specific proteins and also serves as a cleavage site for phosphohydrolases regulating RNA turnover. Therefore, cap analogs containing oligophosphate chain modifications or carrying spectroscopic labels attached to phosphate moieties serve as attractive molecular tools for studies on RNA metabolism and modification of natural RNA properties. Here, we review chemical, enzymatic, and chemoenzymatic approaches that enable preparation of modified cap structures and RNAs carrying such structures, with emphasis on phosphate-modified mRNA cap analogs and their potential applications.
Collapse
Affiliation(s)
- Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland.
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
| |
Collapse
|
6
|
Fuchs AL, Neu A, Sprangers R. A general method for rapid and cost-efficient large-scale production of 5' capped RNA. RNA (NEW YORK, N.Y.) 2016; 22:1454-66. [PMID: 27368341 PMCID: PMC4986899 DOI: 10.1261/rna.056614.116] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/25/2016] [Indexed: 05/03/2023]
Abstract
The eukaryotic mRNA 5' cap structure is indispensible for pre-mRNA processing, mRNA export, translation initiation, and mRNA stability. Despite this importance, structural and biophysical studies that involve capped RNA are challenging and rare due to the lack of a general method to prepare mRNA in sufficient quantities. Here, we show that the vaccinia capping enzyme can be used to produce capped RNA in the amounts that are required for large-scale structural studies. We have therefore designed an efficient expression and purification protocol for the vaccinia capping enzyme. Using this approach, the reaction scale can be increased in a cost-efficient manner, where the yields of the capped RNA solely depend on the amount of available uncapped RNA target. Using a large number of RNA substrates, we show that the efficiency of the capping reaction is largely independent of the sequence, length, and secondary structure of the RNA, which makes our approach generally applicable. We demonstrate that the capped RNA can be directly used for quantitative biophysical studies, including fluorescence anisotropy and high-resolution NMR spectroscopy. In combination with (13)C-methyl-labeled S-adenosyl methionine, the methyl groups in the RNA can be labeled for methyl TROSY NMR spectroscopy. Finally, we show that our approach can produce both cap-0 and cap-1 RNA in high amounts. In summary, we here introduce a general and straightforward method that opens new means for structural and functional studies of proteins and enzymes in complex with capped RNA.
Collapse
Affiliation(s)
- Anna-Lisa Fuchs
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Ancilla Neu
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Remco Sprangers
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| |
Collapse
|
7
|
Ramanathan A, Robb GB, Chan SH. mRNA capping: biological functions and applications. Nucleic Acids Res 2016; 44:7511-26. [PMID: 27317694 PMCID: PMC5027499 DOI: 10.1093/nar/gkw551] [Citation(s) in RCA: 466] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/03/2016] [Indexed: 12/19/2022] Open
Abstract
The 5′ m7G cap is an evolutionarily conserved modification of eukaryotic mRNA. Decades of research have established that the m7G cap serves as a unique molecular module that recruits cellular proteins and mediates cap-related biological functions such as pre-mRNA processing, nuclear export and cap-dependent protein synthesis. Only recently has the role of the cap 2′O methylation as an identifier of self RNA in the innate immune system against foreign RNA has become clear. The discovery of the cytoplasmic capping machinery suggests a novel level of control network. These new findings underscore the importance of a proper cap structure in the synthesis of functional messenger RNA. In this review, we will summarize the current knowledge of the biological roles of mRNA caps in eukaryotic cells. We will also discuss different means that viruses and their host cells use to cap their RNA and the application of these capping machineries to synthesize functional mRNA. Novel applications of RNA capping enzymes in the discovery of new RNA species and sequencing the microbiome transcriptome will also be discussed. We will end with a summary of novel findings in RNA capping and the questions these findings pose.
Collapse
Affiliation(s)
- Anand Ramanathan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - G Brett Robb
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Siu-Hong Chan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| |
Collapse
|
8
|
Rhoads RE. Synthetic mRNA: Production, Introduction into Cells, and Physiological Consequences. Methods Mol Biol 2016; 1428:3-27. [PMID: 27236789 DOI: 10.1007/978-1-4939-3625-0_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent advances have made it possible to synthesize mRNA in vitro that is relatively stable when introduced into mammalian cells, has a diminished ability to activate the innate immune response against exogenous (virus-like) RNA, and can be efficiently translated into protein. Synthetic methods have also been developed to produce mRNA with unique investigational properties such as photo-cross-linking, fluorescence emission, and attachment of ligands through click chemistry. Synthetic mRNA has been proven effective in numerous applications beneficial for human health such as immunizing patients against cancer and infections diseases, alleviating diseases by restoring deficient proteins, converting somatic cells to pluripotent stem cells to use in regenerative medicine therapies, and engineering the genome by making specific alterations in DNA. This introductory chapter provides background information relevant to the following 20 chapters of this volume that present protocols for these applications of synthetic mRNA.
Collapse
Affiliation(s)
- Robert E Rhoads
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA, 71130-3932, USA.
| |
Collapse
|