1
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Zhang Z, Fu Y, Ju X, Zhang F, Zhang P, He M. Advances in Engineering Circular RNA Vaccines. Pathogens 2024; 13:692. [PMID: 39204292 PMCID: PMC11356823 DOI: 10.3390/pathogens13080692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/07/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Engineered circular RNAs (circRNAs) are a class of single-stranded RNAs with head-to-tail covalently linked structures that integrate open reading frames (ORFs) and internal ribosome entry sites (IRESs) with the function of coding and expressing proteins. Compared to mRNA vaccines, circRNA vaccines offer a more improved method that is safe, stable, and simple to manufacture. With the rapid revelation of the biological functions of circRNA and the success of Severe Acute Respiratory Coronavirus Type II (SARS-CoV-2) mRNA vaccines, biopharmaceutical companies and researchers around the globe are attempting to develop more stable circRNA vaccines for illness prevention and treatment. Nevertheless, research on circRNA vaccines is still in its infancy, and more work and assessment are needed for their synthesis, delivery, and use. In this review, based on the current understanding of the molecular biological properties and immunotherapeutic mechanisms of circRNA, we summarize the current preparation methods of circRNA vaccines, including design, synthesis, purification, and identification. We discuss their delivery strategies and summarize the challenges facing the clinical application of circRNAs to provide references for circRNA vaccine-related research.
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Affiliation(s)
- Zhongyan Zhang
- School of Pharmacy, Yantai University, Yantai 264005, China;
| | - Yuanlei Fu
- Yantai Key Laboratory of Nanomedicine & Advanced Preparations, Yantai Institute of Materia Medica, Yantai 264005, China; (Y.F.); (X.J.); (F.Z.)
| | - Xiaoli Ju
- Yantai Key Laboratory of Nanomedicine & Advanced Preparations, Yantai Institute of Materia Medica, Yantai 264005, China; (Y.F.); (X.J.); (F.Z.)
| | - Furong Zhang
- Yantai Key Laboratory of Nanomedicine & Advanced Preparations, Yantai Institute of Materia Medica, Yantai 264005, China; (Y.F.); (X.J.); (F.Z.)
| | - Peng Zhang
- School of Pharmacy, Yantai University, Yantai 264005, China;
| | - Meilin He
- Yantai Key Laboratory of Nanomedicine & Advanced Preparations, Yantai Institute of Materia Medica, Yantai 264005, China; (Y.F.); (X.J.); (F.Z.)
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2
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Ding Q, Liu L. Reprogramming cellular metabolism to increase the efficiency of microbial cell factories. Crit Rev Biotechnol 2024; 44:892-909. [PMID: 37380349 DOI: 10.1080/07388551.2023.2208286] [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: 11/17/2022] [Accepted: 04/11/2023] [Indexed: 06/30/2023]
Abstract
Recent studies are increasingly focusing on advanced biotechnological tools, self-adjusting smart microorganisms, and artificial intelligent networks, to engineer microorganisms with various functions. Microbial cell factories are a vital platform for improving the bioproduction of medicines, biofuels, and biomaterials from renewable carbon sources. However, these processes are significantly affected by cellular metabolism, and boosting the efficiency of microbial cell factories remains a challenge. In this review, we present a strategy for reprogramming cellular metabolism to enhance the efficiency of microbial cell factories for chemical biosynthesis, which improves our understanding of microbial physiology and metabolic control. Current methods are mainly focused on synthetic pathways, metabolic resources, and cell performance. This review highlights the potential biotechnological strategy to reprogram cellular metabolism and provide novel guidance for designing more intelligent industrial microbes with broader applications in this growing field.
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Affiliation(s)
- Qiang Ding
- School of Life Sciences, Anhui University, Hefei, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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3
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Margvelani G, Welden JR, Maquera AA, Van Eyk JE, Murray C, Miranda Sardon SC, Stamm S. Influence of FTDP-17 mutants on circular tau RNAs. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167036. [PMID: 38286213 DOI: 10.1016/j.bbadis.2024.167036] [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: 09/20/2023] [Revised: 12/21/2023] [Accepted: 01/21/2024] [Indexed: 01/31/2024]
Abstract
At least 53 mutations in the microtubule associated protein tau gene (MAPT) have been identified that cause frontotemporal dementia. 47 of these mutations are localized between exons 7 and 13. They could thus affect the formation of circular RNAs (circRNAs) from the MAPT gene that occurs through backsplicing from exon 12 to either exon 10 or exon 7. We analyzed representative mutants and found that five FTDP-17 mutations increase the formation of 12➔7 circRNA and three different mutations increase the amount of 12➔10 circRNA. CircRNAs are translated after undergoing adenosine to inosine RNA editing, catalyzed by ADAR enzymes. We found that the interferon induced ADAR1-p150 isoform has the strongest effect on circTau RNA translation. ADAR1-p150 activity had a stronger effect on circTau RNA expression and strongly decreased 12➔7 circRNA, but unexpectedly increased 12➔10 circRNA. In both cases, ADAR-activity strongly promoted translation of circTau RNAs. Unexpectedly, we found that the 12➔7 circTau protein interacts with eukaryotic initiation factor 4B (eIF4B), which is reduced by four FTDP-17 mutations located in the second microtubule domain. These are the first studies of the effect of human mutations on circular RNA formation and translation. They show that point mutations influence circRNA expression levels, likely through changes in pre-mRNA structures. The effect of the mutations is surpassed by editing of the circular RNAs, leading to their translation. Thus, circular RNAs and their editing status should be considered when analyzing FTDP-17 mutations.
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Affiliation(s)
- Giorgi Margvelani
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Justin R Welden
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA; Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Andrea Arizaca Maquera
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | | | | | - Sandra C Miranda Sardon
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.
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4
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Unti MJ, Jaffrey SR. Highly efficient cellular expression of circular mRNA enables prolonged protein expression. Cell Chem Biol 2024; 31:163-176.e5. [PMID: 37883972 PMCID: PMC10841545 DOI: 10.1016/j.chembiol.2023.09.015] [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: 04/30/2023] [Revised: 08/25/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023]
Abstract
A major problem with mRNA therapeutics is that mRNA is usually degraded within a few hours after entering the cytosol. New approaches for in vitro synthesis of circular mRNA have allowed increased levels and duration of protein synthesis from mRNA therapeutics due to the long half-life of circular mRNA. However, it remains difficult to genetically encode circular mRNAs in mammalian cells. Here, we describe the adaptation of the Tornado (Twister-optimized RNA for durable overexpression) system to achieve in-cell synthesis of circular mRNAs. We screen different promoters and internal ribosomal entry sites (IRESs) and identify combinations that result in high levels of circular mRNA and protein expression. We show that these circular mRNAs can be packaged into virus-like particles (VLPs), thus enabling prolonged protein expression. Overall, these data describe a platform for synthesis of circular mRNAs and how these circular mRNAs can improve VLP therapeutics.
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Affiliation(s)
- Mildred J Unti
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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5
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Gupta R, Arora K, Mehrotra Arora N, Kundu P. Significance of VLPs in Vlp-circRNA vaccines: a vaccine candidate or delivery vehicle? RNA Biol 2024; 21:17-28. [PMID: 39240021 PMCID: PMC11382717 DOI: 10.1080/15476286.2024.2399307] [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: 08/19/2024] [Accepted: 08/26/2024] [Indexed: 09/07/2024] Open
Abstract
Circular RNAs (circRNAs) are a class of single-stranded RNAs with a closed loop lacking 5' and 3' ends. These circRNAs are translatable and, therefore, have a potential in developing vaccine. CircRNA vaccines have been shown to be more stable, safe, easy to manufacture and scale-up production when compared to mRNA vaccines. However, these vaccines also suffer from several drawbacks such as low circularization efficiency for longer RNA precursor and usage of lipid nano particles (LNPs) in their delivery. LNPs have been shown to require large amounts of RNA due to their indirect delivery from endosome to cytosol. Besides, individual components of LNPs provide reactogenicity. Usage of virus like particles (VLPs) can improve the increased production and targeted delivery of circRNA vaccines and show no reactogenicity. Moreover, VLPs has also been used to produce vaccines against several diseases such as hepatitis C virus (HCV) etc. In this article, we will discuss about the methods used to enhance synthesis or circularization efficiency of circRNA. Moreover, we will also discuss about the significance of VLPs as the delivery vehicle for circRNA and their possible usage as the dual vaccine.
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Affiliation(s)
- Reeshu Gupta
- Department of Research and Development, Premas Biotech Pvt Ltd., Industrial Model Township (IMT), Gurugram, India
- Research and Development Cell, Parul University, Vadodara, Gujarat, India
| | - Kajal Arora
- Department of Research and Development, Premas Biotech Pvt Ltd., Industrial Model Township (IMT), Gurugram, India
| | - Nupur Mehrotra Arora
- Department of Research and Development, Premas Biotech Pvt Ltd., Industrial Model Township (IMT), Gurugram, India
| | - Prabuddha Kundu
- Department of Research and Development, Premas Biotech Pvt Ltd., Industrial Model Township (IMT), Gurugram, India
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6
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Xie J, Ye F, Deng X, Tang Y, Liang JY, Huang X, Sun Y, Tang H, Lei J, Zheng S, Zou Y. Circular RNA: A promising new star of vaccine. J Transl Int Med 2023; 11:372-381. [PMID: 38130633 PMCID: PMC10732498 DOI: 10.2478/jtim-2023-0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of single-stranded RNAs with covalently closed structures. Owing to their not having 3' or 5' ends, circRNAs are highly durable and insusceptible to exonuclease-mediated degradation. Moreover, some circRNAs with certain structures are translatable, making them novel vaccines. Vaccines are efficient tools for immunotherapy, such as for the prevention of infectious diseases and cancer treatment. The immune system is activated during immunotherapy to fight against abnormal allies or invaders. CircRNA vaccines represent a potential new avenue in the vaccine era. Recently, several circRNA vaccines have been synthesized and tested in vitro and in vivo. Our review briefly introduces the current understanding of the biology and function of translatable circRNAs, molecular biology, synthetic methods, delivery of circRNA, and current circRNA vaccines. We also discussed the challenges and future directions in the field by summarizing the developments in circRNA vaccines in the past few years.
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Affiliation(s)
- Jindong Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou510060, Guangdong Province, China
| | - Fengxi Ye
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou510060, Guangdong Province, China
| | - Xinpei Deng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou510060, Guangdong Province, China
| | - Yuhui Tang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou510060, Guangdong Province, China
| | - Jie-Ying Liang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou510000, Guangdong Province, China
| | - Xufeng Huang
- Department of Data Science and Visualization, Faculty of Informatics, University of Debrecen, Debrecen, Hungary
| | - Yuying Sun
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou510060, Guangdong Province, China
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou510060, Guangdong Province, China
| | - Jinsong Lei
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou510060, Guangdong Province, China
| | - Shaoquan Zheng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou510060, Guangdong Province, China
- Breast Disease Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou510000, Guangdong Province, China
| | - Yutian Zou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou510060, Guangdong Province, China
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7
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Margvelani G, Welden JR, Maquera AA, Van Eyk JE, Murray C, Miranda Sardon SC, Stamm S. Influence of FTDP-17 mutants on circular Tau RNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.08.556913. [PMID: 37786725 PMCID: PMC10541600 DOI: 10.1101/2023.09.08.556913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
At least 53 mutations in the microtubule associated protein tau gene (MAPT) have been identified that cause frontotemporal dementia. 47 of these mutations are localized between exons 7 and 13. They could thus affect the formation of circular RNAs (circRNAs) from the MAPT gene that occur through backsplicing from exon 12 to either exon 10 or exon 7. We analyzed representative mutants and found that five FTDP-17 mutations increase the formation of 12➔7 circRNA and three different mutations increase the amount of 12➔10 circRNA. CircRNAs are translated after undergoing adenosine to inosine RNA editing, catalyzed by ADAR enzymes. We found that the interferon induced ADAR1-p150 isoform has the strongest effect on circTau RNA translation. ADAR1-p150 activity had a stronger effect on circTau RNA expression and strongly decreased 12➔7 circRNA, but unexpectedly increased 12➔10 circRNA. In both cases, ADAR-activity strongly promoted translation of circTau RNAs. Unexpectedly, we found that the 12➔7 circTau protein interacts with eukaryotic initiation factor 4B (eIF4B), which is reduced by four FTDP-17 mutations located in the second microtubule domain. These are the first studies of the effect of human mutations on circular RNA formation and translation. They show that point mutations influence circRNA expression levels, likely through changes in the secondary pre-mRNA structures. The effect of the mutations is surpassed by editing of the circular RNAs, leading to their translation. Thus, circular RNAs and their editing status should be considered when analyzing FTDP-17 mutations. Highlights 47/53 known FTDP-17 mutations are located in regions that could influence generation of circular RNAs from the MAPT geneCircular Tau RNAs are translated after adenosine to inosine RNA editing, most effectively caused by ADAR1-p150FTDP-17 mutations influence both circTau RNA and circTau protein expression levelsCircTau protein expression levels do not correlate with circTau RNA expression levelsCircTau proteins bind to eukaryotic initiation factor 4B, which is antagonized by FTDP-17 mutations in exon 10. Graphic Abstract
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8
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Unti MJ, Jaffrey SR. Highly efficient cellular expression of circular mRNA enables prolonged protein expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.11.548538. [PMID: 37503010 PMCID: PMC10369907 DOI: 10.1101/2023.07.11.548538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
A major problem with mRNA therapeutics is the limited duration of protein expression due to the short half-life of mRNA. New approaches for generating highly stable circular mRNA in vitro have allowed increased duration of protein expression. However, it remains difficult to genetically encode circular mRNAs in mammalian cells, which limits the use of circular mRNA in cell-derived therapeutics. Here we describe the adaptation of the Tornado (Twister-optimized RNA for durable overexpression) system to achieve in-cell synthesis of circular mRNAs. We identify the promoter and internal ribosomal entry site (IRES) that result in high levels of protein expression in cells. We then show that these circular mRNAs can be packaged into virus-like particles (VLPs) thus enabling prolonged protein expression. Overall, these data describe a platform for synthesis of circular mRNAs and how these circular mRNAs can markedly enhance the ability of VLPs to function as a mRNA delivery tool.
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9
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Wang P, Zhao D, Li J, Su J, Zhang C, Li S, Fan F, Dai Z, Liao X, Mao Z, Bi C, Zhang X. Artificial Diploid Escherichia coli by a CRISPR Chromosome-Doubling Technique. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205855. [PMID: 36642845 PMCID: PMC9982549 DOI: 10.1002/advs.202205855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Synthetic biology has been represented by the creation of artificial life forms at the genomic scale. In this work, a CRISPR-based chromosome-doubling technique is designed to first construct an artificial diploid Escherichia coli cell. The stable single-cell diploid E. coli is isolated by both maximal dilution plating and flow cytometry, and confirmed with quantitative PCR, fluorescent in situ hybridization, and third-generation genome sequencing. The diploid E. coli has a greatly reduced growth rate and elongated cells at 4-5 µm. It is robust against radiation, and the survival rate after exposure to UV increased 40-fold relative to WT. As a novel life form, the artificial diploid E. coli is an ideal substrate for research fundamental questions in life science concerning polyploidy. And this technique may be applied to other bacteria.
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Affiliation(s)
- Pengju Wang
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
| | - Dongdong Zhao
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
| | - Ju Li
- College of Life ScienceTianjin Normal UniversityTianjin300382P. R. China
| | - Junchang Su
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
- School of Biological EngineeringDalian Polytechnic UniversityDalian116034P. R. China
| | - Chunzhi Zhang
- School of Biological EngineeringDalian Polytechnic UniversityDalian116034P. R. China
| | - Siwei Li
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
| | - Feiyu Fan
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
| | - Zhubo Dai
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
| | - Xiaoping Liao
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
- Biodesign CenterKey Laboratory of Systems Microbial BiotechnologyTianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
| | - Zhitao Mao
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
- Biodesign CenterKey Laboratory of Systems Microbial BiotechnologyTianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
| | - Changhao Bi
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
| | - Xueli Zhang
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
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Liu L, Li W, Li J, Zhao D, Li S, Jiang G, Wang J, Chen X, Bi C, Zhang X. Circular Guide RNA for Improved Stability and CRISPR-Cas9 Editing Efficiency in Vitro and in Bacteria. ACS Synth Biol 2023; 12:350-359. [PMID: 36538017 DOI: 10.1021/acssynbio.2c00381] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Due to its intrinsic RNA properties, guide RNA (gRNA) is the least stable component of the CRISPR-Cas9 complex and is a major target for modification and engineering to increase the stability of the system. While most strategies involve chemical modification and special processes, we created a more stable gRNA with an easy-to-use biological technique. Since circular RNAs are theoretically immune to all RNA exonucleases, we attempted to construct a circular gRNA (cgRNA) employing the autocatalytic splicing mechanism of the RNA cyclase ribozyme. First, the formation of the cgRNA, which has a length requirement, was optimized in vivo in E. coli cells. It was found that a cgRNA with an insert length of 251 bp, designated 251cgRNA, was functional. More importantly, cgRNA increased the editing efficiency of the tested base editors relative to normal linear gRNA. The cgRNAs were more stable in vitro under all tested temperature conditions and maintained their function for 24 h at 37 °C, while linear gRNAs completely lost their activity within 8 h. Enzymatically purified 251cgRNA demonstrated even higher stability, which was obviously presented on gels after 48 h at 37 °C, and maintained partial function. By inserting a homologous arm into the 251cgRNA to 251HAcgRNA cassette, the circularization efficiency reached 88.2%, and the half-life of 251HAcgRNA was 30 h, very similar to that of purified 251cgRNA. This work provides a simple innovative strategy to greatly increase the stability of gRNA both in vivo in E. coli and in vitro, with no additional cost or labor. We think this work is very interesting and might revolutionize the form of gRNAs people are using in research and therapeutic applications.
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Affiliation(s)
- Li Liu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300453, China.,China Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,Department of Biomedical Sciences, University of Science and Technology of China, Hefei 230026, P.R. China
| | - Wenbo Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300453, China.,China Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ju Li
- College of Life Science, Tianjin Normal University, Tianjin 300387, China
| | - Dongdong Zhao
- China Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,China Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Siwei Li
- China Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,China Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Guo Jiang
- China Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,China Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jie Wang
- China Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,China Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xuxu Chen
- Guangxi Normal University, Guilin 541001, China
| | - Changhao Bi
- China Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,China Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xueli Zhang
- China Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,China Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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11
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Lao N, Barron N. Enhancing recombinant protein and viral vector production in mammalian cells by targeting the YTHDF readers of N 6 -methyladenosine in mRNA. Biotechnol J 2023; 18:e2200451. [PMID: 36692010 DOI: 10.1002/biot.202200451] [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: 09/02/2022] [Revised: 12/20/2022] [Accepted: 01/19/2023] [Indexed: 01/25/2023]
Abstract
N6 -methyladenosine (m6A) is the most abundant internal modification on eukaryotic mRNA and has been implicated in a wide range of fundamental cellular processes. This modification is regulated and interpreted by a set of writer, eraser, and reader proteins. To date, there have been no reports on the potential of mRNA epigenetic regulators to influence recombinant protein expression in mammalian cells. In this study, the potential of manipulating the expression of the m6A YTH domain-containing readers, YTHDF1, 2 and 3 to improve recombinant protein yield based on their role in regulating mRNA stability and promoting translation were evaluated. Using siRNA-mediated gene depletion, cDNA over-expression, and methylation-specific RNA immunoprecipitation, it is demonstrated that (i) knock-down of YTHDF2 enhances (~2-fold) the levels of recombinant protein derived from GFP and EPO transgenes in CHO cells; (ii) the effects of YTHDF2 depletion on transgene expression is m6A-mediated; and (iii) YTHDF2 depletion, or over-expression of YTHDF1 increases viral protein expression and yield of infectious lentiviral (LV) particles (~2-3-fold) in HEK293 cells. We conclude that various transgenes can be subjected to regulation by m6A regulators in mammalian cell lines and that these findings demonstrate the utility of epitranscriptomic-based approaches to host cell line engineering for improved recombinant protein and viral vector production.
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Affiliation(s)
- Nga Lao
- National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Niall Barron
- National Institute for Bioprocessing Research and Training, Dublin, Ireland.,School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
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12
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Deviatkin AA, Simonov RA, Trutneva KA, Maznina AA, Soroka AB, Kogan AA, Feoktistova SG, Khavina EM, Mityaeva ON, Volchkov PY. Cap-Independent Circular mRNA Translation Efficiency. Vaccines (Basel) 2023; 11:vaccines11020238. [PMID: 36851116 PMCID: PMC9967249 DOI: 10.3390/vaccines11020238] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Recently, the mRNA platform has become the method of choice in vaccine development to find new ways to fight infectious diseases. However, this approach has shortcomings, namely that mRNA vaccines require special storage conditions, which makes them less accessible. This instability is due to the fact that the five-prime and three-prime ends of the mRNA are a substrate for the ubiquitous exoribonucleases. To address the problem, circular mRNAs have been proposed for transgene delivery as they lack these ends. Notably, circular RNAs do not have a capped five-prime end, which makes it impossible to initiate translation canonically. In this review, we summarize the current knowledge on cap-independent translation initiation methods and discuss which approaches might be most effective in developing vaccines and other biotechnological products based on circular mRNAs.
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Affiliation(s)
- Andrei A. Deviatkin
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
- Endocrinology Research Centre, 117036 Moscow, Russia
| | - Ruslan A. Simonov
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Kseniya A. Trutneva
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
- Endocrinology Research Centre, 117036 Moscow, Russia
| | - Anna A. Maznina
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
- Endocrinology Research Centre, 117036 Moscow, Russia
| | - Anastasiia B. Soroka
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
| | - Anna A. Kogan
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
| | - Sofya G. Feoktistova
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
- Endocrinology Research Centre, 117036 Moscow, Russia
| | - Elena M. Khavina
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
- Faculty of Biology, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Olga N. Mityaeva
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
- Endocrinology Research Centre, 117036 Moscow, Russia
| | - Pavel Y. Volchkov
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
- Endocrinology Research Centre, 117036 Moscow, Russia
- Correspondence:
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13
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Welden JR, Margvelani G, Arizaca Maquera KA, Gudlavalleti B, Miranda Sardón S, Campos A, Robil N, Lee D, Hernandez A, Wang WX, Di J, de la Grange P, Nelson P, Stamm S. RNA editing of microtubule-associated protein tau circular RNAs promotes their translation and tau tangle formation. Nucleic Acids Res 2022; 50:12979-12996. [PMID: 36533443 PMCID: PMC9825173 DOI: 10.1093/nar/gkac1129] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/06/2022] [Accepted: 11/09/2022] [Indexed: 12/23/2022] Open
Abstract
Aggregation of the microtubule-associated protein tau characterizes tauopathies, including Alzheimer's disease and frontotemporal lobar degeneration (FTLD-Tau). Gene expression regulation of tau is complex and incompletely understood. Here we report that the human tau gene (MAPT) generates two circular RNAs (circRNAs) through backsplicing of exon 12 to either exon 7 (12→7 circRNA) or exon 10 (12→10 circRNA). Both circRNAs lack stop codons. The 12→7 circRNA contains one start codon and is translated in a rolling circle, generating a protein consisting of multimers of the microtubule-binding repeats R1-R4. For the 12→10 circRNA, a start codon can be introduced by two FTLD-Tau mutations, generating a protein consisting of multimers of the microtubule-binding repeats R2-R4, suggesting that mutations causing FTLD may act in part through tau circRNAs. Adenosine to inosine RNA editing dramatically increases translation of circRNAs and, in the 12→10 circRNA, RNA editing generates a translational start codon by changing AUA to AUI. Circular tau proteins self-aggregate and promote aggregation of linear tau proteins. Our data indicate that adenosine to inosine RNA editing initiates translation of human circular tau RNAs, which may contribute to tauopathies.
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Affiliation(s)
| | - Giorgi Margvelani
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | | | - Bhavani Gudlavalleti
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Sandra C Miranda Sardón
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Alexandre Rosa Campos
- Sanford Burnham Prebys Medical Discovery Institute Proteomics Core, La Jolla, CA, USA
| | | | - Daniel C Lee
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA,Alzheimer's Disease Research Center Neuroscience, University of Kentucky, Lexington, KY, USA
| | | | - Wang-Xia Wang
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA,Alzheimer's Disease Research Center and Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
| | - Jing Di
- Alzheimer's Disease Research Center and Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
| | | | - Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA,Alzheimer's Disease Research Center and Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
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14
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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: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022]
Abstract
Circular RNAs (circRNA) is a class of natural (biogenic) or synthetic closed RNA without 5' or 3' ends. Meanwhile, their unique covalently-closed structures of circRNA prevent RNA degradation by exonucleases, thereby empowering them with high pharmaceutical stability and biostability relative to current standard-of-care linear mRNA. Natural circRNA can be non-coding RNAs as well as protein-coding RNA, the latter of which was recently discovered. The physiological functions of biogenic circRNAs, which largely remain elusive, include protein and gene sponges, cell activity modulators, and protein translation. The discovery that the circRNA levels can be correlated with some human diseases empowers circRNA with the potential as a novel type of disease biomarkers and a noncanonical class of therapeutic targets. Recently, synthetic circRNA have been engineered to explore their applications as a novel class of mRNA therapeutics and vaccines. In this review, we will discuss the current understanding of the biogenesis and physiological functions of natural circRNAs, the approaches to circRNA synthesis, and current research in the exploration of endogenous circRNAs as novel therapeutic targets and testing circRNAs as an emerging class of RNA therapeutics and vaccines.
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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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15
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Engineering Circularized mRNAs for the Production of Spider Silk Proteins. Appl Environ Microbiol 2022; 88:e0002822. [PMID: 35384707 DOI: 10.1128/aem.00028-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Biomaterials offer unique properties that make them irreplaceable for next-generation applications. Fibrous proteins, such as various caterpillar silks and especially spider silk, have strength and toughness not found in human-made materials. In early studies, proteins containing long tandem repeats, such as major ampullate spidroin 1 (MaSp1) and flagelliform silk protein (FSLP), were produced using a large DNA template composed of many tandem repeats. The hierarchical DNA assembly of the DNA template is very time-consuming and labor-intensive, which makes the fibrous proteins difficult to study and engineer. In this study, we designed a circularized mRNA (cmRNA) employing the RNA cyclase ribozyme mechanism. cmRNAs encoding spider silk protein MaSp1 and FSLP were designed based on only one unit of the template sequence but provide ribosomes with a circular and infinite translation template for production of long peptides containing tandem repeats. Using this technique, cmRNAs of MaSp1 and FSLP were successfully generated with circularization efficiencies of 8.5% and 36.7%, respectively, which supported the production of recombinant MaSp1 and FSLP larger than 110 and 88 kDa, containing tens of repeat units. Western blot analysis and mass spectrometry confirmed the authenticity of MaSp1 and FSLP, which were produced at titers of 22.1 and 81.5 mg · liter-1, respectively. IMPORTANCE Spider silk is a biomaterial with superior properties. However, its heterologous expression template is hard to construct. The cmRNA technique simplifies the construction and expression strategy by proving the ribosome a circular translation template for expression of long peptides containing tandem repeats. This revolutionary technique will allow researchers to easily build, study, and experiment with any fiber proteins with sequences either from natural genes or artificial designs. We expect a significantly accelerated development of fibrous protein-based biomaterials with the cmRNA technique.
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16
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Li ZJ, Zhang ZX, Xu Y, Shi TQ, Ye C, Sun XM, Huang H. CRISPR-Based Construction of a BL21 (DE3)-Derived Variant Strain Library to Rapidly Improve Recombinant Protein Production. ACS Synth Biol 2022; 11:343-352. [PMID: 34919397 DOI: 10.1021/acssynbio.1c00463] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Escherichia coli BL21 (DE3) is the most widely used host for recombinant protein expression. However, not every protein can be highly expressed in BL21 (DE3), so individual optimization strategies are often required for different proteins, which is time-consuming and difficult to apply rapidly for industrial production. Constructing more hosts is a good choice to enrich protein expression selection. The expression level of T7 RNAP is the core control node of the pET expression system, so regulating its expression level is an effective way of improving the production of difficult-to-express proteins. Various BL21 (DE3)-derived variant hosts with different translation levels of T7 RNAP could be obtained by changing the ribosomal binding site (RBS) sequences of T7 RNAP in a genome. Here, a BL21 (DE3)-derived variant strain library with different RBS sequences of T7 RNAP was constructed using a base editor and CRISPR-Cas9. Notably, the CRISPR-Cas9 system combined with degenerate primers enabled the construction of an RBS library with 87.5% of the theoretical coverage in single editing, which is more convenient and efficient than the use of a base editor. The expression level of a target gene in the variant strain library ranged from 28 to 220% of the parental strain. Furthermore, a high-throughput host-screening platform for recombinant protein production was constructed, which enabled us to obtain the best expression host for certain target proteins in only 3 days. As a proof of concept, the production of all eight difficult-to-express proteins was greatly improved, including autolytic protein, membrane proteins, antimicrobial peptides, and hardly soluble proteins. Among them, the expression of glucose dehydrogenase in the best host exhibited a 298-fold increase compared to the parental strain. This strategy is simple and effective, requires no advanced equipment, and can be carried out in any laboratory.
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Affiliation(s)
- Zi-Jia Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People’s Republic of China
| | - Zi-Xu Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People’s Republic of China
| | - Yan Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People’s Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People’s Republic of China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People’s Republic of China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People’s Republic of China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People’s Republic of China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People’s Republic of China
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17
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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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18
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Yang Q, Li F, He AT, Yang BB. Circular RNAs: Expression, localization, and therapeutic potentials. Mol Ther 2021; 29:1683-1702. [PMID: 33484969 PMCID: PMC8116570 DOI: 10.1016/j.ymthe.2021.01.018] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/15/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are RNAs with a unique circular structure that is generated from back-splicing processes. These circular molecules were discovered more than 40 years ago but failed to raise scientific interest until lately. Increasing studies have found that these circular RNAs might not just be byproducts of the splicing process but possess important regulatory functions through different cellular events. Most circular RNAs are currently being studied in the field of cancer, and many of them have been confirmed to be involved in the process of tumorigenesis. However, many circular RNAs are implicated in the developmental stages of diseases other than cancer. In this review, we focus on discussing the role of circular RNAs in non-cancer diseases, especially in cardiovascular diseases. Following the summary of the life cycle of circRNAs, we provide input on studying circRNA-protein interactions based on our experience, which modulate protein translocation. Furthermore, we outline the potential of circRNAs to be potent biomarkers, effective therapeutic targets, and potential treatments in cardiovascular diseases as well as other non-cancer fields.
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Affiliation(s)
- Qiwei Yang
- Sunnybrook Research Institute, Toronto, ON, Canada; Medical Research Center, Second Hospital of Jilin University, Changchun, China; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Feiya Li
- Sunnybrook Research Institute, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Alina T He
- Sunnybrook Research Institute, Toronto, ON, Canada
| | - Burton B Yang
- Sunnybrook Research Institute, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada.
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19
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Jiang Y, Chen X, Zhang W. Overexpression-based detection of translatable circular RNAs is vulnerable to coexistent linear RNA byproducts. Biochem Biophys Res Commun 2021; 558:189-195. [PMID: 33940551 DOI: 10.1016/j.bbrc.2021.04.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/12/2021] [Indexed: 12/11/2022]
Abstract
In RNA field, the demarcation between coding and non-coding has been negotiated by the recent discovery of occasionally translated circular RNAs (circRNAs). Although absent of 5' cap structure, circRNAs can be translated cap-independently. Complementary intron-mediated overexpression is one of the most utilized methodologies for circRNA research but not without bearing echoing skepticism for its poorly defined mechanism and latent coexistent side products. In this study, leveraging such circRNA overexpression system, we have interrogated the protein-coding potential of 30 human circRNAs containing infinite open reading frames in HEK293T cells. Surprisingly, pervasive translation signals are detected by immunoblotting. However, intensive mutagenesis reveals that numerous translation signals are generated independently of circRNA synthesis. We have developed a dual tag strategy to isolate translation noise and directly demonstrate that the spurious translation signals originate from cryptically spliced linear transcripts. The concomitant linear RNA byproducts, presumably concatemers, can be translated to allow pseudo rolling circle translation signals, and can involve backsplicing junction (BSJ) to disqualify the BSJ-based evidence for circRNA translation. We also find non-AUG start codons may engage in the translation initiation of circRNAs. Taken together, our systematic evaluation sheds light on heterogeneous translational outputs from circRNA overexpression vector and comes with a caveat that ectopic overexpression technique necessitates extremely rigorous control setup in circRNA translation and functional investigation.
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Affiliation(s)
- Yanyi Jiang
- Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong Province, China.
| | - Xiaofan Chen
- Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong Province, China
| | - Wei Zhang
- Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong Province, China; Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen, Guangdong Province, China.
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20
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Liang X, Chen H, Li L, An R, Komiyama M. Ring-Structured DNA and RNA as Key Players In Vivoand In Vitro. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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21
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Prats AC, David F, Diallo LH, Roussel E, Tatin F, Garmy-Susini B, Lacazette E. Circular RNA, the Key for Translation. Int J Mol Sci 2020; 21:E8591. [PMID: 33202605 PMCID: PMC7697609 DOI: 10.3390/ijms21228591] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
It was thought until the 1990s that the eukaryotic translation machinery was unable to translate a circular RNA. However internal ribosome entry sites (IRESs) and m6A-induced ribosome engagement sites (MIRESs) were discovered, promoting 5' end-independent translation initiation. Today a new family of so-called "noncoding" circular RNAs (circRNAs) has emerged, revealing the pivotal role of 5' end-independent translation. CircRNAs have a strong impact on translational control via their sponge function, and form a new mRNA family as they are translated into proteins with pathophysiological roles. While there is no more doubt about translation of covalently closed circRNA, the linearity of canonical mRNA is only theoretical: it has been shown for more than thirty years that polysomes exhibit a circular form and mRNA functional circularization has been demonstrated in the 1990s by the interaction of initiation factor eIF4G with poly(A) binding protein. More recently, additional mechanisms of 3'-5' interaction have been reported, including m6A modification. Functional circularization enhances translation via ribosome recycling and acceleration of the translation initiation rate. This update of covalently and noncovalently closed circular mRNA translation landscape shows that RNA with circular shape might be the rule for translation with an important impact on disease development and biotechnological applications.
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Affiliation(s)
- Anne-Catherine Prats
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1048, Inserm, Université de Toulouse UT3, 1, Avenue Jean Poulhes, BP 84225, 31432 Toulouse CEDEX 4, France; (F.D.); (L.H.D.); (E.R.); (F.T.); (B.G.-S.); (E.L.)
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22
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Circular RNAs in cancer: limitations in functional studies and diagnostic potential. Semin Cancer Biol 2020; 75:49-61. [PMID: 33035655 DOI: 10.1016/j.semcancer.2020.10.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/15/2020] [Accepted: 10/02/2020] [Indexed: 02/06/2023]
Abstract
Circular RNAs (circRNAs) are a large class of noncoding RNAs, generated from a process called back-splicing, that possess critical regulatory functions in many cellular events. A large body of literature has reported various circRNA functions and their underlying mechanisms, including sponging miRNA, exerting transcriptional and translational regulation, interacting with proteins, and translating into peptides and proteins. CircRNA dysregulation has been implicated in many cancers, including lung, breast, liver, gastric, colorectal, and ovarian cancer. They are detectable in bodily fluids and relatively stable, making them potential cancer biomarker candidates. Furthermore, targeting circRNA expression levels is a potential therapeutic approach for treating cancers. In this review, we describe the functional mechanisms of circRNAs and discuss limitations of current mechanism studies. Following this, we outline the potential of circRNAs to be effective biomarkers in various cancers and present circRNA-based therapeutic approaches. Finally, we discuss challenges in using circRNAs as diagnostic and therapeutic tools and propose future research directions.
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23
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Sun XM, Zhang ZX, Wang LR, Wang JG, Liang Y, Yang HF, Tao RS, Jiang Y, Yang JJ, Yang S. Downregulation of T7 RNA polymerase transcription enhances pET-based recombinant protein production in Escherichia coli BL21 (DE3) by suppressing autolysis. Biotechnol Bioeng 2020; 118:153-163. [PMID: 32897579 DOI: 10.1002/bit.27558] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/25/2020] [Accepted: 08/30/2020] [Indexed: 12/15/2022]
Abstract
Escherichia coli BL21 (DE3) is an excellent and widely used host for recombinant protein production. Many variant hosts were developed from BL21 (DE3), but improving the expression of specific proteins remains a major challenge in biotechnology. In this study, we found that when BL21 (DE3) overexpressed glucose dehydrogenase (GDH), a significant industrial enzyme, severe cell autolysis was induced. Subsequently, we observed this phenomenon in the expression of 10 other recombinant proteins. This precludes a further increase of the produced enzyme activity by extending the fermentation time, which is not conducive to the reduction of industrial enzyme production costs. Analysis of membrane structure and messenger RNA expression analysis showed that cells could underwent a form of programmed cell death (PCD) during the autolysis period. However, blocking three known PCD pathways in BL21 (DE3) did not completely alleviate autolysis completely. Consequently, we attempted to develop a strong expression host resistant to autolysis by controlling the speed of recombinant protein expression. To find a more suitable protein expression rate, the high- and low-strength promoter lacUV5 and lac were shuffled and recombined to yield the promoter variants lacUV5-1A and lac-1G. The results showed that only one base in lac promoter needs to be changed, and the A at the +1 position was changed to a G, resulting in the improved host BL21 (DE3-lac1G), which resistant to autolysis. As a consequence, the GDH activity at 43 h was greatly increased from 37.5 to 452.0 U/ml. In scale-up fermentation, the new host was able to produce the model enzyme with a high rate of 89.55 U/ml/h at 43 h, compared to only 3 U/ml/h achieved using BL21 (DE3). Importantly, BL21 (DE3-lac1G) also successfully improved the production of 10 other enzymes. The engineered E. coli strain constructed in this study conveniently optimizes recombinant protein overexpression by suppressing cell autolysis, and shows great potential for industrial applications.
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Affiliation(s)
- Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Zi-Xu Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Ling-Ru Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu, China
| | | | - Yan Liang
- HuaRui Biotechnology Company, Huzhou, Zhejiang, China
| | - Hai-Feng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Rong-Sheng Tao
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, Zhejiang, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, Zhejiang, China
| | - Jun-Jie Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, Zhejiang, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, Zhejiang, China
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24
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Pre-mRNA structures forming circular RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194410. [DOI: 10.1016/j.bbagrm.2019.194410] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 12/25/2022]
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25
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Reinventing the Wheel: Synthetic Circular RNAs for Mammalian Cell Engineering. Trends Biotechnol 2019; 38:217-230. [PMID: 31421856 DOI: 10.1016/j.tibtech.2019.07.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 12/28/2022]
Abstract
The circular RNA renaissance is upon us. Recent reports demonstrate applications of synthetic circular RNA molecules as gene therapies and in the production of biologics from cell-based expression systems. Circular RNAs are covalently closed loop RNA species that are formed naturally through noncolinear splicing of pre-mRNA. Although once thought to be noncoding artefacts from splicing errors, it is now accepted that circular RNAs are abundant and have diverse functions in gene regulation and protein coding in eukaryotes. Numerous reports have investigated circular RNAs in various diseases, but the promise of synthetic circular RNAs in the production of recombinant proteins and as RNA-based therapies is only now coming into focus. This review highlights reported uses of synthetic circular RNAs and describes methods for generating these molecules.
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Diallo LH, Tatin F, David F, Godet AC, Zamora A, Prats AC, Garmy-Susini B, Lacazette E. How are circRNAs translated by non-canonical initiation mechanisms? Biochimie 2019; 164:45-52. [PMID: 31265859 DOI: 10.1016/j.biochi.2019.06.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/27/2019] [Indexed: 12/22/2022]
Abstract
Circular RNAs (circRNAs) are covalently closed RNA loops produced by a very large number of expressed eukaryotic genes. Initially considered as splicing background and/or splicing side products, recent studies have shown that they are evolutionary conserved and abundant in cells. Yet, their functions remain largely unknown. Because of their circular shape, they were initially categorized as non-coding RNAs. However, recent studies based on mass spectrometry analysis indicate that some cytoplasmic circRNAs are effectively translated into detectable peptides. This raises the interesting question of which mechanisms regulate the translation initiation of those circular transcripts, i.e. unable to recruit the small ribosome subunit through the 5' cap. A possible mechanism for alternative translation initiation is the presence of an IRES (Internal Ribosome Entry Site) that allows direct recruitment of initiation factors and ribosomes on the RNA independently from the cap. This is the case for several circRNAs that exhibit IRESs upstream from the start codon. Yet, another process seems to be involved in initiating the translation of circRNAs: the presence of N6-methyladenosine (m6A) residues. These m6A can promote cap-independent translation and have been shown to be enriched in circRNAs. Interestingly, these two alternative translation initiation processes are generally activated under cellular stress to allow expression of specific stress response genes. These discoveries therefore link circRNA translation to cellular response to stress conditions, raising new enquiries about the regulation of circRNA expression under stress conditions and their functions. This review provides a state of the art on this emerging area.
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Affiliation(s)
- Leïla Halidou Diallo
- UMR 1048-I2MC, Université de Toulouse UT3, INSERM, 1 Avenue Jean Poulhès, BP84225, 31432, Toulouse, Cedex 4, France
| | - Florence Tatin
- UMR 1048-I2MC, Université de Toulouse UT3, INSERM, 1 Avenue Jean Poulhès, BP84225, 31432, Toulouse, Cedex 4, France
| | - Florian David
- UMR 1048-I2MC, Université de Toulouse UT3, INSERM, 1 Avenue Jean Poulhès, BP84225, 31432, Toulouse, Cedex 4, France
| | - Anne-Claire Godet
- UMR 1048-I2MC, Université de Toulouse UT3, INSERM, 1 Avenue Jean Poulhès, BP84225, 31432, Toulouse, Cedex 4, France
| | - Audrey Zamora
- UMR 1048-I2MC, Université de Toulouse UT3, INSERM, 1 Avenue Jean Poulhès, BP84225, 31432, Toulouse, Cedex 4, France
| | - Anne-Catherine Prats
- UMR 1048-I2MC, Université de Toulouse UT3, INSERM, 1 Avenue Jean Poulhès, BP84225, 31432, Toulouse, Cedex 4, France
| | - Barbara Garmy-Susini
- UMR 1048-I2MC, Université de Toulouse UT3, INSERM, 1 Avenue Jean Poulhès, BP84225, 31432, Toulouse, Cedex 4, France
| | - Eric Lacazette
- UMR 1048-I2MC, Université de Toulouse UT3, INSERM, 1 Avenue Jean Poulhès, BP84225, 31432, Toulouse, Cedex 4, France.
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