1
|
Zhang X, Van Treeck B, Horton CA, McIntyre JJR, Palm SM, Shumate JL, Collins K. Harnessing eukaryotic retroelement proteins for transgene insertion into human safe-harbor loci. Nat Biotechnol 2024:10.1038/s41587-024-02137-y. [PMID: 38379101 DOI: 10.1038/s41587-024-02137-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/10/2024] [Indexed: 02/22/2024]
Abstract
Current approaches for inserting autonomous transgenes into the genome, such as CRISPR-Cas9 or virus-based strategies, have limitations including low efficiency and high risk of untargeted genome mutagenesis. Here, we describe precise RNA-mediated insertion of transgenes (PRINT), an approach for site-specifically primed reverse transcription that directs transgene synthesis directly into the genome at a multicopy safe-harbor locus. PRINT uses delivery of two in vitro transcribed RNAs: messenger RNA encoding avian R2 retroelement-protein and template RNA encoding a transgene of length validated up to 4 kb. The R2 protein coordinately recognizes the target site, nicks one strand at a precise location and primes complementary DNA synthesis for stable transgene insertion. With a cultured human primary cell line, over 50% of cells can gain several 2 kb transgenes, of which more than 50% are full-length. PRINT advantages include no extragenomic DNA, limiting risk of deleterious mutagenesis and innate immune responses, and the relatively low cost, rapid production and scalability of RNA-only delivery.
Collapse
Affiliation(s)
- Xiaozhu Zhang
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Briana Van Treeck
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Connor A Horton
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Jeremy J R McIntyre
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Sarah M Palm
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Justin L Shumate
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.
| |
Collapse
|
2
|
Chen MJ, Gatignol A, Scarborough RJ. The discovery and development of RNA-based therapies for treatment of HIV-1 infection. Expert Opin Drug Discov 2023; 18:163-179. [PMID: 36004505 DOI: 10.1080/17460441.2022.2117296] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Long-term control of HIV-1 infection can potentially be achieved using autologous stem cell transplants with gene-modified cells. Non-coding RNAs represent a diverse class of therapeutic agents including ribozymes, RNA aptamers and decoys, small interfering RNAs, short hairpin RNAs, and U1 interference RNAs that can be designed to inhibit HIV-1 replication. They have been engineered for delivery as drugs to complement current HIV-1 therapies and as gene therapies for a potential HIV-1 functional cure. AREAS COVERED This review surveys the past three decades of development of these RNA technologies with a focus on their efficacy and safety for treating HIV-1 infections. We describe the mechanisms of each RNA-based agent, targets they have been developed against, efforts to enhance their stability and efficacy, and we evaluate their performance in past and ongoing preclinical and clinical trials. EXPERT OPINION RNA-based technologies are among the top candidates for gene therapies where they can be stably expressed for long-term suppression of HIV-1. Advances in both gene and drug delivery strategies and improvements to non-coding RNA stability and antiviral properties will cooperatively drive forward progress in improving drug therapy and engineering HIV-1 resistant cells.
Collapse
Affiliation(s)
- Michelle J Chen
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada.,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Anne Gatignol
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada.,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada.,Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Robert J Scarborough
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada.,Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| |
Collapse
|
3
|
Najeh S, Zandi K, Djerroud S, Kharma N, Perreault J. Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes. Methods Mol Biol 2021; 2167:91-111. [PMID: 32712917 DOI: 10.1007/978-1-0716-0716-9_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Pseudoknots are important motifs for stabilizing the structure of functional RNAs. As an example, pseudoknotted hammerhead ribozymes are highly active compared to minimal ribozymes. The design of new RNA sequences that retain the function of a model RNA structure includes taking in account pseudoknots presence in the structure, which is usually a challenge for bioinformatics tools. Our method includes using "Enzymer," a software for designing RNA sequences with desired secondary structures that may include pseudoknots. Enzymer implements an efficient stochastic search and optimization algorithm to sample RNA sequences from low ensemble defect mutational landscape of an initial design template to generate an RNA sequence that is predicted to fold into the desired target structure.
Collapse
Affiliation(s)
- Sabrine Najeh
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, QC, Canada
| | - Kasra Zandi
- Software Engineering and Computer Science Department, Concordia University, Montreal, QC, Canada
| | - Samia Djerroud
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, QC, Canada
| | - Nawwaf Kharma
- Electrical and Computer Engineering Department, Concordia University, Montreal, QC, Canada.
| | - Jonathan Perreault
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, QC, Canada.
| |
Collapse
|
4
|
Lee TS, Radak BK, Harris ME, York DM. A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation. ACS Catal 2016; 6:1853-1869. [PMID: 27774349 DOI: 10.1021/acscatal.5b02158] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA enzymes serve as a potentially powerful platform from which to design catalysts and engineer new biotechnology. A fundamental understanding of these systems provides insight to guide design. The hepatitis delta virus ribozyme (HDVr) is a small, self-cleaving RNA motif widely distributed in nature, that has served as a paradigm for understanding basic principles of RNA catalysis. Nevertheless, questions remain regarding the precise roles of divalent metal ions and key nucleotides in catalysis. In an effort to establish a reaction mechanism model consistent with available experimental data, we utilize molecular dynamics simulations to explore different conformations and metal ion binding modes along the HDVr reaction path. Building upon recent crystallographic data, our results provide a dynamic model of the HDVr reaction mechanism involving a conformational switch between multiple non-canonical G25:U20 base pair conformations in the active site. These local nucleobase dynamics play an important role in catalysis by modulating the metal binding environments of two Mg2+ ions that support catalysis at different steps of the reaction pathway. The first ion plays a structural role by inducing a base pair flip necessary to obtain the catalytic fold in which C75 moves towards to the scissile phosphate in the active site. Ejection of this ion then permits a second ion to bind elsewhere in the active site and facilitate nucleophile activation. The simulations collectively describe a mechanistic scenario that is consistent with currently available experimental data from crystallography, phosphorothioate substitutions, and chemical probing studies. Avenues for further experimental verification are suggested.
Collapse
Affiliation(s)
- Tai-Sung Lee
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Brian K. Radak
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
- Argonne National Laboratory, Argonne, Illinois 60439, United State
| | - Michael E. Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Darrin M. York
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| |
Collapse
|
5
|
Silencing of amyloid precursor protein expression using a new engineered delta ribozyme. Int J Alzheimers Dis 2012; 2012:947147. [PMID: 22482079 PMCID: PMC3296272 DOI: 10.1155/2012/947147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 11/01/2011] [Indexed: 11/17/2022] Open
Abstract
Alzheimer's disease (AD) etiological studies suggest that an elevation in amyloid-β peptides (Aβ) level contributes to aggregations of the peptide and subsequent development of the disease. The major constituent of these amyloid peptides is the 1 to 40–42 residue peptide (Aβ40−42) derived from amyloid protein precursor (APP). Most likely, reducing Aβ levels in the brain may block both its aggregation and neurotoxicity and would be beneficial for patients with AD. Among the several possible ways to lower Aβ accumulation in the cells, we have selectively chosen to target the primary step in the Aβ cascade, namely, to reduce APP gene expression. Toward this end, we engineered specific SOFA-HDV ribozymes, a new generation of catalytic RNA tools, to decrease APP mRNA levels. Additionally, we demonstrated that APP-ribozymes are effective at decreasing APP mRNA and protein levels as well as Aβ levels in neuronal cells. Our results could lay the groundwork for a new protective treatment for AD.
Collapse
|
6
|
Abstract
Small cis-acting ribozymes have been converted into trans-acting ribozymes possessing the ability to cleave RNA substrates. The Hepatitis Delta Virus (HDV) ribozyme is one of the rare examples of these that is derived from an RNA species that is found in human cells. Consequently, it possesses the natural ability to function in the presence of human proteins in addition to an outstanding stability in human cells, two significant advantages in its use. The development of an additional specific on/off adaptor (SOFA) has led to the production of a new generation of HDV ribozymes with improved specificities that provide a tool with significant potential for future development in the fields of both functional genomics and gene -therapy. SOFA-HDV ribozyme-based gene inactivation systems have been reported in both prokaryotic and eukaryotic cells. Here, a step-by-step approach for the efficient design of highly specific SOFA-HDV ribozymes with a minimum investment of time and effort is described.
Collapse
Affiliation(s)
- Michel V Lévesque
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | |
Collapse
|
7
|
Motard J, Rouxel R, Paun A, von Messling V, Bisaillon M, Perreault JP. A novel ribozyme-based prophylaxis inhibits influenza A virus replication and protects from severe disease. PLoS One 2011; 6:e27327. [PMID: 22110627 PMCID: PMC3215696 DOI: 10.1371/journal.pone.0027327] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 10/13/2011] [Indexed: 12/17/2022] Open
Abstract
Influenza A virus seasonal outbreaks and occasional pandemics represent a global health threat. The high genetic instability of this virus permits rapid escape from the host immune system and emergence of resistance to antivirals. There is thus an urgent need to develop novel approaches for efficient treatment of newly emerging strains. Based on a sequence alignment of representatives from every subtype known to infect humans, we identified nucleic acid regions that are conserved amongst these influenza A populations. We then engineered SOFA-HDV-Ribozymes as therapeutic tools recognizing these conserved regions to catalytically cleave the corresponding viral mRNA targets. The most promising ribozymes were chosen based on an initial in silico screening, and their efficacy was assessed using in vitro cleavage assays. Further characterization of their antiviral effect in cell culture and in mice led to the gradual identification of prophylactic SOFA-HDV-Ribozyme combinations, providing proof-of-principle for the potential of this novel strategy to develop antivirals against genetically highly variable viruses.
Collapse
MESH Headings
- Animals
- Antiviral Agents/metabolism
- Antiviral Agents/pharmacology
- Base Sequence
- Biocatalysis
- Female
- HEK293 Cells
- Hepatitis Delta Virus/enzymology
- Humans
- Influenza A Virus, H1N1 Subtype/drug effects
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/physiology
- Influenza, Human/prevention & control
- Influenza, Human/virology
- Mice
- Nucleoproteins/metabolism
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Catalytic/pharmacology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Recombinant Proteins/pharmacology
- Virus Replication/drug effects
Collapse
Affiliation(s)
- Julie Motard
- Département de biochimie, RNA group/Groupe ARN, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Ronan Rouxel
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Canada
| | - Alexandra Paun
- Département de biochimie, RNA group/Groupe ARN, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Canada
| | | | - Martin Bisaillon
- Département de biochimie, RNA group/Groupe ARN, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Canada
- * E-mail: (JPP); (MB)
| | - Jean-Pierre Perreault
- Département de biochimie, RNA group/Groupe ARN, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Canada
- * E-mail: (JPP); (MB)
| |
Collapse
|
8
|
Lévesque MV, Rouleau SG, Perreault JP. Selection of the most potent specific on/off adaptor-hepatitis delta virus ribozymes for use in gene targeting. Nucleic Acid Ther 2011; 21:241-52. [PMID: 21793786 DOI: 10.1089/nat.2011.0301] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The Hepatitis Delta Virus (HDV) ribozyme, which is well adapted to the environment of the human cell, is an excellent candidate for the future development of gene-inactivation systems. On top of this, a new generation of HDV ribozymes now exists that benefits from the addition of a specific on/off adaptor (specifically the SOFA-HDV ribozymes) which greatly increases both the ribozyme's specificity and its cleavage activity. Unlike RNAi and hammerhead ribozymes, the designing of SOFA-HDV ribozymes to cleave, in trans, given RNA species has never been the object of a systematic optimization study, even with their recent use for the gene knockdown of various targets. This report aims at both improving and clarifying the design process of SOFA-HDV ribozymes. Both the ribozyme and the targeted RNA substrate were analyzed in order to provide new criteria that are useful in the selection of the most potent SOFA-HDV ribozymes. The crucial features present in both the ribozyme's biosensor and blocker, as well as at the target site, were identified and characterized. Simple rules were derived and tested using hepatitis C virus NS5B RNA as a model target. Overall, this method should promote the use of the SOFA-HDV ribozymes in a plethora of applications in both functional genomics and gene therapy.
Collapse
Affiliation(s)
- Michel V Lévesque
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke , Sherbrooke, Québec, Canada
| | | | | |
Collapse
|
9
|
Investigating a new generation of ribozymes in order to target HCV. PLoS One 2010; 5:e9627. [PMID: 20224783 PMCID: PMC2835756 DOI: 10.1371/journal.pone.0009627] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 02/17/2010] [Indexed: 02/08/2023] Open
Abstract
For a long time nucleic acid-based approaches directed towards controlling the propagation of Hepatitis C Virus (HCV) have been considered to possess high potential. Towards this end, ribozymes (i.e. RNA enzymes) that specifically recognize and subsequently catalyze the cleavage of their RNA substrate present an attractive molecular tool. Here, the unique properties of a new generation of ribozymes are taken advantage of in order to develop an efficient and durable ribozyme-based technology with which to target HCV (+) RNA strands. These ribozymes resulted from the coupling of a specific on/off adaptor (SOFA) to the ribozyme domain derived from the Hepatitis Delta Virus (HDV). The former switches cleavage activity “on” solely in the presence of the desired RNA substrate, while the latter was the first catalytic RNA reported to function naturally in human cells, specifically in hepatocytes. In order to maximize the chances for success, a step-by-step approach was used for both the design and the selection of the ribozymes. This approach included the use of both bioinformatics and biochemical methods for the identification of the sites possessing the greatest potential for targeting, and the subsequent in vitro testing of the cleavage activities of the corresponding SOFA-HDV ribozymes. These efforts led to a significant improvement in the ribozymes' designs. The ability of the resulting SOFA-HDV ribozymes to inhibit HCV replication was further examined using a luciferase-based replicon. Although some of the ribozymes exhibited high levels of cleavage activity in vitro, none appears to be a potential long term inhibitor in cellulo. Analysis of recent discoveries in the cellular biology of HCV might explain this failure, as well as provide some ideas on the potential limits of using nucleic acid-based drugs to control the propagation of HCV. Finally, the above conclusions received support from experiments performed using a collection of SOFA-HDV ribozymes directed against HCV (−) strands.
Collapse
|
10
|
Beaudoin JD, Perreault JP. Potassium ions modulate a G-quadruplex-ribozyme's activity. RNA (NEW YORK, N.Y.) 2008; 14:1018-1025. [PMID: 18456841 PMCID: PMC2390810 DOI: 10.1261/rna.963908] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Accepted: 03/01/2008] [Indexed: 05/26/2023]
Abstract
Hepatitis delta virus ribozyme folds into a tightly packed tertiary structure. However, unlike other ribozymes, it does not appear to be able to follow alternative folding pathways. Molecular engineering of the hepatitis delta virus ribozyme led to the development of a ribozyme possessing an endoribonuclease activity that is under the control of a G-quadruplex structure (i.e., a G-quartzyme). This latter species represents an entirely new class of ribozyme. Mutants of this ribozyme were then generated in order to shed light on the modulation of the cleavage activity caused by the presence of the G-quadruplex structure. Kinetic characterization of the G-quartzyme was performed under various single turnover conditions. It was found to be active only in the presence of potassium cations that act as counter ions in the positioning of the four coplanar guanines that form the building block of the G-quadruplex structure. The G-quartzyme behaves as an allosteric ribozyme, with the potassium cations acting as positive effectors with a Hill coefficient of 2.9 +/- 0.2. The conformation transition caused by the presence of the potassium ions is supported by enzymatic and chemical probing of both the inactive (off) and active (on) structures. This study shows that it is possible to interfere with the tight structure of the hepatitis delta virus ribozyme by adding an unusual, stable structure. To our knowledge, the G-quartzyme is the sole ribozyme that exhibits a monovalent cation-dependent activity.
Collapse
Affiliation(s)
- Jean-Denis Beaudoin
- RNA Group/Groupe ARN, Département de Biochimie, Université de Sherbrooke, Sherbrooke QC, J1H 5N4, Canada
| | | |
Collapse
|
11
|
Lévesque D, Brière FP, Perreault JP. A modern mode of activation for nucleic acid enzymes. PLoS One 2007; 2:e673. [PMID: 17653287 PMCID: PMC1919428 DOI: 10.1371/journal.pone.0000673] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Accepted: 06/17/2007] [Indexed: 11/19/2022] Open
Abstract
Through evolution, enzymes have developed subtle modes of activation in order to ensure the sufficiently high substrate specificity required by modern cellular metabolism. One of these modes is the use of a target-dependent module (i.e. a docking domain) such as those found in signalling kinases. Upon the binding of the target to a docking domain, the substrate is positioned within the catalytic site. The prodomain acts as a target-dependent module switching the kinase from an off state to an on state. As compared to the allosteric mode of activation, there is no need for the presence of a third partner. None of the ribozymes discovered to date have such a mode of activation, nor does any other known RNA. Starting from a specific on/off adaptor for the hepatitis delta virus ribozyme, that differs but has a mechanism reminiscent of this signalling kinase, we have adapted this mode of activation, using the techniques of molecular engineering, to both catalytic RNAs and DNAs exhibiting various activities. Specifically, we adapted three cleaving ribozymes (hepatitis delta virus, hammerhead and hairpin ribozymes), a cleaving 10-23 deoxyribozyme, a ligating hairpin ribozyme and an artificially selected capping ribozyme. In each case, there was a significant gain in terms of substrate specificity. Even if this mode of control is unreported for natural catalytic nucleic acids, its use needs not be limited to proteinous enzymes. We suggest that the complexity of the modern cellular metabolism might have been an important selective pressure in this evolutionary process.
Collapse
Affiliation(s)
- Dominique Lévesque
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Francis P. Brière
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
12
|
Fiola K, Perreault JP, Cousineau B. Gene targeting in the Gram-Positive bacterium Lactococcus lactis, using various delta ribozymes. Appl Environ Microbiol 2006; 72:869-79. [PMID: 16391129 PMCID: PMC1352214 DOI: 10.1128/aem.72.1.869-879.2006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The trans-acting antigenomic delta ribozyme, isolated from the human hepatitis delta virus, was shown to be highly stable and active in vitro, as well as in mammalian cell lines. However, the stability and gene-targeting competence of this small ribozyme have not been studied previously in bacterial cells. In this paper we describe the use of two variants of the trans-acting antigenomic delta ribozyme targeting the abundant EF-Tu mRNA in the industrially important gram-positive bacterium Lactococcus lactis. These two delta ribozyme variants were expressed at significant levels and were shown to be highly stable in vivo. The half-life of the EF-Tu mRNA was slightly but consistently reduced in the presence of the classical delta ribozymes (7 to 13%). In contrast, delta ribozymes harboring a specific on/off riboswitch (SOFA-delta ribozymes) targeting the same sites on the EF-Tu mRNA considerably reduced the half-life of this mRNA (22 to 47%). The rates of catalysis of the SOFA-delta ribozymes in L. lactis were similar to the rates determined in vitro, showing that this new generation of delta ribozymes was highly efficient in these bacterial cells. Clearly, SOFA-delta ribozymes appear to be an ideal means for development of gene inactivation systems in bacteria.
Collapse
Affiliation(s)
- Karine Fiola
- Department of Microbiology and Immunology, McGill University, Montréal, Québec H3A 2B4, Canada
| | | | | |
Collapse
|
13
|
Bergeron LJ, Reymond C, Perreault JP. Functional characterization of the SOFA delta ribozyme. RNA (NEW YORK, N.Y.) 2005; 11:1858-68. [PMID: 16251383 PMCID: PMC1370874 DOI: 10.1261/rna.2112705] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Molecular engineering has led to the development of a novel target-dependent riboswitch that increases deltaribozyme fidelity. This delta ribozyme possesses a specific on/off adapter (SOFA) that switches the cleavage activity from off (a "safety lock") to on solely in the presence of the desired RNA substrate. In this report, we investigate the influence of both the structure and the sequence of each domain of the SOFA module. Analysis of the cleavage activity, using a large collection of substrates and SOFA-ribozyme mutants, together with RNase H probing provided several insights into the nature of the sequence and the optimal design of each domain of the SOFA module. For example, we determined that (1) the optimal size of the blocker sequence, which keeps the ribozyme off in the absence of the substrate, is 4 nucleotides (nt); (2) a single nucleotide difference between the substrate and the biosensor domain, which is responsible for the initial binding of the substrate that subsequently switches the SOFA-ribozyme on, is sufficient to cause non-recognition of the appropriate substrate; (3) the stabilizer, which joins the 5' and 3' ends of the SOFA-ribozyme, plays only a structural role; and (4) the optimal spacer sequence, which serves to separate the binding regions of the biosensor and catalytic domain of the ribozyme on the substrate, is from 1 to 5 nt long. Together, these data should facilitate the design of more efficient SOFA-ribozymes with significant potential for many applications in gene-inactivation systems.
Collapse
Affiliation(s)
- Lucien Junior Bergeron
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine et des sciences de la santé, Universitéde Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | | | | |
Collapse
|
14
|
Landry P, Perreault JP. Identification of a peach latent mosaic viroid hairpin able to act as a Dicer-like substrate. J Virol 2005; 79:6540-3. [PMID: 15858039 PMCID: PMC1091732 DOI: 10.1128/jvi.79.10.6540-6543.2005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability of several viroids to induce posttranscriptional gene silencing has been demonstrated; however, the structure recognized by the Dicer enzyme(s) responsible for the initiation of this mechanism remains a mystery. Here, we show that the hairpin known to be implicated in the replication of peach latent mosaic viroid has the ability to trigger the Dicer enzyme(s). This domain, which is composed of a succession of several small stems separated by symmetrical bulges, is reminiscent of the precursor micro-RNAs.
Collapse
Affiliation(s)
- Patricia Landry
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | | |
Collapse
|
15
|
Abstract
Ribozymes, RNA molecules that catalyze the cleavage of RNA substrates, provide an interesting alternative to the RNA interference (RNAi) approach to gene inactivation, especially given the fact that RNAi seems to trigger an immunological response. Unfortunately, the limited substrate specificity of ribozymes is considered to be a significant hurdle in their development as molecular tools. Here, we report the molecular engineering of a ribozyme possessing a new biosensor module that switches the cleavage activity from ‘off’ (a ‘safety lock’) to ‘on’ solely in the presence of the appropriate RNA target substrate. Both proof-of-concept and the mechanism of action of this man-made riboswitch are demonstrated using hepatitis delta virus ribozymes that cleave RNA transcripts derived from the hepatitis B and C viruses. To our knowledge, this is the first report of a ribozyme bearing a target-dependent module that is activated by its RNA substrate, an arrangement which greatly diminishes non-specific effects. This new approach provides a highly specific and improved tool with significant potential for application in the fields of both functional genomics and gene therapy.
Collapse
Affiliation(s)
| | - Jean-Pierre Perreault
- To whom correspondence should be addressed. Tel: +1 819 564 5310; Fax: +1 819 564 5340;
| |
Collapse
|
16
|
Sheng J, Al-Anouti F, Ananvoranich S. Engineered delta ribozymes can simultaneously knock down the expression of the genes encoding uracil phosphoribosyltransferase and hypoxanthine-xanthine-guanine phosphoribosyltransferase in Toxoplasma gondii. Int J Parasitol 2004; 34:253-63. [PMID: 15003487 DOI: 10.1016/j.ijpara.2003.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2003] [Revised: 11/06/2003] [Accepted: 11/07/2003] [Indexed: 11/26/2022]
Abstract
Engineered delta ribozymes or HDV ribozymes were used as gene expression modulators in Toxoplasma gondii. The substrate recognition sequence of the trans-acting delta ribozyme, which was derived from the self-cleaving motif located on the antigenomic strand of the hepatitis delta virus genome, was modified to target T. gondii transcripts. The mRNA encoding two well-documented genes, namely uracil phosphoribosyltransferase (UPRT) and hypoxanthine-xanthine-guanine-phosphoribosyltransferase (HXGPRT) of T. gondii were chosen as the targets for the ribozymes. UPRT and HXGPRT are the operative enzymes of the pyrimidine and purine salvage pathway, respectively. The knockdown of UPRT or HXGPRT expression by the engineered ribozymes resulted in parasites with lower levels of the corresponding transcripts and diminished their abilities to assimilate radioactive pyrimidine or purine analogs. Five out of six engineered ribozymes could cleave their substrates and gave rise to the products, which were detected by primer extension assays. Upon electroporation of individual active ribozymes against the UPRT gene, the uracil incorporation was decreased. Similarly, the ribozymes against HXGPRT caused decreased incorporation of hypoxanthine. When the most active ribozyme against UPRT was used in a combination with the best HXGPRT specific ribozyme, the incorporation of both uracil and hypoxanthine were decreased. Northern blot analysis revealed that the target transcripts were lowered to an undetectable level when specific ribozymes were used, and that the transcripts of the housekeeping gene remained intact. The ribozyme system should thus prove to be effective for the study of gene expression in T. gondii.
Collapse
Affiliation(s)
- J Sheng
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ont, Canada N9B 3P4
| | | | | |
Collapse
|
17
|
D’Anjou F, Bergeron LJ, Ben Larbi N, Fournier I, Salzet M, Perreault JP, Day R. Silencing of SPC2 expression using an engineered delta ribozyme in the mouse betaTC-3 endocrine cell line. J Biol Chem 2004; 279:14232-9. [PMID: 14734558 PMCID: PMC2902529 DOI: 10.1074/jbc.m310632200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Endoproteolytic processing is carried out by subtilase-like pro-protein convertases in mammalian cells. In order to understand the distinct roles of a member of this family (SPC2), gene silencing in cultured cells is an ideal approach. Previous studies showed limited success in either the degree of inhibition obtained or the stability of the cell lines. Here we demonstrate the high potential of delta ribozyme as a post-transcriptional gene silencing tool in cultured cells. We used an expression vector based on the RNA polymerase III promoter to establish betaTC-3 stable cell lines expressing the chimeric tRNA(Val)-delta ribozyme transcript targeting SPC2 mRNA. Northern and Western blot hybridizations showed a specific reduction of SPC2 mRNA and protein. Validation of processing effects was tested by measuring the levels of dynorphin A-(1-8), which are present in betaTC-3 cells as a result of the unique cleavage of dynorphin A-(1-17) by SPC2. Moreover, a differential proteomic analysis confirmed these results and allowed identification of secretogranin II as a potential substrate of SPC2. The development of efficient, specific, and durable silencing tools, such as described in the present work, will be of great importance in elucidating the functions of the subtilase-like pro-protein convertases in regard to peptide processing and derived cellular events.
Collapse
Affiliation(s)
- François D’Anjou
- Département de Pharmacologie, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | | | - Nadia Ben Larbi
- Laboratoire de Neuroimmunologie des Annélides, UMR CNRS 8017, Université des Sciences et Technologies de Lille, 59650 Villeneuve d’Ascq, France
| | - Isabelle Fournier
- Laboratoire de Neuroimmunologie des Annélides, UMR CNRS 8017, Université des Sciences et Technologies de Lille, 59650 Villeneuve d’Ascq, France
| | - Michel Salzet
- Laboratoire de Neuroimmunologie des Annélides, UMR CNRS 8017, Université des Sciences et Technologies de Lille, 59650 Villeneuve d’Ascq, France
| | - Jean-Pierre Perreault
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
- Investigator from the Canadian Institutes of Health Research. To whom correspondence may be addressed: Dépt. de Biochimie, RNA Group, Université de Sherbrooke, 3001 12 Ave. Nord, Sherbrooke, Québec J1H 5N4, Canada. Tel.: 819-564-5310; Fax: 819-564-5340;
| | - Robert Day
- Département de Pharmacologie, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
- Senior scholar of the Fonds de la Recherche en Santé du Québec. To whom correspondence may be addressed: Dépt. de Pharmacologie, Institut de Pharmacologie de Sherbrooke Université de Sherbrooke, 3001 12 Ave. Nord, Sherbrooke, Québec J1H 5N4, Canada. Tel.: 819-564-5428; Fax: 819-564-5400;
| |
Collapse
|
18
|
Bergeron LJ, Ouellet J, Perreault JP. Ribozyme-based gene-inactivation systems require a fine comprehension of their substrate specificities; the case of delta ribozyme. Curr Med Chem 2003; 10:2589-97. [PMID: 14529473 PMCID: PMC2902527 DOI: 10.2174/0929867033456486] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The ability of ribozymes (i.e. RNA enzymes) to specifically recognize and subsequently catalyze the cleavage of an RNA substrate makes them attractive for the development of therapeutic tools for the inactivation of both viral RNAs and mRNAs associated with various diseases. Several applicable ribozyme models have been tested both in vitro and in a cellular environment, and have shown significant promise. However, several hurdles remain to be surpassed before we generate a useful gene-inactivation system based on a ribozyme. Among the most important requirements for further progress are a better understanding of the features that contribute to defining the substrate specificity for cleavage by a ribozyme, and the identification of the potential cleavage sites in a given target RNA. The goal of this review is to illustrate the importance of both of these factors at the RNA level in the development of any type of ribozyme based gene-therapy. This is achieved by reviewing the recent progress in both the structure-function relationships and the development of a gene-inactivation system of a model ribozyme, specifically delta ribozyme.
Collapse
Affiliation(s)
| | | | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine, Université de Sherbrooke, Sherbrooke, Québec, JIH 5N4, Canada
| |
Collapse
|
19
|
Deschênes P, Ouellet J, Perreault J, Perreault JP. Formation of the P1.1 pseudoknot is critical for both the cleavage activity and substrate specificity of an antigenomic trans-acting hepatitis delta ribozyme. Nucleic Acids Res 2003; 31:2087-96. [PMID: 12682359 PMCID: PMC153735 DOI: 10.1093/nar/gkg307] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hepatitis delta virus RNAs possess self-cleavage activities that produce 2',3'-cyclic phosphate and 5'-hydroxyl termini (i.e. cis-acting delta ribozyme). Trans-acting delta ribozymes have been engineered by removing a junction from the cis version, thereby producing one molecule possessing the substrate sequence and the other the catalytic domain. According to the pseudoknot model, the secondary structure of the delta ribozyme includes a pseudoknot (i.e. P1.1 stem) formed by two base pairs from residues of the L3 loop and J1/4 junction. A collection of 48 P1.1 stem mutants was synthesized in order to provide an original characterization of both the importance and the structure of this pseudoknot in a trans-acting version of the ribozyme. Several structural differences were noted compared to the results reported for cis-acting ribozymes. For example, a combination of two stable Watson-Crick base pairs composing the essential P1.1 stem was demonstrated to be crucial for a significant level of activity, while the cis version required only one base pair. In addition, we present the first physical evidences revealing that the composition of the P1.1 stem affects the substrate specificity for ribozyme cleavage. Depending on the residues forming the J1/4 junction, non-productive ribozyme-substrate complexes can be observed. This phenomenon is proposed to be important for further development of a gene-inactivation system based on delta ribozyme.
Collapse
Affiliation(s)
- Patrick Deschênes
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | | | | | | |
Collapse
|
20
|
Nishikawa F, Kakiuchi N, Funaji K, Fukuda K, Sekiya S, Nishikawa S. Inhibition of HCV NS3 protease by RNA aptamers in cells. Nucleic Acids Res 2003; 31:1935-43. [PMID: 12655010 PMCID: PMC152807 DOI: 10.1093/nar/gkg291] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Non-structural protein 3 (NS3) of hepatitis C virus (HCV) has two distinct activities, protease and helicase, which are essential for HCV proliferation. In previous work, we obtained RNA aptamers (G9-I, II and III) which specifically bound the NS3 protease domain (DeltaNS3), efficiently inhibiting protease activity in vitro. To utilize these aptamers in vivo, we constructed a G9 aptamer expression system in cultured cells, using the cytomegarovirus enhancer + chicken beta-actin globin (CAG) promoter. By conjugating the cis-acting genomic human hepatitis delta virus (HDV) ribozyme and G9-II aptamer, a chimeric HDV ribozyme-G9-II aptamer (HA) was constructed, which was used to produce stable RNA in vivo and to create tandem repeats of the functional unit. To target the transcribed RNA aptamers to the cytoplasm, the minimal mutant of constitutive transport element (CTE), derived from type D retroviruses, was conjugated at the 3' end of HA (HAC). Transcript RNAs from (HA)(n) and (HAC)(n) were processed into the G9-II aptamer unit by the cis-acting HDV ribozyme, both in vitro and in vivo. Efficient protease inhibition activity of HDV ribozyme-G9-II aptamer expression plasmid was demonstrated in HeLa cells. Protease inhibition activity level of tandem chimeric aptamers, (HA)(n) and (HAC)(n), rose with the increase of n from 1 to 4.
Collapse
Affiliation(s)
- Fumiko Nishikawa
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Sciences and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | | | | | | | | | | |
Collapse
|
21
|
Puerta-Fernández E, Romero-López C, Barroso-delJesus A, Berzal-Herranz A. Ribozymes: recent advances in the development of RNA tools. FEMS Microbiol Rev 2003; 27:75-97. [PMID: 12697343 DOI: 10.1016/s0168-6445(03)00020-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The discovery 20 years ago that some RNA molecules, called ribozymes, are able to catalyze chemical reactions was a breakthrough in biology. Over the last two decades numerous natural RNA motifs endowed with catalytic activity have been described. They all fit within a few well-defined types that respond to a specific RNA structure. The prototype catalytic domain of each one has been engineered to generate trans-acting ribozymes that catalyze the site-specific cleavage of other RNA molecules. On the 20th anniversary of ribozyme discovery we briefly summarize the main features of the different natural catalytic RNAs. We also describe progress towards developing strategies to ensure an efficient ribozyme-based technology, dedicating special attention to the ones aimed to achieve a new generation of therapeutic agents.
Collapse
Affiliation(s)
- Elena Puerta-Fernández
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, Ventanilla 11, 18001 Granada, Spain
| | | | | | | |
Collapse
|
22
|
Bergeron LJ, Perreault JP. Development and comparison of procedures for the selection of delta ribozyme cleavage sites within the hepatitis B virus. Nucleic Acids Res 2002; 30:4682-91. [PMID: 12409459 PMCID: PMC135815 DOI: 10.1093/nar/gkf598] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2002] [Revised: 09/09/2002] [Accepted: 09/09/2002] [Indexed: 01/01/2023] Open
Abstract
Delta ribozyme possesses several unique features related to the fact that it is the only catalytic RNA known to be naturally active in human cells. This makes it attractive as a therapeutic tool for the inactivation of clinically relevant RNAs. However, several hurdles must be overcome prior to the development of useful gene-inactivation systems based on delta ribozyme. We have developed three procedures for the selection of potential delta ribozyme target sites within the hepatitis B virus (HBV) pregenome: (i) the use of bioinformatic tools coupled to biochemical assays; (ii) RNase H hydrolysis with a pool of oligonucleotides; and (iii) cleavage assays with a pool of ribozymes. The results obtained with delta ribozyme show that these procedures are governed by several rules, some of which are different from those both for other catalytic RNAs and antisense oligonucleotides. Together, these procedures identified 12 sites in the HBV pregenome that can be cleaved by delta ribozymes, although with different efficiencies. Clearly, both target site accessibility and the ability to form an active ribozyme-substrate complex constitute interdependent factors that can best be addressed using a combinatorial library of either oligonucleotides or ribozymes.
Collapse
Affiliation(s)
- Lucien Junior Bergeron
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | | |
Collapse
|