1
|
Tsao L, Shepardson-Fungairiño S, Murayama H, Cecere A, Wren E, Núñez M. Assessing the Potential for DNA Quadruplex Formation in the Predatory Bacterium Bdellovibrio bacteriovorus. Biochemistry 2022; 61:2073-2087. [PMID: 36193632 PMCID: PMC9536305 DOI: 10.1021/acs.biochem.2c00443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/25/2022] [Indexed: 11/29/2022]
Abstract
During its life cycle, the predatory bacterium Bdellovibrio bacteriovorus switches between an attack and a growth phase, each of which is characterized by a distinct pattern of gene expression. Twenty-one potential G-quadruplex-forming sequences (PQFS) have been identified in the Bdellovibrio genome. These G-rich sequences are prevalent within open reading frames and nearly evenly distributed between the template and the coding strand, suggesting that they could play a role in gene expression and life cycle switching. Published transcriptomic data show that the genes nearest these sequences are not (de)activated together during the same phases of the life cycle. We explored the biophysical properties of three identified PQFS using circular dichroism (CD) spectroscopy and gel electrophoresis and demonstrated that all three sequences fold into stable unimolecular quadruplexes with distinct topologies. In the presence of their complementary strands, each forms an equilibrium mixture of duplex and quadruplex in which quadruplex formation is favored at higher temperatures. Once the quadruplexes are folded, they are slow to form a duplex when the complementary strand is added, with one sequence requiring the equivalent of many Bdellovibrio lifetimes to do so. Using a variety of cosolutes, we showed that molecular crowding mimicking cellular conditions stabilizes the quadruplex structures and induces structural transitions to the parallel topology regardless of the original topology. Taken together, these experiments suggest that Bdellovibrio PQFS are capable of forming quadruplexes in vivo and thereby playing a role in gene expression.
Collapse
Affiliation(s)
- Lucille
H. Tsao
- Department of Chemistry and
Program in Biochemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Sally Shepardson-Fungairiño
- Department of Chemistry and
Program in Biochemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Hikari Murayama
- Department of Chemistry and
Program in Biochemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Amelia Cecere
- Department of Chemistry and
Program in Biochemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Elizabeth Wren
- Department of Chemistry and
Program in Biochemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Megan Núñez
- Department of Chemistry and
Program in Biochemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| |
Collapse
|
2
|
Tickner ZJ, Farzan M. Riboswitches for Controlled Expression of Therapeutic Transgenes Delivered by Adeno-Associated Viral Vectors. Pharmaceuticals (Basel) 2021; 14:ph14060554. [PMID: 34200913 PMCID: PMC8230432 DOI: 10.3390/ph14060554] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/28/2021] [Accepted: 06/04/2021] [Indexed: 11/16/2022] Open
Abstract
Vectors developed from adeno-associated virus (AAV) are powerful tools for in vivo transgene delivery in both humans and animal models, and several AAV-delivered gene therapies are currently approved for clinical use. However, AAV-mediated gene therapy still faces several challenges, including limited vector packaging capacity and the need for a safe, effective method for controlling transgene expression during and after delivery. Riboswitches, RNA elements which control gene expression in response to ligand binding, are attractive candidates for regulating expression of AAV-delivered transgene therapeutics because of their small genomic footprints and non-immunogenicity compared to protein-based expression control systems. In addition, the ligand-sensing aptamer domains of many riboswitches can be exchanged in a modular fashion to allow regulation by a variety of small molecules, proteins, and oligonucleotides. Riboswitches have been used to regulate AAV-delivered transgene therapeutics in animal models, and recently developed screening and selection methods allow rapid isolation of riboswitches with novel ligands and improved performance in mammalian cells. This review discusses the advantages of riboswitches in the context of AAV-delivered gene therapy, the subsets of riboswitch mechanisms which have been shown to function in human cells and animal models, recent progress in riboswitch isolation and optimization, and several examples of AAV-delivered therapeutic systems which might be improved by riboswitch regulation.
Collapse
Affiliation(s)
- Zachary J. Tickner
- Department of Immunology and Microbiology, the Scripps Research Institute, Jupiter, FL 33458, USA;
- Correspondence:
| | - Michael Farzan
- Department of Immunology and Microbiology, the Scripps Research Institute, Jupiter, FL 33458, USA;
- Emmune, Inc., Jupiter, FL 33458, USA
| |
Collapse
|
3
|
Catalytic RNA, ribozyme, and its applications in synthetic biology. Biotechnol Adv 2019; 37:107452. [DOI: 10.1016/j.biotechadv.2019.107452] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/21/2022]
|
4
|
Lim CS, Brown C. A new class of ribozyme from hepatitis B virus. FEBS J 2017; 284:1182-1183. [PMID: 28414880 DOI: 10.1111/febs.14062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this issue, Chakraborty and Ghosh present initial in vitro data indicating a 53-base part of the hepatitis B virus (HBV) epsilon region is a ribozyme with unusual properties. Self-cleavage first occurred at the HBV non-canonical polyadenylation signal UAUAAA and the "centre bulge" of the epsilon region, releasing a ribozyme. The released ribozyme then acted as a new class of trans-cleaving ribozyme cleaving other RNAs.
Collapse
Affiliation(s)
- Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Christopher Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| |
Collapse
|
5
|
Chakraborty D, Ghosh S. The epsilon motif of hepatitis B virusRNAexhibits a potassium‐dependent ribonucleolytic activity. FEBS J 2017; 284:1184-1203. [DOI: 10.1111/febs.14050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/21/2017] [Accepted: 02/22/2017] [Indexed: 12/01/2022]
|
6
|
Abd Rahman N, Ibrahim F, Yafouz B. Dielectrophoresis for Biomedical Sciences Applications: A Review. SENSORS 2017; 17:s17030449. [PMID: 28245552 PMCID: PMC5375735 DOI: 10.3390/s17030449] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/10/2016] [Accepted: 12/20/2016] [Indexed: 12/18/2022]
Abstract
Dielectrophoresis (DEP) is a label-free, accurate, fast, low-cost diagnostic technique that uses the principles of polarization and the motion of bioparticles in applied electric fields. This technique has been proven to be beneficial in various fields, including environmental research, polymer research, biosensors, microfluidics, medicine and diagnostics. Biomedical science research is one of the major research areas that could potentially benefit from DEP technology for diverse applications. Nevertheless, many medical science research investigations have yet to benefit from the possibilities offered by DEP. This paper critically reviews the fundamentals, recent progress, current challenges, future directions and potential applications of research investigations in the medical sciences utilizing DEP technique. This review will also act as a guide and reference for medical researchers and scientists to explore and utilize the DEP technique in their research fields.
Collapse
Affiliation(s)
- Nurhaslina Abd Rahman
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
- Centre for Innovation in Medical Engineering (CIME), Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Fatimah Ibrahim
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
- Centre for Innovation in Medical Engineering (CIME), Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Bashar Yafouz
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
- Centre for Innovation in Medical Engineering (CIME), Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
- Faculty of Engineering and Information Technology, Taiz University, 6803 Taiz, Yemen.
| |
Collapse
|
7
|
Felletti M, Hartig JS. Ligand-dependent ribozymes. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27687155 DOI: 10.1002/wrna.1395] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/12/2016] [Accepted: 08/23/2016] [Indexed: 12/20/2022]
Abstract
The discovery of catalytic RNA (ribozymes) more than 30 years ago significantly widened the horizon of RNA-based functions in natural systems. Similarly to the activity of protein enzymes that are often modulated by the presence of an interaction partner, some examples of naturally occurring ribozymes are influenced by ligands that can either act as cofactors or allosteric modulators. Recent discoveries of new and widespread ribozyme motifs in many different genetic contexts point toward the existence of further ligand-dependent RNA catalysts. In addition to the presence of ligand-dependent ribozymes in nature, researchers have engineered ligand dependency into natural and artificial ribozymes. Because RNA functions can often be assembled in a truly modular way, many different systems have been obtained utilizing different ligand-sensing domains and ribozyme activities in diverse applications. We summarize the occurrence of ligand-dependent ribozymes in nature and the many examples realized by researchers that engineered ligand-dependent catalytic RNA motifs. We will also highlight methods for obtaining ligand dependency as well as discuss the many interesting applications of ligand-controlled catalytic RNAs. WIREs RNA 2017, 8:e1395. doi: 10.1002/wrna.1395 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Michele Felletti
- Department of Chemistry and Konstanz Research School of Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry and Konstanz Research School of Chemical Biology, University of Konstanz, Konstanz, Germany
| |
Collapse
|
8
|
K+-responsive off-to-on switching of hammerhead ribozyme through dual G-quadruplex formation requiring no heating and cooling treatment. Biochem Biophys Res Commun 2015; 468:27-31. [DOI: 10.1016/j.bbrc.2015.10.173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 10/31/2015] [Indexed: 11/23/2022]
|
9
|
Rossier BC, Baker ME, Studer RA. Epithelial sodium transport and its control by aldosterone: the story of our internal environment revisited. Physiol Rev 2015; 95:297-340. [PMID: 25540145 DOI: 10.1152/physrev.00011.2014] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Transcription and translation require a high concentration of potassium across the entire tree of life. The conservation of a high intracellular potassium was an absolute requirement for the evolution of life on Earth. This was achieved by the interplay of P- and V-ATPases that can set up electrochemical gradients across the cell membrane, an energetically costly process requiring the synthesis of ATP by F-ATPases. In animals, the control of an extracellular compartment was achieved by the emergence of multicellular organisms able to produce tight epithelial barriers creating a stable extracellular milieu. Finally, the adaptation to a terrestrian environment was achieved by the evolution of distinct regulatory pathways allowing salt and water conservation. In this review we emphasize the critical and dual role of Na(+)-K(+)-ATPase in the control of the ionic composition of the extracellular fluid and the renin-angiotensin-aldosterone system (RAAS) in salt and water conservation in vertebrates. The action of aldosterone on transepithelial sodium transport by activation of the epithelial sodium channel (ENaC) at the apical membrane and that of Na(+)-K(+)-ATPase at the basolateral membrane may have evolved in lungfish before the emergence of tetrapods. Finally, we discuss the implication of RAAS in the origin of the present pandemia of hypertension and its associated cardiovascular diseases.
Collapse
Affiliation(s)
- Bernard C Rossier
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland; Division of Nephrology-Hypertension, University of California San Diego, La Jolla, California; and Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Michael E Baker
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland; Division of Nephrology-Hypertension, University of California San Diego, La Jolla, California; and Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Romain A Studer
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland; Division of Nephrology-Hypertension, University of California San Diego, La Jolla, California; and Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| |
Collapse
|
10
|
Yamaoki Y, Mashima T, Nagata T, Katahira M. Boosting of activity enhancement of K+-responsive quadruplex hammerhead ribozyme. Chem Commun (Camb) 2015; 51:5898-901. [DOI: 10.1039/c5cc00961h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Second-generation quadruplex hammerhead ribozymes, whose activity enhances in response to K+, were developed. New strategies suppressed the basal activity and boosted the activity enhancement upon the addition of K+ to 21-fold.
Collapse
Affiliation(s)
- Yudai Yamaoki
- Institute of Advanced Energy
- Graduate School of Energy Science
- Kyoto University
- Gokasho
- Uji
| | - Tsukasa Mashima
- Institute of Advanced Energy
- Graduate School of Energy Science
- Kyoto University
- Gokasho
- Uji
| | - Takashi Nagata
- Institute of Advanced Energy
- Graduate School of Energy Science
- Kyoto University
- Gokasho
- Uji
| | - Masato Katahira
- Institute of Advanced Energy
- Graduate School of Energy Science
- Kyoto University
- Gokasho
- Uji
| |
Collapse
|
11
|
Métifiot M, Amrane S, Litvak S, Andreola ML. G-quadruplexes in viruses: function and potential therapeutic applications. Nucleic Acids Res 2014; 42:12352-66. [PMID: 25332402 PMCID: PMC4227801 DOI: 10.1093/nar/gku999] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/26/2014] [Accepted: 10/06/2014] [Indexed: 12/15/2022] Open
Abstract
G-rich nucleic acids can form non-canonical G-quadruplex structures (G4s) in which four guanines fold in a planar arrangement through Hoogsteen hydrogen bonds. Although many biochemical and structural studies have focused on DNA sequences containing successive, adjacent guanines that spontaneously fold into G4s, evidence for their in vivo relevance has recently begun to accumulate. Complete sequencing of the human genome highlighted the presence of ∼300,000 sequences that can potentially form G4s. Likewise, the presence of putative G4-sequences has been reported in various viruses genomes [e.g., Human immunodeficiency virus (HIV-1), Epstein-Barr virus (EBV), papillomavirus (HPV)]. Many studies have focused on telomeric G4s and how their dynamics are regulated to enable telomere synthesis. Moreover, a role for G4s has been proposed in cellular and viral replication, recombination and gene expression control. In parallel, DNA aptamers that form G4s have been described as inhibitors and diagnostic tools to detect viruses [e.g., hepatitis A virus (HAV), EBV, cauliflower mosaic virus (CaMV), severe acute respiratory syndrome virus (SARS), simian virus 40 (SV40)]. Here, special emphasis will be given to the possible role of these structures in a virus life cycle as well as the use of G4-forming oligonucleotides as potential antiviral agents and innovative tools.
Collapse
Affiliation(s)
- Mathieu Métifiot
- CNRS UMR-5234, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Samir Amrane
- INSERM, U869, IECB, ARNA laboratory, Université de Bordeaux, 2 Rue Robert Escarpit 33600 Pessac, France
| | - Simon Litvak
- CNRS UMR-5234, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Marie-Line Andreola
- CNRS UMR-5234, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
| |
Collapse
|
12
|
Nomura Y, Zhou L, Miu A, Yokobayashi Y. Controlling mammalian gene expression by allosteric hepatitis delta virus ribozymes. ACS Synth Biol 2013; 2:684-9. [PMID: 23697539 PMCID: PMC3874218 DOI: 10.1021/sb400037a] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
We engineered small molecule responsive
allosteric ribozymes based
on the genomic hepatitis delta virus (HDV) ribozyme by replacing the
P4-L4 stem-loop with an RNA aptamer through a connector stem. When
embedded in the 3′ untranslated region of a reporter gene mRNA,
these RNA devices enabled regulation of cis-gene
expression by theophylline and guanine by up to 29.5-fold in mammalian
cell culture. Furthermore, a NOR logic gate device was constructed
by placing two engineered ribozymes in tandem, demonstrating the modularity
of the RNA devices. The significant improvement in the regulatory
dynamic range (ON/OFF ratio) of the RNA devices based on the HDV ribozyme
should provide new opportunities for practical applications.
Collapse
Affiliation(s)
- Yoko Nomura
- Department
of Biomedical Engineering, University of California, Davis, 451 Health Sciences
Drive, Davis, California 95616, United States
| | - Linlin Zhou
- Department
of Biomedical Engineering, University of California, Davis, 451 Health Sciences
Drive, Davis, California 95616, United States
| | - Anh Miu
- Department
of Biomedical Engineering, University of California, Davis, 451 Health Sciences
Drive, Davis, California 95616, United States
| | - Yohei Yokobayashi
- Department
of Biomedical Engineering, University of California, Davis, 451 Health Sciences
Drive, Davis, California 95616, United States
| |
Collapse
|
13
|
Agarwala P, Pandey S, Maiti S. G-quadruplexes as tools for synthetic biology. Chembiochem 2013; 14:2077-81. [PMID: 24106165 DOI: 10.1002/cbic.201300456] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Indexed: 11/07/2022]
Abstract
With the potential to engineer biological systems, synthetic biology is an emerging field that combines various disciplines of sciences. It encompasses combinations of DNA, RNA and protein modules for constructing desired systems and the "rewiring" of existing signalling networks. Despite recent advances, this field still lags behind in the artificial reconstruction of cellular processes, and thus demands new modules and switches to create "genetic circuits". The widely characterised noncanonical nucleic acid secondary structures, G-quadruplexes are promising candidates to be used as biological modules in synthetic biology. Structural plasticity and functional versatility are significant G-quadruplex traits for its integration into a biological system and for diverse applications in synthetic circuits.
Collapse
Affiliation(s)
- Prachi Agarwala
- Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007 (India)
| | | | | |
Collapse
|
14
|
Adams DS, Levin M. Endogenous voltage gradients as mediators of cell-cell communication: strategies for investigating bioelectrical signals during pattern formation. Cell Tissue Res 2013; 352:95-122. [PMID: 22350846 PMCID: PMC3869965 DOI: 10.1007/s00441-012-1329-4] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 01/12/2012] [Indexed: 01/07/2023]
Abstract
Alongside the well-known chemical modes of cell-cell communication, we find an important and powerful system of bioelectrical signaling: changes in the resting voltage potential (Vmem) of the plasma membrane driven by ion channels, pumps and gap junctions. Slow Vmem changes in all cells serve as a highly conserved, information-bearing pathway that regulates cell proliferation, migration and differentiation. In embryonic and regenerative pattern formation and in the disorganization of neoplasia, bioelectrical cues serve as mediators of large-scale anatomical polarity, organ identity and positional information. Recent developments have resulted in tools that enable a high-resolution analysis of these biophysical signals and their linkage with upstream and downstream canonical genetic pathways. Here, we provide an overview for the study of bioelectric signaling, focusing on state-of-the-art approaches that use molecular physiology and developmental genetics to probe the roles of bioelectric events functionally. We highlight the logic, strategies and well-developed technologies that any group of researchers can employ to identify and dissect ionic signaling components in their own work and thus to help crack the bioelectric code. The dissection of bioelectric events as instructive signals enabling the orchestration of cell behaviors into large-scale coherent patterning programs will enrich on-going work in diverse areas of biology, as biophysical factors become incorporated into our systems-level understanding of cell interactions.
Collapse
Affiliation(s)
- Dany S Adams
- Department of Biology, and Center for Regenerative and Developmental Biology, Tufts University, 200 Boston Ave, Medford, MA 02155, USA
| | | |
Collapse
|
15
|
Rouleau SG, Jodoin R, Bisaillon M, Perreault JP. Programming a highly structured ribozyme into complex allostery using RNA oligonucleotides. ACS Chem Biol 2012; 7:1802-6. [PMID: 22950875 DOI: 10.1021/cb300319m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA possesses great potential for expanding the toolbox currently available to synthetic biologists. Here, the modulation of the Hepatitis Delta Virus ribozyme's activity with a series of rationally designed aptamers and effector RNA oligonucleotides is described. The ribozyme was initially fused with an 18-nucleotide hairpin structure that abolished its self-cleaving activity. The binding of a 14-mer oligonucleotide to the hairpin rescued the self-cleavage in a concentration-dependent manner. This modified ribozyme was inserted into the 5' UTR of a reporter gene, and the resulting construct was used to demonstrate that it is possible to modulate the ribozyme activity in cellulo with the oligonucleotide. Subsequently, ribozymes possessing specialized aptamers respecting other logic gates were also successfully designed and found to be functional in vitro. To our knowledge, this is the first example of HDV ribozyme regulation by oligonucleotides, as well as the first allosteric regulation of HDV ribozyme in mammalian cells.
Collapse
Affiliation(s)
- Samuel G. Rouleau
- RNA group/Groupe
ARN, Département de biochimie,
Faculté de médecine et des sciences de la santé,
Pavillon de Recherche Appliquée sur le Cancer, Université de Sherbrooke, 3201 Jean-Mignault,
Sherbrooke, Québec J1E 4K8, Canada
| | - Rachel Jodoin
- RNA group/Groupe
ARN, Département de biochimie,
Faculté de médecine et des sciences de la santé,
Pavillon de Recherche Appliquée sur le Cancer, Université de Sherbrooke, 3201 Jean-Mignault,
Sherbrooke, Québec J1E 4K8, Canada
| | - Martin Bisaillon
- RNA group/Groupe
ARN, Département de biochimie,
Faculté de médecine et des sciences de la santé,
Pavillon de Recherche Appliquée sur le Cancer, Université de Sherbrooke, 3201 Jean-Mignault,
Sherbrooke, Québec J1E 4K8, Canada
| | - Jean-Pierre Perreault
- RNA group/Groupe
ARN, Département de biochimie,
Faculté de médecine et des sciences de la santé,
Pavillon de Recherche Appliquée sur le Cancer, Université de Sherbrooke, 3201 Jean-Mignault,
Sherbrooke, Québec J1E 4K8, Canada
| |
Collapse
|
16
|
Nagata T, Sakurai Y, Hara Y, Mashima T, Kodaki T, Katahira M. ‘Intelligent’ ribozyme whose activity is altered in response to K+ as a result of quadruplex formation. FEBS J 2012; 279:1456-63. [DOI: 10.1111/j.1742-4658.2012.08538.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
17
|
Levin M, Stevenson CG. Regulation of cell behavior and tissue patterning by bioelectrical signals: challenges and opportunities for biomedical engineering. Annu Rev Biomed Eng 2012; 14:295-323. [PMID: 22809139 PMCID: PMC10472538 DOI: 10.1146/annurev-bioeng-071811-150114] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Achieving control over cell behavior and pattern formation requires molecular-level understanding of regulatory mechanisms. Alongside transcriptional networks and biochemical gradients, there functions an important system of cellular communication and control: transmembrane voltage gradients (V(mem)). Bioelectrical signals encoded in spatiotemporal changes of V(mem) control cell proliferation, migration, and differentiation. Moreover, endogenous bioelectrical gradients serve as instructive cues mediating anatomical polarity and other organ-level aspects of morphogenesis. In the past decade, significant advances in molecular physiology have enabled the development of new genetic and biophysical tools for the investigation and functional manipulation of bioelectric cues. Recent data implicate V(mem) as a crucial epigenetic regulator of patterning events in embryogenesis, regeneration, and cancer. We review new conceptual and methodological developments in this fascinating field. Bioelectricity offers a novel way of quantitatively understanding regulation of growth and form in vivo, and it reveals tractable, powerful control points that will enable truly transformative applications in bioengineering, regenerative medicine, and synthetic biology.
Collapse
Affiliation(s)
- Michael Levin
- Department of Biology, Center for Regenerative and Developmental Biology, Tufts University, Medford, Massachusetts 02155, USA.
| | | |
Collapse
|
18
|
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
|
19
|
McManus SA, Li Y. The structural diversity of deoxyribozymes. Molecules 2010; 15:6269-84. [PMID: 20877222 PMCID: PMC6257715 DOI: 10.3390/molecules15096269] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 08/23/2010] [Accepted: 09/02/2010] [Indexed: 11/16/2022] Open
Abstract
When not constrained to long double-helical arrangements, DNA is capable of forming structural arrangements that enable specific sequences to perform functions such as binding and catalysis under defined conditions. Through a process called in vitro selection, numerous catalytic DNAs, known as deoxyribozymes or DNAzymes, have been isolated. Many of these molecules have the potential to act as therapeutic agents and diagnostic tools. As such, a better understanding of the structural arrangements present in these functional DNAs will aid further efforts in the development and optimization of these useful molecules. Structural characterization of several deoxyribozymes through mutagenesis, in vitro re-selection, chemical probing and circular dichroism has revealed many distinct and elaborate structural classes. Deoxyribozymes have been found to contain diverse structural elements including helical junctions, pseudoknots, triplexes, and guanine quadruplexes. Some of these studies have further shown the repeated isolation of similar structural motifs in independent selection experiments for the same type of chemical reaction, suggesting that some structural motifs are well suited for catalyzing a specific chemical reaction. To investigate the extent of structural diversity possible in deoxyribozymes, a group of kinase deoxyribozymes have been extensively characterized. Such studies have discovered some interesting structural features of these DNAzymes while revealing some novel DNA structures.
Collapse
Affiliation(s)
- Simon A. McManus
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada; E-Mail:
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada; E-Mail:
- Department of Chemistry and Chemical Biology, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-905-528-9140 ext. 22462
| |
Collapse
|
20
|
Lamm G, Pack GR. Counterion condensation and shape within Poisson-Boltzmann theory. Biopolymers 2010; 93:619-39. [PMID: 20213767 DOI: 10.1002/bip.21421] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
An analytical approximation to the nonlinear Poisson-Boltzmann (PB) equation is applied to charged macromolecules that possess one-dimensional symmetry and can be modeled by a plane, infinite cylinder, or sphere. A functional substitution allows the nonlinear PB equation subject to linear boundary conditions to be transformed into an approximate linear (Debye-Hückel-type) equation subject to nonlinear boundary conditions. A simple analytical result for the surface potential of such polyelectrolytes follows, leading to expressions for the amount of condensed (or renormalized) charge and the electrostatic Helmholtz energy for polyelectrolytes. Analytical high-charge/low-salt and low-charge/high-salt limits are shown to be similar to results obtained by others based on PB or counterion condensation theory. Several important general observations concerning polyelectrolytes treated within the context of PB theory can be made including: (1) all charged surfaces display some counterion condensation for finite electrolyte concentration, (2) the effect of surface geometry is described primarily by the sum of the Debye constant and the mean curvature of the surface, (3) two surfaces with the same surface charge density and mean curvature condense approximately identical fractions of counterions, (4) the amount of condensation is not determined by a predefined "condensation distance" although such a distance can be determined uniquely from it, and (5) substantial condensation occurs if the Debye constant of the electrolyte is much less than the mean curvature of a highly charged polyelectrolyte.
Collapse
Affiliation(s)
- Gene Lamm
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA
| | | |
Collapse
|
21
|
Beaudoin JD, Perreault JP. 5'-UTR G-quadruplex structures acting as translational repressors. Nucleic Acids Res 2010; 38:7022-36. [PMID: 20571090 PMCID: PMC2978341 DOI: 10.1093/nar/gkq557] [Citation(s) in RCA: 175] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Given that greater than 90% of the human genome is expressed, it is logical to assume that post-transcriptional regulatory mechanisms must be the primary means of controlling the flow of information from mRNA to protein. This report describes a robust approach that includes in silico, in vitro and in cellulo experiments permitting an in-depth evaluation of the impact of G-quadruplexes as translational repressors. Sequences including potential G-quadruplexes were selected within nine distinct genes encoding proteins involved in various biological processes. Their abilities to fold into G-quadruplex structures in vitro were evaluated using circular dichroism, thermal denaturation and the novel use of in-line probing. Six sequences were observed to fold into G-quadruplex structures in vitro, all of which exhibited translational inhibition in cellulo when linked to a reporter gene. Sequence analysis, direct mutagenesis and subsequent experiments were performed in order to define the rules governing the folding of G-quadruplexes. In addition, the impact of single-nucleotide polymorphism was shown to be important in the formation of G-quadruplexes located within the 5'-untranslated region of an mRNA. In light of these results, clearly the 5'-UTR G-quadruplexes represent a class of translational repressors that is broadly distributed in the cell.
Collapse
Affiliation(s)
- Jean-Denis Beaudoin
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, QC, J1H 5N4, Canada
| | | |
Collapse
|
22
|
Reymond C, Beaudoin JD, Perreault JP. Modulating RNA structure and catalysis: lessons from small cleaving ribozymes. Cell Mol Life Sci 2009; 66:3937-50. [PMID: 19718544 PMCID: PMC2777235 DOI: 10.1007/s00018-009-0124-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 07/30/2009] [Accepted: 07/31/2009] [Indexed: 01/12/2023]
Abstract
RNA is a key molecule in life, and comprehending its structure/function relationships is a crucial step towards a more complete understanding of molecular biology. Even though most of the information required for their correct folding is contained in their primary sequences, we are as yet unable to accurately predict both the folding pathways and active tertiary structures of RNA species. Ribozymes are interesting molecules to study when addressing these questions because any modifications in their structures are often reflected in their catalytic properties. The recent progress in the study of the structures, the folding pathways and the modulation of the small ribozymes derived from natural, self-cleaving, RNA motifs have significantly contributed to today's knowledge in the field.
Collapse
Affiliation(s)
- Cedric Reymond
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
| | - Jean-Denis Beaudoin
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
| |
Collapse
|