1
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Kirsebom LA, Liu F, McClain WH. The discovery of a catalytic RNA within RNase P and its legacy. J Biol Chem 2024; 300:107318. [PMID: 38677513 PMCID: PMC11143913 DOI: 10.1016/j.jbc.2024.107318] [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: 09/18/2023] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024] Open
Abstract
Sidney Altman's discovery of the processing of one RNA by another RNA that acts like an enzyme was revolutionary in biology and the basis for his sharing the 1989 Nobel Prize in Chemistry with Thomas Cech. These breakthrough findings support the key role of RNA in molecular evolution, where replicating RNAs (and similar chemical derivatives) either with or without peptides functioned in protocells during the early stages of life on Earth, an era referred to as the RNA world. Here, we cover the historical background highlighting the work of Altman and his colleagues and the subsequent efforts of other researchers to understand the biological function of RNase P and its catalytic RNA subunit and to employ it as a tool to downregulate gene expression. We primarily discuss bacterial RNase P-related studies but acknowledge that many groups have significantly contributed to our understanding of archaeal and eukaryotic RNase P, as reviewed in this special issue and elsewhere.
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Affiliation(s)
- Leif A Kirsebom
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
| | - Fenyong Liu
- School of Public Health, University of California, Berkeley, California, USA.
| | - William H McClain
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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2
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Story S, Bhaduri S, Ganguly S, Dakarapu R, Wicks SL, Bhadra J, Kwange S, Arya DP. Understanding Antisense Oligonucleotide Efficiency in Inhibiting Prokaryotic Gene Expression. ACS Infect Dis 2024; 10:971-987. [PMID: 38385613 DOI: 10.1021/acsinfecdis.3c00645] [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] [Indexed: 02/23/2024]
Abstract
Oligonucleotides offer a unique opportunity for sequence specific regulation of gene expression in bacteria. A fundamental question to address is the choice of oligonucleotide, given the large number of options available. Different modifications varying in RNA binding affinities and cellular uptake are available but no comprehensive comparisons have been performed. Herein, the efficiency of blocking expression of β-galactosidase (β-Gal) in E. coli was evaluated utilizing different antisense oligomers (ASOs). Fluorescein (FAM)-labeled oligomers were used to understand their differences in bacterial uptake. Flow cytometry analysis revealed significant differences in uptake, with high fluorescence seen in cells treated with FAM-labeled peptidic nucleic acid (PNA), phosphorodiamidate morpholino oligonucleotide (PMO) and phosphorothioate (PS) oligomers, and low fluorescence observed in cells treated with phosphodiester (PO) oligomers. Thermal denaturation (Tm) of oligomer:RNA duplexes and isothermal titration calorimetry (ITC) studies reveal that ASO binding to target RNA demonstrates a good correlation between Tm and Kd values. There was no correlation between Kd values and reduction of β-Gal activity in bacterial cells. However, cell-free translation assays demonstrated a direct relationship between Kd values and inhibition of gene expression by antisense oligomers, with tight binding oligomers such as LNA being the most efficient. Membrane active compounds such as polymyxin B and A22 further improved the cellular uptake of FAM-PNA and FAM-PS oligomers in wild-type E. coli cells. PNA and PMO were most effective in cellular uptake and reducing β-Gal activity as compared to oligomers with PS or those with PO linkages. Overall, cell uptake of the oligomers is shown as the key determinant in predicting their differences in bacterial antisense inhibition, and the RNA affinity is the key determinant in inhibition of gene expression in cell free systems.
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Affiliation(s)
- Sandra Story
- NUBAD, LLC, Greenville, South Carolina 29605, United States
| | | | - Sudakshina Ganguly
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | | | - Sarah L Wicks
- NUBAD, LLC, Greenville, South Carolina 29605, United States
| | - Jhuma Bhadra
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Simeon Kwange
- NUBAD, LLC, Greenville, South Carolina 29605, United States
| | - Dev P Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
- NUBAD, LLC, Greenville, South Carolina 29605, United States
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3
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Magaña AJ, Sklenicka J, Pinilla C, Giulianotti M, Chapagain P, Santos R, Ramirez MS, Tolmasky ME. Restoring susceptibility to aminoglycosides: identifying small molecule inhibitors of enzymatic inactivation. RSC Med Chem 2023; 14:1591-1602. [PMID: 37731693 PMCID: PMC10507813 DOI: 10.1039/d3md00226h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/21/2023] [Indexed: 09/22/2023] Open
Abstract
Growing resistance to antimicrobial medicines is a critical health problem that must be urgently addressed. Adding to the increasing number of patients that succumb to infections, there are other consequences to the rise in resistance like the compromise of several medical procedures and dental work that are heavily dependent on infection prevention. Since their introduction in the clinics, aminoglycoside antibiotics have been a critical component of the armamentarium to treat infections. Still, the increase in resistance and their side effects led to a decline in their utilization. However, numerous current factors, like the urgent need for antimicrobials and their favorable properties, led to renewed interest in these drugs. While efforts to design new classes of aminoglycosides refractory to resistance mechanisms and with fewer toxic effects are starting to yield new promising molecules, extending the useful life of those already in use is essential. For this, numerous research projects are underway to counter resistance from different angles, like inhibition of expression or activity of resistance components. This review focuses on selected examples of one aspect of this quest, the design or identification of small molecule inhibitors of resistance caused by enzymatic modification of the aminoglycoside. These compounds could be developed as aminoglycoside adjuvants to overcome resistant infections.
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Affiliation(s)
- Angel J Magaña
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
| | - Jan Sklenicka
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
| | - Clemencia Pinilla
- Center for Translational Science, Florida International University Port St. Lucie FL 34987 USA
| | - Marc Giulianotti
- Center for Translational Science, Florida International University Port St. Lucie FL 34987 USA
| | - Prem Chapagain
- Department of Physics, Florida International University Miami FL 33199 USA
- Biomolecular Sciences Institute, Florida International University Miami FL 33199 USA
| | - Radleigh Santos
- Department of Mathematics, Nova Southeastern University Fort Lauderdale FL 33314 USA
| | - Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
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4
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Altman S, Angele-Martinez C. Inactivating Gene Expression with Antisense Modified Oligonucleotides. Acta Naturae 2021; 13:101-105. [PMID: 34707901 PMCID: PMC8526185 DOI: 10.32607/actanaturae.11522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 09/21/2021] [Indexed: 11/20/2022] Open
Abstract
Modified nucleotides, including phosphoramidates and mesyl nucleotides, are
very effective in inactivating gene expression in bacteria. Gyr A
is the target gene in several organisms, including Plasmodium
falciparum. Antisense reactions with bacteria infecting citrus plants
are promising but incomplete. Human tissue culture cells assayed with a
different target are also susceptible to the presence of mesyl oligonucleotides.
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Affiliation(s)
- Sidney Altman
- Yale University New Haven CT USA, Arizona State University, Tempe AZUSA
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5
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Popella L, Jung J, Popova K, Ðurica-Mitić S, Barquist L, Vogel J. Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics. Nucleic Acids Res 2021; 49:4705-4724. [PMID: 33849070 PMCID: PMC8096218 DOI: 10.1093/nar/gkab242] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
Antisense peptide nucleic acids (PNAs) inhibiting mRNAs of essential genes provide a straight-forward way to repurpose our knowledge of bacterial regulatory RNAs for development of programmable species-specific antibiotics. While there is ample proof of PNA efficacy, their target selectivity and impact on bacterial physiology are poorly understood. Moreover, while antibacterial PNAs are typically designed to block mRNA translation, effects on target mRNA levels are not well-investigated. Here, we pioneer the use of global RNA-seq analysis to decipher PNA activity in a transcriptome-wide manner. We find that PNA-based antisense oligomer conjugates robustly decrease mRNA levels of the widely-used target gene, acpP, in Salmonella enterica, with limited off-target effects. Systematic analysis of several different PNA-carrier peptides attached not only shows different bactericidal efficiency, but also activation of stress pathways. In particular, KFF-, RXR- and Tat-PNA conjugates especially induce the PhoP/Q response, whereas the latter two additionally trigger several distinct pathways. We show that constitutive activation of the PhoP/Q response can lead to Tat-PNA resistance, illustrating the utility of RNA-seq for understanding PNA antibacterial activity. In sum, our study establishes an experimental framework for the design and assessment of PNA antimicrobials in the long-term quest to use these for precision editing of microbiota.
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Affiliation(s)
- Linda Popella
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Jakob Jung
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Kristina Popova
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Svetlana Ðurica-Mitić
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
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6
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Silencing Antibiotic Resistance with Antisense Oligonucleotides. Biomedicines 2021; 9:biomedicines9040416. [PMID: 33921367 PMCID: PMC8068983 DOI: 10.3390/biomedicines9040416] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/07/2021] [Accepted: 04/10/2021] [Indexed: 02/06/2023] Open
Abstract
Antisense technologies consist of the utilization of oligonucleotides or oligonucleotide analogs to interfere with undesirable biological processes, commonly through inhibition of expression of selected genes. This field holds a lot of promise for the treatment of a very diverse group of diseases including viral and bacterial infections, genetic disorders, and cancer. To date, drugs approved for utilization in clinics or in clinical trials target diseases other than bacterial infections. Although several groups and companies are working on different strategies, the application of antisense technologies to prokaryotes still lags with respect to those that target other human diseases. In those cases where the focus is on bacterial pathogens, a subset of the research is dedicated to produce antisense compounds that silence or reduce expression of antibiotic resistance genes. Therefore, these compounds will be adjuvants administered with the antibiotic to which they reduce resistance levels. A varied group of oligonucleotide analogs like phosphorothioate or phosphorodiamidate morpholino residues, as well as peptide nucleic acids, locked nucleic acids and bridge nucleic acids, the latter two in gapmer configuration, have been utilized to reduce resistance levels. The major mechanisms of inhibition include eliciting cleavage of the target mRNA by the host’s RNase H or RNase P, and steric hindrance. The different approaches targeting resistance to β-lactams include carbapenems, aminoglycosides, chloramphenicol, macrolides, and fluoroquinolones. The purpose of this short review is to summarize the attempts to develop antisense compounds that inhibit expression of resistance to antibiotics.
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7
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Danilin NA, Matveev AL, Tikunova NV, Venyaminova AG, Novopashina DS. Conjugates of RNase P-Guiding Oligonucleotides with Oligo(N-Methylpyrrole) as Prospective Antibacterial Agents. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Pifer R, Greenberg DE. Antisense antibacterial compounds. Transl Res 2020; 223:89-106. [PMID: 32522669 DOI: 10.1016/j.trsl.2020.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 02/08/2023]
Abstract
Extensive antibiotic use combined with poor historical drug stewardship practices have created a medical crisis in which once treatable bacterial infections are now increasingly unmanageable. To combat this, new antibiotics will need to be developed and safeguarded. An emerging class of antibiotics based upon nuclease-stable antisense technologies has proven valuable in preclinical testing against a variety of bacterial pathogens. This review describes the current state of development of antisense-based antibiotics, the mechanisms thus far employed by these compounds, and possible future avenues of research.
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Affiliation(s)
- Reed Pifer
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - David E Greenberg
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas.
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9
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Sandoval-Mojica AF, Altman S, Hunter WB, Pelz-Stelinski KS. Peptide conjugated morpholinos for management of the huanglongbing pathosystem. PEST MANAGEMENT SCIENCE 2020; 76:3217-3224. [PMID: 32358830 DOI: 10.1002/ps.5877] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/27/2020] [Accepted: 05/01/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND 'Candidatus Liberibacter asiaticus' (CLas) is the causal agent of the devastating citrus disease Huanglongbing (HLB) and is transmitted by the insect vector Diaphorina citri (Hemiptera: Liviidae). A potential approach for treating CLas infection is the use of synthetic nucleic acid-like oligomers to silence bacterial gene expression. Peptide conjugated morpholinos (PPMOs) targeting essential genes in CLas and the psyllid vector's endosymbiotic bacteria, Wolbachia (-Diaphorina, wDi), were evaluated using in vitro and in vivo assays. RESULTS Expression of the wDi gyrA gene was significantly reduced following incubation of wDi cells with PPMOs. In addition, the viability of isolated wDi cells was greatly reduced when treated with PPMOs as compared to untreated cells. Feeding D. citri adults with a complementary PPMO (CLgyrA-14) showed significantly reduced (70% lower) expression of the CLas gyrA gene. CLas relative density was significantly lower in the psyllids fed with CLgyrA-14, when compared to untreated insects. Psyllids that were treated with CLgyrA-14 were less successful in transmitting the pathogen into uninfected plants, compared to untreated insects. CONCLUSION The expression of essential genes in the D. citri symbiont, wDi and the HLB pathogen were suppressed in response to PPMO treatments. This study demonstrates the potential of PPMOs as a novel strategy for management of bacterial pathogens of fruit trees, such as HLB. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Andrés F Sandoval-Mojica
- Department of Entomology and Nematology, Citrus Research and Education Center, University of Florida, Lake Alfred, FL, USA
| | - Sidney Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT,, USA
| | - Wayne B Hunter
- U.S Department of Agriculture, Agricultural Research Service, Fort Pierce, FL, USA
| | - Kirsten S Pelz-Stelinski
- Department of Entomology and Nematology, Citrus Research and Education Center, University of Florida, Lake Alfred, FL, USA
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10
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Danilin NA, Koroleva LS, Novopashina DS, Venyaminova AG. RNase P-Guiding Peptide Conjugates of Oligo(2'-O-methylribonucleotides) as Prospective Antibacterial Agents. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s106816201906013x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Novopashina DS, Nazarov AS, Vorobjeva MA, Kuprushkin MS, Davydova AS, Lomzov AA, Pyshnyi DV, Altman S, Venyaminova AG. Modified Oligonucleotides for Guiding RNA Cleavage Using Bacterial RNase P. Mol Biol 2018. [DOI: 10.1134/s0026893318060134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Davies-Sala C, Jani S, Zorreguieta A, Tolmasky ME. Identification of the Acinetobacter baumannii Ribonuclease P Catalytic Subunit: Cleavage of a Target mRNA in the Presence of an External Guide Sequence. Front Microbiol 2018; 9:2408. [PMID: 30349524 PMCID: PMC6186949 DOI: 10.3389/fmicb.2018.02408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/20/2018] [Indexed: 11/17/2022] Open
Abstract
The bacterial ribonuclease P or RNase P holoenzyme is usually composed of a catalytic RNA subunit, M1, and a cofactor protein, C5. This enzyme was first identified for its role in maturation of tRNAs by endonucleolytic cleavage of the pre-tRNA. The RNase P endonucleolytic activity is characterized by having structural but not sequence substrate requirements. This property led to development of EGS technology, which consists of utilizing a short antisense oligonucleotide that when forming a duplex with a target RNA induces its cleavage by RNase P. This technology is being explored for designing therapies that interfere with expression of genes, in the case of bacterial infections EGS technology could be applied to target essential, virulence, or antibiotic resistant genes. Acinetobacter baumannii is a problematic pathogen that is commonly resistant to multiple antibiotics, and EGS technology could be utilized to design alternative therapies. To better understand the A. baumannii RNase P we first identified and characterized the catalytic subunit. We identified a gene coding for an RNA species, M1Ab, with the expected features of the RNase P M1 subunit. A recombinant clone coding for M1Ab complemented the M1 thermosensitive mutant Escherichia coli BL21(DE3) T7A49, which upon transformation was able to grow at the non-permissive temperature. M1Ab showed in vitro catalytic activity in combination with the C5 protein cofactor from E. coli as well as with that from A. baumannii, which was identified, cloned and partially purified. M1Ab was also able to cleave a target mRNA in the presence of an EGS with efficiency comparable to that of the E. coli M1, suggesting that EGS technology could be a viable option for designing therapeutic alternatives to treat multiresistant A. baumannii infections.
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Affiliation(s)
- Carol Davies-Sala
- Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University, Fullerton, Fullerton, CA, United States.,Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.,Facultad de Ciencias Exactas y Naturales de la Universidad de Buenos Aires, University of Buenos Aires, Buenos Aires, Argentina
| | - Saumya Jani
- Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University, Fullerton, Fullerton, CA, United States
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.,Facultad de Ciencias Exactas y Naturales de la Universidad de Buenos Aires, University of Buenos Aires, Buenos Aires, Argentina
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University, Fullerton, Fullerton, CA, United States
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13
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Chow G, Morcos PA, Moulton HM. Aggregation and Disaggregation of Morpholino Oligomers in Solution. Methods Mol Biol 2018; 1565:31-38. [PMID: 28364231 DOI: 10.1007/978-1-4939-6817-6_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Morpholino oligomers are effective antisense molecules to regulate gene expression and the US FDA has approved a Morpholino drug for the treatment of Duchenne muscular dystrophy. However, it has been observed that the antisense activities of aqueous solutions of some Morpholinos decrease over time. We hypothesize that the decreased activity is caused by the formation of soluble aggregates of the Morpholinos. Here, we analyzed three Morpholino sequences by size exclusion chromatography and found two of them have over time formed soluble aggregates in water. The degree of aggregation is sequence-, temperature-, and time-dependent. We describe a simple procedure for detecting and breaking down the aggregates to return the Morpholinos to their monomeric forms.
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Affiliation(s)
- Garrick Chow
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, 105 Magruder Hall, Corvallis, OR, 97331, USA
| | | | - Hong M Moulton
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, 105 Magruder Hall, Corvallis, OR, 97331, USA.
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14
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Jani S, Jackson A, Davies-Sala C, Chiem K, Soler-Bistué A, Zorreguieta A, Tolmasky ME. Assessment of External Guide Sequences' (EGS) Efficiency as Inducers of RNase P-Mediated Cleavage of mRNA Target Molecules. Methods Mol Biol 2018; 1737:89-98. [PMID: 29484589 DOI: 10.1007/978-1-4939-7634-8_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
RNase P is a ribozyme consisting of a catalytic RNA molecule and, depending on the organism, one or more cofactor proteins. It was initially identified as the enzyme that mediates cleavage of precursor tRNAs at the 5'-end termini to generate the mature tRNAs. An important characteristic of RNase P is that its specificity depends on the structure rather than the sequence of the RNA substrate. Any RNA species that interacts with an antisense molecule (called external guide sequence, EGS) and forms the appropriate structure can be cleaved by RNase P. This property is the basis for EGS technology, an antisense methodology for inhibiting gene expression by eliciting RNase P-mediated cleavage of a target mRNA molecule. EGS technology is being developed to design therapies against a large variety of diseases. An essential milestone in developing EGSs as therapies is the assessment of the efficiency of antisense molecules to induce cleavage of the target mRNA and evaluate their effect in vivo. Here, we describe simple protocols to test the ability of EGSs to induce cleavage of a target mRNA in vitro and to induce a phenotypic change in growing cells.
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Affiliation(s)
- Saumya Jani
- Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - Alexis Jackson
- Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
- Fundación Instituto Leloir, IIBBA-CONICET, and FCEyN, University of Buenos Aires, Aires, Argentina
| | - Carol Davies-Sala
- Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
- Fundación Instituto Leloir, IIBBA-CONICET, and FCEyN, University of Buenos Aires, Aires, Argentina
| | - Kevin Chiem
- Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - Alfonso Soler-Bistué
- Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
- Fundación Instituto Leloir, IIBBA-CONICET, and FCEyN, University of Buenos Aires, Aires, Argentina
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, IIBBA-CONICET, and FCEyN, University of Buenos Aires, Aires, Argentina
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA.
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15
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Hegarty JP, Stewart DB. Advances in therapeutic bacterial antisense biotechnology. Appl Microbiol Biotechnol 2017; 102:1055-1065. [PMID: 29209794 DOI: 10.1007/s00253-017-8671-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/16/2017] [Accepted: 11/17/2017] [Indexed: 12/15/2022]
Abstract
Antisense therapeutics are a biotechnological form of antibiotic therapy using chemical analogues of short single-stranded nucleic acid sequences modified to form stable oligomers. These molecules are termed antisense oligonucleotides (ASOs) because their sequence is complementary, via Watson-Crick specific base pairing, to their target messenger RNA (mRNA). ASOs modify gene expression in this sequence-dependent manner by binding to its complementary mRNA and inhibiting its translation into protein through steric blockage and/or through RNase degradation of the ASO/RNA duplex. The widespread use of conventional antibiotics has led to the increasing emergence of multiple drug-resistant pathogenic bacteria. There is an urgent need to develop alternative therapeutic strategies to reduce the morbidity and mortality associated with bacterial infections, and until recently, the use of ASOs as therapeutic agents has been essentially limited to eukaryotic cells, with ASOs as antibacterials having been largely unexplored primarily due to the poor uptake efficiency of antisense molecules by bacteria. There are conceptual advantages to bacterial antisense antibiotic therapies, including a sequence-dependent approach that allows for a rational design to multiple specific molecular targets. This review summarizes the current knowledge of antisense bacterial biotechnology and highlights the recent progress and the current obstacles in their development for therapeutic applications.
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Affiliation(s)
- John P Hegarty
- College of Medicine, Department of Surgery, The Pennsylvania State University, 500 University Drive, H137, P.O. Box 850, Hershey, PA, 17033-0850, USA
| | - David B Stewart
- College of Medicine, Department of Surgery, The Pennsylvania State University, 500 University Drive, H137, P.O. Box 850, Hershey, PA, 17033-0850, USA.
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16
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Métris A, Sudhakar P, Fazekas D, Demeter A, Ari E, Olbei M, Branchu P, Kingsley RA, Baranyi J, Korcsmáros T. SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation. NPJ Syst Biol Appl 2017; 3:31. [PMID: 29057095 PMCID: PMC5647365 DOI: 10.1038/s41540-017-0034-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 09/19/2017] [Accepted: 09/22/2017] [Indexed: 12/31/2022] Open
Abstract
Salmonella enterica is a prominent bacterial pathogen with implications on human and animal health. Salmonella serovars could be classified as gastro-intestinal or extra-intestinal. Genome-wide comparisons revealed that extra-intestinal strains are closer relatives of gastro-intestinal strains than to each other indicating a parallel evolution of this trait. Given the complexity of the differences, a systems-level comparison could reveal key mechanisms enabling extra-intestinal serovars to cause systemic infections. Accordingly, in this work, we introduce a unique resource, SalmoNet, which combines manual curation, high-throughput data and computational predictions to provide an integrated network for Salmonella at the metabolic, transcriptional regulatory and protein-protein interaction levels. SalmoNet provides the networks separately for five gastro-intestinal and five extra-intestinal strains. As a multi-layered, multi-strain database containing experimental data, SalmoNet is the first dedicated network resource for Salmonella. It comprehensively contains interactions between proteins encoded in Salmonella pathogenicity islands, as well as regulatory mechanisms of metabolic processes with the option to zoom-in and analyze the interactions at specific loci in more detail. Application of SalmoNet is not limited to strain comparisons as it also provides a Salmonella resource for biochemical network modeling, host-pathogen interaction studies, drug discovery, experimental validation of novel interactions, uncovering new pathological mechanisms from emergent properties and epidemiological studies. SalmoNet is available at http://salmonet.org.
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Affiliation(s)
- Aline Métris
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK.,Present Address: Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedfordshire UK
| | - Padhmanand Sudhakar
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK.,Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK
| | - David Fazekas
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK.,Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117 Budapest, Hungary
| | - Amanda Demeter
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK.,Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK.,Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117 Budapest, Hungary
| | - Eszter Ari
- Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117 Budapest, Hungary.,Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Marton Olbei
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK.,Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK
| | - Priscilla Branchu
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK.,IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Rob A Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK
| | - Jozsef Baranyi
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK
| | - Tamas Korcsmáros
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK.,Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK
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17
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Hurley KA, Santos TMA, Nepomuceno GM, Huynh V, Shaw JT, Weibel DB. Targeting the Bacterial Division Protein FtsZ. J Med Chem 2016; 59:6975-98. [DOI: 10.1021/acs.jmedchem.5b01098] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Katherine A. Hurley
- Department of Pharmaceutical Sciences, University of Wisconsin—Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Thiago M. A. Santos
- Department
of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Gabriella M. Nepomuceno
- Department of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
| | - Valerie Huynh
- Department of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
| | - Jared T. Shaw
- Department of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
| | - Douglas B. Weibel
- Department
of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Department of Biomedical Engineering, University of Wisconsin—Madison, 1550 Engineering Drive, Madison, Wisconsin 53706, United States
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18
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Jackson A, Jani S, Sala CD, Soler-Bistué AJC, Zorreguieta A, Tolmasky ME. Assessment of configurations and chemistries of bridged nucleic acids-containing oligomers as external guide sequences: a methodology for inhibition of expression of antibiotic resistance genes. Biol Methods Protoc 2016; 1. [PMID: 27857983 PMCID: PMC5108630 DOI: 10.1093/biomethods/bpw001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
External guide sequences (EGSs) are short antisense oligoribonucleotides that elicit RNase P-mediated cleavage of a target mRNA, which results in inhibition of gene expression. EGS technology is used to inhibit expression of a wide variety of genes, a strategy that may lead to development of novel treatments of numerous diseases, including multidrug-resistant bacterial and viral infections. Successful development of EGS technology depends on finding nucleotide analogs that resist degradation by nucleases present in biological fluids and the environment but still elicit RNase P-mediated degradation when forming a duplex with a target mRNA. Previous results suggested that locked nucleic acids (LNA)/DNA chimeric oligomers have these properties. LNA are now considered the first generation of compounds collectively known as bridged nucleic acids (BNAs) – modified ribonucleotides that contain a bridge at the 2ʹ,4ʹ-position of the ribose. LNA and the second-generation BNA, known as BNANC, differ in the chemical nature of the bridge. Chimeric oligomers containing LNA or BNANC and deoxynucleotide monomers in different configurations are nuclease resistant and could be excellent EGS compounds. However, not all configurations may be equally active as EGSs. RNase P cleavage assays comparing LNA/DNA and BNANC/DNA chimeric oligonucleotides that share identical nucleotide sequence but with different configurations were carried out using as target the amikacin resistance aac(6ʹ)-Ib mRNA. LNA/DNA gapmers with 5 and 3/4 LNA residues at the 5ʹ- and 3ʹ-ends, respectively, were the most efficient EGSs while all BNANC/DNA gapmers showed very poor activity. When the most efficient LNA/DNA gapmer was covalently bound to a cell-penetrating peptide, the hybrid compound conserved the EGS activity as determined by RNase P cleavage assays and reduced the levels of resistance to amikacin when added to Acinetobacter baumannii cells in culture, an indication of cellular uptake and biological activity.
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Affiliation(s)
- Alexis Jackson
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA, USA
| | - Saumya Jani
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA, USA
| | - Carol Davies Sala
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA, USA; Fundación Instituto Leloir, IIBBA-CONICET, and FCEyN, University of Buenos Aires, Argentina
| | - Alfonso J C Soler-Bistué
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA, USA; Fundación Instituto Leloir, IIBBA-CONICET, and FCEyN, University of Buenos Aires, Argentina
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, IIBBA-CONICET, and FCEyN, University of Buenos Aires, Argentina
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA, USA
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19
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Hitrik A, Abboud-Jarrous G, Orlovetskie N, Serruya R, Jarrous N. Targeted inhibition of WRN helicase by external guide sequence and RNase P RNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:572-80. [PMID: 26808708 DOI: 10.1016/j.bbagrm.2016.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 12/29/2015] [Accepted: 01/21/2016] [Indexed: 01/04/2023]
Abstract
Human WRN, a RecQ helicase encoded by the Werner syndrome gene, is implicated in genome maintenance, including replication, recombination, excision repair and DNA damage response. These genetic processes and expression of WRN are concomitantly upregulated in many types of cancers. Therefore, targeted destruction of this helicase could be useful for elimination of cancer cells. Here, we provide a proof of concept for applying the external guide sequence (EGS) approach in directing an RNase P RNA to efficiently cleave the WRN mRNA in cultured human cell lines, thus abolishing translation and activity of this distinctive 3'-5' DNA helicase-nuclease. Remarkably, EGS-directed knockdown of WRN leads to severe inhibition of cell viability. Hence, further assessment of this targeting system could be beneficial for selective cancer therapies, particularly in the light of the recent improvements introduced into EGSs.
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Affiliation(s)
- Anna Hitrik
- Department of Microbiology and Molecular Genetics, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Ghada Abboud-Jarrous
- Institute for Dental Sciences, The Hebrew University-Hadassah School of Dental Medicine, Jerusalem 91120, Israel
| | - Natalie Orlovetskie
- Department of Microbiology and Molecular Genetics, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Raphael Serruya
- Department of Microbiology and Molecular Genetics, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Nayef Jarrous
- Department of Microbiology and Molecular Genetics, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; Institute for Dental Sciences, The Hebrew University-Hadassah School of Dental Medicine, Jerusalem 91120, Israel.
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20
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RNase P-Mediated Sequence-Specific Cleavage of RNA by Engineered External Guide Sequences. Biomolecules 2015; 5:3029-50. [PMID: 26569326 PMCID: PMC4693268 DOI: 10.3390/biom5043029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/16/2015] [Accepted: 10/29/2015] [Indexed: 01/06/2023] Open
Abstract
The RNA cleavage activity of RNase P can be employed to decrease the levels of specific RNAs and to study their function or even to eradicate pathogens. Two different technologies have been developed to use RNase P as a tool for RNA knockdown. In one of these, an external guide sequence, which mimics a tRNA precursor, a well-known natural RNase P substrate, is used to target an RNA molecule for cleavage by endogenous RNase P. Alternatively, a guide sequence can be attached to M1 RNA, the (catalytic) RNase P RNA subunit of Escherichia coli. The guide sequence is specific for an RNA target, which is subsequently cleaved by the bacterial M1 RNA moiety. These approaches are applicable in both bacteria and eukaryotes. In this review, we will discuss the two technologies in which RNase P is used to reduce RNA expression levels.
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21
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Sala CD, Soler-Bistué A, Bonomo R, Zorreguieta A, Tolmasky ME. External guide sequence technology: a path to development of novel antimicrobial therapeutics. Ann N Y Acad Sci 2015; 1354:98-110. [PMID: 25866265 PMCID: PMC4600001 DOI: 10.1111/nyas.12755] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/14/2015] [Accepted: 03/03/2015] [Indexed: 12/11/2022]
Abstract
RNase P is a ribozyme originally identified for its role in maturation of tRNAs by cleavage of precursor tRNAs (pre-tRNAs) at the 5'-end termini. RNase P is a ribonucleoprotein consisting of a catalytic RNA molecule and, depending on the organism, one or more cofactor proteins. The site of cleavage of a pre-tRNA is identified by its tertiary structure; and any RNA molecule can be cleaved by RNase P as long as the RNA forms a duplex that resembles the regional structure in the pre-tRNA. When the antisense sequence that forms the duplex with the strand that is subsequently cleaved by RNase P is in a separate molecule, it is called an external guide sequence (EGS). These fundamental observations are the basis for EGS technology, which consists of inhibiting gene expression by utilizing an EGS that elicits RNase P-mediated cleavage of a target mRNA molecule. EGS technology has been used to inhibit expression of a wide variety of genes, and may help development of novel treatments of diseases, including multidrug-resistant bacterial and viral infections.
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Affiliation(s)
- Carol Davies Sala
- Fundación Instituto Leloir, IIBBA-CONICET, and FCEyN, University of
Buenos Aires, Argentina
- Center for Applied Biotechnology Studies, College of Natural Sciences and
Mathematics, California State University Fullerton, Fullerton, California
| | - Alfonso Soler-Bistué
- Fundación Instituto Leloir, IIBBA-CONICET, and FCEyN, University of
Buenos Aires, Argentina
- Center for Applied Biotechnology Studies, College of Natural Sciences and
Mathematics, California State University Fullerton, Fullerton, California
| | - Robert Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine,
Cleveland, Ohio
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, IIBBA-CONICET, and FCEyN, University of
Buenos Aires, Argentina
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, College of Natural Sciences and
Mathematics, California State University Fullerton, Fullerton, California
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22
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Chaudhary AK, Na D, Lee EY. Rapid and high-throughput construction of microbial cell-factories with regulatory noncoding RNAs. Biotechnol Adv 2015; 33:914-30. [PMID: 26027891 DOI: 10.1016/j.biotechadv.2015.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/27/2015] [Accepted: 05/27/2015] [Indexed: 12/11/2022]
Abstract
Due to global crises such as pollution and depletion of fossil fuels, sustainable technologies based on microbial cell-factories have been garnering great interest as an alternative to chemical factories. The development of microbial cell-factories is imperative in cutting down the overall manufacturing cost. Thus, diverse metabolic engineering strategies and engineering tools have been established to obtain a preferred genotype and phenotype displaying superior productivity. However, these tools are limited to only a handful of genes with permanent modification of a genome and significant labor costs, and this is one of the bottlenecks associated with biofactory construction. Therefore, a groundbreaking rapid and high-throughput engineering tool is needed for efficient construction of microbial cell-factories. During the last decade, copious small noncoding RNAs (ncRNAs) have been discovered in bacteria. These are involved in substantial regulatory roles like transcriptional and post-transcriptional gene regulation by modulating mRNA elongation, stability, or translational efficiency. Because of their vulnerability, ncRNAs can be used as another layer of conditional control over gene expression without modifying chromosomal sequences, and hence would be a promising high-throughput tool for metabolic engineering. Here, we review successful design principles and applications of ncRNAs for high-throughput metabolic engineering or physiological studies of diverse industrially important microorganisms.
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Affiliation(s)
- Amit Kumar Chaudhary
- Department of Chemical Engineering, Kyung Hee University, Gyeonggi-do 446-701, Republic of Korea
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 156-756, Republic of Korea.
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Gyeonggi-do 446-701, Republic of Korea.
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23
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Mondhe M, Chessher A, Goh S, Good L, Stach JEM. Species-selective killing of bacteria by antimicrobial peptide-PNAs. PLoS One 2014; 9:e89082. [PMID: 24558473 PMCID: PMC3928365 DOI: 10.1371/journal.pone.0089082] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 01/19/2014] [Indexed: 12/31/2022] Open
Abstract
Broad-spectrum antimicrobials kill indiscriminately, a property that can lead to negative clinical consequences and an increase in the incidence of resistance. Species-specific antimicrobials that could selectively kill pathogenic bacteria without targeting other species in the microbiome could limit these problems. The pathogen genome presents an excellent target for the development of such antimicrobials. In this study we report the design and evaluation of species-selective peptide nucleic acid (PNA) antibacterials. Selective growth inhibition of B. subtilis, E. coli, K. pnuemoniae and S. enterica serovar Typhimurium in axenic or mixed culture could be achieved with PNAs that exploit species differences in the translation initiation region of essential genes. An S. Typhimurium-specific PNA targeting ftsZ resulted in elongated cells that were not observed in E. coli, providing phenotypic evidence of the selectivity of PNA-based antimicrobials. Analysis of the genomes of E. coli and S. Typhimurium gave a conservative estimate of >150 PNA targets that could potentially discriminate between these two closely related species. This work provides a basis for the development of a new class of antimicrobial with a tuneable spectrum of activity.
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Affiliation(s)
- Madhav Mondhe
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ashley Chessher
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Shan Goh
- Department of Pathology and Infectious Diseases, Royal Veterinary College, University of London, London, United Kingdom
| | | | - James E. M. Stach
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
- * E-mail:
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24
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McLeod FSA, Simmonds RS. Penicillin facilitates the entry of antisense constructs into Streptococcus mutans. FEMS Microbiol Lett 2013; 349:25-31. [PMID: 24111714 DOI: 10.1111/1574-6968.12286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 09/13/2013] [Indexed: 12/01/2022] Open
Abstract
Antisense oligonucleotides (AS-ODN) target genes in a sequence-specific manner inhibit gene function and have potential use as antimicrobial agents. Cell barriers, such as peptidoglycan, cell surface proteins and lipopolysaccharide membranes, prevent delivery of AS-ODN into the bacterial cell, limiting their use as an effective treatment option. The β-lactam antibiotic penicillin was examined for its ability to deliver phosphorothioate oligodeoxyribonucleotides (PS-ODNs) and γ(32) P-ODN into Streptococcus mutans OMZ175. Treatment of lag-phase S. mutans OMZ175 cells with penicillin and FBA (PS-ODN targeting the fructose-biphosphate aldolase gene), resulted in prolonged suppression of growth (> 24 h) and fba expression (656.9 ± 194.4-fold decrease at 5 h). Suppression of both cell growth and fba expression corresponded with a greater amount of γ(32) P-ODN becoming cell associated, with a maximum γ(32) P-ODN concentration per cell achieved 5 h after penicillin treatment (6.50 ± 1.39 × 10(8) molecules per CFU). This study confirms that for S. mutans OMZ175, the peptidoglycan layer acts as a major barrier preventing AS-ODN penetration and suggests that the use of agents such as penicillin that interfere with peptidoglycan integrity can significantly increase the uptake of PS-ODN by these cells.
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Affiliation(s)
- Felicity S A McLeod
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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25
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Synthetic RNA Silencing of Actinorhodin Biosynthesis in Streptomyces coelicolor A3(2). PLoS One 2013; 8:e67509. [PMID: 23826310 PMCID: PMC3694883 DOI: 10.1371/journal.pone.0067509] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 05/24/2013] [Indexed: 01/15/2023] Open
Abstract
We demonstrate the first application of synthetic RNA gene silencers in Streptomyces coelicolor A3(2). Peptide nucleic acid and expressed antisense RNA silencers successfully inhibited actinorhodin production. Synthetic RNA silencing was target-specific and is a new tool for gene regulation and metabolic engineering studies in Streptomyces.
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26
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Sawyer AJ, Wesolowski D, Gandotra N, Stojadinovic A, Izadjoo M, Altman S, Kyriakides TR. A peptide-morpholino oligomer conjugate targeting Staphylococcus aureus gyrA mRNA improves healing in an infected mouse cutaneous wound model. Int J Pharm 2013; 453:651-5. [PMID: 23727592 DOI: 10.1016/j.ijpharm.2013.05.041] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 04/24/2013] [Accepted: 05/14/2013] [Indexed: 11/26/2022]
Abstract
Management of skin wound infections presents a serious problem in the clinic, in the community, and in both civilian and military clinical treatment centers. Staphylococcus aureus is one of the most common microbial pathogens in cutaneous wounds. Peptide-morpholino oligomer (PMO) conjugates targeted to S. aureus gyrase A mRNA have shown the ability to reduce bacterial viability by direct site-specific mRNA cleavage via RNase P. As a treatment, these conjugates have the added advantages of not being susceptible to resistance due to genetic mutations and are effective against drug resistant strains. While this strategy has proven effective in liquid culture, it has yet to be evaluated in an animal model of infected surface wounds. In the present study, we combined PMO conjugates with a thermoresponsive gel delivery system to treat full-thickness mouse cutaneous wounds infected with S. aureus. Wounds treated with a single dose of PMO conjugate displayed improved healing that was associated with increased epithelialization, reduced bacterial load, and increased matrix deposition. Taken together, our findings demonstrate the efficacy and flexibility of the PMO conjugate drug delivery system and make it an attractive and novel topical antimicrobial agent.
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Affiliation(s)
- Andrew J Sawyer
- Department of Pathology, Yale University, New Haven, CT 06520, USA
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27
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Microbial competition in polar soils: a review of an understudied but potentially important control on productivity. BIOLOGY 2013; 2:533-54. [PMID: 24832797 PMCID: PMC3960893 DOI: 10.3390/biology2020533] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 03/11/2013] [Accepted: 03/12/2013] [Indexed: 01/29/2023]
Abstract
Intermicrobial competition is known to occur in many natural environments, and can result from direct conflict between organisms, or from differential rates of growth, colonization, and/or nutrient acquisition. It has been difficult to extensively examine intermicrobial competition in situ, but these interactions may play an important role in the regulation of the many biogeochemical processes that are tied to microbial communities in polar soils. A greater understanding of how competition influences productivity will improve projections of gas and nutrient flux as the poles warm, may provide biotechnological opportunities for increasing the degradation of contaminants in polar soil, and will help to predict changes in communities of higher organisms, such as plants.
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28
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Traglia GM, Sala CD, Fuxman Bass JI, Soler-Bistué AJC, Zorreguieta A, Ramírez MS, Tolmasky ME. Internalization of Locked Nucleic Acids/DNA Hybrid Oligomers into Escherichia coli. Biores Open Access 2013; 1:260-3. [PMID: 23515318 PMCID: PMC3559211 DOI: 10.1089/biores.2012.0257] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Delivery inside the cells is essential for practical application of antisense technologies. The hybrid locked nucleic acid (LNA)/DNA CAAGTACTGTTCCACCA (LNA residues are underlined) was labeled by conjugation to Alexa Fluor 488 (fLNA/DNA) and tested to determine its ability to penetrate Escherichia coli cells and reach the cytoplasm. Flow cytometry analysis showed that the fLNA/DNA was associated with 14% of cells from a stationary phase culture, while association with a labeled isosequential oligodeoxynucleotide was negligible. Laser scanning confocal microscopy confirmed that the fLNA/DNA was located inside the cytoplasm.
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Affiliation(s)
- German M Traglia
- Institute of Microbiology and Medical Parasitology, National Scientific and Technical Research Council (CONICET), University of Buenos Aires , Buenos Aires, Argentina
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29
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Inhibition of cell division induced by external guide sequences (EGS Technology) targeting ftsZ. PLoS One 2012; 7:e47690. [PMID: 23110089 PMCID: PMC3479136 DOI: 10.1371/journal.pone.0047690] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 09/18/2012] [Indexed: 01/20/2023] Open
Abstract
EGS (external guide sequence) technology is a promising approach to designing new antibiotics. EGSs are short antisense oligoribonucleotides that induce RNase P-mediated cleavage of a target RNA by forming a precursor tRNA-like complex. The ftsZ mRNA secondary structure was modeled and EGSs complementary to two regions with high probability of being suitable targets were designed. In vitro reactions showed that EGSs targeting these regions bound ftsZ mRNA and elicited RNase P-mediated cleavage of ftsZ mRNA. A recombinant plasmid, pEGSb1, coding for an EGS that targets region “b” under the control of the T7 promoter was generated. Upon introduction of this plasmid into Escherichia coli BL21(DE3)(pLysS) the transformant strain formed filaments when expression of the EGS was induced. Concomitantly, E. coli harboring pEGSb1 showed a modest but significant inhibition of growth when synthesis of the EGSb1 was induced. Our results indicate that EGS technology could be a viable strategy to generate new antimicrobials targeting ftsZ.
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30
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Gene selective mRNA cleavage inhibits the development of Plasmodium falciparum. Proc Natl Acad Sci U S A 2012; 109:6235-40. [PMID: 22474358 DOI: 10.1073/pnas.1203516109] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unique peptide-morpholino oligomer (PMO) conjugates have been designed to bind and promote the cleavage of specific mRNA as a tool to inhibit gene function and parasite growth. The new conjugates were validated using the P. falciparum gyrase mRNA as a target (PfGyrA). Assays in vitro demonstrated a selective degradation of the PfGyrA mRNA directed by the external guide sequences, which are morpholino oligomers in the conjugates. Fluorescence microscopy revealed that labeled conjugates are delivered into Plasmodium-infected erythrocytes during all intraerythrocytic stages of parasite development. Consistent with the expression of PfGyrA in all stages of parasite development, proliferation assays showed that these conjugates have potent antimalarial activity, blocking early development, maturation, and replication of the parasite. The conjugates were equally effective against drug sensitive and resistant P. falciparum strains. The potency, selectivity, and predicted safety of PMO conjugates make this approach attractive for the development of a unique class of target-specific antimalarials and for large-scale functional analysis of the malarial genome.
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31
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Kole R, Krainer AR, Altman S. RNA therapeutics: beyond RNA interference and antisense oligonucleotides. Nat Rev Drug Discov 2012; 11:125-40. [PMID: 22262036 PMCID: PMC4743652 DOI: 10.1038/nrd3625] [Citation(s) in RCA: 892] [Impact Index Per Article: 68.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Here, we discuss three RNA-based therapeutic technologies exploiting various oligonucleotides that bind to RNA by base pairing in a sequence-specific manner yet have different mechanisms of action and effects. RNA interference and antisense oligonucleotides downregulate gene expression by inducing enzyme-dependent degradation of targeted mRNA. Steric-blocking oligonucleotides block the access of cellular machinery to pre-mRNA and mRNA without degrading the RNA. Through this mechanism, steric-blocking oligonucleotides can redirect alternative splicing, repair defective RNA, restore protein production or downregulate gene expression. Moreover, they can be extensively chemically modified to acquire more drug-like properties. The ability of RNA-blocking oligonucleotides to restore gene function makes them best suited for the treatment of genetic disorders. Positive results from clinical trials for the treatment of Duchenne muscular dystrophy show that this technology is close to achieving its clinical potential.
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Affiliation(s)
- Ryszard Kole
- AVI BioPharma, 3450 Monte Villa Parkway, Bothell, Washington 98021, USA.
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32
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Abstract
The gene coding for the RNA subunit of ribonuclease P (RNase P) is essential in all free-living organisms. The RNA subunit, itself, is an enzyme and, from its evolutionary tree, we can infer that it is a very ancient molecule. The specificity of this enzyme is that it cleaves other RNA molecules at the junction of single-stranded and the 5' end of double-stranded regions of RNA. One can speculate that this molecule was very useful in an ancient world in cleaving long pieces of RNA, which must have contained hairpin regions in it, into shorter molecules with the capability of different functions from the longer parent. Today, the specificity of the enzyme can be used in designing drug therapies.
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Affiliation(s)
- Sidney Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.
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Basic peptide-morpholino oligomer conjugate that is very effective in killing bacteria by gene-specific and nonspecific modes. Proc Natl Acad Sci U S A 2011; 108:16582-7. [PMID: 21949365 DOI: 10.1073/pnas.1112561108] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Basic peptides covalently linked to nucleic acids, or chemically modified nucleic acids, enable the insertion of such a conjugate into bacteria grown in liquid medium and mammalian cells in tissue culture. A unique peptide, derived from human T cells, has been employed in a chemical synthesis to make a conjugate with a morpholino oligonucleotide. This new conjugate is at least 10- to 100-fold more effective than previous peptides used in altering the phenotype of host bacteria if the external guide sequence methodology is employed in these experiments. Bacteria with target genes expressing chloramphenicol resistance, penicillin resistance, or gyrase A function can effectively be reduced in their expression and the host cells killed. Several bacteria are susceptible to this treatment, which has a broad range of potency. The loss in viability of bacteria is not due only to complementarity with a target RNA and the action of RNase P, but also to a non-gene-specific tight binding of the complexed nontargeted RNA to the basic polypeptide-morpholino oligonucleotide.
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Cho IM, Kazakov SA, Gopalan V. Evidence for recycling of external guide sequences during cleavage of bipartite substrates in vitro by reconstituted archaeal RNase P. J Mol Biol 2011; 405:1121-7. [PMID: 21144851 PMCID: PMC3025773 DOI: 10.1016/j.jmb.2010.11.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 11/25/2010] [Accepted: 11/30/2010] [Indexed: 11/18/2022]
Abstract
RNA-mediated RNA cleavage events are being increasingly exploited to disrupt RNA function, an important objective in post-genomic biology. RNase P, a ribonucleoprotein enzyme that catalyzes the removal of 5'-leaders from precursor tRNAs, has previously been utilized for sequence-specific cleavage of cellular RNAs. In one of these strategies, borne out in bacterial and mammalian cell culture, an external guide sequence (EGS) RNA base-paired to a target RNA makes the latter a substrate for endogenous RNase P by rendering the bipartite target RNA-EGS complex a precursor tRNA structural mimic. In this study, we first obtained evidence that four different mesophilic and thermophilic archaeal RNase P holoenzymes, reconstituted in vitro using their respective constituent RNA and protein subunits, recognize and cleave such substrate-EGS complexes. We further demonstrate that these EGSs engage in multiple rounds of substrate recognition while assisting archaeal RNase P-mediated cleavage of a target RNA in vitro. Taken together, the EGS-based approach merits consideration as a gene knockdown tool in archaea.
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Affiliation(s)
- I-Ming Cho
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | | | - Venkat Gopalan
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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Aarthi JJ, Darendeliler MA, Pushparaj PN. Dissecting the role of the S1P/S1PR axis in health and disease. J Dent Res 2011; 90:841-54. [PMID: 21248363 DOI: 10.1177/0022034510389178] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Sphingosine-1-phosphate (S1P) is a pleiotropic sphingophospholipid generated from the phosphorylation of sphingosine by sphingosine kinases (SPHKs). S1P has been experimentally demonstrated to modulate an array of cellular processes such as cell proliferation, cell survival, cell invasion, vascular maturation, and angiogenesis by binding with any of the five known G-protein-coupled sphingosine 1 phosphate receptors (S1P1-5) on the cell surface in an autocrine as well as a paracrine manner. Recent studies have shown that the S1P receptors (S1PRs) and SPHKs are the key targets for modulating the pathophysiological consequences of various debilitating diseases, such as cancer, sepsis, rheumatoid arthritis, ulcerative colitis, and other related illnesses. In this article, we recapitulate these novel discoveries relative to the S1P/S1PR axis, necessary for the proper maintenance of health, as well as the induction of tumorigenic, angiogenic, and inflammatory stimuli that are vital for the development of various diseases, and the novel therapeutic tools to modulate these responses in oral biology and medicine.
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Affiliation(s)
- J J Aarthi
- Department of Orthodontics, Faculty of Dentistry, The University of Sydney, Sydney, New South Wales, NSW 2010, Australia
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36
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Zhang H, Jiang T. Synthetic circuits, devices and modules. Protein Cell 2010; 1:974-8. [PMID: 21153514 DOI: 10.1007/s13238-010-0133-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 11/09/2010] [Indexed: 12/19/2022] Open
Abstract
The aim of synthetic biology is to design artificial biological systems for novel applications. From an engineering perspective, construction of biological systems of defined functionality in a hierarchical way is fundamental to this emerging field. Here, we highlight some current advances on design of several basic building blocks in synthetic biology including the artificial gene control elements, synthetic circuits and their assemblies into devices and modules. Such engineered basic building blocks largely expand the synthetic toolbox and contribute to our understanding of the underlying design principles of living cells.
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Affiliation(s)
- Hong Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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Xiao G, Wesolowski D, Izadjoo M, Altman S. Morpholino oligonucleotides do not participate perfectly in standard Watson-Crick complexes with RNA. RNA (NEW YORK, N.Y.) 2010; 16:2218-25. [PMID: 20817753 PMCID: PMC2957060 DOI: 10.1261/rna.2256610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
RNase P from E. coli will cleave a RNA at a site designated in a complex with an external guide sequence (EGS). The location of the site is determined by the Watson-Crick complementary sequence that can be formed between the RNA and the EGS. Morpholino oligonucleotides (PMOs) that have the same base sequences as any particular EGS will not direct cleavage by RNase P of the target RNA at the expected site in three mRNAs. Instead, cleavage occurs at a secondary site that does not correspond exactly to the expected Watson-Crick sequence in the PMO. This cleavage in the mRNA for a drug resistance gene, CAT mRNA, is at least second order in the concentration of the PMOs, but the mechanism is not understood yet and might be more complicated than a simple second-order reaction. EGSs and PMOs inhibit the reactions of each other effectively in a competitive fashion. A basic peptide attached to the PMO (PPMO) is more effective because of its binding properties to the mRNA as a substrate. However, a PMO is just as efficient as a PPMO on a mRNA that is mutated so that the canonical W-C site has been altered. The altered mRNA is not recognizable by effective extensive W-C pairing to an EGS or PMO. The complex of a PMO on a mutated mRNA as a substrate shows that the dimensions of the modified oligonucleotide cannot be the same as a naked piece of single-stranded RNA.
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Affiliation(s)
- Gaoping Xiao
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
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38
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Abstract
Nuclear ribonuclease (RNase) P is a ubiquitous essential ribonucleoprotein complex, one of only two known RNA-based enzymes found in all three domains of life. The RNA component is the catalytic moiety of RNases P across all phylogenetic domains; it contains a well-conserved core, whereas peripheral structural elements are diverse. RNA components of eukaryotic RNases P tend to be less complex than their bacterial counterparts, a simplification that is accompanied by a dramatic reduction of their catalytic ability in the absence of protein. The size and complexity of the protein moieties increase dramatically from bacterial to archaeal to eukaryotic enzymes, apparently reflecting the delegation of some structural functions from RNA to proteins and, perhaps, in response to the increased complexity of the cellular environment in the more evolutionarily advanced organisms; the reasons for the increased dependence on proteins are not clear. We review current information on RNase P and the closely related universal eukaryotic enzyme RNase MRP, focusing on their functions and structural organization.
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Affiliation(s)
- Olga Esakova
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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39
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Abstract
The ability to interfere with gene expression is of crucial importance to unravel the function of genes and is also a promising therapeutic strategy. Here we discuss methodologies for inhibition of target RNAs based on the cleavage activity of the essential enzyme, Ribonuclease P (RNase P). RNase P-mediated cleavage of target RNAs can be directed by external guide sequences (EGSs) or by the use of the catalytic M1 RNA from E. coli linked to a guide sequence (M1GSs). These are not only basic tools for functional genetic studies in prokaryotic and eukaryotic cells but also promising antibacterial, anticancer and antiviral agents.
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Affiliation(s)
- Eirik Wasmuth Lundblad
- Reference Centre for Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway.
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40
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Hatamoto M, Ohashi A, Imachi H. Peptide nucleic acids (PNAs) antisense effect to bacterial growth and their application potentiality in biotechnology. Appl Microbiol Biotechnol 2010; 86:397-402. [PMID: 20135118 DOI: 10.1007/s00253-009-2387-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Revised: 11/26/2009] [Accepted: 11/27/2009] [Indexed: 11/29/2022]
Abstract
Peptide nucleic acids (PNAs) are nucleic acid analogs having attractive properties such as quiet stability against nucleases and proteases, and they form strong complexes with complementary strands of DNA or RNA. Because of this attractive nature, PNA is often used in antisense technology to inhibit gene expression and microbial cell growth with high specificity. Many bacterial antisense or antiribosomal studies using PNA oligomers have been reported so far, and parameters to design effective antisense PNAs and to improve PNA cell entry for efficient inhibition of bacterial growth have been presented. However, there are still several obstacles such as low cellular uptake of PNA while applying antisense PNAs to a complex microbial community. On overcoming these problems, the PNA antisense technique might become a very attractive tool not only for controlling the microbial growth but also for further elucidating microbial ecology in complex microbial consortia. Here, we summarize and present recent studies on the development of antimicrobial PNAs targeting mRNAs and rRNAs. In addition, the application potentiality of antisense techniques in nonclinical biotechnology fields is discussed.
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Affiliation(s)
- Masashi Hatamoto
- Department of Social and Environmental Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8527, Japan.
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McClain WH, Lai LB, Gopalan V. Trials, travails and triumphs: an account of RNA catalysis in RNase P. J Mol Biol 2010; 397:627-46. [PMID: 20100492 DOI: 10.1016/j.jmb.2010.01.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 01/12/2010] [Accepted: 01/19/2010] [Indexed: 12/16/2022]
Abstract
Last December marked the 20th anniversary of the Nobel Prize in Chemistry to Sidney Altman and Thomas Cech for their discovery of RNA catalysts in bacterial ribonuclease P (an enzyme catalyzing 5' maturation of tRNAs) and a self-splicing rRNA of Tetrahymena, respectively. Coinciding with the publication of a treatise on RNase P, this review provides a historical narrative, a brief report on our current knowledge, and a discussion of some research prospects on RNase P.
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Affiliation(s)
- William H McClain
- Department of Bacteriology, College of Agriculture & Life Sciences, University of Wisconsin, Madison, WI 53706, USA.
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Inhibition of aac(6')-Ib-mediated amikacin resistance by nuclease-resistant external guide sequences in bacteria. Proc Natl Acad Sci U S A 2009; 106:13230-5. [PMID: 19666539 DOI: 10.1073/pnas.0906529106] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inhibition of bacterial gene expression by RNase P-directed cleavage is a promising strategy for the development of antibiotics and pharmacological agents that prevent expression of antibiotic resistance. The rise in multiresistant bacteria harboring AAC(6')-Ib has seriously limited the effectiveness of amikacin and other aminoglycosides. We have recently shown that recombinant plasmids coding for external guide sequences (EGS), short antisense oligoribonucleotides (ORN) that elicit RNase P-mediated cleavage of a target mRNA, induce inhibition of expression of aac(6')-Ib and concomitantly induce a significant decrease in the levels of resistance to amikacin. However, since ORN are rapidly degraded by nucleases, development of a viable RNase P-based antisense technology requires the design of nuclease-resistant RNA analog EGSs. We have assayed a variety of ORN analogs of which selected LNA/DNA co-oligomers elicited RNase P-mediated cleavage of mRNA in vitro. Although we found an ideal configuration of LNA/DNA residues, there seems not to be a correlation between number of LNA substitutions and level of activity. Exogenous administration of as low as 50 nM of an LNA/DNA co-oligomer to the hyperpermeable E. coli AS19 harboring the aac(6')-Ib inhibited growth in the presence of amikacin. Our experiments strongly suggest an RNase P-mediated mechanism in the observed antisense effect.
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