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Chandler M, Panigaj M, Rolband LA, Afonin KA. Challenges to optimizing RNA nanostructures for large scale production and controlled therapeutic properties. Nanomedicine (Lond) 2020; 15:1331-1340. [PMID: 32452262 PMCID: PMC7304434 DOI: 10.2217/nnm-2020-0034] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/16/2020] [Indexed: 02/06/2023] Open
Abstract
Nucleic acids have been utilized to construct an expansive collection of nanoarchitectures varying in design, physicochemical properties, cellular processing and biomedical applications. However, the broader therapeutic adaptation of nucleic acid nanoassemblies in general, and RNA-based nanoparticles in particular, have faced several challenges in moving towards (pre)clinical settings. For one, the large-batch synthesis of nucleic acids is still under development, with multi-stranded and chemically modified assemblies requiring greater production capacity while maintaining consistent medical-grade outputs. Furthermore, the unknown immunostimulation by these nanomaterials poses additional challenges, necessary to be overcome for optimizing future development of clinically approved RNA nanoparticles.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Martin Panigaj
- Institute of Biology & Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice, Slovak Republic
| | - Lewis A Rolband
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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2
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Higuchi-Takeuchi M, Numata K. Marine Purple Photosynthetic Bacteria as Sustainable Microbial Production Hosts. Front Bioeng Biotechnol 2019; 7:258. [PMID: 31681740 PMCID: PMC6798066 DOI: 10.3389/fbioe.2019.00258] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/25/2019] [Indexed: 12/01/2022] Open
Abstract
Photosynthetic microorganisms can serve as the ideal hosts for the sustainable production of high-value compounds. Purple photosynthetic bacteria are typical anoxygenic photosynthetic microorganisms and are expected to be one of the suitable microorganisms for industrial production. Purple photosynthetic bacteria are reported to produce polyhydroxyalkanoate (PHA), extracellular nucleic acids and hydrogen gas. We characterized PHA production as a model compound in purple photosynthetic bacteria, especially focused on marine strains. PHA is a family of biopolyesters synthesized by a variety of microorganisms as carbon and energy storage materials. PHA have recently attracted attention as an alternative to conventional petroleum-based plastics. Production of extracellular nucleic acids have been studied in Rhodovulum sulfidophilum, a marine purple non-sulfur bacterium. Several types of artificial RNAs have been successfully produced in R. sulfidophilum. Purple photosynthetic bacteria produce hydrogen via nitrogenase, and genetic engineering strategies have been investigated to enhance the hydrogen production. This mini review describes the microbial production of these high-value compounds using purple photosynthetic bacteria as the host microorganism.
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Affiliation(s)
- Mieko Higuchi-Takeuchi
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan
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Kikuchi Y, Umekage S. Extracellular nucleic acids of the marine bacterium Rhodovulum sulfidophilum and recombinant RNA production technology using bacteria. FEMS Microbiol Lett 2019; 365:4705897. [PMID: 29228187 DOI: 10.1093/femsle/fnx268] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/05/2017] [Indexed: 12/21/2022] Open
Abstract
Extracellular nucleic acids of high molecular weight are detected ubiquitously in seawater. Recent studies have indicated that these nucleic acids are, at least in part, derived from active production by some bacteria. The marine bacterium Rhodovulum sulfidophilum is one of those bacteria. Rhodovulumsulfidophilum is a non-sulfur phototrophic marine bacterium that is known to form structured communities of cells called flocs, and to produce extracellular nucleic acids in culture media. Recently, it has been revealed that this bacterium produces gene transfer agent-like particles and that this particle production may be related to the extracellular nucleic acid production mechanism. This review provides a summary of recent physiological and genetic studies of these phenomena and also introduces a new method for extracellular production of artificial and biologically functional RNAs using this bacterium. In addition, artificial RNA production using Escherichia coli, which is related to this topic, will also be described.
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Affiliation(s)
- Yo Kikuchi
- Department of Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - So Umekage
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
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Komatsu H, Yamamoto J, Suzuki H, Nagao N, Hirose Y, Ohyama T, Umekage S, Kikuchi Y. Involvement of the response regulator CtrA in the extracellular DNA production of the marine bacterium Rhodovulum sulfidophilum. J GEN APPL MICROBIOL 2018. [PMID: 29526925 DOI: 10.2323/jgam.2017.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The marine bacterium Rhodovulum sulfidophilum is a nonsulfur phototrophic bacterium, which is known to produce extracellular nucleic acids in soluble form in culture medium. In the present paper, constructing the response regulator ctrA-deficient mutant of R. sulfidophilum, we found that this mutation causes a significant decrease in the extracellular DNA production. However, by the introduction of a plasmid containing the wild type ctrA gene into the mutant, the amount of extracellular DNA produced was recovered. This is the first and clear evidence that the extracellular DNA production is actively controlled by the CtrA in R. sulfidophilum.
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Affiliation(s)
- Hiroyuki Komatsu
- Department of Environmental and Life Sciences, Toyohashi University of Technology
| | - Junya Yamamoto
- Department of Environmental and Life Sciences, Toyohashi University of Technology
| | - Hiromichi Suzuki
- Department of Environmental and Life Sciences, Toyohashi University of Technology
| | - Nobuyoshi Nagao
- Department of Environmental and Life Sciences, Toyohashi University of Technology
| | - Yuu Hirose
- Department of Environmental and Life Sciences, Toyohashi University of Technology
| | - Takashi Ohyama
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University.,Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University
| | - So Umekage
- Department of Environmental and Life Sciences, Toyohashi University of Technology
| | - Yo Kikuchi
- Department of Environmental and Life Sciences, Toyohashi University of Technology.,Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University
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Amano R, Aoki K, Miyakawa S, Nakamura Y, Kozu T, Kawai G, Sakamoto T. NMR monitoring of the SELEX process to confirm enrichment of structured RNA. Sci Rep 2017; 7:283. [PMID: 28325909 PMCID: PMC5428055 DOI: 10.1038/s41598-017-00273-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/15/2017] [Indexed: 01/20/2023] Open
Abstract
RNA aptamers are RNA molecules that bind to a target molecule with high affinity and specificity using uniquely-folded tertiary structures. RNA aptamers are selected from an RNA pool typically comprising up to 1015 different sequences generated by iterative steps of selection and amplification known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Over several rounds of SELEX, the diversity of the RNA pool decreases and the aptamers are enriched. Hence, monitoring of the enrichment of these RNA pools is critical for the successful selection of aptamers, and several methods for monitoring them have been developed. In this study, we measured one-dimensional imino proton NMR spectra of RNA pools during SELEX. The spectrum of the initial RNA pool indicates that the RNAs adopt tertiary structures. The structural diversity of the RNA pools was shown to depend highly on the design of the primer-binding sequence. Furthermore, we demonstrate that enrichment of RNA aptamers can be monitored using NMR. The RNA pools can be recovered from the NMR tube after measurement of NMR spectra. We also can monitor target binding in the NMR tubes. Thus, we propose using NMR to monitor the enrichment of structured aptamers during the SELEX process.
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Affiliation(s)
- Ryo Amano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan
| | - Kazuteru Aoki
- Ribomic Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - Shin Miyakawa
- Ribomic Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - Yoshikazu Nakamura
- Ribomic Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan.
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Pereira P, Pedro AQ, Tomás J, Maia CJ, Queiroz JA, Figueiras A, Sousa F. Advances in time course extracellular production of human pre-miR-29b from Rhodovulum sulfidophilum. Appl Microbiol Biotechnol 2016; 100:3723-34. [DOI: 10.1007/s00253-016-7350-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 01/12/2016] [Accepted: 01/23/2016] [Indexed: 02/08/2023]
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Nagao N, Yamamoto J, Komatsu H, Suzuki H, Hirose Y, Umekage S, Ohyama T, Kikuchi Y. The gene transfer agent-like particle of the marine phototrophic bacterium Rhodovulum sulfidophilum. Biochem Biophys Rep 2015; 4:369-374. [PMID: 29124226 PMCID: PMC5669443 DOI: 10.1016/j.bbrep.2015.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 10/29/2015] [Accepted: 11/02/2015] [Indexed: 11/20/2022] Open
Abstract
Gene transfer agents (GTAs) are shaped like bacteriophage particles but have many properties that distinguish them from bacteriophages. GTAs play a role in horizontal gene transfer in nature and thus affect the evolution of prokaryotic genomes. In the course of studies on the extracellular production of designed RNAs using the marine bacterium Rhodovulum sulfidophilum, we found that this bacterium produces a GTA-like particle. The particle contains DNA fragments of 4.5 kb, which consist of randomly fragmented genomic DNA from the bacterium. This 4.5-kb DNA production was prevented while quorum sensing was inhibited. Direct observation of the particle by transmission electron microscopy revealed that the particle resembles a tailed phage and has a head diameter of about 40 nm and a tail length of about 60 nm. We also identified the structural genes for the GTA in the genome. Translated amino acid sequences and gene positions are closely related to those of the genes that encode the Rhodobacter capsulatus GTA. This is the first report of a GTA-like particle from the genus Rhodovulum. However, gene transfer activity of this particle has not yet been confirmed. The differences between this particle and other GTAs are discussed. Rhodovulum sulfidophilum produces the GTA-like particle. The GTA-like particle contains 4.5 kbp DNA. The GTA-like particle was directly observed by TEM. The structural genes for the particle were identified in the host genome.
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Affiliation(s)
- Nobuyoshi Nagao
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Junya Yamamoto
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Hiroyuki Komatsu
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Hiromichi Suzuki
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Yuu Hirose
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - So Umekage
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Takashi Ohyama
- Department of Integrative Bioscience and Biomedical Engineering, Graduate School of Advanced Science and Engineering, Waseda University, Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yo Kikuchi
- Department of Integrative Bioscience and Biomedical Engineering, Graduate School of Advanced Science and Engineering, Waseda University, Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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Nagao N, Suzuki H, Numano R, Umekage S, Kikuchi Y. Short hairpin RNAs of designed sequences can be extracellularly produced by the marine bacterium Rhodovulum sulfidophilum. J GEN APPL MICROBIOL 2015; 60:222-6. [PMID: 25742972 DOI: 10.2323/jgam.60.222] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Previously, we proposed a new method for production of RNA aptamers using the marine bacterium Rhodovulum sulfidophilum. A streptavidin RNA aptamer (an RNA which binds to streptavidin) was extracellularly produced by this bacterium containing engineered plasmid. The aptamer had full biological function. As a next step we attempted to produce another functional RNA, short hairpin RNAs (shRNAs) using this bacterial system. We have designed two types of shRNAs targeted to the luciferase gene. Here we report that shRNAs are successfully produced extracellularly by this system. Even if the shRNA has a long stem-loop structure which is thought to interfere with transcription in bacterial cells, the yield of the shRNA is almost the same as that of the streptavidin RNA aptamer. During the course of these experiments, we also found a new type of RNA processing for the double-stranded region of the shRNA.
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Affiliation(s)
- Nobuyoshi Nagao
- Department of Environmental and Life Sciences, Toyohashi University of Technology
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Complete Genome Sequence of Rhodovulum sulfidophilum DSM 2351, an Extracellular Nucleic Acid-Producing Bacterium. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00388-15. [PMID: 25931606 PMCID: PMC4417702 DOI: 10.1128/genomea.00388-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Rhodovulum sulfidophilum DSM 2351 is the nonsulfur photosynthetic bacterium that efficiently releases nucleic acids into the extracellular milieu, which leads to flocculation. In this study, we determined the complete genome sequence of R. sulfidophilum DSM 2351, which will provide new insights into the mechanism of its unique nucleic acid release.
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Pereira P, Sousa Â, Queiroz JA, Figueiras A, Sousa F. Pharmaceutical-grade pre-miR-29 purification using an agmatine monolithic support. J Chromatogr A 2014; 1368:173-82. [DOI: 10.1016/j.chroma.2014.09.080] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 09/14/2014] [Accepted: 09/27/2014] [Indexed: 02/08/2023]
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Purification of pre-miR-29 by a new O-phospho-l-tyrosine affinity chromatographic strategy optimized using design of experiments. J Chromatogr A 2014; 1343:119-27. [DOI: 10.1016/j.chroma.2014.03.071] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 03/14/2014] [Accepted: 03/27/2014] [Indexed: 01/01/2023]
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12
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Pereira P, Sousa Â, Queiroz J, Correia I, Figueiras A, Sousa F. Purification of pre-miR-29 by arginine-affinity chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 951-952:16-23. [DOI: 10.1016/j.jchromb.2014.01.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/12/2014] [Accepted: 01/14/2014] [Indexed: 11/26/2022]
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