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Ueda T, Nishimura KI, Nishiyama Y, Tominaga Y, Miyazaki K, Furuta H, Matsumura S, Ikawa Y. Pairwise Engineering of Tandemly Aligned Self-Splicing Group I Introns for Analysis and Control of Their Alternative Splicing. Biomolecules 2023; 13:biom13040654. [PMID: 37189401 DOI: 10.3390/biom13040654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
Alternative splicing is an important mechanism in the process of eukaryotic nuclear mRNA precursors producing multiple protein products from a single gene. Although group I self-splicing introns usually perform regular splicing, limited examples of alternative splicing have also been reported. The exon-skipping type of splicing has been observed in genes containing two group I introns. To characterize splicing patterns (exon-skipping/exon-inclusion) of tandemly aligned group I introns, we constructed a reporter gene containing two Tetrahymena introns flanking a short exon. To control splicing patterns, we engineered the two introns in a pairwise manner to design pairs of introns that selectively perform either exon-skipping or exon-inclusion splicing. Through pairwise engineering and biochemical characterization, the structural elements important for the induction of exon-skipping splicing were elucidated.
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Affiliation(s)
- Tomoki Ueda
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Kei-ichiro Nishimura
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yuka Nishiyama
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Yuto Tominaga
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Katsushi Miyazaki
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
- Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
- Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
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2
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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3
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Abstract
The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an 'RNA world', notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pK a values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.
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4
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Qiu H, Weng D, Chen T, Shen L, Chen SS, Wei YR, Wu Q, Zhao MM, Li QH, Hu Y, Zhang Y, Zhou Y, Su YL, Zhang F, Lu LQ, Zhou NY, Li SL, Zhang LL, Wang C, Li HP. Stimulator of Interferon Genes Deficiency in Acute Exacerbation of Idiopathic Pulmonary Fibrosis. Front Immunol 2017; 8:1756. [PMID: 29312299 PMCID: PMC5732537 DOI: 10.3389/fimmu.2017.01756] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/27/2017] [Indexed: 12/25/2022] Open
Abstract
The stimulator of interferon genes (STING) is a key adaptor protein mediating innate immune defense against DNA viruses. To investigate the role of STING in acute exacerbation of idiopathic pulmonary fibrosis (AE-IPF), we isolated primary peripheral blood mononuclear cells (PBMCs) from patients and healthy controls (HCs). Raw264.7 and A549 cells were infected with herpes simplex virus type 1 (HSV-1). Mice with bleomycin-induced lung fibrosis were infected with HSV-1 to stimulate acute exacerbation of the lung fibrosis. Global gene expression profiling revealed a substantial downregulation of interferon-regulated genes (downstream of STING) in the AE-IPF group compared with the HC and stable IPF groups. The PBMCs of the AE-IPF group showed significantly reduced STING protein levels, increased levels of endoplasmic reticulum (ER) stress markers, and elevated apoptosis. HSV-1 infection decreased STING expression and stimulated the ER stress pathways in Raw264.7 and A549 cells in a time- and dose-dependent manner. HSV-1 infection exacerbated the bleomycin-induced lung injury in mice. In the primary bone marrow-derived macrophages of mice treated with bleomycin and HSV-1, STING protein expression was substantially reduced; ER stress was stimulated. Tauroursodeoxycholic acid, a known inhibitor of ER stress, partially reversed those HSV-1-mediated adverse effects in mice with bleomycin-induced lung injury. STING levels in PBMCs increased after treatment in patients showing improvement but remained at low levels in patients with deterioration. Viral infection may trigger ER stress, resulting in STING deficiency and AE-IPF onset.
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Affiliation(s)
- Hui Qiu
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Dong Weng
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Tao Chen
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Li Shen
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | | | - Ya-Ru Wei
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qin Wu
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Meng-Meng Zhao
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qiu-Hong Li
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yang Hu
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yuan Zhang
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ying Zhou
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yi-Liang Su
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fen Zhang
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Li-Qin Lu
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Nian-Yu Zhou
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Sen-Lin Li
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Le-Le Zhang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chen Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Hui-Ping Li
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
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5
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Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life. Life (Basel) 2016; 6:life6010012. [PMID: 26999216 PMCID: PMC4810243 DOI: 10.3390/life6010012] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/26/2016] [Accepted: 03/04/2016] [Indexed: 11/17/2022] Open
Abstract
The origins of the components of genetic coding are examined in the present study. Genetic information arose from replicator induction by metabolite in accordance with the metabolic expansion law. Messenger RNA and transfer RNA stemmed from a template for binding the aminoacyl-RNA synthetase ribozymes employed to synthesize peptide prosthetic groups on RNAs in the Peptidated RNA World. Coevolution of the genetic code with amino acid biosynthesis generated tRNA paralogs that identify a last universal common ancestor (LUCA) of extant life close to Methanopyrus, which in turn points to archaeal tRNA introns as the most primitive introns and the anticodon usage of Methanopyrus as an ancient mode of wobble. The prediction of the coevolution theory of the genetic code that the code should be a mutable code has led to the isolation of optional and mandatory synthetic life forms with altered protein alphabets.
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Barrett R, Ornelas L, Yeager N, Mandefro B, Sahabian A, Lenaeus L, Targan SR, Svendsen CN, Sareen D. Reliable generation of induced pluripotent stem cells from human lymphoblastoid cell lines. Stem Cells Transl Med 2014; 3:1429-34. [PMID: 25298370 DOI: 10.5966/sctm.2014-0121] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Patient-specific induced pluripotent stem cells (iPSCs) hold great promise for many applications, including disease modeling to elucidate mechanisms involved in disease pathogenesis, drug screening, and ultimately regenerative medicine therapies. A frequently used starting source of cells for reprogramming has been dermal fibroblasts isolated from skin biopsies. However, numerous repositories containing lymphoblastoid cell lines (LCLs) generated from a wide array of patients also exist in abundance. To date, this rich bioresource has been severely underused for iPSC generation. We first attempted to create iPSCs from LCLs using two existing methods but were unsuccessful. Here we report a new and more reliable method for LCL reprogramming using episomal plasmids expressing pluripotency factors and p53 shRNA in combination with small molecules. The LCL-derived iPSCs (LCL-iPSCs) exhibited identical characteristics to fibroblast-derived iPSCs (fib-iPSCs), wherein they retained their genotype, exhibited a normal pluripotency profile, and readily differentiated into all three germ-layer cell types. As expected, they also maintained rearrangement of the heavy chain immunoglobulin locus. Importantly, we also show efficient iPSC generation from LCLs of patients with spinal muscular atrophy and inflammatory bowel disease. These LCL-iPSCs retained the disease mutation and could differentiate into neurons, spinal motor neurons, and intestinal organoids, all of which were virtually indistinguishable from differentiated cells derived from fib-iPSCs. This method for reliably deriving iPSCs from patient LCLs paves the way for using invaluable worldwide LCL repositories to generate new human iPSC lines, thus providing an enormous bioresource for disease modeling, drug discovery, and regenerative medicine applications.
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Affiliation(s)
- Robert Barrett
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Loren Ornelas
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Nicole Yeager
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Berhan Mandefro
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Anais Sahabian
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lindsay Lenaeus
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Stephan R Targan
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Clive N Svendsen
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dhruv Sareen
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
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7
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Romero-López C, Díaz-González R, Berzal-Herranz A. RNA Selection and EvolutionIn Vitro:Powerful Techniques for the Analysis and Identification of new Molecular Tools. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2007.10817461] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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8
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Nakamura Y, Ishiguro A, Miyakawa S. RNA plasticity and selectivity applicable to therapeutics and novel biosensor development. Genes Cells 2012; 17:344-64. [PMID: 22487172 PMCID: PMC3444689 DOI: 10.1111/j.1365-2443.2012.01596.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 02/03/2012] [Indexed: 12/25/2022]
Abstract
Aptamers are short, single-stranded nucleic acid sequences that are selected in vitro from large oligonucleotide libraries based on their high affinity to a target molecule. Hence, aptamers can be thought of as a nucleic acid analog to antibodies. However, several viewpoints hold that the potential of aptamers arises from interesting characteristics that are distinct from, or in some cases, superior to those of antibodies. This review summarizes the recent achievements in aptamer programs developed in our laboratory against basic and therapeutic protein targets. Through these studies, we became aware of the remarkable conformational plasticity and selectivity of RNA, on which the published report has not shed much light even though this is evidently a crucial feature for the strong specificity and affinity of RNA aptamers.
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Affiliation(s)
- Yoshikazu Nakamura
- Department of Basic Medical Sciences, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
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9
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Synthetic translational regulation by an L7Ae–kink-turn RNP switch. Nat Chem Biol 2009; 6:71-8. [DOI: 10.1038/nchembio.273] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 10/16/2009] [Indexed: 12/25/2022]
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10
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Kashiwagi N, Yamashita K, Furuta H, Ikawa Y. Designed RNAs with Two Peptide-Binding Units as Artificial Templates for Native Chemical Ligation of RNA-Binding Peptides. Chembiochem 2009; 10:2745-52. [DOI: 10.1002/cbic.200900392] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Abstract
Comparison of phylogenetically diverse ribonucleoprotein (RNP) enzymes and information about their biochemistry have stimulated hypotheses about their evolution. Instead of the canonical view, in which catalysis proceeds from ribozyme to RNP enzyme to protein enzyme, RNP enzymes and proteins are seen to share contemporary catalysis. Furthermore, the RNA components of RNP enzymes show no evidence of fading out but instead, in some cases, have elaborated new functions.
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12
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Kashiwagi N, Furuta H, Ikawa Y. Primitive templated catalysis of a peptide ligation by self-folding RNAs. Nucleic Acids Res 2009; 37:2574-83. [PMID: 19264804 PMCID: PMC2677871 DOI: 10.1093/nar/gkp111] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
RNA–polypeptide complexes (RNPs), which play various roles in extant biological systems, have been suggested to have been important in the early stages of the molecular evolution of life. At a certain developmental stage of ancient RNPs, their RNA and polypeptide components have been proposed to evolve in a reciprocal manner to establish highly elaborate structures and functions. We have constructed a simple model system, from which a cooperative evolution system of RNA and polypeptide components could be developed. Based on the observation that several RNAs modestly accelerated the chemical ligation of the two basic peptides. We have designed an RNA molecule possessing two peptide binding sites that capture the two peptides. This designed RNA can also accelerate the peptide ligation. The resulting ligated peptide, which has two RNA-binding sites, can in turn function as a trans-acting factor that enhances the endonuclease activity catalyzed by the designed RNA.
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Affiliation(s)
- Norimasa Kashiwagi
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
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13
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Saito H, Inoue T. Synthetic biology with RNA motifs. Int J Biochem Cell Biol 2008; 41:398-404. [PMID: 18775792 DOI: 10.1016/j.biocel.2008.08.017] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 08/05/2008] [Accepted: 08/05/2008] [Indexed: 12/23/2022]
Abstract
Structural motifs in naturally occurring RNAs and RNPs can be employed as new molecular parts for synthetic biology to facilitate the development of novel devices and systems that modulate cellular functions. In this review, we focus on the following: (i) experimental evolution techniques of RNA molecules in vitro and (ii) their applications for regulating gene expression systems in vivo. For experimental evolution, new artificial RNA aptamers and RNA enzymes (ribozymes) have been selected in vitro. These functional RNA molecules are likely to be applicable in the reprogramming of existing gene regulatory systems. Furthermore, they may be used for designing hypothetical RNA-based living systems in the so-called RNA world. For the regulation of gene expressions in living cells, the development of new riboswitches allows us to modulate the target gene expression in a tailor-made manner. Moreover, recently RNA-based synthetic genetic circuits have been reported by employing functional RNA molecules, expanding the repertory of synthetic biology with RNA motifs.
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Affiliation(s)
- Hirohide Saito
- Department of Gene Mechanisms, Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.
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14
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Ohuchi SP, Ikawa Y, Nakamura Y. Selection of a novel class of RNA-RNA interaction motifs based on the ligase ribozyme with defined modular architecture. Nucleic Acids Res 2008; 36:3600-7. [PMID: 18460545 PMCID: PMC2441787 DOI: 10.1093/nar/gkn206] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
To develop molecular tools for the detection and control of RNA molecules whose functions rely on their 3D structures, we have devised a selection system to isolate novel RNA motifs that interact with a target RNA structure within a given structural context. In this system, a GAAA tetraloop and its specific receptor motif (11-ntR) from an artificial RNA ligase ribozyme with modular architecture (the DSL ribozyme) were replaced with a target structure and random sequence, respectively. Motifs recognizing the target structure can be identified by in vitro selection based on ribozyme activity. A model selection targeting GAAA-loop successfully identified motifs previously known as GAAA-loop receptors. In addition, a new selection targeting a C-loop motif also generated novel motifs that interact with this structure. Biochemical analysis of one of the C-loop receptor motifs revealed that it could also function as an independent structural unit.
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Affiliation(s)
- Shoji P Ohuchi
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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15
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Saito H, Inoue T. RNA and RNP as new molecular parts in synthetic biology. J Biotechnol 2007; 132:1-7. [PMID: 17875338 DOI: 10.1016/j.jbiotec.2007.07.952] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Accepted: 07/22/2007] [Indexed: 12/29/2022]
Abstract
Synthetic biology has a promising outlook in biotechnology and for understanding the self-organizing principle of biological molecules in life. However, synthetic biologists have been looking for new molecular "parts" that function as modular units required in designing and constructing new "devices" and "systems" for regulating cell function because the number of such parts is strictly limited at present. In this review, we focus on RNA/ribonucleoprotein (RNP) architectures that hold promise as new "parts" for synthetic biology. They are constructed with molecular design and an experimental evolution technique. So far, designed self-folding RNAs, RNA (RNP) enzymes, and nanoscale RNA architectures have been successfully constructed by utilizing Watson-Crick base-pairs together with specific RNA-RNA or RNA-protein binding motifs of known defined 3D structures. Riboregulators for regulating targeted gene expression have also been designed and produced in vitro as well as in vivo. Lately, RNA and ribonucleoprotein complexes have been strongly attracting the attention of molecular biologists because a variety of noncoding RNAs discovered in nature perform spatiotemporal gene expressions. Thus we hope that newly accumulating knowledge on naturally occurring RNAs and RNP complexes will provide a variety of new parts, devices and systems for synthetic biology.
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Affiliation(s)
- Hirohide Saito
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; ICORP, Japan Science and Technology Corporation (JST), Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.
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16
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Abstract
Natural and engineered RNA 'parts' can perform a variety of functions, including hybridizing to targets, binding ligands and undergoing programmed conformational changes, and catalyzing reactions. These RNA parts can in turn be assembled into synthetic genetic circuits that regulate gene expression by acting either in cis or in trans on mRNAs. As more parts are discovered and engineered, it should be increasingly possible to create synthetic RNA circuits that are able to carry out complex logical operations in cells, either superimposed on or autonomous to extant gene regulation.
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Affiliation(s)
- Eric A Davidson
- Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, 1 University Station/A4800, University of Texas at Austin, Austin, Texas 78712, USA
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17
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Süleymanoĝlu E. Molecular phylogenetics and functional evolution of major RNA recognition domains of recently cloned and characterized autoimmune RNA-binding particle. GENOMICS PROTEOMICS & BIOINFORMATICS 2005; 1:310-20. [PMID: 15629060 PMCID: PMC5172410 DOI: 10.1016/s1672-0229(03)01037-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are spliceosomal macromolecular assemblages and thus actively participate in pre-mRNA metabolism. They are composed of evolutionarily conserved and tandemly repeated motifs, where both RNA-binding and protein-protein recognition occur to achieve cellular activities. By yet unknown mechanisms, these ribonucleoprotein (RNP) particles are targeted by autoantibodies and hence play significant role in a variety of human systemic autoimmune diseases. This feature makes them important prognostic markers in terms of molecular epidemiology and pathogenesis of autoimmunity. Since RNP domain is one of the most conserved and widespread scaffolds, evolutionary analyses of these RNA-binding domains can provide further clues on disease-specific epitope formation. The study presented herein represents a sequence comparison of RNA-recognition regions of recently cloned and characterized human hnRNP A3 with those of other relevant hnRNP A/B-type proteins. Their implications in human autoimmunity are particularly emphasized.
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Affiliation(s)
- Erhan Süleymanoĝlu
- Medical Faculty, Vienna Biocenter, Institute of Biochemistry, University of Vienna, Vienna, Austria.
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18
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Abstract
Ribonuclease P (RNase P) is an essential enzyme that processes the 5' leader sequence of precursor tRNA. Eubacterial RNase P is an RNA enzyme, while its eukaryotic counterpart acts as catalytic ribonucleoprotein, consisting of RNA and numerous protein subunits. To study the latter form, we reconstitute human RNase P activity, demonstrating that the subunits H1 RNA, Rpp21, and Rpp29 are sufficient for 5' cleavage of precursor tRNA. The reconstituted RNase P precisely delineates its cleavage sites in various substrates and hydrolyzes the phosphodiester bond. Rpp21 and Rpp29 facilitate catalysis by H1 RNA, which seems to require a phylogenetically conserved pseudoknot structure for function. Unexpectedly, Rpp29 forms a catalytic complex with M1 RNA of E. coli RNase P. The results uncover the core components of eukaryotic RNase P, reveal its evolutionary origin in translation, and provide a paradigm for studying RNA-based catalysis by other nuclear and nucleolar ribonucleoprotein enzymes.
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Affiliation(s)
- Hagit Mann
- Department of Molecular Biology, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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19
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Ikawa Y, Tsuda K, Matsumura S, Atsumi S, Inoue T. Putative intermediary stages for the molecular evolution from a ribozyme to a catalytic RNP. Nucleic Acids Res 2003; 31:1488-96. [PMID: 12595557 PMCID: PMC149818 DOI: 10.1093/nar/gkg225] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A hypothetical evolutionary pathway from a ribozyme to a catalytic RNA-protein complex (RNP) is proposed and examined. In this hypothesis for an early phase of molecular evolution, one RNA-RNA interaction in the starting ribozyme is replaced with an RNA-protein interaction via two intermediary stages. At each stage, the original RNA-RNA interaction and a newly introduced RNA-protein interaction are designed to coexist. The catalytic RNPs corresponding to the intermediary stages were constructed by employing the Tetrahymena ribozyme together with molecular modeling. Analyses of the RNPs indicate that the protein can fully replace the original role of the RNA-RNA interaction in the starting ribozyme and that the association of a protein with a ribozyme might be beneficial for improving the ribozymatic activity.
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Affiliation(s)
- Yoshiya Ikawa
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
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Atsumi S, Ikawa Y, Shiraishi H, Inoue T. Selections for constituting new RNA-protein interactions in catalytic RNP. Nucleic Acids Res 2003; 31:661-9. [PMID: 12527775 PMCID: PMC140506 DOI: 10.1093/nar/gkg140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In vitro and in vivo selection techniques are developed to constitute new RNA-peptide interactions. The selection strategy is designed by employing a catalytic RNP consisting of a derivative of the Tetrahymena ribozyme and an artificial RNA-binding protein. An arginine-rich RNA-binding motif and its target RNA motif in the RNP are substituted with randomized sequences and used for the selection experiments. Previously unknown binding motifs are obtained and the newly established interactions have been indispensable for assembling a catalytically active RNP. The method employed in this study is useful for making customized self-splicing intron RNAs whose activity is regulated by protein cofactors.
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Affiliation(s)
- Shota Atsumi
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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Thompson KM, Syrett HA, Knudsen SM, Ellington AD. Group I aptazymes as genetic regulatory switches. BMC Biotechnol 2002; 2:21. [PMID: 12466025 PMCID: PMC139998 DOI: 10.1186/1472-6750-2-21] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2002] [Accepted: 12/04/2002] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Allosteric ribozymes (aptazymes) that have extraordinary activation parameters have been generated in vitro by design and selection. For example, hammerhead and ligase ribozymes that are activated by small organic effectors and protein effectors have been selected from random sequence pools appended to extant ribozymes. Many ribozymes, especially self-splicing introns, are known control gene regulation or viral replication in vivo. We attempted to generate Group I self-splicing introns that were activated by a small organic effector, theophylline, and to show that such Group I aptazymes could mediate theophylline-dependent splicing in vivo. RESULTS By appending aptamers to the Group I self-splicing intron, we have generated a Group I aptazyme whose in vivo splicing is controlled by exogenously added small molecules. Substantial differences in gene regulation could be observed with compounds that differed by as little as a single methyl group. The effector-specificity of the Group I aptazyme could be rationally engineered for new effector molecules. CONCLUSION Group I aptazymes may find applications as genetic regulatory switches for generating conditional knockouts at the level of mRNA or for developing economically viable gene therapies.
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Affiliation(s)
- Kristin M Thompson
- Present address: Archemix Corp., 1 Hampshire St., Cambridge, MA 02139, USA
| | - Heather A Syrett
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Scott M Knudsen
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Andrew D Ellington
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
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Hartig JS, Najafi-Shoushtari SH, Grüne I, Yan A, Ellington AD, Famulok M. Protein-dependent ribozymes report molecular interactions in real time. Nat Biotechnol 2002; 20:717-22. [PMID: 12089558 DOI: 10.1038/nbt0702-717] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Most approaches to monitoring interactions between biological macromolecules require large amounts of material, rely upon the covalent modification of an interaction partner, or are not amenable to real-time detection. We have developed a generalizable assay system based on interactions between proteins and reporter ribozymes. The assay can be configured in a modular fashion to monitor the presence and concentration of a protein or of molecules that modulate protein function. We report two applications of the assay: screening for a small molecule that disrupts protein binding to its nucleic acid target and screening for protein protein interactions. We screened a structurally diverse library of antibiotics for small molecules that modulate the activity of HIV-1 Rev-responsive ribozymes by binding to Rev. We identified an inhibitor that subsequently inhibited HIV-1 replication in cells. A simple format switch allowed reliable monitoring of domain-specific interactions between the blood-clotting factor thrombin and its protein partners. The rapid identification of interactions between proteins or of compounds that disrupt such interactions should have substantial utility for the drug-discovery process.
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Affiliation(s)
- Jörg S Hartig
- Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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Abstract
RNA and DNA molecules can be engineered to function as molecular switches that trigger catalytic events when a specific target molecule becomes bound. Recent studies on the underlying biochemical properties of these constructs indicate that a significant untapped potential exists for the practical application of allosteric nucleic acids. Engineered molecular switches can be used to report the presence of specific analytes in complex mixtures, making possible the creation of new types of biosensor devices and genetic control elements.
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Affiliation(s)
- Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA.
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