1
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Liu T, Pyle AM. Highly Reactive Group I Introns Ubiquitous in Pathogenic Fungi. J Mol Biol 2024; 436:168513. [PMID: 38447889 DOI: 10.1016/j.jmb.2024.168513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
Systemic fungal infections are a growing public health threat, and yet viable antifungal drug targets are limited as fungi share a similar proteome with humans. However, features of RNA metabolism and the noncoding transcriptomes in fungi are distinctive. For example, fungi harbor highly structured RNA elements that humans lack, such as self-splicing introns within key housekeeping genes in the mitochondria. However, the location and function of these mitochondrial riboregulatory elements has largely eluded characterization. Here we used an RNA-structure-based bioinformatics pipeline to identify the group I introns interrupting key mitochondrial genes in medically relevant fungi, revealing their fixation within a handful of genetic hotspots and their ubiquitous presence across divergent phylogenies of fungi, including all highest priority pathogens such as Candida albicans, Candida auris, Aspergillus fumigatus and Cryptococcus neoformans. We then biochemically characterized two representative introns from C. albicans and C. auris, demonstrating their exceptionally efficient splicing catalysis relative to previously-characterized group I introns. Indeed, the C. albicans mitochondrial intron displays extremely rapid catalytic turnover, even at ambient temperatures and physiological magnesium ion concentrations. Our results unmask a significant new set of players in the RNA metabolism of pathogenic fungi, suggesting a promising new type of antifungal drug target.
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Affiliation(s)
- Tianshuo Liu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.
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2
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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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3
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Jurich CP, Yesselman JD. Automated 3D Design and Evaluation of RNA Nanostructures with RNAMake. Methods Mol Biol 2023; 2586:251-261. [PMID: 36705909 DOI: 10.1007/978-1-0716-2768-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Despite growing interest in applying RNA's unique structural characteristics to solve diverse biotechnology and nanotechnology problems, there are few computational tools for targeted tertiary design. As a result, RNA 3D design is traditionally slow, resource-consuming, and dependent on expert modeling. In this chapter, we discuss our recently developed software package: RNAMake, a set of applications capable of designing RNA tertiary structures to solve various relevant nanotechnology problems and provide basic thermodynamic calculations for the generated designs. We provide in-depth examples and instructions for designing example RNA nanostructures such as minimal RNA sequences containing a single tertiary contact, generating RNAs that stabilize small-molecule ligands, and building tethers that link ribosomal subunits together. We also highlight the addition of a new Monte Carlo design algorithm and the ability to estimate the thermodynamic contribution of helical elements in RNA 3D structures.
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Affiliation(s)
- Chris P Jurich
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Joseph D Yesselman
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
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4
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Box-shaped ribozyme octamer formed by face-to-face dimerization of a pair of square-shaped ribozyme tetramers. J Biosci Bioeng 2022; 134:195-202. [PMID: 35810135 DOI: 10.1016/j.jbiosc.2022.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 11/21/2022]
Abstract
Naturally occurring ribozymes with defined three-dimensional (3D) structures serve as promising platforms for the design and construction of artificial RNA nanostructures. We constructed a hexameric ribozyme nanostructure by face-to-face dimerization of a pair of triangular ribozyme trimers, unit RNAs of which were derived from the Tetrahymena group I ribozyme. In this study, we have expanded the dimerization strategy to a square-shaped ribozyme tetramer by introducing four pillar units. The resulting box-shaped nanostructures, which contained eight ribozyme units, can be assembled from either four or two components of their unit RNAs.
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5
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Wang X, Wang J, Li S, Lu C, Sui N. An overview of RNA splicing and functioning of splicing factors in land plant chloroplasts. RNA Biol 2022; 19:897-907. [PMID: 35811474 PMCID: PMC9275481 DOI: 10.1080/15476286.2022.2096801] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
RNA splicing refers to a process by which introns of a pre-mRNA are excised and the exons at both ends are joined together. Chloroplast introns are inherently self-splicing ribozymes, but over time, they have lost self-splicing ability due to the degeneration of intronic elements. Thus, the splicing of chloroplast introns relies heavily on nuclear-encoded splicing factors, which belong to diverse protein families. Different splicing factors and their shared intron targets are supposed to form ribonucleoprotein particles (RNPs) to facilitate intron splicing. As characterized in a previous review, around 14 chloroplast intron splicing factors were identified until 2010. However, only a few genetic and biochemical evidence has shown that these splicing factors are required for the splicing of one or several introns. The roles of splicing factors are generally believed to facilitate intron folding; however, the precise role of each protein in RNA splicing remains ambiguous. This may be because the precise binding site of most of these splicing factors remains unexplored. In the last decade, several new splicing factors have been identified. Also, several splicing factors were found to bind to specific sequences within introns, which enhanced the understanding of splicing factors. Here, we summarize recent progress on the splicing factors in land plant chloroplasts and discuss their possible roles in chloroplast RNA splicing based on previous studies.
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Affiliation(s)
- Xuemei Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, Western Shandong, China
| | - Jingyi Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, Western Shandong, China
| | - Simin Li
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, Western Shandong, China
| | - Congming Lu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Western Shandong, China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, Western Shandong, China
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6
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Dobirul Islam M, Motiar Rahman M, Matsumura S, Ikawa Y. Effects of chain length of polyethylene glycol molecular crowders on a mutant Tetrahymena group I ribozyme lacking large peripheral module. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:867-883. [PMID: 34402751 DOI: 10.1080/15257770.2021.1956531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
While current group I ribozymes use several distinct strategies to function under conditions of low Mg2+ concentration (≤ 3 mM), a deletion mutant of the Tetrahymena ribozyme (ΔP5 ribozyme) is virtually inactive with 3 mM Mg2+ due to removal of the large peripheral module, P5abc, supporting the active conformation of the core module. We investigated the molecular crowding effects of synthetic polyethylene glycols (PEGs) on the activity of the ΔP5 ribozyme. Among PEG molecules with different chain lengths, PEG600 improved the activity of the ΔP5 ribozyme most effectively in the presence of 3 mM Mg2+.
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Affiliation(s)
- Md Dobirul Islam
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan
| | - Md Motiar Rahman
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan
| | - Shigeyoshi Matsumura
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan.,Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Yoshiya Ikawa
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan.,Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
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7
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Mori Y, Oi H, Suzuki Y, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Flexible Assembly of Engineered Tetrahymena Ribozymes Forming Polygonal RNA Nanostructures with Catalytic Ability. Chembiochem 2021; 22:2168-2176. [PMID: 33876531 DOI: 10.1002/cbic.202100109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/11/2021] [Indexed: 11/11/2022]
Abstract
Ribozymes with modular architecture constitute an attractive class of structural platforms for design and construction of nucleic acid nanostructures with biological functions. Through modular engineering of the Tetrahymena ribozyme, we have designed unit RNAs (L-RNAs), assembly of which formed ribozyme-based closed trimers and closed tetramers. Their catalytic activity was dependent on oligomer formation. In this study, the structural variety of L-RNA oligomers was extended by tuning their structural elements, yielding closed pentamers and closed hexamers. Their assembly properties were analyzed by electrophoretic mobility shift assay (EMSA) and atomic force microscopy (AFM).
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Affiliation(s)
- Yuki Mori
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, 930-8555, Toyama, Japan
| | - Hiroki Oi
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, 930-8555, Toyama, Japan
| | - Yuki Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, 606-8502, Kyoto, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, 606-8502, Kyoto, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, 606-8502, Kyoto, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, 606-8502, Kyoto, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, 606-8502, Kyoto, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, 930-8555, Toyama, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, 930-8555, Toyama, Japan
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8
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Deng Y, Wu X, Wen D, Huang H, Chen Y, Mukhtar I, Yue L, Wang L, Wen Z. Intraspecific Mitochondrial DNA Comparison of Mycopathogen Mycogone perniciosa Provides Insight Into Mitochondrial Transfer RNA Introns. PHYTOPATHOLOGY 2021; 111:639-648. [PMID: 32886023 DOI: 10.1094/phyto-07-20-0281-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mycogone perniciosa is the main causative agent of wet bubble disease, which causes severe damage to the production of the cultivated mushroom Agaricus bisporus around the world. Whole-genome sequencing of 12 isolates of M. perniciosa was performed using the Illumina sequencing platform, and the obtained paired-end reads were used to assemble complete mitochondrial genomes. Intraspecific comparisons of conserved protein-coding genes, transfer RNA (tRNA) and ribosomal RNA (rRNA) genes, introns, and intergenic regions were conducted. Five different mitochondrial DNA (mtDNA) haplotypes were detected among the tested isolates, ranging from 89,080 to 93,199 bp in length. All of the mtDNAs contained the same set of 14 protein-coding genes and 2 rRNA and 27 tRNA genes, which shared high sequence similarity. In contrast, the number, insertion sites, and sequences of introns varied greatly among the mtDNAs. Eighteen of 43 intergenic regions differed among the isolates, reflecting 65 single nucleotide polymorphisms, 76 indels, and the gain/loss of nine long fragments. Intraspecific comparison revealed that two introns were located within tRNA genes, which is the first detailed description of mitochondrial tRNA introns. Intronic sequence comparison within the same insertion sites revealed the formation process of two introns, which also illustrated a fast evolutionary rate of introns among M. perniciosa isolates. Based on the intron distribution pattern, a pair of universal primers and four pairs of isolate-specific primers were designed and were used to identify the five mtDNA types. In summary, the rapid gain or loss of mitochondrial introns could be an ideal marker for population genetics analysis.
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Affiliation(s)
- Youjin Deng
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin Wu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Die Wen
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haichen Huang
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yilei Chen
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Irum Mukhtar
- Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Liyun Yue
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Li Wang
- Shandong Key Laboratory of Microbiology, College of Plant Protection, Shandong Agricultural University, Taian 271000, China
| | - Zhiqiang Wen
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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9
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Abstract
RNA enzymes or ribozymes catalyze some of the most important reactions in biology and are thought to have played a central role in the origin and evolution of life on earth. Catalytic function in RNA has evolved in crowded cellular environments that are different from dilute solutions in which most in vitro assays are performed. The presence of molecules such as amino acids, polypeptides, alcohols, and sugars in the cell introduces forces that modify the kinetics and thermodynamics of ribozyme-catalyzed reactions. Synthetic molecules are routinely used in in vitro studies to better approximate the properties of biomolecules under in vivo conditions. This review discusses the various forces that operate within simulated crowded solutions in the context of RNA structure, folding, and catalysis. It also explores ideas about how crowding could have been beneficial to the evolution of functional RNAs and the development of primitive cellular systems in a prebiotic milieu.
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Affiliation(s)
- Saurja DasGupta
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.
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10
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Kiyooka R, Akagi J, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Catalytic RNA nano-objects formed by self-assembly of group I ribozyme dimers serving as unit structures. J Biosci Bioeng 2020; 130:253-259. [PMID: 32451246 DOI: 10.1016/j.jbiosc.2020.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/16/2020] [Accepted: 04/24/2020] [Indexed: 12/24/2022]
Abstract
Ribozymes with modular structures are attractive platforms for the construction of nanoscale RNA objects with biological functions. We designed group I ribozyme dimers as unit ribozyme dimers (Urds), which self-assembled to form their polymeric states and also oligomeric states with defined numbers of Urds. Assembly of Urds yielded catalytic ability of a pair of distinct ribozyme units to cleave two distinct substrates. The morphologies of the assembled ribozyme structures were observed directly by atomic force microscopy (AFM).
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Affiliation(s)
- Ryuji Kiyooka
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Junya Akagi
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8502, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, 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.
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11
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Thirumalai D, Lorimer GH, Hyeon C. Iterative annealing mechanism explains the functions of the GroEL and RNA chaperones. Protein Sci 2019; 29:360-377. [PMID: 31800116 DOI: 10.1002/pro.3795] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/16/2022]
Abstract
Molecular chaperones are ATP-consuming machines, which facilitate the folding of proteins and RNA molecules that are kinetically trapped in misfolded states. Unassisted folding occurs by the kinetic partitioning mechanism according to which folding to the native state, with low probability as well as misfolding to one of the many metastable states, with high probability, occur rapidly. GroEL is an all-purpose stochastic machine that assists misfolded substrate proteins to fold. The RNA chaperones such as CYT-19, which are ATP-consuming enzymes, help the folding of ribozymes that get trapped in metastable states for long times. GroEL does not interact with the folded proteins but CYT-19 disrupts both the folded and misfolded ribozymes. The structures of GroEL and RNA chaperones are strikingly different. Despite these differences, the iterative annealing mechanism (IAM) quantitatively explains all the available experimental data for assisted folding of proteins and ribozymes. Driven by ATP binding and hydrolysis and GroES binding, GroEL undergoes a catalytic cycle during which it samples three allosteric states, T (apo), R (ATP bound), and R″ (ADP bound). Analyses of the experimental data show that the efficiency of the GroEL-GroES machinery and mutants is determined by the resetting rate k R ″ → T , which is largest for the wild-type (WT) GroEL. Generalized IAM accurately predicts the folding kinetics of Tetrahymena ribozyme and its variants. Chaperones maximize the product of the folding rate and the steady-state native state fold by driving the substrates out of equilibrium. Neither the absolute yield nor the folding rate is optimized.
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Affiliation(s)
- D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas
| | - George H Lorimer
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland
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12
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Tsuruga R, Uehara N, Suzuki Y, Furuta H, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Oligomerization of a modular ribozyme assembly of which is controlled by a programmable RNA–RNA interface between two structural modules. J Biosci Bioeng 2019; 128:410-415. [DOI: 10.1016/j.jbiosc.2019.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/14/2022]
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13
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Gulshan MA, Rahman MM, Matsumura S, Higuchi T, Umezawa N, Ikawa Y. Biogenic triamine and tetraamine activate core catalytic ability of Tetrahymena group I ribozyme in the absence of its large activator module. Biochem Biophys Res Commun 2018; 496:594-600. [DOI: 10.1016/j.bbrc.2018.01.085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 01/11/2018] [Indexed: 10/18/2022]
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14
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Mitchell D, Ritchey LE, Park H, Babitzke P, Assmann SM, Bevilacqua PC. Glyoxals as in vivo RNA structural probes of guanine base-pairing. RNA (NEW YORK, N.Y.) 2018; 24:114-124. [PMID: 29030489 PMCID: PMC5733565 DOI: 10.1261/rna.064014.117] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/10/2017] [Indexed: 05/09/2023]
Abstract
Elucidation of the folded structures that RNA forms in vivo is vital to understanding its functions. Chemical reagents that modify the Watson-Crick (WC) face of unprotected nucleobases are particularly useful in structure elucidation. Dimethyl sulfate penetrates cell membranes and informs on RNA base-pairing and secondary structure but only modifies the WC face of adenines and cytosines. We present glyoxal, methylglyoxal, and phenylglyoxal as potent in vivo reagents that target the WC face of guanines as well as cytosines and adenines. Tests on rice (Oryza sativa) 5.8S rRNA in vitro read out by reverse transcription and gel electrophoresis demonstrate specific modification of almost all guanines in a time- and pH-dependent manner. Subsequent in vivo tests on rice, a eukaryote, and Bacillus subtilis and Escherichia coli, Gram-positive and Gram-negative bacteria, respectively, showed that all three reagents enter living cells without prior membrane permeabilization or pH adjustment of the surrounding media and specifically modify solvent-exposed guanine, cytosine, and adenine residues.
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Affiliation(s)
- David Mitchell
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Laura E Ritchey
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Hongmarn Park
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Paul Babitzke
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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15
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Use of a Fluorescent Aptamer RNA as an Exonic Sequence to Analyze Self-Splicing Ability of aGroup I Intron from Structured RNAs. BIOLOGY 2016; 5:biology5040043. [PMID: 27869660 PMCID: PMC5192423 DOI: 10.3390/biology5040043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 11/17/2022]
Abstract
Group I self-splicing intron constitutes an important class of functional RNA molecules that can promote chemical transformation. Although the fundamental mechanism of the auto-excision from its precursor RNA has been established, convenient assay systems for its splicing activity are still useful for a further understanding of its detailed mechanism and of its application. Because some host RNA sequences, to which group I introns inserted form stable three-dimensional (3D) structures, the effects of the 3D structures of exonic elements on the splicing efficiency of group I introns are important but not a fully investigated issue. We developed an assay system for group I intron self-splicing by employing a fluorescent aptamer RNA (spinach RNA) as a model exonic sequence inserted by the Tetrahymena group I intron. We investigated self-splicing of the intron from spinach RNA, serving as a model exonic sequence with a 3D structure.
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16
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Abstract
Introns inserted within introns are commonly referred to as twintrons, however the original definition for twintron implied that splicing of the external member of the twintron could only proceed upon splicing of the internal member. This review examines the various types of twintron-like arrangements that have been reported and assigns them to either nested or twintron categories that are subdivided further into subtypes based on differences of their mode of splicing. Twintron-like arrangements evolved independently by fortuitous events among different types of introns but once formed they offer opportunities for the evolution of new regulatory strategies and/or novel genetic elements.
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Affiliation(s)
- Mohamed Hafez
- a Department of Biochemistry ; Faculty of Medicine; University of Montreal ; Montréal , QC Canada.,b Department of Botany and Microbiology ; Faculty of Science; Suez University ; Suez , Egypt
| | - Georg Hausner
- c Department of Microbiology ; University of Manitoba ; Winnipeg , MB Canada
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17
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Hori N, Denesyuk NA, Thirumalai D. Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension. J Mol Biol 2016; 428:2847-59. [PMID: 27315694 DOI: 10.1016/j.jmb.2016.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 12/24/2022]
Abstract
Because of the potential link between -1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single-molecule pulling experiments have been performed on PKs to decipher the mechanism of programmed ribosomal frameshifting. Motivated in part by these experiments, we performed simulations using a coarse-grained model of RNA to describe the response of a PK over a range of mechanical forces (fs) and monovalent salt concentrations (Cs). The coarse-grained simulations quantitatively reproduce the multistep thermal melting observed in experiments, thus validating our model. The free energy changes obtained in simulations are in excellent agreement with experiments. By varying f and C, we calculated the phase diagram that shows a sequence of structural transitions, populating distinct intermediate states. As f and C are changed, the stem-loop tertiary interactions rupture first, followed by unfolding of the 3'-end hairpin (I⇌F). Finally, the 5'-end hairpin unravels, producing an extended state (E⇌I). A theoretical analysis of the phase boundaries shows that the critical force for rupture scales as (logCm)(α) with α=1(0.5) for E⇌I (I⇌F) transition. This relation is used to obtain the preferential ion-RNA interaction coefficient, which can be quantitatively measured in single-molecule experiments, as done previously for DNA hairpins. A by-product of our work is the suggestion that the frameshift efficiency is likely determined by the stability of the 5'-end hairpin that the ribosome first encounters during translation.
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Affiliation(s)
- Naoto Hori
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Natalia A Denesyuk
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - D Thirumalai
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
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18
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Wierzchowski J, Antosiewicz JM, Shugar D. 8-Azapurines as isosteric purine fluorescent probes for nucleic acid and enzymatic research. MOLECULAR BIOSYSTEMS 2015; 10:2756-74. [PMID: 25124808 DOI: 10.1039/c4mb00233d] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The 8-azapurines, and their 7-deaza and 9-deaza congeners, represent a unique class of isosteric (isomorphic) analogues of the natural purines, frequently capable of substituting for the latter in many biochemical processes. Particularly interesting is their propensity to exhibit pH-dependent room-temperature fluorescence in aqueous medium, and in non-polar media. We herein review the physico-chemical properties of this class of compounds, with particular emphasis on the fluorescence emission properties of their neutral and/or ionic species, which has led to their widespread use as fluorescent probes in enzymology, including enzymes involved in purine metabolism, agonists/antagonists of adenosine receptors, mechanisms of catalytic RNAs, RNA editing, etc. They are also exceptionally useful fluorescent probes for analytical and clinical applications in crude cell homogenates.
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Affiliation(s)
- Jacek Wierzchowski
- Department of Biophysics, University of Varmia & Masuria, Oczapowskiego 4, 10-719 Olsztyn, Poland.
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19
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Matsumura S, Ito T, Tanaka T, Furuta H, Ikawa Y. Modulation of group I ribozyme activity by cationic porphyrins. BIOLOGY 2015; 4:251-63. [PMID: 25811638 PMCID: PMC4498298 DOI: 10.3390/biology4020251] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/03/2015] [Indexed: 11/16/2022]
Abstract
The effects of cationic porphyrins on the catalytic activities of four group I ribozymes were investigated. A cationic porphyrin possessing four pyridinium moieties (pPyP) inhibited two group IC3 ribozymes (Syn Rz and Azo Rz) and a group IC1 ribozyme (Tet Rz). In the case of a group IA2 ribozyme (Td Rz), however, pPyP served not only as an inhibitor but also as an activator, and the effects of pPyP were dependent on its concentration. To analyze the structural and electronic factors determining the effects of pPyP on group I ribozymes, three cationic porphyrins (pPyNCP, pPyF4P, and TMPyP) were also examined. As interactions between small organic molecules and nucleic acids are attractive and important issues in biochemistry and biotechnology, this study contributes to the development of porphyrin-based molecules that can modulate functions of structured RNA molecules.
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Affiliation(s)
- Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan.
| | - Tatsunobu Ito
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Takahiro Tanaka
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan.
- Center for Molecular Systems, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan.
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20
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García-Sacristán A, Moreno M, Ariza-Mateos A, López-Camacho E, Jáudenes RM, Vázquez L, Gómez J, Martín-Gago JÁ, Briones C. A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy. Nucleic Acids Res 2014; 43:565-80. [PMID: 25510496 PMCID: PMC4288189 DOI: 10.1093/nar/gku1299] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The 5' untranslated region of hepatitis C virus (HCV) genomic RNA contains an internal ribosome entry site (IRES) element, composed of domains II-IV, which is required for cap-independent translation initiation. Little information on the 3D structure of the whole functional HCV IRES is still available. Here, we use atomic force microscopy to visualize the HCV IRES conformation in its natural sequence context, which includes the upstream domain I and the essential, downstream domains V and VI. The 574 nt-long molecule analyzed underwent an unexpected, Mg(2+)-induced switch between two alternative conformations: from 'open', elongated morphologies at 0-2 mM Mg(2+) concentration to a 'closed', comma-shaped conformation at 4-6 mM Mg(2+). This sharp transition, confirmed by gel-shift analysis and partial RNase T1 cleavage, was hindered by the microRNA miR-122. The comma-shaped IRES-574 molecules visualized at 4-6 mM Mg(2+) in the absence of miR-122 showed two arms. Our data support that the first arm would contain domain III, while the second one would be composed of domains (I-II)+(V-VI) thanks to a long-range RNA interaction between the I-II spacer and the basal region of domain VI. This reinforces the previously described structural continuity between the HCV IRES and its flanking domains I, V and VI.
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Affiliation(s)
- Ana García-Sacristán
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain Centro de Investigaciones Biomédicas en Red de Enfermedades Hepáticas y Digestivas, (CIBERehd), Spain
| | - Miguel Moreno
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain
| | - Ascensión Ariza-Mateos
- Centro de Investigaciones Biomédicas en Red de Enfermedades Hepáticas y Digestivas, (CIBERehd), Spain Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina 'López-Neyra' (CSIC), Parque Tecnológico Ciencias de la Salud, Armilla, Granada 18016, Spain
| | - Elena López-Camacho
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain Instituto de Ciencia de Materiales de Madrid (CSIC), Cantoblanco, Madrid 28049, Spain
| | - Rosa M Jáudenes
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain
| | - Luis Vázquez
- Instituto de Ciencia de Materiales de Madrid (CSIC), Cantoblanco, Madrid 28049, Spain
| | - Jordi Gómez
- Centro de Investigaciones Biomédicas en Red de Enfermedades Hepáticas y Digestivas, (CIBERehd), Spain Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina 'López-Neyra' (CSIC), Parque Tecnológico Ciencias de la Salud, Armilla, Granada 18016, Spain
| | - José Ángel Martín-Gago
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain Instituto de Ciencia de Materiales de Madrid (CSIC), Cantoblanco, Madrid 28049, Spain
| | - Carlos Briones
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain Centro de Investigaciones Biomédicas en Red de Enfermedades Hepáticas y Digestivas, (CIBERehd), Spain
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21
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Sowa SW, Vazquez-Anderson J, Clark CA, De La Peña R, Dunn K, Fung EK, Khoury MJ, Contreras LM. Exploiting post-transcriptional regulation to probe RNA structures in vivo via fluorescence. Nucleic Acids Res 2014; 43:e13. [PMID: 25416800 PMCID: PMC4333371 DOI: 10.1093/nar/gku1191] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
While RNA structures have been extensively characterized in vitro, very few techniques exist to probe RNA structures inside cells. Here, we have exploited mechanisms of post-transcriptional regulation to synthesize fluorescence-based probes that assay RNA structures in vivo. Our probing system involves the co-expression of two constructs: (i) a target RNA and (ii) a reporter containing a probe complementary to a region in the target RNA attached to an RBS-sequestering hairpin and fused to a sequence encoding the green fluorescent protein (GFP). When a region of the target RNA is accessible, the area can interact with its complementary probe, resulting in fluorescence. By using this system, we observed varied patterns of structural accessibility along the length of the Tetrahymena group I intron. We performed in vivo DMS footprinting which, along with previous footprinting studies, helped to explain our probing results. Additionally, this novel approach represents a valuable tool to differentiate between RNA variants and to detect structural changes caused by subtle mutations. Our results capture some differences from traditional footprinting assays that could suggest that probing in vivo via oligonucleotide hybridization facilitates the detection of folding intermediates. Importantly, our data indicate that intracellular oligonucleotide probing can be a powerful complement to existing RNA structural probing methods.
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Affiliation(s)
- Steven W Sowa
- Microbiology Graduate Program, University of Texas at Austin, 100 E. 24th Street, A6500, Austin, TX 78712, USA
| | - Jorge Vazquez-Anderson
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX 78712, USA
| | - Chelsea A Clark
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX 78712, USA
| | - Ricardo De La Peña
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX 78712, USA
| | - Kaitlin Dunn
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX 78712, USA
| | - Emily K Fung
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX 78712, USA
| | - Mark J Khoury
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX 78712, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX 78712, USA
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22
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Tourasse NJ, Stabell FB, Kolstø AB. Survey of chimeric IStron elements in bacterial genomes: multiple molecular symbioses between group I intron ribozymes and DNA transposons. Nucleic Acids Res 2014; 42:12333-51. [PMID: 25324310 PMCID: PMC4227781 DOI: 10.1093/nar/gku939] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
IStrons are chimeric genetic elements composed of a group I intron associated with an insertion sequence (IS). The group I intron is a catalytic RNA providing the IStron with self-splicing ability, which renders IStron insertions harmless to the host genome. The IS element is a DNA transposon conferring mobility, and thus allowing the IStron to spread in genomes. IStrons are therefore a striking example of a molecular symbiosis between unrelated genetic elements endowed with different functions. In this study, we have conducted the first comprehensive survey of IStrons in sequenced genomes that provides insights into the distribution, diversity, origin and evolution of IStrons. We show that IStrons have a restricted phylogenetic distribution limited to two bacterial phyla, the Firmicutes and the Fusobacteria. Nevertheless, diverse IStrons representing two major groups targeting different insertion site motifs were identified. This taken with the finding that while the intron components of all IStrons belong to the same structural class, they are fused to different IS families, indicates that multiple intron–IS symbioses have occurred during evolution. In addition, introns and IS elements related to those that were at the origin of IStrons were also identified.
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Affiliation(s)
- Nicolas J Tourasse
- Laboratory for Microbial Dynamics (LaMDa), Department of Pharmaceutical Biosciences, University of Oslo, Oslo, Norway Institut de Biologie Physico-Chimique, UMR CNRS 7141, Université Pierre et Marie Curie, Paris, France
| | - Fredrik B Stabell
- Laboratory for Microbial Dynamics (LaMDa), Department of Pharmaceutical Biosciences, University of Oslo, Oslo, Norway
| | - Anne-Brit Kolstø
- Laboratory for Microbial Dynamics (LaMDa), Department of Pharmaceutical Biosciences, University of Oslo, Oslo, Norway
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23
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Sachsenmaier N, Handl S, Debeljak F, Waldsich C. Mapping RNA structure in vitro using nucleobase-specific probes. Methods Mol Biol 2014; 1086:79-94. [PMID: 24136599 DOI: 10.1007/978-1-62703-667-2_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
RNAs have to adopt specific three-dimensional structures to fulfill their biological functions. Therefore exploring RNA structure is of interest to understand RNA-dependent processes. Chemical probing in vitro is a very powerful tool to investigate RNA molecules under a variety of conditions. Among the most frequently used chemical reagents are the nucleobase-specific probes dimethyl sulfate (DMS), 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluenesulfonate (CMCT) and β-ethoxy-α-ketobutyraldehyde (kethoxal). These chemical reagents modify nucleotides which are not involved in hydrogen bonding or protected by a ligand, such as proteins or metabolites. Upon performing modification reactions with all three chemicals the accessibility of all four nucleobases can be determined. With this fast and inexpensive method local changes in RNA secondary and tertiary structure, as well as the formation of contacts between RNA and its ligands can be detected independent of the RNA's length.
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Affiliation(s)
- Nora Sachsenmaier
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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24
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Ward WL, Plakos K, DeRose VJ. Nucleic acid catalysis: metals, nucleobases, and other cofactors. Chem Rev 2014; 114:4318-42. [PMID: 24730975 PMCID: PMC4002065 DOI: 10.1021/cr400476k] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Indexed: 12/17/2022]
Affiliation(s)
- W. Luke Ward
- Department of Chemistry and Biochemistry and Institute of
Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Kory Plakos
- Department of Chemistry and Biochemistry and Institute of
Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Victoria J. DeRose
- Department of Chemistry and Biochemistry and Institute of
Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
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25
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Tanaka T, Furuta H, Ikawa Y. Installation of orthogonality to the interface that assembles two modular domains in the Tetrahymena group I ribozyme. J Biosci Bioeng 2014; 117:407-12. [DOI: 10.1016/j.jbiosc.2013.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/04/2013] [Accepted: 10/07/2013] [Indexed: 01/08/2023]
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26
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Hausner G, Hafez M, Edgell DR. Bacterial group I introns: mobile RNA catalysts. Mob DNA 2014; 5:8. [PMID: 24612670 PMCID: PMC3984707 DOI: 10.1186/1759-8753-5-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 02/24/2014] [Indexed: 12/02/2022] Open
Abstract
Group I introns are intervening sequences that have invaded tRNA, rRNA and protein coding genes in bacteria and their phages. The ability of group I introns to self-splice from their host transcripts, by acting as ribozymes, potentially renders their insertion into genes phenotypically neutral. Some group I introns are mobile genetic elements due to encoded homing endonuclease genes that function in DNA-based mobility pathways to promote spread to intronless alleles. Group I introns have a limited distribution among bacteria and the current assumption is that they are benign selfish elements, although some introns and homing endonucleases are a source of genetic novelty as they have been co-opted by host genomes to provide regulatory functions. Questions regarding the origin and maintenance of group I introns among the bacteria and phages are also addressed.
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Affiliation(s)
- Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2 N2, Canada
| | - Mohamed Hafez
- Department of Biochemistry, Faculty of Medicine, University of Montreal, Montréal, QC H3C 3 J7, Canada
- Department of Botany, Faculty of Science, Suez University, Suez, Egypt
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
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27
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Wildauer M, Zemora G, Liebeg A, Heisig V, Waldsich C. Chemical probing of RNA in living cells. Methods Mol Biol 2014; 1086:159-76. [PMID: 24136603 DOI: 10.1007/978-1-62703-667-2_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
RNAs need to adopt a specific architecture to exert their task in cells. While significant progress has been made in describing RNA folding landscapes in vitro, understanding intracellular RNA structure formation is still in its infancy. This is in part due to the complex nature of the cellular environment but also to the limited availability of suitable methodologies. To assess the intracellular structure of large RNAs, we recently applied a chemical probing technique and a metal-induced cleavage assay in vivo. These methods are based on the fact that small molecules, like dimethyl sulfate (DMS), or metal ions, such as Pb(2+), penetrate and spread throughout the cell very fast. Hence, these chemicals are able to modify accessible RNA residues or to induce cleavage of the RNA strand in the vicinity of a metal ion in living cells. Mapping of these incidents allows inferring information on the intracellular conformation, metal ion binding sites or ligand-induced structural changes of the respective RNA molecule. Importantly, in vivo chemical probing can be easily adapted to study RNAs in different cell types.
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Affiliation(s)
- Michael Wildauer
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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28
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Papaioannou IA, Dimopoulou CD, Typas MA. "Cryptic" group-I introns in the nuclear SSU-rRNA gene of Verticillium dahliae. Curr Genet 2013; 60:135-48. [PMID: 24258678 DOI: 10.1007/s00294-013-0417-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 10/24/2013] [Accepted: 11/06/2013] [Indexed: 11/30/2022]
Abstract
Group-I introns are widespread--though irregularly distributed--in eukaryotic organisms, and they have been extensively used for discrimination and phylogenetic analyses. Within the Verticillium genus, which comprises important phytopathogenic fungi, a group-I intron was previously identified in the SSU-rRNA (18S) gene of only V. longisporum. In this work, we aimed at elucidating the SSU-located intron distribution in V. dahliae and other Verticillium species, and the assessment of heterogeneity regarding intron content among rDNA repeats of fungal strains. Using conserved PCR primers for the amplification of the SSU gene, a structurally similar novel intron (sub-group IC1) was detected in only a few V. dahliae isolates. However, when intron-specific primers were used for the screening of a diverse collection of Verticillium isolates that originally failed to produce intron-containing SSU amplicons, most were found to contain one or both intron types, at variable rDNA repeat numbers. This marked heterogeneity was confirmed with qRT-PCR by testing rDNA copy numbers (varying from 39 to 70 copies per haploid genome) and intron copy ratios in selected isolates. Our results demonstrate that (a) IC1 group-I introns are not specific to V. longisporum within the Verticillium genus, (b) V. dahliae isolates of vegetative compatibility groups (VCGs) 4A and 6, which bear the novel intron at most of their rDNA repeats, are closely related, and (c) there is considerable intra-genomic heterogeneity for the presence or absence of introns among the ribosomal repeats. These findings underline that distributions of introns in the highly heterogeneous repetitive rDNA complex should always be verified with sensitive methods to avoid misleading conclusions for the phylogeny of fungi and other organisms.
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Affiliation(s)
- Ioannis A Papaioannou
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
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29
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Guo Y, Zhang W. Molecular dynamics simulation of RNA pseudoknot unfolding pathway. WUHAN UNIVERSITY JOURNAL OF NATURAL SCIENCES 2013. [PMCID: PMC7149040 DOI: 10.1007/s11859-013-0905-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Many biological functions of RNA molecules are related to their pseudoknot structures. It is significant for predicting the structure and function of RNA that learning about the stability and the process of RNA pseudoknot folding and unfolding. The structural features of mouse mammary tumor virus (MMTV) RNA pseudoknot in different ion concentration, the unfolding process of the RNA pseudoknot, and the two hairpin helices that constitute the RNA pseudoknot were studied with all atom molecule dynamics simulation method in this paper. We found that the higher cation concentration can cause structure of the RNA molecules more stable, and ions played an indispensable role in keeping the structure of RNA molecules stable; the unfolding process of hairpin structure was corresponding to the antiprocess of its folding process. The main pathway of pseudoknot unfolding was that the inner base pair opened first, and then, the two helices, which formed the RNA pseudoknot opened decussately, while the folding pathway of the RNA pseudoknot was a helix folding after formation of the other helix. Therefore, the unfolding process of RNA pseudoknot is different from the antiprocess of its folding process, and the unfolding process of each helix in the RNA pseudoknot is similar to the hairpin structure’s unfolding process, which means that both are the unzipping process.
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Abstract
RNA folding is an essential aspect underlying RNA-mediated cellular processes. Many RNAs, including large, multi-domain ribozymes, are capable of folding to the native, functional state without assistance of a protein cofactor in vitro. In the cell, trans-acting factors, such as proteins, are however known to modulate the structure and thus the fate of an RNA. DEAD-box proteins, including Mss116p, were recently found to assist folding of group I and group II introns in vitro and in vivo. The underlying mechanism(s) have been studied extensively to explore the contribution of ATP hydrolysis and duplex unwinding in helicase-stimulated intron splicing. Here we summarize the ongoing efforts to understand the novel role of DEAD-box proteins in RNA folding.
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Affiliation(s)
- Nora Sachsenmaier
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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31
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Desbouis D, Troitsky IP, Belousoff MJ, Spiccia L, Graham B. Copper(II), zinc(II) and nickel(II) complexes as nuclease mimetics. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.12.005] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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32
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Abstract
Phosphoryl transfer onto backbone hydroxyls is a recognized catalytic activity of nucleic acids. We find that kinase ribozyme K28 possesses an unusually complex active site that promotes (thio)phosphorylation of two residues widely separated in primary sequence. After allowing the ribozyme to radiolabel itself by phosphoryl transfer from [γ-32P]GTP, DNAzyme-mediated cleavage yielded two radiolabeled cleavage fragments, indicating phosphorylation sites within each of the two cleavage fragments. These sites were mapped by alkaline digestion and primer extension pausing. Enzymatic digestion and mutational analysis identified nucleotides important for activity and established the active structure as being a constrained pseudoknot with unusual connectivity that may juxtapose the two reactive sites. Nuclease sensitivities for nucleotides near the pseudoknot core were altered in the presence of GTPγS, indicating donor-induced folding. The 5′ target site was more strongly favored in full-length ribozyme K28 (128 nt) than in truncated RNAs (58 nt). Electrophoretic mobilities of self-thiophosphorylated products on organomercurial gels are distinct from the 5′ mono-thiophosphorylated product produced by reaction with polynucleotide kinase, potentially indicating simultaneous labeling of both sites within individual RNA strands. Our evidence supports a single, compact structure with local dynamics, rather than global rearrangement, as being responsible for dual-site phosphorylation.
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Affiliation(s)
- Elisa Biondi
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, MO 65211, USA.
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33
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Hafez M, Iranpour M, Mullineux ST, Sethuraman J, Wosnitza KM, Lehn P, Kroeker J, Loewen PC, Reid J, Hausner G. Identification of group I introns within the SSU rDNA gene in species of Ceratocystiopsis and related taxa. Fungal Biol 2012; 116:98-111. [DOI: 10.1016/j.funbio.2011.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 10/17/2011] [Accepted: 10/18/2011] [Indexed: 11/28/2022]
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Abstract
Coxiella burnetii is an extremely infectious, zoonotic agent that causes Q fever in humans. With the exception of New Zealand, the bacterium is distributed worldwide. Coxiella is classified as a select agent based on its past and potential use as a bioweapon and its threat to public health. Despite decades of research, we know relatively little regarding Coxiella?s molecular pathogenesis, and a vaccine is not widely available. This article briefly reviews the unusual genetics of C. burnetii; a pathogen that retains telltale genetic mementos collected over the course of its evolutionary path from a free-living bacterium to an obligate intracellular parasite of eukaryotic host cell phagosomes. Understanding why these genetic elements are maintained may help us better understand the biology of this fascinating pathogen.
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Affiliation(s)
- Michael F Minnick
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA.
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35
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Mitra S, Laederach A, Golden BL, Altman RB, Brenowitz M. RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways. RNA (NEW YORK, N.Y.) 2011; 17:1589-1603. [PMID: 21712400 PMCID: PMC3153981 DOI: 10.1261/rna.2694811] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 05/19/2011] [Indexed: 05/31/2023]
Abstract
Functional and kinetic constraints must be efficiently balanced during the folding process of all biopolymers. To understand how homologous RNA molecules with different global architectures fold into a common core structure we determined, under identical conditions, the folding mechanisms of three phylogenetically divergent group I intron ribozymes. These ribozymes share a conserved functional core defined by topologically equivalent tertiary motifs but differ in their primary sequence, size, and structural complexity. Time-resolved hydroxyl radical probing of the backbone solvent accessible surface and catalytic activity measurements integrated with structural-kinetic modeling reveal that each ribozyme adopts a unique strategy to attain the conserved functional fold. The folding rates are not dictated by the size or the overall structural complexity, but rather by the strength of the constituent tertiary motifs which, in turn, govern the structure, stability, and lifetime of the folding intermediates. A fundamental general principle of RNA folding emerges from this study: The dominant folding flux always proceeds through an optimally structured kinetic intermediate that has sufficient stability to act as a nucleating scaffold while retaining enough conformational freedom to avoid kinetic trapping. Our results also suggest a potential role of naturally selected peripheral A-minor interactions in balancing RNA structural stability with folding efficiency.
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Affiliation(s)
- Somdeb Mitra
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Barbara L. Golden
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Russ B. Altman
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Michael Brenowitz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Spitzer R, Kloiber K, Tollinger M, Kreutz C. Kinetics of DNA refolding from longitudinal exchange NMR spectroscopy. Chembiochem 2011; 12:2007-10. [PMID: 21739562 DOI: 10.1002/cbic.201100318] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Indexed: 12/22/2022]
Affiliation(s)
- Romana Spitzer
- Institute of Organic Chemistry, University of Innsbruck, Innrain 52a, 6020 Innsbruck, Austria
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Bégu D, Castandet B, Araya A. RNA editing restores critical domains of a group I intron in fern mitochondria. Curr Genet 2011; 57:317-25. [DOI: 10.1007/s00294-011-0349-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 06/07/2011] [Accepted: 06/10/2011] [Indexed: 11/28/2022]
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Abstract
As important functional structures, RNA pseudoknots provide excellent models for studying the interplay between secondary and tertiary structures and the roles of triplexes, noncanonical interactions, and coaxial stacking in the folding/unfolding process. Here we report a first atomistic and statistical analysis of the unfolding of the pseudoknot within gene 32 mRNA of bacteriophage T2. Multiple unfolding pathways, diverse transition states, and various intermediate structures were observed. Water molecules were found to be coupled with the unfolding process via the expulsion or concurrent mechanism.
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Affiliation(s)
- Yujie Zhang
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China
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39
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Pollack L. Time resolved SAXS and RNA folding. Biopolymers 2011; 95:543-9. [PMID: 21328311 DOI: 10.1002/bip.21604] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/19/2011] [Accepted: 01/19/2011] [Indexed: 01/04/2023]
Abstract
Small angle X-ray scattering provides low resolution structural information about macromolecules in solution. When coupled with rapid mixing methods, SAXS reports time-dependent conformational changes of RNA induced by the addition of Mg(2+) to trigger folding. Thus time-resolved SAXS provides unique information about the global or overall structures of transient intermediates populated during folding. Notably, SAXS provides information about the earliest folding events, which can evade detection by other methods.
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Affiliation(s)
- Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.
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Watts T, Khalimonchuk O, Wolf RZ, Turk EM, Mohr G, Winge DR. Mne1 is a novel component of the mitochondrial splicing apparatus responsible for processing of a COX1 group I intron in yeast. J Biol Chem 2011; 286:10137-46. [PMID: 21257754 DOI: 10.1074/jbc.m110.205625] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Saccharomyces cerevisiae cells lacking Mne1 are deficient in intron splicing in the gene encoding the Cox1 subunit of cytochrome oxidase but contain wild-type levels of the bc(1) complex. Thus, Mne1 has no role in splicing of COB introns or expression of the COB gene. Northern experiments suggest that splicing of the COX1 aI5β intron is dependent on Mne1 in addition to the previously known Mrs1, Mss116, Pet54, and Suv3 factors. Processing of the aI5β intron is similarly impaired in mne1Δ and mrs1Δ cells and overexpression of Mrs1 partially restores the respiratory function of mne1Δ cells. Mrs1 is known to function in the initial transesterification reaction of splicing. Mne1 is a mitochondrial matrix protein loosely associated with the inner membrane and is found in a high mass ribonucleoprotein complex specifically associated with the COX1 mRNA even within an intronless strain. Mne1 does not appear to have a secondary function in COX1 processing or translation, because disruption of MNE1 in cells containing intronless mtDNA does not lead to a respiratory growth defect. Thus, the primary defect in mne1Δ cells is splicing of the aI5β intron in COX1.
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Affiliation(s)
- Talina Watts
- Department of Medicine, University of Utah Health Sciences Center, Salt Lake City, Utah 84132, USA
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A maturase that specifically stabilizes and activates its cognate group I intron at high temperatures. Biochimie 2010; 93:533-41. [PMID: 21129434 DOI: 10.1016/j.biochi.2010.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 11/22/2010] [Indexed: 11/23/2022]
Abstract
Folding of large structured RNAs into their functional tertiary structures at high temperatures is challenging. Here we show that I-TnaI protein, a small LAGLIDADG homing endonuclease encoded by a group I intron from a hyperthermophilic bacterium, acts as a maturase that is essential for the catalytic activity of this intron at high temperatures and physiological cationic conditions. I-TnaI specifically binds to and induces tertiary packing of the P4-P6 domain of the intron; this RNA-protein complex might serve as a thermostable platform for active folding of the entire intron. Interestingly, the binding affinity of I-TnaI to its cognate intron RNA largely increases with temperature; over 30-fold stronger binding at higher temperatures relative to 37 °C correlates with a switch from an entropy-driven (37 °C) to an enthalpy-driven (55-60 °C) interaction mode. This binding mode may represent a novel strategy how an RNA binding protein can promote the function of its target RNA specifically at high temperatures.
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Zhang J, Lau MW, Ferré-D'Amaré AR. Ribozymes and riboswitches: modulation of RNA function by small molecules. Biochemistry 2010; 49:9123-31. [PMID: 20931966 DOI: 10.1021/bi1012645] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Diverse small molecules interact with catalytic RNAs (ribozymes) as substrates and cofactors, and their intracellular concentrations are sensed by gene-regulatory mRNA domains (riboswitches) that modulate transcription, splicing, translation, or RNA stability. Although recognition mechanisms vary from RNA to RNA, structural analyses reveal recurring strategies that arise from the intrinsic properties of RNA such as base pairing and stacking with conjugated heterocycles, and cation-dependent recognition of anionic functional groups. These studies also suggest that, to a first approximation, the magnitude of ligand-induced reorganization of an RNA is inversely proportional to the complexity of the riboswitch or ribozyme. How these small molecule binding-induced changes in RNA lead to alteration in gene expression is less well understood. While different riboswitches have been proposed to be under either kinetic or thermodynamic control, the biochemical and structural mechanisms that give rise to regulatory consequences downstream of small molecule recognition by RNAs mostly remain to be elucidated.
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Affiliation(s)
- Jinwei Zhang
- Howard Hughes Medical Institute, Seattle, Washington 98109-1024, USA
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Abstract
RNA folding is the most essential process underlying RNA function. While significant progress has been made in understanding the forces driving RNA folding in vitro, exploring the rules governing intracellular RNA structure formation is still in its infancy. The cellular environment hosts a great diversity of factors that potentially influence RNA folding in vivo. For example, the nature of transcription and translation is known to shape the folding landscape of RNA molecules. Trans-acting factors such as proteins, RNAs and metabolites, among others, are also able to modulate the structure and thus the fate of an RNA. Here we summarize the ongoing efforts to uncover how RNA folds in living cells.
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Affiliation(s)
- Georgeta Zemora
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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Duncan CDS, Weeks KM. Nonhierarchical ribonucleoprotein assembly suggests a strain-propagation model for protein-facilitated RNA folding. Biochemistry 2010; 49:5418-25. [PMID: 20533823 DOI: 10.1021/bi100267g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteins play diverse and critical roles in cellular ribonucleoproteins (RNPs) including promoting formation of and stabilizing active RNA conformations. Yet, the conformational changes required to convert large RNAs into active RNPs have proven difficult to characterize fully. Here we use high-resolution approaches to monitor both local nucleotide flexibility and solvent accessibility for nearly all nucleotides in the bI3 group I intron RNP in four assembly states: the free RNA, maturase-bound RNA, Mrs1-bound RNA, and the complete six-component holocomplex. The free RNA is misfolded relative to the secondary structure required for splicing. The maturase and Mrs1 proteins each stabilized long-range tertiary interactions, but neither protein alone induced folding into the functional secondary structure. In contrast, simultaneous binding by both proteins results in large secondary structure rearrangements in the RNA and yielded the catalytically active group I intron structure. Secondary and tertiary folding of the RNA component of the bI3 RNP are thus not independent: RNA folding is strongly nonhierarchical. These results emphasize that protein-mediated stabilization of RNA tertiary interactions functions to pull the secondary structure into an energetically disfavored, but functional, conformation and emphasize a new role for facilitator proteins in RNP assembly.
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Affiliation(s)
- Caia D S Duncan
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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Abstract
Controlling RNA splicing opens up possibilities for the synthetic biologist. The Tetrahymena ribozyme is a model group I self-splicing ribozyme that has been shown to be useful in synthetic circuits. To create additional splicing ribozymes that can function in synthetic circuits, we generated synthetic ribozyme variants by rationally mutating the Tetrahymena ribozyme. We present an alignment visualization for the ribozyme termed as structure information diagram that is similar to a sequence logo but with alignment data mapped on to secondary structure information. Using the alignment data and known biochemical information about the Tetrahymena ribozyme, we designed synthetic ribozymes with different primary sequences without altering the secondary structure. One synthetic ribozyme with 110 nt mutated retained 12% splicing efficiency in vivo. The results indicate that our biochemical understanding of the ribozyme is accurate enough to engineer a family of active splicing ribozymes with similar secondary structure but different primary sequences.
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Affiliation(s)
- Austin J Che
- Computer Science and Artificial Intelligence Laboratory, Masschusetts Institute of Technology, 32 Vassar St, Cambridge, MA 02139, USA.
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46
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Fiskaa T, Birgisdottir AB. RNA reprogramming and repair based on trans-splicing group I ribozymes. N Biotechnol 2010; 27:194-203. [PMID: 20219714 DOI: 10.1016/j.nbt.2010.02.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
While many traditional gene therapy strategies attempt to deliver new copies of wild-type genes back to cells harboring the defective genes, RNA-directed strategies offer a range of novel therapeutic applications. Revision or reprogramming of mRNA is a form of gene therapy that modifies mRNA without directly changing the transcriptional regulation or the genomic gene sequence. Group I ribozymes can be engineered to act in trans by recognizing a separate RNA molecule in a sequence-specific manner, and to covalently link a new RNA sequence to this separate RNA molecule. Group I ribozymes have been shown to repair defective transcripts that cause human genetic or malignant diseases, as well as to replace transcript sequences by foreign RNA resulting in new cellular functions. This review provides an overview of current strategies using trans-splicing group I ribozymes in RNA repair and reprogramming.
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Affiliation(s)
- Tonje Fiskaa
- RNA and Transcriptomics Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway.
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47
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Duncan CDS, Weeks KM. The Mrs1 splicing factor binds the bI3 group I intron at each of two tetraloop-receptor motifs. PLoS One 2010; 5:e8983. [PMID: 20126554 PMCID: PMC2813881 DOI: 10.1371/journal.pone.0008983] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 01/11/2010] [Indexed: 11/18/2022] Open
Abstract
Most large ribozymes require protein cofactors in order to function efficiently. The yeast mitochondrial bI3 group I intron requires two proteins for efficient splicing, Mrs1 and the bI3 maturase. Mrs1 has evolved from DNA junction resolvases to function as an RNA cofactor for at least two group I introns; however, the RNA binding site and the mechanism by which Mrs1 facilitates splicing were unknown. Here we use high-throughput RNA structure analysis to show that Mrs1 binds a ubiquitous RNA tertiary structure motif, the GNRA tetraloop-receptor interaction, at two sites in the bI3 RNA. Mrs1 also interacts at similar tetraloop-receptor elements, as well as other structures, in the self-folding Azoarcus group I intron and in the RNase P enzyme. Thus, Mrs1 recognizes general features found in the tetraloop-receptor motif. Identification of the two Mrs1 binding sites now makes it possible to create a model of the complete six-component bI3 ribonucleoprotein. All protein cofactors bind at the periphery of the RNA such that every long-range RNA tertiary interaction is stabilized by protein binding, involving either Mrs1 or the bI3 maturase. This work emphasizes the strong evolutionary pressure to bolster RNA tertiary structure with RNA-binding interactions as seen in the ribosome, spliceosome, and other large RNA machines.
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Affiliation(s)
- Caia D. S. Duncan
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
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48
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Turk EM, Caprara MG. Splicing of yeast aI5beta group I intron requires SUV3 to recycle MRS1 via mitochondrial degradosome-promoted decay of excised intron ribonucleoprotein (RNP). J Biol Chem 2010; 285:8585-94. [PMID: 20064926 DOI: 10.1074/jbc.m109.090761] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Yeast Suv3p is a member of the DEXH/D box family of RNA helicases and is a critical component of the mitochondrial degradosome, which also includes a 3' --> 5' exonuclease, Dss1p. Defects in the degradosome result in accumulation of aberrant transcripts, unprocessed transcripts, and excised group I introns. In addition, defects in SUV3 result in decreased splicing of the aI5beta and bI3 group I introns. Whereas a role for Suv3p in RNA degradation is well established, the function of Suv3p in splicing of group I introns has remained elusive. It has been particularly challenging to determine if Suv3p effects group I intron splicing through RNA degradation as part of the degradosome, or has a direct role in splicing as a chaperone, because nearly all perturbations of SUV3 or DSS1 result in loss of the mitochondrial genome. Here we utilized the suv3-1 allele, which is defective in RNA metabolism and yet maintains a stable mitochondrial genome, to investigate the role of Suv3p in splicing of the aI5beta group I intron. We provide genetic evidence that Mrs1p is a limiting cofactor for aI5beta splicing, and this evidence also suggests that Suv3p activity is required to recycle the excised aI5beta ribonucleoprotein. We also show that Suv3p acts indirectly as a component of the degradosome to promote aI5beta splicing. We present a model whereby defects in Suv3p result in accumulation of stable, excised group I intron ribonucleoproteins, which result in sequestration of Mrs1p, and a concomitant reduction in splicing of aI5beta.
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Affiliation(s)
- Edward M Turk
- Center for RNA Molecular Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA.
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Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures. Proc Natl Acad Sci U S A 2009; 106:17349-54. [PMID: 19805055 DOI: 10.1073/pnas.0906625106] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Understanding how RNA molecules navigate their rugged folding landscapes holds the key to describing their roles in a variety of cellular functions. To dissect RNA folding at the molecular level, we performed simulations of three pseudoknots (MMTV and SRV-1 from viral genomes and the hTR pseudoknot from human telomerase) using coarse-grained models. The melting temperatures from the specific heat profiles are in good agreement with the available experimental data for MMTV and hTR. The equilibrium free energy profiles, which predict the structural transitions that occur at each melting temperature, are used to propose that the relative stabilities of the isolated helices control their folding mechanisms. Kinetic simulations, which corroborate the inferences drawn from the free energy profiles, show that MMTV folds by a hierarchical mechanism with parallel paths, i.e., formation of one of the helices nucleates the assembly of the rest of the structure. The SRV-1 pseudoknot, which folds in a highly cooperative manner, assembles in a single step in which the preformed helices coalesce nearly simultaneously to form the tertiary structure. Folding occurs by multiple pathways in the hTR pseudoknot, the isolated structural elements of which have similar stabilities. In one of the paths, tertiary interactions are established before the formation of the secondary structures. Our work shows that there are significant sequence-dependent variations in the folding landscapes of RNA molecules with similar fold. We also establish that assembly mechanisms can be predicted using the stabilities of the isolated secondary structures.
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Shi X, Mollova ET, Pljevaljcić G, Millar DP, Herschlag D. Probing the dynamics of the P1 helix within the Tetrahymena group I intron. J Am Chem Soc 2009; 131:9571-8. [PMID: 19537712 DOI: 10.1021/ja902797j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
RNA conformational transformations are integral to RNA's biological functions. Further, structured RNA molecules exist as a series of dynamic intermediates in the course of folding or complexation with proteins. Thus, an understanding of RNA folding and function will require deep and incisive understanding of its dynamic behavior. However, existing tools to investigate RNA dynamics are limited. Here, we introduce a powerful fluorescence polarization anisotropy approach that utilizes a rare base analogue that retains substantial fluorescence when incorporated into helices. We show that 6-methylisoxanthopterin (6-MI) can be used to follow the nanosecond dynamics of individual helices. We then use 6-MI to probe the dynamics of an individual helix, referred to as P1, within the 400nt Tetrahymena group I ribozyme. Comparisons of the dynamics of the P1 helix in wild type and mutant ribozymes and in model constructs reveal a highly immobilized docked state of the P1 helix, as expected, and a relatively mobile "open complex" or undocked state. This latter result rules out a model in which slow docking of the P1 helix into its cognate tertiary interactions arises from a stable alternatively docked conformer. The results are consistent with a model in which stacking and tertiary interactions of the A(3) tether connecting the P1 helix to the body of the ribozyme limit P1 mobility and slow its docking, and this model is supported by cross-linking results. The ability to isolate the nanosecond motions of individual helices within complex RNAs and RNA/protein complexes will be valuable in distinguishing between functional models and in discerning the fundamental behavior of important biological species.
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Affiliation(s)
- Xuesong Shi
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
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