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Cheng F, Chapman T, Zhang S, Morsch M, Chung R, Lee A, Rayner SL. Understanding age-related pathologic changes in TDP-43 functions and the consequence on RNA splicing and signalling in health and disease. Ageing Res Rev 2024; 96:102246. [PMID: 38401571 DOI: 10.1016/j.arr.2024.102246] [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: 10/26/2023] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 02/26/2024]
Abstract
TAR DNA binding protein-43 (TDP-43) is a key component in RNA splicing which plays a crucial role in the aging process. In neurodegenerative diseases such as amyotrophic lateral sclerosis, frontotemporal dementia and limbic-predominant age-related TDP-43 encephalopathy, TDP-43 can be mutated, mislocalised out of the nucleus of neurons and glial cells and form cytoplasmic inclusions. These TDP-43 alterations can lead to its RNA splicing dysregulation and contribute to mis-splicing of various types of RNA, such as mRNA, microRNA, and circular RNA. These changes can result in the generation of an altered transcriptome and proteome within cells, ultimately changing the diversity and quantity of gene products. In this review, we summarise the findings of novel atypical RNAs resulting from TDP-43 dysfunction and their potential as biomarkers or targets for therapeutic development.
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Affiliation(s)
- Flora Cheng
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia.
| | - Tyler Chapman
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Selina Zhang
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Marco Morsch
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Roger Chung
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Albert Lee
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Stephanie L Rayner
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia.
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Mafi A, Keshavarzmotamed A, Hedayati N, Boroujeni ZY, Reiter RJ, Dehmordi RM, Aarabi MH, Rezaee M, Asemi Z. Melatonin targeting non-coding RNAs in cancer: Focus on mechanisms and potential therapeutic targets. Eur J Pharmacol 2023; 950:175755. [PMID: 37119959 DOI: 10.1016/j.ejphar.2023.175755] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/15/2023] [Accepted: 04/26/2023] [Indexed: 05/01/2023]
Abstract
Despite, melatonin is mainly known as a regulatory factor for circadian rhythm, its notable role in other fundamental biological processes, such as redox homeostasis and programmed cell death, has been found. In this line, a growing body of evidence indicated that melatonin could apply an inhibitory effect on the tumorigenic processes. Hence, melatonin might be considered an efficient adjuvant agent for cancer treatment. Besides, the physiological and pathological functions of non-coding RNAs (ncRNAs) in various disease, particularly cancers, have been expanded over the past two decades. It is well-established that ncRNAs can modulate the gene expression at various levels, thereby, ncRNAs. can regulate the numerous biological processes, including cell proliferation, cell metabolism, apoptosis, and cell cycle. Recently, targeting the ncRNAs expression provides a novel insight in the therapeutic approaches for cancer treatment. Moreover, accumulating investigations have revealed that melatonin could impact the expression of different ncRNAs in a multiple disorders, including cancer. Therefore, in the precent study, we discuss the potential roles of melatonin in modulating the expression of ncRNAs and the related molecular pathways in different types of cancer. Also, we highlighted its importance in therapeutic application and translational medicine in cancer treatment.
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Affiliation(s)
- Alireza Mafi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran; Nutrition and Food Security Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
| | | | - Neda Hedayati
- School of Medicine, Iran University of Medical Science, Tehran, Iran.
| | - Zahra Yeganeh Boroujeni
- School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Russel J Reiter
- Department of Cell Systems and Anatomy, UT Health. Long School of Medicine, San Antonio, TX, USA.
| | - Rohollah Mousavi Dehmordi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Mohammad-Hossein Aarabi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Malihe Rezaee
- Department of Pharmacology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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3
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Lian K, Furulund BMN, Tveita AA, Haugen P, Johansen SD. Mobile group I introns at nuclear rDNA position L2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal introns. Mob DNA 2022; 13:23. [PMID: 36209098 PMCID: PMC9548176 DOI: 10.1186/s13100-022-00280-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/28/2022] [Indexed: 11/24/2022] Open
Abstract
Background Mobile group I introns encode homing endonucleases that confer intron mobility initiated by a double-strand break in the intron-lacking allele at the site of insertion. Nuclear ribosomal DNA of some fungi and protists contain mobile group I introns harboring His-Cys homing endonuclease genes (HEGs). An intriguing question is how protein-coding genes embedded in nuclear ribosomal DNA become expressed. To address this gap of knowledge we analyzed nuclear L2066 group I introns from myxomycetes and ascomycetes. Results A total of 34 introns were investigated, including two identified mobile-type introns in myxomycetes with HEGs oriented in sense or antisense directions. Intriguingly, both HEGs are interrupted by spliceosomal introns. The intron in Didymium squamulosum, which harbors an antisense oriented HEG, was investigated in more detail. The group I intron RNA self-splices in vitro, thus generating ligated exons and full-length intron circles. The intron HEG is expressed in vivo in Didymium cells, which involves removal of a 47-nt spliceosomal intron (I-47) and 3′ polyadenylation of the mRNA. The D. squamulosum HEG (lacking the I-47 intron) was over-expressed in E. coli, and the corresponding protein was purified and shown to confer endonuclease activity. The homing endonuclease was shown to cleave an intron-lacking DNA and to produce a pentanucleotide 3′ overhang at the intron insertion site. Conclusions The L2066 family of nuclear group I introns all belong to the group IE subclass. The D. squamulosum L2066 intron contains major hallmarks of a true mobile group I intron by encoding a His-Cys homing endonuclease that generates a double-strand break at the DNA insertion site. We propose a potential model to explain how an antisense HEG becomes expressed from a nuclear ribosomal DNA locus. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00280-4.
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Affiliation(s)
- Kjersti Lian
- Nofima AS, Muninbakken 9-13, Breivika, 9291, Tromsø, Norway
| | - Betty M N Furulund
- Genomics division, Faculty of Biosciences and Aquaculture, Nord University, N-8049, Bodø, Norway
| | - Anders A Tveita
- Medical Department, Bærum Hospital, Vestre Viken Hospital Trulst, Drammen, Norway
| | - Peik Haugen
- Department of Chemistry and Center for Bioinformatics, Faculty of Science and Technology, UiT-The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Steinar D Johansen
- Genomics division, Faculty of Biosciences and Aquaculture, Nord University, N-8049, Bodø, Norway.
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4
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Abstract
Covalently closed, single-stranded circular RNAs can be produced from viral RNA genomes as well as from the processing of cellular housekeeping noncoding RNAs and precursor messenger RNAs. Recent transcriptomic studies have surprisingly uncovered that many protein-coding genes can be subjected to backsplicing, leading to widespread expression of a specific type of circular RNAs (circRNAs) in eukaryotic cells. Here, we discuss experimental strategies used to discover and characterize diverse circRNAs at both the genome and individual gene scales. We further highlight the current understanding of how circRNAs are generated and how the mature transcripts function. Some circRNAs act as noncoding RNAs to impact gene regulation by serving as decoys or competitors for microRNAs and proteins. Others form extensive networks of ribonucleoprotein complexes or encode functional peptides that are translated in response to certain cellular stresses. Overall, circRNAs have emerged as an important class of RNAmolecules in gene expression regulation that impact many physiological processes, including early development, immune responses, neurogenesis, and tumorigenesis.
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Affiliation(s)
- Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China;
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, Texas, USA;
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China;
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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5
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CircRNA: An emerging star in the progression of glioma. Biomed Pharmacother 2022; 151:113150. [PMID: 35623170 DOI: 10.1016/j.biopha.2022.113150] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/12/2022] [Accepted: 05/15/2022] [Indexed: 11/21/2022] Open
Abstract
Circular RNAs (circRNAs), a class of single-stranded noncoding RNAs with a covalently closed loop structure, are recognized as promising biomarkers and targets for diagnosing and treating dozens of diseases, especially cancers. CircRNAs are extremely stable, abundant and conserved and have tissue- or developmental stage-specific expression. Currently, the biogenesis and biological functions of circRNAs have been increasingly revealed with deep sequencing and bioinformatics. Studies have indicated that circRNAs are frequently expressed in brain tissues and that their expression levels change in different stages of neural development, suggesting that circRNAs may play an important role in diseases of the nervous system, such as glioma. However, because the biogenesis and functions of circRNAs do not depend on a single mechanism but are coregulated by multiple factors, it is necessary to further explore the underlying mechanisms. In this review, we summarized the classification, mechanisms of biogenesis and biological functions of circRNAs. Meanwhile, we emphatically expounded on the process of abnormal expression of circRNAs, methods used in circRNA research, and their effects on the malignant biological capabilities of glioma.
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Structural Organization of S516 Group I Introns in Myxomycetes. Genes (Basel) 2022; 13:genes13060944. [PMID: 35741706 PMCID: PMC9223047 DOI: 10.3390/genes13060944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 02/04/2023] Open
Abstract
Group I introns are mobile genetic elements encoding self-splicing ribozymes. Group I introns in nuclear genes are restricted to ribosomal DNA of eukaryotic microorganisms. For example, the myxomycetes, which represent a distinct protist phylum with a unique life strategy, are rich in nucleolar group I introns. We analyzed and compared 75 group I introns at position 516 in the small subunit ribosomal DNA from diverse and distantly related myxomycete taxa. A consensus secondary structure revealed a conserved group IC1 ribozyme core, but with a surprising RNA sequence complexity in the peripheral regions. Five S516 group I introns possess a twintron organization, where a His-Cys homing endonuclease gene insertion was interrupted by a small spliceosomal intron. Eleven S516 introns contained direct repeat arrays with varying lengths of the repeated motif, a varying copy number, and different structural organizations. Phylogenetic analyses of S516 introns and the corresponding host genes revealed a complex inheritance pattern, with both vertical and horizontal transfers. Finally, we reconstructed the evolutionary history of S516 nucleolar group I introns from insertion of mobile-type introns at unoccupied cognate sites, through homing endonuclease gene degradation and loss, and finally to the complete loss of introns. We conclude that myxomycete S516 introns represent a family of genetic elements with surprisingly dynamic structures despite a common function in RNA self-splicing.
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A Phylogenetic Approach to Structural Variation in Organization of Nuclear Group I Introns and Their Ribozymes. Noncoding RNA 2021; 7:ncrna7030043. [PMID: 34449660 PMCID: PMC8395846 DOI: 10.3390/ncrna7030043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 01/22/2023] Open
Abstract
Nuclear group I introns are restricted to the ribosomal DNA locus where they interrupt genes for small subunit and large subunit ribosomal RNAs at conserved sites in some eukaryotic microorganisms. Here, the myxomycete protists are a frequent source of nuclear group I introns due to their unique life strategy and a billion years of separate evolution. The ribosomal DNA of the myxomycete Mucilago crustacea was investigated and found to contain seven group I introns, including a direct repeat-containing intron at insertion site S1389 in the small subunit ribosomal RNA gene. We collected, analyzed, and compared 72 S1389 group IC1 introns representing diverse myxomycete taxa. The consensus secondary structure revealed a conserved ribozyme core, but with surprising sequence variations in the guanosine binding site in segment P7. Some S1389 introns harbored large extension sequences in the peripheral region of segment P9 containing direct repeat arrays. These repeats contained up to 52 copies of a putative internal guide sequence motif. Other S1389 introns harbored homing endonuclease genes in segment P1 encoding His-Cys proteins. Homing endonuclease genes were further interrupted by small spliceosomal introns that have to be removed in order to generate the open reading frames. Phylogenetic analyses of S1389 intron and host gene indicated both vertical and horizontal intron transfer during evolution, and revealed sporadic appearances of direct repeats, homing endonuclease genes, and guanosine binding site variants among the myxomycete taxa.
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The Mitochondrial Genome of the Sea Anemone Stichodactyla haddoni Reveals Catalytic Introns, Insertion-Like Element, and Unexpected Phylogeny. Life (Basel) 2021; 11:life11050402. [PMID: 33924866 PMCID: PMC8146996 DOI: 10.3390/life11050402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 01/15/2023] Open
Abstract
A hallmark of sea anemone mitochondrial genomes (mitogenomes) is the presence of complex catalytic group I introns. Here, we report the complete mitogenome and corresponding transcriptome of the carpet sea anemone Stichodactyla haddoni (family Stichodactylidae). The mitogenome is vertebrate-like in size, organization, and gene content. Two mitochondrial genes encoding NADH dehydrogenase subunit 5 (ND5) and cytochrome c oxidase subunit I (COI) are interrupted with complex group I introns, and one of the introns (ND5-717) harbors two conventional mitochondrial genes (ND1 and ND3) within its sequence. All the mitochondrial genes, including the group I introns, are expressed at the RNA level. Nonconventional and optional mitochondrial genes are present in the mitogenome of S. haddoni. One of these gene codes for a COI-884 intron homing endonuclease and is organized in-frame with the upstream COI exon. The insertion-like orfA is expressed as RNA and translocated in the mitogenome as compared with other sea anemones. Phylogenetic analyses based on complete nucleotide and derived protein sequences indicate that S. haddoni is embedded within the family Actiniidae, a finding that challenges current taxonomy.
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A Singular and Widespread Group of Mobile Genetic Elements: RNA Circles with Autocatalytic Ribozymes. Cells 2020; 9:cells9122555. [PMID: 33260527 PMCID: PMC7761336 DOI: 10.3390/cells9122555] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/19/2020] [Accepted: 11/26/2020] [Indexed: 11/16/2022] Open
Abstract
Circular DNAs, such as most prokaryotic and phage genomes, are a frequent form of nucleic acids, whereas circular RNAs had been regarded as unusual macromolecules until very recently. The first reported RNA circles were the family of small infectious genomes of viroids and circular RNA (circRNA) satellites of plant viruses, some of which contain small self-cleaving RNA motifs, such as the hammerhead (HHR) and hairpin ribozymes. A similar infectious circRNA, the unique human hepatitis delta virus (HDV), is another viral satellite that also encodes self-cleaving motifs called HDV ribozymes. Very recently, different animals have been reported to contain HDV-like circRNAs with typical HDV ribozymes, but also conserved HHR motifs, as we describe here. On the other hand, eukaryotic and prokaryotic genomes encode sequences able to self-excise as circRNAs, like the autocatalytic Group I and II introns, which are widespread genomic mobile elements. In the 1990s, the first circRNAs encoded in a mammalian genome were anecdotally reported, but their abundance and importance have not been unveiled until recently. These gene-encoded circRNAs are produced by events of alternative splicing in a process generally known as backsplicing. However, we have found a second natural pathway of circRNA expression conserved in numerous plant and animal genomes, which efficiently promotes the accumulation of small non-coding RNA circles through the participation of HHRs. Most of these genome-encoded circRNAs with HHRs are the transposition intermediates of a novel family of non-autonomous retrotransposons called retrozymes, with intriguing potential as new forms of gene regulation.
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10
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Cavalcante GC, Magalhães L, Ribeiro-dos-Santos Â, Vidal AF. Mitochondrial Epigenetics: Non-Coding RNAs as a Novel Layer of Complexity. Int J Mol Sci 2020; 21:E1838. [PMID: 32155913 PMCID: PMC7084767 DOI: 10.3390/ijms21051838] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 01/29/2020] [Accepted: 02/02/2020] [Indexed: 12/12/2022] Open
Abstract
Mitochondria are organelles responsible for several functions involved in cellular balance, including energy generation and apoptosis. For decades now, it has been well-known that mitochondria have their own genetic material (mitochondrial DNA), which is different from nuclear DNA in many ways. More recently, studies indicated that, much like nuclear DNA, mitochondrial DNA is regulated by epigenetic factors, particularly DNA methylation and non-coding RNAs (ncRNAs). This field is now called mitoepigenetics. Additionally, it has also been established that nucleus and mitochondria are constantly communicating to each other to regulate different cellular pathways. However, little is known about the mechanisms underlying mitoepigenetics and nuclei-mitochondria communication, and also about the involvement of the ncRNAs in mitochondrial functions and related diseases. In this context, this review presents the state-of-the-art knowledge, focusing on ncRNAs as new players in mitoepigenetic regulation and discussing future perspectives of these fields.
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Affiliation(s)
- Giovanna C. Cavalcante
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
| | - Leandro Magalhães
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
| | - Ândrea Ribeiro-dos-Santos
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Researches, Federal University of Pará, Rua dos Mundurucus, 4487, 66073-005 Belém, PA, Brazil
| | - Amanda F. Vidal
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
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11
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Patop IL, Wüst S, Kadener S. Past, present, and future of circRNAs. EMBO J 2019; 38:e100836. [PMID: 31343080 PMCID: PMC6694216 DOI: 10.15252/embj.2018100836] [Citation(s) in RCA: 766] [Impact Index Per Article: 153.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 05/15/2019] [Accepted: 06/03/2019] [Indexed: 12/28/2022] Open
Abstract
Exonic circular RNAs (circRNAs) are covalently closed RNA molecules generated by a process named back-splicing. circRNAs are highly abundant in eukaryotes, and many of them are evolutionary conserved. In metazoans, circular RNAs are expressed in a tissue-specific manner, are highly stable, and accumulate with age in neural tissues. circRNA biogenesis can regulate the production of the linear RNA counterpart in cis as back-splicing competes with linear splicing. Recent reports also demonstrate functions for some circRNAs in trans: Certain circRNAs interact with microRNAs, some are translated, and circRNAs have been shown to regulate immune responses and behavior. Here, we review current knowledge about animal circRNAs and summarize new insights into potential circRNA functions, concepts of their origin, and possible future directions in the field.
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Affiliation(s)
| | - Stas Wüst
- Department of BiologyBrandeis UniversityWalthamMAUSA
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12
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Chi SI, Dahl M, Emblem Å, Johansen SD. Giant group I intron in a mitochondrial genome is removed by RNA back-splicing. BMC Mol Biol 2019; 20:16. [PMID: 31153363 PMCID: PMC6545197 DOI: 10.1186/s12867-019-0134-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 05/23/2019] [Indexed: 01/29/2023] Open
Abstract
Background The mitochondrial genomes of mushroom corals (Corallimorpharia) are remarkable for harboring two complex group I introns; ND5-717 and COI-884. How these autocatalytic RNA elements interfere with mitochondrial RNA processing is currently not known. Here, we report experimental support for unconventional processing events of ND5-717 containing RNA. Results We obtained the complete mitochondrial genome sequences and corresponding mitochondrial transcriptomes of the two distantly related corallimorpharian species Ricordea yuma and Amplexidiscus fenestrafer. All mitochondrial genes were found to be expressed at the RNA-level. Both introns were perfectly removed by autocatalytic splicing, but COI-884 excision appeared more efficient than ND5-717. ND5-717 was organized into giant group I intron elements of 18.1 kb and 19.3 kb in A. fenestrafer and R. yuma, respectively. The intron harbored almost the entire mitochondrial genome embedded within the P8 peripheral segment. Conclusion ND5-717 was removed by group I intron splicing from a small primary transcript that contained a permutated intron–exon arrangement. The splicing pathway involved a circular exon-containing RNA intermediate, which is a hallmark of RNA back-splicing. ND5-717 represents the first reported natural group I intron that becomes excised by back-splicing from a permuted precursor RNA. Back-splicing may explain why Corallimorpharia mitochondrial genomes tolerate giant group I introns. Electronic supplementary material The online version of this article (10.1186/s12867-019-0134-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sylvia Ighem Chi
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Mikael Dahl
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Åse Emblem
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Steinar D Johansen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway. .,Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
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13
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Circular RNAs in gynecological disease: promising biomarkers and diagnostic targets. Biosci Rep 2019; 39:BSR20181641. [PMID: 30996117 PMCID: PMC6522738 DOI: 10.1042/bsr20181641] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 03/28/2019] [Accepted: 04/14/2019] [Indexed: 12/15/2022] Open
Abstract
Circular RNAs (circRNAs) are a category of RNA molecules with covalently closed circles lacking both a 5′ cap and a 3′ tail. In recent years, circRNAs have attracted much attention and become a research hotspot of the RNA field following miRNAs and lncRNAs. CircRNAs exhibit tissue specificity, structural stability, and evolutionary conservation. Although the biological effects of circRNAs are still underestimated, many studies have shown that circRNAs have functions including regulation of transcription, translation into proteins and miRNA sponges. In this review, we briefly described the biogenesis and function of circRNAs and present circular transcripts in gynecological disease.
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Holdt LM, Kohlmaier A, Teupser D. Molecular functions and specific roles of circRNAs in the cardiovascular system. Noncoding RNA Res 2018; 3:75-98. [PMID: 30159442 PMCID: PMC6096412 DOI: 10.1016/j.ncrna.2018.05.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/11/2018] [Accepted: 05/11/2018] [Indexed: 12/25/2022] Open
Abstract
As part of the superfamily of long noncoding RNAs, circular RNAs (circRNAs) are emerging as a new type of regulatory molecules that partake in gene expression control. Here, we review the current knowledge about circRNAs in cardiovascular disease. CircRNAs are not only associated with different types of cardiovascular disease, but they have also been identified as intracellular effector molecules for pathophysiological changes in cardiovascular tissues, and as cardiovascular biomarkers. This evidence is put in the context of the current understanding of general circRNA biogenesis and of known interactions of circRNAs with DNA, RNA, and proteins.
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Affiliation(s)
- Lesca M. Holdt
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Germany
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15
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Soslau G. Circular RNA (circRNA) was an important bridge in the switch from the RNA world to the DNA world. J Theor Biol 2018; 447:32-40. [PMID: 29567323 DOI: 10.1016/j.jtbi.2018.03.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/10/2018] [Accepted: 03/14/2018] [Indexed: 12/01/2022]
Abstract
The concept that life on Earth began as an RNA world has been built upon extensive experimentation demonstrating that many of the building blocks required for living cells could be synthesized in the laboratory under conditions approximating our primordial world. Many of the building blocks for life have also been found in meteorites indicating that meteors may have been a source for these molecules, or more likely, that they represent the chemical library present in most/all bodies in the universe after the big bang. Perhaps the most important support for the concept comes from the fact that some RNA species possess catalytic activity, ribozymes, and that RNA could be reverse transcribe to DNA. The thrust of numerous papers on this topic has been to explore how the available molecules on Earth, at its birth, gave rise to life as we know it today. This paper focuses more on a reverse view of the topic. The "how" molecular building blocks were synthesized is not addressed nor how the "first" RNA molecules were synthesized. We can clearly speculate on the variable environmental conditions and chemistry available on Earth billions of years ago. However, we can never truly replicate the changing conditions or know the chemical composition of Earth at the beginning of time. We can, however, confirm that over millions, perhaps billions of years the basic building blocks for life accumulated sufficiently to initiate evolution to an RNA world followed by our RNA/DNA world. Here we are attempting to take the information from our current knowledge of biology and by inference and extrapolation work backward to hypothesize biological events in the march forward from RNA to DNA. It is proposed that the primordial replicating RNA cell, the ribocyte, evolved from liposomes encompassing required reactants and products for "life" and that ribonucleopeptide complexes formed membrane pores to support bidirectional ion and molecular transport to maintain biological functions and osmolarity. Circular RNA, circRNA, is proposed as a critical stable RNA molecule that served as the genetic precursor for the switch to DNA and the replication of circRNA by a rolling circle mechanism gave rise to the RNA complexity required for the genetic functions of the cell. The replicating ribocyte would have required protein synthesis as well as RNA replication and a model for non-coded and primordial coded protein synthesis is proposed. Finally, the switch from the RNA to the DNA world would have involved the synthesis of an RNA:DNA hybrid prior to the formation of dsDNA. If the hybrid was a circular molecule that ultimately yielded a circular dsDNA molecule, it could predict that the primordial DNA cell would evolve into a bacterial cell with a single circular chromosome. One would hope that continued speculation of the origin of life will spur new directions of research that may never fully answer the questions of the past but add to our ability to regulate potentially harmful biological events in the present and in the future.
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Affiliation(s)
- Gerald Soslau
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th ST, Philadelphia, PA 19102, United States.
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16
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Holdt LM, Kohlmaier A, Teupser D. Molecular roles and function of circular RNAs in eukaryotic cells. Cell Mol Life Sci 2018; 75:1071-1098. [PMID: 29116363 PMCID: PMC5814467 DOI: 10.1007/s00018-017-2688-5] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/29/2017] [Accepted: 10/17/2017] [Indexed: 12/27/2022]
Abstract
Protein-coding and noncoding genes in eukaryotes are typically expressed as linear messenger RNAs, with exons arranged colinearly to their genomic order. Recent advances in sequencing and in mapping RNA reads to reference genomes have revealed that thousands of genes express also covalently closed circular RNAs. Many of these circRNAs are stable and contain exons, but are not translated into proteins. Here, we review the emerging understanding that both, circRNAs produced by co- and posttranscriptional head-to-tail "backsplicing" of a downstream splice donor to a more upstream splice acceptor, as well as circRNAs generated from intronic lariats during colinear splicing, may exhibit physiologically relevant regulatory functions in eukaryotes. We describe how circRNAs impact gene expression of their host gene locus by affecting transcriptional initiation and elongation or splicing, and how they partake in controlling the function of other molecules, for example by interacting with microRNAs and proteins. We conclude with an outlook how circRNA dysregulation affects disease, and how the stability of circRNAs might be exploited in biomedical applications.
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Affiliation(s)
- Lesca M Holdt
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany.
| | - Alexander Kohlmaier
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- Faculty of Biology, Genetics, LMU Munich, Großhaderner Str. 2-4, 82152, Martinsried, Germany
| | - Daniel Teupser
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
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17
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Beermann J, Piccoli MT, Viereck J, Thum T. Non-coding RNAs in Development and Disease: Background, Mechanisms, and Therapeutic Approaches. Physiol Rev 2017; 96:1297-325. [PMID: 27535639 DOI: 10.1152/physrev.00041.2015] [Citation(s) in RCA: 1262] [Impact Index Per Article: 180.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Advances in RNA-sequencing techniques have led to the discovery of thousands of non-coding transcripts with unknown function. There are several types of non-coding linear RNAs such as microRNAs (miRNA) and long non-coding RNAs (lncRNA), as well as circular RNAs (circRNA) consisting of a closed continuous loop. This review guides the reader through important aspects of non-coding RNA biology. This includes their biogenesis, mode of actions, physiological function, as well as their role in the disease context (such as in cancer or the cardiovascular system). We specifically focus on non-coding RNAs as potential therapeutic targets and diagnostic biomarkers.
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Affiliation(s)
- Julia Beermann
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany; and National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Maria-Teresa Piccoli
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany; and National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Janika Viereck
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany; and National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany; and National Heart and Lung Institute, Imperial College London, London, United Kingdom
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18
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Andersen KL, Beckert B, Masquida B, Johansen SD, Nielsen H. Accumulation of Stable Full-Length Circular Group I Intron RNAs during Heat-Shock. Molecules 2016; 21:molecules21111451. [PMID: 27809244 PMCID: PMC6274462 DOI: 10.3390/molecules21111451] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 02/07/2023] Open
Abstract
Group I introns in nuclear ribosomal RNA of eukaryotic microorganisms are processed by splicing or circularization. The latter results in formation of full-length circular introns without ligation of the exons and has been proposed to be active in intron mobility. We applied qRT-PCR to estimate the copy number of circular intron RNA from the myxomycete Didymium iridis. In exponentially growing amoebae, the circular introns are nuclear and found in 70 copies per cell. During heat-shock, the circular form is up-regulated to more than 500 copies per cell. The intron harbours two ribozymes that have the potential to linearize the circle. To understand the structural features that maintain circle integrity, we performed chemical and enzymatic probing of the splicing ribozyme combined with molecular modeling to arrive at models of the inactive circular form and its active linear counterpart. We show that the two forms have the same overall structure but differ in key parts, including the catalytic core element P7 and the junctions at which reactions take place. These differences explain the relative stability of the circular species, demonstrate how it is prone to react with a target molecule for circle integration and thus supports the notion that the circular form is a biologically significant molecule possibly with a role in intron mobility.
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Affiliation(s)
- Kasper L Andersen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
| | - Bertrand Beckert
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
- Molecular Genetics Genomics Microbiology, Université de Strasbourg, CNRS, UMR 7156, Strasbourg 67081, France.
| | - Benoit Masquida
- Molecular Genetics Genomics Microbiology, Université de Strasbourg, CNRS, UMR 7156, Strasbourg 67081, France.
| | - Steinar D Johansen
- Department of Medical Biology, UiT, The Arctic University of Norway, Tromsø N-9037, Norway.
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
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Abstract
Non-coding RNAs have gained increasing attention, as their physiological and pathological functions are being gradually uncovered. MicroRNAs are the most well-studied ncRNAs, which play essential roles in translational repression and mRNA degradation. In contrast, long non-coding RNAs are distinguished from other small/short non-coding RNAs by length and regulate chromatin remodeling, gene transcription and posttranscriptional modifications. Recently, circular RNAs have emerged as endogenous, abundant, conserved and stable in mammalian cells. It has been demonstrated that circular RNAs can function as miRNA sponges. Other possible biological functions of circular RNAs are still under investigation. In this review, the biogenesis and biological functions of the three major types of ncRNAs, including miRNAs, lncRNAs and circRNAs, are overviewed. In addition, the role of ncRNAs in human diseases and potential clinical applications of ncRNAs are discussed.
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Affiliation(s)
- Nan Wu
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Burton B Yang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
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20
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Petkovic S, Müller S. RNA circularization strategies in vivo and in vitro. Nucleic Acids Res 2015; 43:2454-65. [PMID: 25662225 PMCID: PMC4344496 DOI: 10.1093/nar/gkv045] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 01/07/2015] [Accepted: 01/12/2015] [Indexed: 12/30/2022] Open
Abstract
In the plenitude of naturally occurring RNAs, circular RNAs (circRNAs) and their biological role were underestimated for years. However, circRNAs are ubiquitous in all domains of life, including eukaryotes, archaea, bacteria and viruses, where they can fulfill diverse biological functions. Some of those functions, as for example playing a role in the life cycle of viral and viroid genomes or in the maturation of tRNA genes, have been elucidated; other putative functions still remain elusive. Due to the resistance to exonucleases, circRNAs are promising tools for in vivo application as aptamers, trans-cleaving ribozymes or siRNAs. How are circRNAs generated in vivo and what approaches do exist to produce ring-shaped RNAs in vitro? In this review we illustrate the occurrence and mechanisms of RNA circularization in vivo, survey methods for the generation of circRNA in vitro and provide appropriate protocols.
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Affiliation(s)
- Sonja Petkovic
- Institut für Biochemie, Ernst Moritz Arndt Universität Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Ernst Moritz Arndt Universität Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
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21
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Hassall J, MacDonald P, Cordero T, Rostain W, Jaramillo A. Design and Characterization of Topological Small RNAs. Methods Mol Biol 2015; 1316:149-167. [PMID: 25967060 DOI: 10.1007/978-1-4939-2730-2_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
RNA can self-assemble into complex structures through base pairing, as well as encode information and bind with proteins to induce enzymatic activity. Furthermore, RNA can possess intrinsic enzymatic-like (ribozymatic) activity, a property that, if necessary, can be activated only upon the binding of a small molecule or another RNA (as is the case in aptazymes). As such, RNA could be of use in nanotechnology as a programmable polymer capable of self-assembling into complex topological structures. In this chapter we describe a method for designing advanced topological structures using self-circulating RNA, exemplified by three tiers of topologically manipulated self-assembling synthetic RNA systems. The first tier of topological manipulation, the RNA knot is a physically locked structure, formed by circularizing one monomer of knotted single-stranded RNA left with loose ends (an "open" knot). The second tier, a two interlocking ring system, is made by interlocking two circular RNA components: a circular RNA target, and an RNA lasso designed to intercalate the target before circularizing. The third tier naturally extends this system into a string of topologically locked circular RNA molecules (an RNA chain). We detail the methodology used for designing such topologically complex RNAs, including computational predictions of secondary structure, and where appropriate, RNA-RNA interactions, illustrated by examples. We then describe the experimental methods used for characterizing such structures, and provide sequences of building blocks that can be used for topological manipulation of RNA.
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Affiliation(s)
- Jack Hassall
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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22
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Abstract
It is now clear that there is a diversity of circular RNAs in biological systems. Circular RNAs can be produced by the direct ligation of 5' and 3' ends of linear RNAs, as intermediates in RNA processing reactions, or by "backsplicing," wherein a downstream 5' splice site (splice donor) is joined to an upstream 3' splice site (splice acceptor). Circular RNAs have unique properties including the potential for rolling circle amplification of RNA, the ability to rearrange the order of genomic information, protection from exonucleases, and constraints on RNA folding. Circular RNAs can function as templates for viroid and viral replication, as intermediates in RNA processing reactions, as regulators of transcription in cis, as snoRNAs, and as miRNA sponges. Herein, we review the breadth of circular RNAs, their biogenesis and metabolism, and their known and anticipated functions.
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Affiliation(s)
- Erika Lasda
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Roy Parker
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado 80309, USA
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23
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Tang Y, Nielsen H, Masquida B, Gardner PP, Johansen SD. Molecular characterization of a new member of the lariat capping twin-ribozyme introns. Mob DNA 2014; 5:25. [PMID: 25342998 PMCID: PMC4167309 DOI: 10.1186/1759-8753-5-25] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/03/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Twin-ribozyme introns represent a complex class of mobile group I introns that harbour a lariat capping (LC) ribozyme and a homing endonuclease gene embedded in a conventional self-splicing group I ribozyme (GIR2). Twin-ribozyme introns have so far been confined to nucleolar DNA in Naegleria amoeboflagellates and the myxomycete Didymium iridis. RESULTS We characterize structural organization, catalytic properties and molecular evolution of a new twin-ribozyme intron in Allovahlkampfia (Heterolobosea). The intron contains two ribozyme domains with different functions in ribosomal RNA splicing and homing endonuclease mRNA maturation. We found Allovahlkampfia GIR2 to be a typical group IC1 splicing ribozyme responsible for addition of the exogenous guanosine cofactor (exoG), exon ligation and circularization of intron RNA. The Allovahlkampfia LC ribozyme, by contrast, represents an efficient self-cleaving ribozyme that generates a small 2',5' lariat cap at the 5' end of the homing endonuclease mRNA, and thus contributes to intron mobility. CONCLUSIONS The discovery of a twin-ribozyme intron in a member of Heterolobosea expands the distribution pattern of LC ribozymes. We identify a putative regulatory RNA element (AP2.1) in the Allovahlkampfia LC ribozyme that involves homing endonuclease mRNA coding sequences as an important structural component.
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Affiliation(s)
- Yunjia Tang
- RNA and Molecular Pathology group, Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, MH-building Breivika, N-9037 Tromsø, Norway
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Benoît Masquida
- Génétique Moléculaire, Génomique, Microbiologie, IPCB, Université de Strasbourg, CNRS, Strasbourg, France
| | - Paul P Gardner
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Steinar D Johansen
- RNA and Molecular Pathology group, Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, MH-building Breivika, N-9037 Tromsø, Norway
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24
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Abstract
The lariat-capping (LC) ribozyme is a natural ribozyme isolated from eukaryotic microorganisms. Despite apparent structural similarity to group I introns, the LC ribozyme catalyzes cleavage by a 2',5' branching reaction, leaving the 3' product with a 3-nt lariat cap that functionally substitutes for a conventional mRNA cap in the downstream pre-mRNA encoding a homing endonuclease. We describe the crystal structures of the precleavage and postcleavage LC ribozymes, which suggest that structural features inherited from group I ribozymes have undergone speciation due to profound changes in molecular selection pressure, ultimately giving rise to an original branching ribozyme family. The structures elucidate the role of key elements that regulate the activity of the LC ribozyme by conformational switching and suggest a mechanism by which the signal for branching is transmitted to the catalytic core. The structures also show how conserved interactions twist residues, forming the lariat to join chemical groups involved in branching.
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25
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Dalby SJ, Bonen L. Impact of low temperature on splicing of atypical group II introns in wheat mitochondria. Mitochondrion 2013; 13:647-55. [PMID: 24056090 DOI: 10.1016/j.mito.2013.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/14/2013] [Accepted: 09/06/2013] [Indexed: 12/31/2022]
Abstract
To investigate the impact of cold on group II intron splicing, we compared the physical forms of excised mitochondrial introns from wheat embryos germinated at room temperature and 4°C. For introns which deviate from the conventional branchpoint structure, we observed predominantly heterogeneous circularized introns in the cold rather than linear polyadenylated forms arising from a hydrolytic pathway as seen at room temperature. In addition, intron-containing precursors are elevated relative to mature mRNAs upon cold treatment. Our findings indicate that low temperature growth not only reduces splicing efficiency, but also shifts the splicing biochemistry of atypical group II introns to novel, yet productive, pathways.
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Affiliation(s)
- Stephen J Dalby
- Biology Department, University of Ottawa, Ottawa K1N 6N5, Canada
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26
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Hedberg A, Johansen SD. Nuclear group I introns in self-splicing and beyond. Mob DNA 2013; 4:17. [PMID: 23738941 PMCID: PMC3679873 DOI: 10.1186/1759-8753-4-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 05/14/2013] [Indexed: 01/09/2023] Open
Abstract
Group I introns are a distinct class of RNA self-splicing introns with an ancient origin. All known group I introns present in eukaryote nuclei interrupt functional ribosomal RNA genes located in ribosomal DNA loci. The discovery of the Tetrahymena intron more than 30 years ago has been essential to our understanding of group I intron catalysis, higher-order RNA structure, and RNA folding, but other intron models have provided information about the biological role. Nuclear group I introns appear widespread among eukaryotic microorganisms, and the plasmodial slime molds (myxomycetes) contain an abundance of self-splicing introns. Here, we summarize the main conclusions from previous work on the Tetrahymena intron on RNA self-splicing catalysis as well as more recent work on myxomycete intron biology. Group I introns in myxomycetes that represent different evolutionary stages, biological roles, and functional settings are discussed.
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Affiliation(s)
- Annica Hedberg
- RNA lab-RAMP, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø N-9037, Norway.
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27
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Gupta AK, Panigrahi SK, Bhattacharya A, Bhattacharya S. Self-circularizing 5'-ETS RNAs accumulate along with unprocessed pre ribosomal RNAs in growth-stressed Entamoeba histolytica. Sci Rep 2012; 2:303. [PMID: 22396851 PMCID: PMC3294279 DOI: 10.1038/srep00303] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 02/15/2012] [Indexed: 01/13/2023] Open
Abstract
The primary transcript of rRNA genes is a large pre rRNA which is precisely processed to release the mature rRNAs. The 5'-external transcribed spacer (ETS) of rRNA genes contains important sites for pre rRNA processing. Once the processing is accomplished the ETS is rapidly degraded. We show that in growth-stressed cells of the human parasitic protist Entamoeba histolytica the A'-A(0) sub-fragment of the 5'-ETS accumulates to high levels as a family of RNA molecules of size 666 to 912 nt. These etsRNAs are circular in vivo and can spontaneously self-circularize in vitro. The accumulation of etsRNAs is accompanied by accumulation of unprocessed pre rRNA, indicating a possible role of etsRNAs in inhibition of processing during growth stress. Our data shows for the first time that processed etsRNA is not a mere by-product destined for degradation but is stabilized by circularization and could play a regulatory role as noncoding RNA.
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28
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Danan M, Schwartz S, Edelheit S, Sorek R. Transcriptome-wide discovery of circular RNAs in Archaea. Nucleic Acids Res 2011; 40:3131-42. [PMID: 22140119 PMCID: PMC3326292 DOI: 10.1093/nar/gkr1009] [Citation(s) in RCA: 433] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Circular RNA forms had been described in all domains of life. Such RNAs were shown to have diverse biological functions, including roles in the life cycle of viral and viroid genomes, and in maturation of permuted tRNA genes. Despite their potentially important biological roles, discovery of circular RNAs has so far been mostly serendipitous. We have developed circRNA-seq, a combined experimental/computational approach that enriches for circular RNAs and allows profiling their prevalence in a whole-genome, unbiased manner. Application of this approach to the archaeon Sulfolobus solfataricus P2 revealed multiple circular transcripts, a subset of which was further validated independently. The identified circular RNAs included expected forms, such as excised tRNA introns and rRNA processing intermediates, but were also enriched with non-coding RNAs, including C/D box RNAs and RNase P, as well as circular RNAs of unknown function. Many of the identified circles were conserved in Sulfolobus acidocaldarius, further supporting their functional significance. Our results suggest that circular RNAs, and particularly circular non-coding RNAs, are more prevalent in archaea than previously recognized, and might have yet unidentified biological roles. Our study establishes a specific and sensitive approach for identification of circular RNAs using RNA-seq, and can readily be applied to other organisms.
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Affiliation(s)
- Miri Danan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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29
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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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30
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Group I introns and inteins: disparate origins but convergent parasitic strategies. J Bacteriol 2009; 191:6193-202. [PMID: 19666710 DOI: 10.1128/jb.00675-09] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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31
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Vicens Q, Cech TR. A natural ribozyme with 3',5' RNA ligase activity. Nat Chem Biol 2009; 5:97-9. [PMID: 19125157 PMCID: PMC2897744 DOI: 10.1038/nchembio.136] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 12/08/2008] [Indexed: 01/10/2023]
Abstract
Using electrophoresis, sequencing and enzymatic digestion, we show that the group I intron from the cyanobacterium Anabaena sp. PCC 7120 catalyzes phosphodiester bond formation using a triphosphate on the 5'-terminal nucleotide, much like protein polymerases and engineered ribozymes. In the process, this ribozyme forms a unique circular RNA that incorporates the exogenous guanosine cofactor added during self-splicing. This finding may have relevance to a prebiotic RNA world and to modern biology.
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Affiliation(s)
- Quentin Vicens
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, UCB 215, Boulder, Colorado 80309-0215, USA.
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32
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Vicens Q, Paukstelis PJ, Westhof E, Lambowitz AM, Cech TR. Toward predicting self-splicing and protein-facilitated splicing of group I introns. RNA (NEW YORK, N.Y.) 2008; 14:2013-2029. [PMID: 18768647 PMCID: PMC2553746 DOI: 10.1261/rna.1027208] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2008] [Accepted: 07/08/2008] [Indexed: 05/26/2023]
Abstract
In the current era of massive discoveries of noncoding RNAs within genomes, being able to infer a function from a nucleotide sequence is of paramount interest. Although studies of individual group I introns have identified self-splicing and nonself-splicing examples, there is no overall understanding of the prevalence of self-splicing or the factors that determine it among the >2300 group I introns sequenced to date. Here, the self-splicing activities of 12 group I introns from various organisms were assayed under six reaction conditions that had been shown previously to promote RNA catalysis for different RNAs. Besides revealing that assessing self-splicing under only one condition can be misleading, this survey emphasizes that in vitro self-splicing efficiency is correlated with the GC content of the intron (>35% GC was generally conductive to self-splicing), and with the ability of the introns to form particular tertiary interactions. Addition of the Neurospora crassa CYT-18 protein activated splicing of two nonself-splicing introns, but inhibited the second step of self-splicing for two others. Together, correlations between sequence, predicted structure and splicing begin to establish rules that should facilitate our ability to predict the self-splicing activity of any group I intron from its sequence.
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Affiliation(s)
- Quentin Vicens
- Howard Hughes Medical Institute, University of Colorado, Department of Chemistry and Biochemistry, Boulder, Colorado 80309-0215, USA.
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Dotson PP, Sinha J, Testa SM. Kinetic characterization of the first step of the ribozyme-catalyzed trans excision-splicing reaction. FEBS J 2008; 275:3110-22. [PMID: 18479464 DOI: 10.1111/j.1742-4658.2008.06464.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Group I introns catalyze the self-splicing reaction, and their derived ribozymes are frequently used as model systems for the study of RNA folding and catalysis, as well as for the development of non-native catalytic reactions. Utilizing a group I intron-derived ribozyme from Pneumocystis carinii, we previously reported a non-native reaction termed trans excision-splicing (TES). In this reaction, an internal segment of RNA is excised from an RNA substrate, resulting in the covalent reattachment of the flanking regions. TES proceeds through two consecutive phosphotransesterification reactions, which are similar to the reaction steps of self-splicing. One key difference is that TES utilizes the 3'-terminal guanosine of the ribozyme as the first-step nucleophile, whereas self-splicing utilizes an exogenous guanosine. To further aid in our understanding of ribozyme reactions, a kinetic framework for the first reaction step (substrate cleavage) was established. The results demonstrate that the substrate binds to the ribozyme at a rate expected for simple helix formation. In addition, the rate constant for the first step of the TES reaction is more than one order of magnitude lower than the analogous step in self-splicing. Results also suggest that a conformational change, likely similar to that in self-splicing, exists between the two reaction steps of TES. Finally, multiple turnover is curtailed because dissociation of the cleavage product is slower than the rate of chemistry.
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Affiliation(s)
- P Patrick Dotson
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
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Sethuraman J, Okoli CV, Majer A, Corkery TLC, Hausner G. The sporadic occurrence of a group I intron-like element in the mtDNA rnl gene of Ophiostoma novo-ulmi subsp. americana. ACTA ACUST UNITED AC 2007; 112:564-82. [PMID: 18406119 DOI: 10.1016/j.mycres.2007.11.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Revised: 07/20/2007] [Accepted: 11/29/2007] [Indexed: 11/16/2022]
Abstract
The presence of group I intron-like elements within the U7 region of the mtDNA large ribosomal subunit RNA gene (rnl) was investigated in strains of Ophiostoma novo-ulmi subsp. americana from Canada, Europe and Eurasia, and in selected strains of O. ips, O. minus, O. piceae, O. ulmi, and O. himal-ulmi. This insertion is of interest as it has been linked previously to the generation of plasmid-like mtDNA elements in diseased strains of O. novo-ulmi. Among 197 O. novo-ulmi subsp. americana strains tested, 61 contained a 1.6kb insertion within the rnl-U7 region and DNA sequence analysis suggests the presence of a group I intron (IA1 type) that encodes a potential double motif LAGLIDADG homing endonuclease-like gene (HEG). Phylogenetic analysis of rnl-U7 intron encoded HEG-like elements supports the view that double motif HEGs originated from a duplication event of a single-motif HEG followed by a fusion event that combined the two copies into one open reading frame (ORF). The data also show that rnl-U7 intron encoded ORFs belong to a clade that includes ORFs inserted into different types of group I introns, e.g. IB, ID, IC3, IA1, present within a variety of different mtDNA genes, such as the small ribosomal subunit RNA gene (rns), apo-cytochrome b gene (cob), NADH dehydrogenase subunit 5 (nad5), cytochrome oxidase subunit 1 gene (coxI), and ATPase subunit 9 gene (atp9). We also compared the occurrence of the rnl-U7 intron in our collection of 227 strains with the presence of the rnl-U11 group I intron and concluded that the U7 intron appears to be an optional element and the U11 intron is probably essential among the strains tested.
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Affiliation(s)
- Jyothi Sethuraman
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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Haugen P, Bhattacharya D, Palmer JD, Turner S, Lewis LA, Pryer KM. Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns. BMC Evol Biol 2007; 7:159. [PMID: 17825109 PMCID: PMC1995217 DOI: 10.1186/1471-2148-7-159] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Accepted: 09/08/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Group I introns are one of the four major classes of introns as defined by their distinct splicing mechanisms. Because they catalyze their own removal from precursor transcripts, group I introns are referred to as autocatalytic introns. Group I introns are common in fungal and protist nuclear ribosomal RNA genes and in organellar genomes. In contrast, they are rare in all other organisms and genomes, including bacteria. RESULTS Here we report five group I introns, each containing a LAGLIDADG homing endonuclease gene (HEG), in large subunit (LSU) rRNA genes of cyanobacteria. Three of the introns are located in the LSU gene of Synechococcus sp. C9, and the other two are in the LSU gene of Synechococcus lividus strain C1. Phylogenetic analyses show that these introns and their HEGs are closely related to introns and HEGs located at homologous insertion sites in organellar and bacterial rDNA genes. We also present a compilation of group I introns with homing endonuclease genes in bacteria. CONCLUSION We have discovered multiple HEG-containing group I introns in a single bacterial gene. To our knowledge, these are the first cases of multiple group I introns in the same bacterial gene (multiple group I introns have been reported in at least one phage gene and one prophage gene). The HEGs each contain one copy of the LAGLIDADG motif and presumably function as homodimers. Phylogenetic analysis, in conjunction with their patchy taxonomic distribution, suggests that these intron-HEG elements have been transferred horizontally among organelles and bacteria. However, the mode of transfer and the nature of the biological connections among the intron-containing organisms are unknown.
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Affiliation(s)
- Peik Haugen
- Department of Biological Sciences and Roy J. Carver Center for Comparative Genomics, University of Iowa, 446 Biology Building, Iowa City, IA 52242, USA
- Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, N-9037 Tromsø, Norway
| | - Debashish Bhattacharya
- Department of Biological Sciences and Roy J. Carver Center for Comparative Genomics, University of Iowa, 446 Biology Building, Iowa City, IA 52242, USA
| | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Seán Turner
- National Center for Biotechnology Information, National Institutes of Health, 45 Center Drive, MSC 6510, Bethesda, MD 20892, USA
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, The University of Connecticut, Storrs, CT 06269, USA
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Johansen SD, Haugen P, Nielsen H. Expression of protein-coding genes embedded in ribosomal DNA. Biol Chem 2007; 388:679-86. [PMID: 17570819 DOI: 10.1515/bc.2007.089] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Ribosomal DNA (rDNA) is a specialised chromosomal location that is dedicated to high-level transcription of ribosomal RNA genes. Interestingly, rDNAs are frequently interrupted by parasitic elements, some of which carry protein genes. These are non-LTR retrotransposons and group II introns that encode reverse transcriptase-like genes, and group I introns and archaeal introns that encode homing endonuclease genes (HEGs). Although rDNA-embedded protein genes are widespread in nuclei, organelles and bacteria, there is surprisingly little information available on how these genes are expressed. Exceptions include a handful of HEGs from group I introns. Recent studies have revealed unusual and essential roles of group I and group I-like ribozymes in the endogenous expression of HEGs. Here we discuss general aspects of rDNA-embedded protein genes and focus on HEG expression from group I introns in the nucleolus.
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Affiliation(s)
- Steinar D Johansen
- Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, Tromsø, Norway.
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Fiskaa T, Lundblad EW, Henriksen JR, Johansen SD, Einvik C. RNA reprogramming of α-mannosidase mRNA sequencesin vitroby myxomycete group IC1 and IE ribozymes. FEBS J 2006; 273:2789-800. [PMID: 16817905 DOI: 10.1111/j.1742-4658.2006.05295.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Trans-splicing group I ribozymes have been introduced in order to mediate RNA reprogramming (including RNA repair) of therapeutically relevant RNA transcripts. Efficient RNA reprogramming depends on the appropriate efficiency of the reaction, and several attempts, including optimization of target recognition and ribozyme catalysis, have been performed. In most studies, the Tetrahymena group IC1 ribozyme has been applied. Here we investigate the potential of group IC1 and group IE intron ribozymes, derived from the myxomycetes Didymium and Fuligo, in addition to the Tetrahymena ribozyme, for RNA reprogramming of a mutated alpha-mannosidase mRNA sequence. Randomized internal guide sequences were introduced for all four ribozymes and used to select accessible sites within isolated mutant alpha-mannosidase mRNA from mammalian COS-7 cells. Two accessible sites common to all the group I ribozymes were identified and further investigated in RNA reprogramming by trans-splicing analyses. All the myxomycete ribozymes performed the trans-splicing reaction with high fidelity, resulting in the conversion of mutated alpha-mannosidase RNA into wild-type sequence. RNA protection analysis revealed that the myxomycete ribozymes perform trans-splicing at approximately similar efficiencies as the Tetrahymena ribozyme. Interestingly, the relative efficiency among the ribozymes tested correlates with structural features of the P4-P6-folding domain, consistent with the fact that efficient folding is essential for group I intron trans-splicing.
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Affiliation(s)
- Tonje Fiskaa
- Department of Molecular Biotechnology, RNA Research group, Institute of Medical Biology, University of Tromsø, Norway
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38
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Wikmark OG, Einvik C, De Jonckheere JF, Johansen SD. Short-term sequence evolution and vertical inheritance of the Naegleria twin-ribozyme group I intron. BMC Evol Biol 2006; 6:39. [PMID: 16670006 PMCID: PMC1464144 DOI: 10.1186/1471-2148-6-39] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2005] [Accepted: 05/02/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ribosomal DNA of several species of the free-living Naegleria amoeba harbors an optional group I intron within the nuclear small subunit ribosomal RNA gene. The intron (Nae.S516) has a complex organization of two ribozyme domains (NaGIR1 and NaGIR2) and a homing endonuclease gene (NaHEG). NaGIR2 is responsible for intron excision, exon ligation, and full-length intron RNA circularization, reactions typical for nuclear group I intron ribozymes. NaGIR1, however, is essential for NaHEG expression by generating the 5' end of the homing endonuclease messenger RNA. Interestingly, this unusual class of ribozyme adds a lariat-cap at the mRNA. RESULTS To elucidate the evolutionary history of the Nae.S516 twin-ribozyme introns we have analyzed 13 natural variants present in distinct Naegleria isolates. Structural variabilities were noted within both the ribozyme domains and provide strong comparative support to the intron secondary structure. One of the introns, present in N. martinezi NG872, contains hallmarks of a degenerated NaHEG. Phylogenetic analyses performed on separate data sets representing NaGIR1, NaGIR2, NaHEG, and ITS1-5.8S-ITS2 ribosomal DNA are consistent with an overall vertical inheritance pattern of the intron within the Naegleria genus. CONCLUSION The Nae.S516 twin-ribozyme intron was gained early in the Naegleria evolution with subsequent vertical inheritance. The intron was lost in the majority of isolates (70%), leaving a widespread but scattered distribution pattern. Why the apparent asexual Naegleria amoebae harbors active intron homing endonucleases, dependent on sexual reproduction for its function, remains a puzzle.
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Affiliation(s)
- Odd-Gunnar Wikmark
- Department of Molecular Biotechnology, RNA Research Group, Institute of Medical Biology, University of Tromsø, N-9037 Tromsø, Norway
| | - Christer Einvik
- Department of Molecular Biotechnology, RNA Research Group, Institute of Medical Biology, University of Tromsø, N-9037 Tromsø, Norway
- Department of Pediatrics, University Hospital of North Norway, N-9038 Tromsø, Norway
| | - Johan F De Jonckheere
- Protozoology Laboratory, Scientific Institute Public Health, B1050 Brussels, Belgium
| | - Steinar D Johansen
- Department of Molecular Biotechnology, RNA Research Group, Institute of Medical Biology, University of Tromsø, N-9037 Tromsø, Norway
- Department of Fisheries and Natural Sciences, Bodø University College, N-8049 Bodø, Norway
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Hofacker IL, Stadler PF. Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics 2006; 22:1172-6. [PMID: 16452114 DOI: 10.1093/bioinformatics/btl023] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND A small class of RNA molecules, in particular the tiny genomes of viroids, are circular. Yet most structure prediction algorithms handle only linear RNAs. The most straightforward approach is to compute circular structures from 'internal' and 'external' substructures separated by a base pair. This is incompatible, however, with the memory-saving approach of the Vienna RNA Package which builds a linear RNA structure from shorter (internal) structures only. RESULT Here we describe how circular secondary structures can be obtained without additional memory requirements as a kind of 'post-processing' of the linear structures. AVAILABILITY The circular folding algorithm is implemented in the current version of the of RNAfold program of the Vienna RNA Package, which can be downloaded from http://www.tbi.univie.ac.at/RNA/
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Affiliation(s)
- Ivo L Hofacker
- Institute for Theoretical Chemistry, University of Vienna Währingerstr. 17, A-1090 Vienna, Austria
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Birgisdottir AB, Johansen SD. Reverse splicing of a mobile twin-ribozyme group I intron into the natural small subunit rRNA insertion site. Biochem Soc Trans 2005; 33:482-4. [PMID: 15916547 DOI: 10.1042/bst0330482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A mobile group I intron containing two ribozyme domains and a homing endonuclease gene (twin-ribozyme intron organization) can integrate by reverse splicing into the small subunit rRNA of bacteria and yeast. The integration is sequence-specific and corresponds to the natural insertion site (homing site) of the intron. The reverse splicing is independent of the homing endonuclease gene, but is dependent on the group I splicing ribozyme domain. The observed distribution of group I introns in nature can be explained by horizontal transfer between natural homing sites by reverse splicing and subsequent spread in populations by endonuclease-dependent homing.
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Affiliation(s)
- A B Birgisdottir
- Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, Tromsø, Norway
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41
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Haugen P, Wikmark OG, Vader A, Coucheron DH, Sjøttem E, Johansen SD. The recent transfer of a homing endonuclease gene. Nucleic Acids Res 2005; 33:2734-41. [PMID: 15891115 PMCID: PMC1110740 DOI: 10.1093/nar/gki564] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The myxomycete Didymium iridis (isolate Panama 2) contains a mobile group I intron named Dir.S956-1 after position 956 in the nuclear small subunit (SSU) rRNA gene. The intron is efficiently spread through homing by the intron-encoded homing endonuclease I-DirI. Homing endonuclease genes (HEGs) usually spread with their associated introns as a unit, but infrequently also spread independent of introns (or inteins). Clear examples of HEG mobility are however sparse. Here, we provide evidence for the transfer of a HEG into a group I intron named Dir.S956-2 that is inserted into the SSU rDNA of the Costa Rica 8 isolate of D.iridis. Similarities between intron sequences that flank the HEG and rDNA sequences that flank the intron (the homing endonuclease recognition sequence) suggest that the HEG invaded the intron during the recent evolution in a homing-like event. Dir.S956-2 is inserted into the same SSU site as Dir.S956-1. Remarkably, the two group I introns encode distantly related splicing ribozymes with phylogenetically related HEGs inserted on the opposite strands of different peripheral loop regions. The HEGs are both interrupted by small spliceosomal introns that must be removed during RNA maturation.
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Affiliation(s)
| | | | | | | | | | - Steinar D. Johansen
- To whom correspondence should be addressed. Tel: +47 77 64 53 67; Fax: +47 77 64 53 50;
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Birgisdottir ÅB, Johansen S. Site-specific reverse splicing of a HEG-containing group I intron in ribosomal RNA. Nucleic Acids Res 2005; 33:2042-51. [PMID: 15817568 PMCID: PMC1074745 DOI: 10.1093/nar/gki341] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The wide, but scattered distribution of group I introns in nature is a result of two processes; the vertical inheritance of introns with or without losses, and the occasional transfer of introns across species barriers. Reversal of the group I intron self-splicing reaction, termed reverse splicing, coupled with reverse transcription and genomic integration potentially mediate an RNA-based intron mobility pathway. Compared to the well characterized endonuclease-mediated intron homing, reverse splicing is less specific and represents a likely explanation for many intron transpositions into new genomic sites. However, the frequency and general role of an RNA-based mobility pathway in the spread of natural group I introns is still unclear. We have used the twin-ribozyme intron (Dir.S956-1) from the myxomycete Didymium iridis to test how a mobile group I intron containing a homing endonuclease gene (HEG) selects between potential insertion sites in the small subunit (SSU) rRNA in vitro, in Escherichia coli and in yeast. Surprisingly, the results show a site-specific RNA-based targeting of Dir.S956-1 into its natural (S956) SSU rRNA site. Our results suggest that reverse splicing, in addition to the established endonuclease-mediated homing mechanism, potentially accounts for group I intron spread into the homologous sites of different strains and species.
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Affiliation(s)
- Åsa B. Birgisdottir
- Department of Molecular Biotechnology, Institute of Medical Biology, University of TromsøN-9037 Tromsø, Norway
| | - Steinar Johansen
- Department of Molecular Biotechnology, Institute of Medical Biology, University of TromsøN-9037 Tromsø, Norway
- Faculty of Fisheries and Natural Sciences, Bodø Regional UniversityN-8049 Bodø, Norway
- To whom correspondence should be addressed. Tel: +47 77 64 53 67; Fax: +47 77 64 53 50;
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Lundblad EW, Haugen P, Johansen SD. Trans-splicing of a mutated glycosylasparaginase mRNA sequence by a group I ribozyme deficient in hydrolysis. ACTA ACUST UNITED AC 2004; 271:4932-8. [PMID: 15606781 DOI: 10.1111/j.1432-1033.2004.04462.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
RNA reprogramming represents a new concept in correcting genetic defects at the RNA level. However, for the technique to be useful for therapy, the level of reprogramming must be appropriate. To improve the efficiency of group I ribozyme-mediated RNA reprogramming, when using the Tetrahymena ribozyme, regions complementary to the target RNA have previously been extended in length and accessible sites in the target RNAs have been identified. As an alternative to the Tetrahymena model ribozyme, the DiGIR2 group I ribozyme, derived from a mobile group I intron in rDNA of the myxomycete Didymium iridis, represents a new and attractive tool in RNA reprogramming. We reported recently that the deletion of a structural element within the P9 domain of DiGIR2 turns off hydrolysis at the 3' splice site (side reaction) without affecting self-splicing [Haugen, P., Andreassen, M., Birgisdottir, A.B. & Johansen, S.D. (2004) Eur. J. Biochem. 271, 1015-1024]. Here we analyze the potential of the modified ribozyme, deficient in hydrolysis at the 3' splice site, for application in group I ribozyme-mediated trans-splicing of RNA. The improved ribozyme catalyses both cis-splicing and trans-splicing in vitro of a human glycosylasparaginase mRNA sequence with the same efficiency as the original DiGIR2 ribozyme, but without detectable levels of the unwanted hydrolysis.
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Affiliation(s)
- Eirik W Lundblad
- Department of Molecular Biotechnology, RNA Research group, Institute of Medical Biology, University of Tromsø, Norway
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Haugen P, Runge HJ, Bhattacharya D. Long-term evolution of the S788 fungal nuclear small subunit rRNA group I introns. RNA (NEW YORK, N.Y.) 2004; 10:1084-96. [PMID: 15208444 PMCID: PMC1370599 DOI: 10.1261/rna.5202704] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
More than 1000 group I introns have been identified in fungal rDNA. Little is known, however, of the splicing and secondary structure evolution of these ribozymes. Here, we use a combination of comparative and biochemical methods to address the evolution and splicing of a vertically inherited group I intron found at position 788 in the fungal small subunit (S) rRNA. The ancestral state of the S788 intron contains a highly conserved core and an extended P5 domain typical of IC1 introns. In contrast, the more derived introns have lost most of P5, and have an accelerated divergence rate within the core region with three functionally important substitutions that unambiguously separate them from the ancestral pool. Of 14 S788 group I introns that were tested for splicing, five, all of the ancestral type, were able to self-splice and produced intron RNA circles in vitro. The more derived S788 introns did not self-splice, and potentially rely on fungal-specific factors to facilitate splicing. In summary, we demonstrate one possible fate of vertically inherited group I introns, the loss of secondary structure elements, lessened selective constraints in the intron core, and ultimately, dependence on host-mediated splicing.
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Affiliation(s)
- Peik Haugen
- Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, 210 Biology Building, Iowa City, IA 52242-1324, USA
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45
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Haugen P, Andreassen M, Birgisdottir AB, Johansen S. Hydrolytic cleavage by a group I intron ribozyme is dependent on RNA structures not important for splicing. ACTA ACUST UNITED AC 2004; 271:1015-24. [PMID: 15009213 DOI: 10.1111/j.1432-1033.2004.04003.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DiGIR2 is the group I splicing-ribozyme of the mobile twin-ribozyme intron Dir.S956-1, present in Didymium nuclear ribosomal DNA. DiGIR2 is responsible for intron excision, exon ligation, 3'-splice site hydrolysis, and full-length intron RNA circle formation. We recently reported that DiGIR2 splicing (intron excision and exon ligation) competes with hydrolysis and subsequent full-length intron circularization. Here we present experimental evidence that hydrolysis at the 3'-splice site in DiGIR2 is dependent on structural elements within the P9 subdomain not involved in splicing. Whereas the GCGA tetra-loop in P9b was found to be important in hydrolytic cleavage, probably due to tertiary RNA-RNA interactions, the P9.2 hairpin structure was found to be essential for hydrolysis. The most important positions in P9.2 include three adenosines in the terminal loop (L9.2) and a consensus kink-turn motif in the proximal stem. We suggest that the L9.2 adenosines and the kink-motif represent key regulatory elements in the splicing and hydrolytic reaction pathways.
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Affiliation(s)
- Peik Haugen
- Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, Norway
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46
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Lundblad EW, Einvik C, Rønning S, Haugli K, Johansen S. Twelve Group I introns in the same pre-rRNA transcript of the myxomycete Fuligo septica: RNA processing and evolution. Mol Biol Evol 2004; 21:1283-93. [PMID: 15034133 DOI: 10.1093/molbev/msh126] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The ribosomal DNA region of the myxomycete Fuligo septica was investigated and found to contain 12 group I introns (four in the small subunit and eight in the large subunit ribosomal RNAs). We have performed molecular and phylogenetic analyses to provide insight into intron structure and function, intron-host biology, and intron origin and evolution. The introns vary in size from 398 to 943 nt, all lacking detectable open reading frames. Secondary structure models revealed considerable structural diversity, but all, except one (subclass IB), represent the common group IC1 intron subclass. In vitro splicing analysis revealed that 10 of the 12 introns were able to self-splice as naked RNA, but all 12 introns were able to splice out from the precursor rRNA in vivo as evaluated by reverse transcription PCR analysis on total F. septica RNA. Furthermore, RNA processing analyses in vitro and in vivo showed that 10 of 12 introns perform hydrolytic cleavage at the 3' splice site, as well as intron circularization. Full-length intron RNA circles were detected in vivo. The order of splicing was analyzed by a reverse transcription PCR approach on cellular RNA, but no strict order of intron excision could be detected. Phylogenetic analysis indicated that most Fuligo introns were distantly related to each other and were independently gained in ribosomal DNA during evolution.
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Affiliation(s)
- Eirik W Lundblad
- Department of Molecular Biotechnology, RNA research group, Institute of Medical Biology, University of Tromso, Tromso, Norway
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