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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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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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Fang X, Jiang Y, Li K, Zeng Q. F-CphI represents a new homing endonuclease family using the Endo VII catalytic motif. Mob DNA 2018; 9:27. [PMID: 30100927 PMCID: PMC6083498 DOI: 10.1186/s13100-018-0132-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/31/2018] [Indexed: 11/16/2022] Open
Abstract
Background There are six known families of homing endonucleases, LAGLIDADG, GIY-YIG, HNH, His-Cys box, PD-(D/E)-XK, and EDxHD, which are characterized by their conserved residues. Previously, we discovered a novel homing endonuclease F-CphI encoded by ORF177 of cyanophage S-PM2. F-CphI does not resemble any characterized homing endonucleases. Instead, the C-terminus of F-CphI aligns well with the N-terminal catalytic domain of a Holliday junction DNA resolvase, phage T4 endonuclease VII (Endo VII). Results A PSI-BLAST search resulted in a total of 313 Endo VII motif–containing sequences in sequenced genomes. Multiple sequence alignment showed that the catalytically important residues of T4 Endo VII were all well conserved in these proteins. Our site-directed mutagenesis studies further confirmed that the catalytically important residues of T4 Endo VII were also essential for F-CphI activity, and thus F-CphI might use a similar protein fold as Endo VII for DNA cleavage. A phylogenetic tree of the Endo VII motif–containing sequences showed that putative resolvases grouped into one clade while putative homing endonucleases and restriction endonucleases grouped into another clade. Conclusions Based on the unique conserved residues, we proposed that F-CphI represents a new homing endonuclease family, which was named the DHHRN family. Our phylogenetic analysis could be used to predict the functions of many previously unknown proteins. Electronic supplementary material The online version of this article (10.1186/s13100-018-0132-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoting Fang
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - YongLiang Jiang
- 2School of Life Sciences, University of Science and Technology of China, Hefei, 230027 Anhui China
| | - Kim Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.,HKUST Shenzhen Research Institute, Shenzhen, China
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4
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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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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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The Naegleria genome: a free-living microbial eukaryote lends unique insights into core eukaryotic cell biology. Res Microbiol 2011; 162:607-18. [PMID: 21392573 DOI: 10.1016/j.resmic.2011.03.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 01/29/2011] [Indexed: 11/24/2022]
Abstract
Naegleria gruberi, a free-living protist, has long been treasured as a model for basal body and flagellar assembly due to its ability to differentiate from crawling amoebae into swimming flagellates. The full genome sequence of Naegleria gruberi has recently been used to estimate gene families ancestral to all eukaryotes and to identify novel aspects of Naegleria biology, including likely facultative anaerobic metabolism, extensive signaling cascades, and evidence for sexuality. Distinctive features of the Naegleria genome and nuclear biology provide unique perspectives for comparative cell biology, including cell division, RNA processing and nucleolar assembly. We highlight here exciting new and novel aspects of Naegleria biology identified through genomic analysis.
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Marcaida MJ, Muñoz IG, Blanco FJ, Prieto J, Montoya G. Homing endonucleases: from basics to therapeutic applications. Cell Mol Life Sci 2010; 67:727-48. [PMID: 19915993 PMCID: PMC11115532 DOI: 10.1007/s00018-009-0188-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Revised: 10/16/2009] [Accepted: 10/19/2009] [Indexed: 10/20/2022]
Abstract
Homing endonucleases (HE) are double-stranded DNAses that target large recognition sites (12-40 bp). HE-encoding sequences are usually embedded in either introns or inteins. Their recognition sites are extremely rare, with none or only a few of these sites present in a mammalian-sized genome. However, these enzymes, unlike standard restriction endonucleases, tolerate some sequence degeneracy within their recognition sequence. Several members of this enzyme family have been used as templates to engineer tools to cleave DNA sequences that differ from their original wild-type targets. These custom HEs can be used to stimulate double-strand break homologous recombination in cells, to induce the repair of defective genes with very low toxicity levels. The use of tailored HEs opens up new possibilities for gene therapy in patients with monogenic diseases that can be treated ex vivo. This review provides an overview of recent advances in this field.
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Affiliation(s)
- Maria J. Marcaida
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain
| | - Inés G. Muñoz
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain
| | - Francisco J. Blanco
- Ikerbasque Professor Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Vizcaya, 48160 Derio, Spain
| | - Jesús Prieto
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain
| | - Guillermo Montoya
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain
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Thomas V, Loret JF, Jousset M, Greub G. Biodiversity of amoebae and amoebae-resisting bacteria in a drinking water treatment plant. Environ Microbiol 2008; 10:2728-45. [DOI: 10.1111/j.1462-2920.2008.01693.x] [Citation(s) in RCA: 210] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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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Machouart M, Lacroix C, Bui H, Feuilhade de Chauvin M, Derouin F, Lorenzo F. Polymorphisms and intronic structures in the 18S subunit ribosomal RNA gene of the fungiScytalidium dimidiatumandScytalidium hyalinum. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09789.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Haugen P, Coucheron DH, Rønning SB, Haugli K, Johansen S. The molecular evolution and structural organization of self-splicing group I introns at position 516 in nuclear SSU rDNA of myxomycetes. J Eukaryot Microbiol 2004; 50:283-92. [PMID: 15132172 DOI: 10.1111/j.1550-7408.2003.tb00135.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Group I introns are relatively common within nuclear ribosomal DNA of eukaryotic microorganisms, especially in myxomycetes. Introns at position S516 in the small subunit ribosomal RNA gene are particularly common, but have a sporadic occurrence in myxomycetes. Fuligo septica, Badhamia gracilis, and Physarum flavicomum, all members of the family Physaraceae, contain related group IC1 introns at this site. The F. septica intron was studied at the molecular level and found to self-splice as naked RNA and to generate full-length intron RNA circles during incubation. Group I introns at position S516 appear to have a particularly widespread distribution among protists and fungi. Secondary structural analysis of more than 140 S516 group I introns available in the database revealed five different types of organization, including IC1 introns with and without His-Cys homing endonuclease genes, complex twin-ribozyme introns, IE introns, and degenerate group I-like introns. Both intron structural and phylogenetic analyses indicate a multiple origin of the S516 introns during evolution. The myxomycete introns are related to S516 introns in the more distantly related brown algae and Acanthamoeba species. Possible mechanisms of intron transfer both at the RNA- and DNA-levels are discussed in order to explain the observed widespread, but scattered, phylogenetic distribution.
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Affiliation(s)
- Peik Haugen
- Department of Molecular Biotechnology, RNA Research Group, Institute of Medical Biology, University of Tromsø, N-9037 Tromsø, Norway
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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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Abstract
The gene coding for the small ribosomal subunit RNA of Ploeotia costata contains an actively splicing group I intron (Pco.S516) which is unique among euglenozoans. Secondary structure predictions indicate that paired segments P1-P10 as well as several conserved elements typical of group I introns and of subclass IC1 in particular are present. Phylogenetic analyses of SSU rDNA sequences demonstrate a well-supported placement of Ploeotia costata within the Euglenozoa; whereas, analyses of intron data sets uncover a close phylogenetic relation of Pco.S516 to S-516 introns from Acanthamoeba, Aureoumbra lagunensis (Stramenopila) and red algae of the order Bangiales. Discrepancies between SSU rDNA and intron phylogenies suggest horizontal spread of the group I intron. Monophyly of IC1 516 introns from Ploeotia costata, A. lagunensis and rhodophytes is supported by a unique secondary structure element: helix P5b possesses an insertion of 19 nt length with a highly conserved tetraloop which is supposed to take part in tertiary interactions. Neither functional nor degenerated ORFs coding for homing endonucleases can be identified in Pco.S516. Nevertheless, degenerated ORFs with His-Cys box motifs in closely related intron sequences indicate that homing may have occurred during evolution of the investigated intron group.
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Affiliation(s)
- Ingo Busse
- Fakultät für Biologie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
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Abstract
The catalytic mechanisms of type II restriction endonucleases and homing endonucleases are discussed and compared. Brief reviews of the chemistry of phosphoryl transfers and canonical one-metal and two-metal endonucleolytic mechanisms are provided along with possible future directions in the study of endonuclease active sites. The discussion of type II restriction endonucleases is comprised of a description of the general architecture of the canonical active site structural motif followed by more in-depth examples of one- and two-metal mechanisms. The homing endonuclease section is comprised of four sections describing what is known regarding the cleavage mechanisms of the four group I intron homing endonuclease families: LAGLIDADG, His-Cys box, H-N-H, and GIY-YIG.
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Affiliation(s)
- Eric A Galburt
- Fred Hutchinson Cancer Research Center and Graduate Program in Biomolecular Structure and Design, University of Washington, 1100 Fairview Avenue North, A3-023, Seattle, Washington 98109, USA
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Yokoyama E, Yamagishi K, Hara A. Group-I intron containing a putative homing endonuclease gene in the small subunit ribosomal DNA of Beauveria bassiana IFO 31676. Mol Biol Evol 2002; 19:2022-5. [PMID: 12411610 DOI: 10.1093/oxfordjournals.molbev.a004025] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Johansen S, Einvik C, Nielsen H. DiGIR1 and NaGIR1: naturally occurring group I-like ribozymes with unique core organization and evolved biological role. Biochimie 2002; 84:905-12. [PMID: 12458083 DOI: 10.1016/s0300-9084(02)01443-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The group I-like ribozyme GIR1 is a unique example of a naturally occurring ribozyme with an evolved biological function. GIR1 generates the 5'-end of a nucleolar encoded messenger RNA involved in intron mobility. GIR1 is found as a cis-cleaving ribozyme within two very different rDNA group I introns (twin-ribozyme introns) in distantly related organisms. The Didymium GIR1 (DiGIR1) and Naegleria GIR1 (NaGIR1) share fundamental features in structural organization and reactivity, and display significant differences when compared to the related group I splicing ribozymes. GIR1 lacks the characteristic P1 segment present in all group I splicing ribozymes, it has a novel core organization, and it catalyses two site-specific hydrolytic cleavages rather than splicing. DiGIR1 and NaGIR1 appear to have originated from eubacterial group I introns in order to fulfil a common biological challenge: the expression of a protein encoding gene in a nucleolar context.
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Affiliation(s)
- Steinar Johansen
- RNA Research Group, Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, 037 Tromsø, Norway.
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Haugen P, De Jonckheere JF, Johansen S. Characterization of the self-splicing products of two complex Naegleria LSU rDNA group I introns containing homing endonuclease genes. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:1641-9. [PMID: 11895434 DOI: 10.1046/j.1432-1327.2002.02802.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The two group I introns Nae.L1926 and Nmo.L2563, found at two different sites in nuclear LSU rRNA genes of Naegleria amoebo-flagellates, have been characterized in vitro. Their structural organization is related to that of the mobile Physarum intron Ppo.L1925 (PpLSU3) with ORFs extending the L1-loop of a typical group IC1 ribozyme. Nae.L1926, Nmo.L2563 and Ppo.L1925 RNAs all self-splice in vitro, generating ligated exons and full-length intron circles as well as internal processed excised intron RNAs. Formation of full-length intron circles is found to be a general feature in RNA processing of ORF-containing nuclear group I introns. Both Naegleria LSU rDNA introns contain a conserved polyadenylation signal at exactly the same position in the 3' end of the ORFs close to the internal processing sites, indicating an RNA polymerase II-like expression pathway of intron proteins in vivo. The intron proteins I-NaeI and I-NmoI encoded by Nae.L1926 and Nmo.L2563, respectively, correspond to His-Cys homing endonucleases of 148 and 175 amino acids. I-NaeI contains an additional sequence motif homologous to the unusual DNA binding motif of three antiparallel beta sheets found in the I-PpoI endonuclease, the product of the Ppo.L1925 intron ORF.
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Affiliation(s)
- Peik Haugen
- RNA Research group, Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, Tromsø, Norway
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Chevalier BS, Stoddard BL. Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res 2001; 29:3757-74. [PMID: 11557808 PMCID: PMC55915 DOI: 10.1093/nar/29.18.3757] [Citation(s) in RCA: 334] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Homing endonucleases confer mobility to their host intervening sequence, either an intron or intein, by catalyzing a highly specific double-strand break in a cognate allele lacking the intervening sequence. These proteins are characterized by their ability to bind long DNA target sites (14-40 bp) and their tolerance of minor sequence changes in these sites. A wealth of biochemical and structural data has been generated for these enzymes over the past few years. Herein we review our current understanding of homing endonucleases, including their diversity and evolution, DNA-binding and catalytic mechanisms, and attempts to engineer them to bind novel DNA substrates.
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Affiliation(s)
- B S Chevalier
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center and Graduate Program in Molecular and Cell Biology, University of Washington, 1100 Fairview Avenue North A3-023, Seattle, WA 98109, USA
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