1
|
Analysis of small and large subunit rDNA introns from several ectomycorrhizal fungi species. PLoS One 2021; 16:e0245714. [PMID: 33720962 PMCID: PMC7959364 DOI: 10.1371/journal.pone.0245714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 01/06/2021] [Indexed: 11/19/2022] Open
Abstract
The small (18S) and large (28S) nuclear ribosomal DNA (rDNA) introns have been researched and sequenced in a variety of ectomycorrhizal fungal taxa in this study, it is found that both 18S and 28S rDNA would contain introns and display some degree variation in size, nucleotide sequences and insertion positions within the same fungi species (Meliniomyces). Under investigations among the tested isolates, 18S rDNA has four sites for intron insertions, 28S rDNA has two sites for intron insertions. Both 18S and 28S rDNA introns among the tested isolates belong to group I introns with a set of secondary structure elements designated P1-P10 helics and loops. We found a 12 nt nucleotide sequences TACCACAGGGAT at site 2 in the 3'-end of 28S rDNA, site 2 introns just insert the upstream or the downstream of the12 nt nucleotide sequences. Afters sequence analysis of all 18S and 28S rDNA introns from tested isolates, three high conserved regions around 30 nt nucleotides (conserved 1, conserved 2, conserved 3) and identical nucleotides can be found. Conserved 1, conserved 2 and conserved 3 regions have high GC content, GC percentage is almost more than 60%. From our results, it seems that the more convenient host sites, intron sequences and secondary structures, or isolates for 18S and 28S rDNA intron insertion and deletion, the more popular they are. No matter 18S rDNA introns or 18S rDNA introns among tested isolates, complementary base pairing at the splicing sites in P1-IGS-P10 tertiary helix around 5'-end introns and exons were weak.
Collapse
|
2
|
Krogh N, Pietschmann M, Schmid M, Jensen TH, Nielsen H. Lariat capping as a tool to manipulate the 5' end of individual yeast mRNA species in vivo. RNA (NEW YORK, N.Y.) 2017; 23:683-695. [PMID: 28159804 PMCID: PMC5393178 DOI: 10.1261/rna.059337.116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 01/31/2017] [Indexed: 06/06/2023]
Abstract
The 5' cap structure of eukaryotic mRNA is critical for its processing, transport, translation, and stability. The many functions of the cap and the fact that most, if not all, mRNA carries the same type of cap makes it difficult to analyze cap function in vivo at individual steps of gene expression. We have used the lariat capping ribozyme (LCrz) from the myxomycete Didymium to replace the mRNA m7G cap of a single reporter mRNA species with a tiny lariat in which the first and the third nucleotide are joined by a 2', 5' phosphodiester bond. We show that the ribozyme functions in vivo in the budding yeast Saccharomyces cerevisiae presumably without cofactors and that lariat capping occurs cotranscriptionally. The lariat-capped reporter mRNA is efficiently exported to the cytoplasm where it is found to be oligoadenylated and evenly distributed. Both the oligoadenylated form and a lariat-capped mRNA with a templated poly(A) tail translates poorly, underlining the critical importance of the m7G cap in translation. Finally, the lariat-capped RNA exhibits a threefold longer half-life compared to its m7G-capped counterpart, consistent with a key role for the m7G cap in mRNA turnover. Our study emphasizes important activities of the m7G cap and suggests new utilities of lariat capping as a molecular tool in vivo.
Collapse
Affiliation(s)
- Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Max Pietschmann
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
|
5
|
Nielsen H, Einvik C, Lentz TE, Hedegaard MM, Johansen SD. A conformational switch in the DiGIR1 ribozyme involved in release and folding of the downstream I-DirI mRNA. RNA (NEW YORK, N.Y.) 2009; 15:958-967. [PMID: 19329537 PMCID: PMC2673072 DOI: 10.1261/rna.669209] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2008] [Accepted: 01/23/2009] [Indexed: 05/27/2023]
Abstract
DiGIR1 is a group I-like cleavage ribozyme found as a structural domain within a nuclear twin-ribozyme group I intron. DiGIR1 catalyzes cleavage by branching at an Internal Processing Site (IPS) leading to formation of a lariat cap at the 5'-end of the 3'-cleavage product. The 3'-cleavage product is subsequently processed into an mRNA encoding a homing endonuclease. By analysis of combinations of 5'- and 3'-deletions, we identify a hairpin in the 5'-UTR of the mRNA (HEG P1) that is formed by conformational switching following cleavage. The formation of HEG P1 inhibits the reversal of the branching reaction, thus giving it directionality. Furthermore, the release of the mRNA is a consequence of branching rather than hydrolytic cleavage. A model is put forward that explains the release of the I-DirI mRNA with a lariat cap and a structured 5'-UTR as a direct consequence of the DiGIR1 branching reaction. The role of HEG P1 in GIR1 branching is reminiscent of that of hairpin P-1 in splicing of the Tetrahymena rRNA group I intron and illustrates a general principle in RNA-directed RNA processing.
Collapse
Affiliation(s)
- Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, DK-2200N Copenhagen, Denmark.
| | | | | | | | | |
Collapse
|
6
|
Wikmark OG, Haugen P, Lundblad EW, Haugli K, Johansen SD. The molecular evolution and structural organization of group I introns at position 1389 in nuclear small subunit rDNA of myxomycetes. J Eukaryot Microbiol 2007; 54:49-56. [PMID: 17300520 DOI: 10.1111/j.1550-7408.2006.00145.x] [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: 11/27/2022]
Abstract
The number of nuclear group I introns from myxomycetes is rapidly increasing in GenBank as more rDNA sequences from these organisms are being sequenced. They represent an interesting and complex group of intervening sequences because several introns are mobile (or inferred to be mobile) and many contain large and unusual insertions in peripheral loops. Here we describe related group I introns at position 1389 in the small subunit rDNA of representatives from the myxomycete family Didymiaceae. Phylogenetic analyses support a common origin and mainly vertical inheritance of the intron. All S1389 introns from the Didymiaceae belong to the IC1 subclass of nuclear group I introns. The central catalytic core region of about 100 nt appears divergent in sequence composition even though the introns reside in closely related species. Furthermore, unlike the majority of group I introns from myxomycetes the S1389 introns do not self-splice as naked RNA in vitro under standard conditions, consistent with a dependence on host factors for folding or activity. Finally, the myxomycete S1389 introns are exclusively found within the family Didymiaceae, which suggests that this group I intron was acquired after the split between the families Didymiaceae and Physaraceae.
Collapse
Affiliation(s)
- Odd-Gunnar Wikmark
- Department of Molecular Biotechnology, RNA Research Group, Institute of Medical Biology, University of Tromsø, N-9037 Tromsø, Norway
| | | | | | | | | |
Collapse
|
7
|
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.
Collapse
Affiliation(s)
- Steinar D Johansen
- Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, Tromsø, Norway.
| | | | | |
Collapse
|
8
|
Nielsen H, Johansen SD. A new RNA branching activity: the GIR1 ribozyme. Blood Cells Mol Dis 2006; 38:102-9. [PMID: 17188534 DOI: 10.1016/j.bcmd.2006.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Accepted: 11/07/2006] [Indexed: 11/27/2022]
Abstract
The formation of lariat intermediates during the first step of splicing of group II introns and spliceosomal introns is a well-studied fundamental reaction in molecular biology. Apart from this prominent example, there are surprisingly few occurrences of branched nucleotides or even 2',5'-phosphodiester bonds in biology. We recently described a new ribozyme, the GIR1 branching ribozyme, which catalyzes the formation of a tiny lariat that caps an mRNA. This new example together with work on artificial branching ribozymes and deoxyribozymes shows that branching is facile and points to the possibility that branching reactions could be more prevalent than previously recognized.
Collapse
Affiliation(s)
- Henrik Nielsen
- Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Denmark.
| | | |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Nielsen H, Westhof E, Johansen S. An mRNA is capped by a 2', 5' lariat catalyzed by a group I-like ribozyme. Science 2005; 309:1584-7. [PMID: 16141078 DOI: 10.1126/science.1113645] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Twin-ribozyme introns are formed by two ribozymes belonging to the group I family and occur in some ribosomal RNA transcripts. The group I-like ribozyme, GIR1, liberates the 5' end of a homing endonuclease messenger RNA in the slime mold Didymium iridis. We demonstrate that this cleavage occurs by a transesterification reaction with the joining of the first and the third nucleotide of the messenger by a 2',5'-phosphodiester linkage. Thus, a group I-like ribozyme catalyzes an RNA branching reaction similar to the first step of splicing in group II introns and spliceosomal introns. The resulting short lariat, by forming a protective 5' cap, might have been useful in a primitive RNA world.
Collapse
Affiliation(s)
- Henrik Nielsen
- Department of Medical Biochemistry and Genetics, Panum Institute, University of Copenhagen, DK-2200N Copenhagen, Denmark.
| | | | | |
Collapse
|
11
|
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.
Collapse
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;
| |
Collapse
|
12
|
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
|
13
|
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.
Collapse
Affiliation(s)
- Peik Haugen
- Department of Molecular Biotechnology, RNA Research Group, Institute of Medical Biology, University of Tromsø, N-9037 Tromsø, Norway
| | | | | | | | | |
Collapse
|
14
|
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.
Collapse
Affiliation(s)
- Eirik W Lundblad
- Department of Molecular Biotechnology, RNA research group, Institute of Medical Biology, University of Tromso, Tromso, Norway
| | | | | | | | | |
Collapse
|
15
|
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.
Collapse
Affiliation(s)
- Steinar Johansen
- RNA Research Group, Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, 037 Tromsø, Norway.
| | | | | |
Collapse
|
16
|
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.
Collapse
Affiliation(s)
- Peik Haugen
- RNA Research group, Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, Tromsø, Norway
| | | | | |
Collapse
|
17
|
Elde M, Willassen NP, Johansen S. Functional characterization of isoschizomeric His-Cys box homing endonucleases from Naegleria. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:7257-66. [PMID: 11106439 DOI: 10.1046/j.1432-1327.2000.01862.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Several species within the amoeboflagellate genus Naegleria harbor an optional ORF containing group I introns in their nuclear small subunit ribosomal DNA. The different ORFs encode homing endonucleases with 65 to 95% identity at the amino-acid level. I-NjaI, I-NanI and I-NitI, from introns in Naegleria jamiesoni, N. andersoni and N. italica, respectively, were analyzed in more detail and found to be isoschizomeric endonucleases that recognize and cleave an approximal 19-bp partially symmetrical sequence, creating a pentanucleotide 3' overhang upon cleavage. The optimal conditions for cleavage activity with respect to temperature, pH, salt and divalent metal ions were investigated. The optimal cleavage temperature for all three endonucleases was found to be 37 degrees C and the activity was dependent on the concentration of NaCl with an optimum at 200 mM. Divalent metal ions, primarily Mg2+, are essential for Naegleria endonuclease activity. Whereas both Mn2+ and Ca2+ could substitute for Mg2+, but with a slower cleavage rate, Zn2+ was unable to support cleavage. Interestingly, the pH dependence of DNA cleavage was found to vary significantly between the I-NitI and I-NjaI/I-NanI endonucleases with optimal pH values at 6.5 and 9, respectively. Site-directed mutagenesis of conserved I-NjaI residues strongly supports the hypothesis that Naegleria homing endonucleases share a similar zinc-binding structure and active site with the His-Cys box homing endonuclease I-PpoI.
Collapse
Affiliation(s)
- M Elde
- Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromso, Norway
| | | | | |
Collapse
|
18
|
Einvik C, Nielsen H, Nour R, Johansen S. Flanking sequences with an essential role in hydrolysis of a self-cleaving group I-like ribozyme. Nucleic Acids Res 2000; 28:2194-200. [PMID: 10773091 PMCID: PMC105364 DOI: 10.1093/nar/28.10.2194] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
DiGIR1 is a group I-like ribozyme derived from the mobile twin ribozyme group I intron DiSSU1 in the nuclear ribosomal DNA of the myxomycete Didymium iridis. This ribozyme is responsible for intron RNA processing in vitro and in vivo at two internal sites close to the 5'-end of the intron endo-nuclease open reading frame and is a unique example of a group I ribozyme with an evolved biological function. DiGIR1 is the smallest functional group I ribozyme known from nature and has an unusual core organization including the 6 bp P15 pseudoknot. Here we report results of functional and structural analyses that identify RNA elements critical for hydrolysis outside the DiGIR1 ribozyme core moiety. Results from deletion analysis, disruption/compensation mutagenesis and RNA structure probing analysis all support the existence of two new segments, named P2 and P2.1, involved in the hydrolysis of DiGIR1. Significant decreases in the hydrolysis rate, k (obs), were observed in disruption mutants involving both segments. These effects were restored by compensatory base pairing mutants. The possible role of P2 is to tether the ribozyme core, whereas P2.1 appears to be more directly involved in catalysis.
Collapse
Affiliation(s)
- C Einvik
- Department of Molecular Cell Biology, Institute of Medical Biology, University of Tromsø, N-9037 Tromsø, Norway
| | | | | | | |
Collapse
|
19
|
Lin J, Vogt VM. Functional alpha-fragment of beta-galactosidase can be expressed from the mobile group I intron PpLSU3 embedded in yeast pre-ribosomal RNA derived from the chromosomal rDNA locus. Nucleic Acids Res 2000; 28:1428-38. [PMID: 10684939 PMCID: PMC111048 DOI: 10.1093/nar/28.6.1428] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/1999] [Revised: 01/11/2000] [Accepted: 01/21/2000] [Indexed: 11/14/2022] Open
Abstract
PpLSU3, a mobile group I intron found in the ribo-somal RNA genes of Physarum polycephalum, encodes the I-PpoI homing endonuclease. This enzyme represents one of the rare cases in nature where a protein is expressed from an RNA polymerase I transcript. Our previous results showed that the full length intron, but not a further processed species, is the messenger for I-PpoI, implying a role of the untranslated region (UTR) in gene expression. To study the function of the 3'-UTR in expression of the endonuclease and in splicing of the intron, we replaced the I-PpoI gene in PpLSU3 with the gene for the alpha-fragment of Escherichia coli beta-galactosidase, and then integrated this chimeric intron into all the chromosomal rDNA repeats of yeast. The resulting cells synthesized functional alpha-fragment, as evidenced by a complementation assay analogous to that used in E.coli. The beta-galactosidase activity thus provides an unusual and potentially valuable readout for Pol I transcription from chromosomal rDNA. This is the first example in which a eucaryotic homing endonuclease gene has been successfully replaced by a heterologous gene. Using deletion mutagenesis and a novel randomization approach with the alpha-fragment as a reporter, we found that a small segment of the 3'-UTR dramatically influences both splicing and protein expression.
Collapse
Affiliation(s)
- J Lin
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
| | | |
Collapse
|