Complex group-I introns in nuclear SSU rDNA of red and green algae: Evidence of homing-endonuclease pseudogenes in the Bangiophyceae

Current Genetics

Volumn 36, Issue 6, 1999, Pages 345-353

  Haugen, Peik ^a   Huss, Volker A R ^c   Nielsen, Henrik ^d   Johansen, Steinar ^a,b  

^a UNIVERSITY OF TROMSØ   (Norway)

^b University of Tromsö   (Norway)

^c UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

^d UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Group I intron; Homing endonuclease; Porphyra; Ribosomal DNA; Scenedesmus

Indexed keywords

ENDONUCLEASE; RIBOSOME DNA; RIBOSOME PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; DELETION MUTANT; EXON; FRAMESHIFT MUTATION; GREEN ALGA; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PSEUDOGENE; RED ALGA; RNA GENE; RNA SPLICING; RNA STRUCTURE;

ALGAE; BACTERIA (MICROORGANISMS); BANGIA; BANGIOPHYCEAE; CHLOROPHYTA; EUKARYOTA; PORPHYRA; PORPHYRA SPIRALIS; SCENEDESMUS; SCENEDESMUS PUPUKENSIS;

EID: 0033390654     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002940050509     Document Type: Article

References (43)

1. Bhattacharya D, Surek B, Rüsing M, Damberger S, Melkonian M (1994) Group-I introns are inherited through common ancestry in the nuclear-encoded rRNA of Zygnematales (Charophyceae). Proc Natl Acad Sci USA 91:9916-9920
2. Beagley CT, Okada NA, Wolstenholme DR (1996) Two mitochondrial group-I introns in a metazoan, the sea anemone Metridium senile: one intron contains genes for subunits 1 and 3 of NADH dehydrogenase. Proc Natl Acad Sci USA 93:5619-5623
3. Belfort M, Roberts RJ (1997) Homing endonucleases; keeping the house in order. Nucleic Acids Res 25:3379-3388
4. Burke JM, RajBhandary UL (1982) Introns within the large rRNA gene of N. crassa mitochondria: a long open reading frame and a consensus sequence possibly important in splicing. Cell 31:509-520
5. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna JA (1996) Crystal structure of a group-I ribozyme domain: principles of RNA packing. Science 273:1678-1685
6. Cech TR, Herschlag D (1996) Group-I ribozymes: substrate recognition, catalytic strategies, and comparative mechanistic analysis. Nucleic Acids Mol Biol 10:1-17
7. Cech TR, Damberger SH, Gutell RR (1994) Representation of the secondary and tertiary structure of group-I introns. Nature Struct Biol 1:273-280
8. Cummings DJ, McNally KL, Domenico JM, Matsuura ET (1990) The complete DNA sequence of the mitochondrial genome of Podospora anserina. Curr Genet 18:375-402
9. Decatur WA, Einvik C, Johansen S, Vogt VM (1995) Two group-I ribozymes with different functions in a nuclear rDNA intron. EMBO J 14:4558-4568
10. De Jonckheere JF, Brown S (1998) Three different group-I introns in the nuclear large subunit ribosomal DNA of the amoebo-flagellate Naegleria. Nucleic Acids Res 26:456-461
11. Einvik C, Decatur WA, Embley TM, Vogt VM, Johansen S (1997) Naegleria nucleolar introns contain two group-I ribozymes with different functions in RNA splicing and processing. RNA 3:710-720
12. Einvik C, Nielsen H, Westhof E, Michel F, Johansen S (1998) Group-I-like ribozymes with a novel core organization perform obligate sequential hydrolytic cleavages at two processing sites. RNA 4:530-541
13. Eide M, Haugen P, Willassen NP, Johansen S (1999) I-NjaI, a nuclear intron-encoded homing endonuclease from Naegleria, generates a pentanucleotide 3′ cleavage-overhang within a 19 base-pair partially symmetric DNA recognition site. Eur J Biochem 259:281-288
14. Flick KE, Jurica MS, Monnat RJ Jr, Stoddard BL (1998) DNA binding and cleavage by the nuclear intron-encoded endonuclease I-PpoI. Nature 394:96-101
15. Golden BL, Gooding AR, Podell ER, Cech TR (1998) A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science 282:259-264
16. Hausner G, Monteiro-Vitorello CB, Searles DB, Maland M, Fulbright DW, Bertrand H (1999) A long open reading frame in the mitochondrial LSL rRNA group-I intron of Cryphonectria parasitica encodes a putative S5 ribosomal protein fused to a maturase. Curr Genet 35:109-117
17. Holst-Jensen A, Vaage M, Schumacher T, Johansen S (1999) Structural characteristics and possible horizontal transfer of group-I introns between closely related plant pathogenic fungi. Mol Biol Evol 16:114-126
18. Jansson Å, Gillin F, Kagardt U, Hagblom P (1994) Coding of hemolysins within the ribosomal RNA repeat on a plasmid in Entamoeba histolytica. Science 263:1440-1443
19. Johansen S, Haugen P (1999) A complex group-I intron in Nectria galligena rDNA. Microbiology 145:516-517
20. Johansen S, Vogt VM (1994) An intron in the nuclear ribosomal DNA of Didymium iridis codes for a group-I ribozyme and a novel ribozyme that cooperate in self-splicing. Cell 76:725-734
21. Johansen S, Embley TM, Willassen NP (1993) A family of nuclear homing endonucleases. Nucleic Acids Res 21:4405
22. Johansen S, Muscarella DE, Vogt VM (1996) Insertion elements in ribosomal DNA. In: Zimmermann RA, Dahlberg AE (eds) Ribosomal RNA: structure, evolution, processing, and function in biosynthesis. CRC Press, Boca Raton, Florida, pp 89-108
23. Johansen S, Elde M, Vader A, Haugen P, Haugli K, Haugli F (1997) In vivo mobility of a group-I twintron in nuclear ribosomal DNA of the myxomycete Didymium iridis. Mol Microbiol 24:737-745
24. Kessler E, Schäfer M, Hümmer C, Kloboucek A, Huss VAR (1997) Physiological, biochemical, and molecular characters for the taxonomy of the subgenera of Scenedesmus (Chlorococcales, Chlorophyta). Bot Acta 110:244-250
25. Kunimoto M, Yamamoto Y, Kaminishi Y, Mizukami Y, Kilo H (1998) A discrimination of Porphyra species (Rhodophyta) based on the sequences of the small subunit ribosomal RNA gene. DDBJ/ EMBL/ GenBank database accession number AB013176
26. Lehnert V, Jaeger L, Michel F, Westhof E (1996) New loop-loop tertiary interactions in self-splicing introns of subgroups IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem Biol 3:993-1009
27. Lin J, Vogt VM (1998) I-PpoI, the endonuclease encoded by the group-I intron PpLSU3, is expressed from an RNA polymerase-I transcript. Mol Cell Biol 18:665-675
28. Loizos N, Tillier ERM, Belfort M (1994) Evolution of mobile group-I introns: recognition of intron sequences by an intron-encoded endonuclease. Proc Natl Acad Sci USA 91:11983-11987
29. Margulis L, Schwartz KV (1998) Five kingdoms. An illustrated guide to the phyla of life on earth. 3rd edn. WH Freeman, New York
30. Michel F, Westhof E (1990) Modelling of the three-dimensional architecture of group-I catalytic introns based on comparative sequence analysis. J Mol Biol 216:585-610
31. Muscarella DE, Vogt VM (1989) A mobile group-I intron in the nuclear rDNA of Physarum polycephalum. Cell 56:443-454
32. Muscarella DE, Vogt VM (1993) A mobile group-I intron from Physarum polycephalum can insert itself and induce point mutations in the nuclear ribosomal DNA of Saccharomyces cerevisiae. Mol Cell Biol 13:1023-1033
33. Muscarella DE, Ellison EL, Ruoff BM, Vogt VM (1990) Characterization of I-Ppo. an intron-encoded endonuclease that mediates homing of a group-I intron in the ribosomal DNA of Physarum polycephalum. Mol Cell Biol 10:3386-3396
34. Nishida H, Tajiri Y, Sugiyama J (1998) Multiple origins of fungal group-I introns located in the same position of the nuclear SSU rRNA gene. J Mol Evol 46:442-448
35. Oliveira MC, Ragan MA (1994) Variant forms of a group-I intron in nuclear small-subunit rRNA genes of the marine red alga Porphyra spiralis var. amplifolia. Mol Biol Evol 11:195-207
36. Roman J, Rubin MN, Woodson SA (1999) Sequence specificity of in vivo reverse splicing of the Tetrahymena group-I intron. RNA 5:1-13
37. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
38. Sellem CH, Belcour L (1997) Intron open reading frames as mobile elements and evolution of a group-I intron. Mol Biol Evol 14:518-526
39. Shinohara ML, LoBuglio KF, Rogers SO (1996) Group-I intron family in the nuclear ribosomal RNA small subunit genes of Cenacoccum geophilum isolates. Curr Genet 29:377-387
40. Upcroft JA, Healey A, Mitchell R, Boreham PFL, Upcroft P (1990) Antigen expression from the ribosomal DNA repeat unit of Giardia intestinalis. Nucleic Acids Res 18:7077-7081
41. Vader A, Næss J, Haugli K, Haugli F, Johansen S (1994) Nucleolar introns from Physarum flavicomum contain insertion elements that may explain how mobile group-I introns gained their open reading frames. Nucleic Acids Res 22:4553-4559
42. Vader A, Nielsen H, Johansen S (1999) In vivo expression of the nucleolar group-I intron-encoded I-DirI homing endonuclease involves the removal of a spliceosomal intron. EMBO J 18:1003-1013
43. Woodson SA, Cech TR (1989) Reverse self-splicing of the Tetrahymena group-I intron: implication for the directionality of splicing and for intron transposition. Cell 57:335-345