Journal of Molecular Evolution

, Volume 57, Issue 6, pp 710–720 | Cite as

Phylogeny and Self-Splicing Ability of the Plastid tRNA-Leu Group I Intron

  • Dawn Simon
  • David Fewer
  • Thomas Friedl
  • Debashish BhattacharyaEmail author


Group I introns are mobile RNA enzymes (ribozymes) that encode conserved primary and secondary structures required for autocatalysis. The group I intron that interrupts the tRNA-Leu gene in cyanobacteria and plastids is remarkable because it is the oldest known intervening sequence and may have been present in the common ancestor of the cyanobacteria (i.e., 2.7–3.5 billion years old). This intron entered the eukaryotic domain through primary plastid endosymbiosis. We reconstructed the phylogeny of the tRNA-Leu intron and tested the in vitro self-splicing ability of a diverse collection of these ribozymes to address the relationship between intron stability and autocatalysis. Our results suggest that the present-day intron distribution in plastids is best explained by strict vertical transmission, with no intron losses in land plants or a subset of the Stramenopiles (xanthophyceae/phaeophyceae) and frequent loss among green algae, as well as in the red algae and their secondary plastid derivatives (except the xanthophyceae/phaeophyceae lineage). Interestingly, all tested land plant introns could not self-splice in vitro and presumably have become dependent on a host factor to facilitate in vivo excision. The host dependence likely evolved once in the common ancestor of land plants. In all other plastid lineages, these ribozymes could either self-splice or complete only the first step of autocatalysis.


Autocatalysis Cyanobacteria Group I intron Intron mobility Plastid endosymbiosis Self-splicing ability tRNA-Leu gene 



This work was supported by a grant awarded to D.B. from the National Science Foundation (MCB 01-10252) and a grant from the Deutsche Forschungsgemeinschaft to T.F. (Fr 905/7-1,2). D.F. received financial support from the GlaxoSmithKline Corporation and a Sigma Xi Grant-in-Aid award. D.S. was supported by a Stanley Fellowship from the University of Iowa. We also thank Hwan Su Yoon (Iowa) and Peik Haugen (Iowa) for helpful discussions and technical advice.


  1. 1.
    Anderson, RA, Potter, D, Bidigare, RR, Latosa, M, Rowan, K, O’Kelly, CJ 1998Characterization and phylogenetic position of the enigmatic golden alga Phaeothamnion confervicola: Ultrastructure, pigment composition, and partial SSU rDNA Sequence.J Phycol34286298CrossRefGoogle Scholar
  2. 2.
    Anderson, RA, Van de Peer, Y, Potter, D, Sexton, JP, Kawachi, M, LaJeunesse, T 1999Phylogenetic analysis of the SSU rRNA from members of the Chrysophyceae.Protist1507184PubMedGoogle Scholar
  3. 3.
    Asmussen, CB, Chase, MW 2001Coding and noncoding plastid DNA in palm systematics.Am J Bot8811031117PubMedGoogle Scholar
  4. 4.
    Barfod, ET, Cech, TR 1988Deletion of nonconserved helices near the 3′ end of the rRNA intron of Tetrahymena thermophila alters self-splicing but not core catalytic activity.Genes Dev2652653PubMedGoogle Scholar
  5. 5.
    Beaudry, AA, Joyce, GF 1990Minimum secondary structure requirements for catalytic activity of a self-splicing group I intron.Biochemistry2965346539PubMedGoogle Scholar
  6. 6.
    Besendahl, A, Qiu, Y-L, Lee, J, Palmer, JD, Bhattacharya, D 2000The cyanobacterial origin and vertical transmission of the plastid tRNALeu group-I intron.Curr Genet371223Google Scholar
  7. 7.
    Bhattacharya, D, Medlin, L 1995The phylogeny of plastids: A review based on comparisons of small subunit ribosomal RNA coding regions.J Phycol31489498Google Scholar
  8. 8.
    Bhattacharya, D, Surek, B, Ruesing, M, Damberger, S, Melkonian, M 1994Group I introns are inherited through common ancestry in the nuclear-encoded rRNA of Zygnematales (Charophyceae).Proc Natl Acad Sci USA9199169920PubMedGoogle Scholar
  9. 9.
    Bhattacharya, D, Cannone, JJ, Gutell, RR 2001Group I intron lateral transfer between red and brown algal ribosomal RNA.Curr Genet408290CrossRefPubMedGoogle Scholar
  10. 10.
    Bhattacharya, D, Friedl, T, Helms, G 2002Vertical evolution and intragenic spread of lichen-fungal group I introns.J Mol Evol557484CrossRefPubMedGoogle Scholar
  11. 11.
    Butterfield, N 2000 Bangiomorpha pubescens n. gen., n. sp.: Implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes.Paleobiol26386404Google Scholar
  12. 12.
    Brocks, JJ, Logan, GA, Buick, R, Summons, RE 1999Archean molecular fossils and the early rise of eukaryotes.Science28510331036CrossRefPubMedGoogle Scholar
  13. 13.
    Buchheim, MA, Michalopulos, EA, Buchheim, JA 2001Phylogeny of the Chlorophyceae with special reference to the Sphaeropleales: A study of 18S and 26S rDNA data.J Phycol37819835CrossRefGoogle Scholar
  14. 14.
    Cech, TR 1988Conserved sequences and structures of group I introns: Building an active site for RNA catalysis—A review.Gene73259271PubMedGoogle Scholar
  15. 15.
    Cech, TR 1990Self-splicing of group I introns.Annu Rev Biochem59543568PubMedGoogle Scholar
  16. 16.
    Cech, TR, Damberger, SH, Gutell, RR 1994Representation of the secondary and tertiary structure of group I introns.Nature Struct Biol1273280Google Scholar
  17. 17.
    Costa, JL, Paulsrud, P, Lindblad, P 2002The cyanobacterial tRNA(Leu) (UAA) intron: Evolutionary patterns in a genetic marker.Mol Biol Evol19850857PubMedGoogle Scholar
  18. 18.
    Damberger, SH, Gutell, RR 1994A comparative database of group I intron structures.Nucleic Acids Res2235083510PubMedGoogle Scholar
  19. 19.
    Daros, JA, Flores, R 1996A group I plant intron accumulates as circular RNA forms with extensive 5′ deletions in vivo.RNA2928936PubMedGoogle Scholar
  20. 20.
    Daugbjerg, N, Guillou, L 2001Phylogenetic analyses of Bolidophyceae (Heterokontophyta) using rbcL gene sequences support their sister group relationship to diatoms.Phycologia40153161Google Scholar
  21. 21.
    Delwiche, CF, Palmer, JD 1997Plastid origin and secondary symbiosis.Bhattacharya, D eds. Origins of algae and their plastids.SpringerWien5386Google Scholar
  22. 22.
    Douglas, SE, Penny, SL 1999The plastid genome of the cryptophyte alga, Guillardia theta: Complete sequence and conserved synteny groups confirm its common ancestry with red algae.J Mol Evol48236244PubMedGoogle Scholar
  23. 23.
    Draisma, SGA, Prud’homme van Reine, WF, Stam, WT, Olsen, JL 2001A reassesment of phylogenetic relationships within the phaeophyceae based on rubisco large subunit and ribosomal DNA sequences.J Phycol37586603CrossRefGoogle Scholar
  24. 24.
    Felsenstein, J 1985Confidence intervals on phylogenies: An approach using the bootstrap.Evolution39783791Google Scholar
  25. 25.
    Friedl, T 1997The evolution of the green algae.Bhattacharya, D eds. Origins of algae and their plastids.SpringerWien87102Google Scholar
  26. 26.
    Friedl, T, O’Kelly, CJ 2002Phylogenetic relationships of green algae assigned to the genus Planophila (Chlorophyta): Evidence from 18S rDNA sequence data and ultrastructure.Eur J Phycol37373384CrossRefGoogle Scholar
  27. 27.
    Gilbert D (2001) SeqApp: A Macintosh biosequence editor, analyzer, and network handyman. Available at Scholar
  28. 28.
    Gilbert, W 1986The RNA world.Nature319618Google Scholar
  29. 29.
    Glockner, G, Rosenthal, A, Valentin, K 2000The structure and gene repertoire of an ancient red algal plastid genome.J Mol Evol51382390PubMedGoogle Scholar
  30. 30.
    Goddard, MR, Burt, A 1999Recurrent invasion and extinction of a selfish gene.Proc Natl Acad Sci USA961388013885CrossRefPubMedGoogle Scholar
  31. 31.
    Helmchen, T, Bhattacharya, D, Melkonian, M 1995Analyses of ribosomal RNA sequences from glaucocystophyte cyanelles provide new insights into the evolutionary relationships of plastids.J Mol Evol41203210PubMedGoogle Scholar
  32. 32.
    Huelsenbeck, JP, Ronquist, F 2001MrBayes: Bayesian inference of phylogeny.Bioinformatics17754755CrossRefPubMedGoogle Scholar
  33. 33.
    Inoue, T, Sullivan, FX, Cech, TR 1986New reactions of the ribosomal RNA precursor of Tetrahymena and the mechanism of self-splicing.J Mol Biol189143165PubMedGoogle Scholar
  34. 34.
    Karol, KG, McCourt, RM, Cimino, MT, Delwiche, CF 2002The closest living relatives of land plants.Science29423512353CrossRefGoogle Scholar
  35. 35.
    Kenrick, P, Crane, PR 1997The origin and early evolution of plants on land.Nature3893339CrossRefGoogle Scholar
  36. 36.
    Kuhsel, MG, Strickland, R, Palmer, JD 1990An ancient group-I intron shared by eubacteria and chloroplasts.Science25015701573PubMedGoogle Scholar
  37. 37.
    Lambowitz, AM, Caprara, MG, Zimmerly, S, Perlman, PS 1999Group I and group II ribozymes as RNPs: Clues to the past and guides to the future.Gesteland, RFCech, TRAtkins, J eds. The RNA world, 2nd ed.Cold Spring Harbor Laboratory PressCold Spring Harbor, NY451485Google Scholar
  38. 38.
    Martin, W, Stoebe, B, Goremykin, V, Hansmann, S, Hasegawa, M, Kowallik, K 1998Gene transfer to the nucleus and the evolution of chloroplasts.Nature393162165PubMedGoogle Scholar
  39. 39.
    Michel, F, Westhof, E 1990Modelling the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis.J Mol Biol216585610PubMedGoogle Scholar
  40. 40.
    Moore, MJ, Query, CC, Sharp, PA 1993Splicing of precursors to mRNA by the spliceosome.Gesteland, RFAtkins, JF eds. The RNA world.Cold Spring Harbor Laboratory PressCold Spring Harbor, NY303357Google Scholar
  41. 41.
    Nakamura, T, Ohta, M, Sugiura, M, Sugita, M 1999Chloroplast ribonucleoproteins are associated with both mRNAs and intron-containing precursor tRNAs.FEBS Lett460437441CrossRefPubMedGoogle Scholar
  42. 42.
    Nickrent, DL, Parkinson, CL, Palmer, JD, Duff, RJ 2000Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants.Mol Biol Evol1718851895PubMedGoogle Scholar
  43. 43.
    Ohta, N 1997Analysis of a plastid gene cluster reveals a close relationship between Cyanidioschyzon and Cyanidium.J Plant Res110235245Google Scholar
  44. 44.
    Pace, NR, Marsh, TK 1985RNA catalysis and the origin of life.Origins of Life1697116PubMedGoogle Scholar
  45. 45.
    Palmer, JD, Delwiche, CF 1996Second-hand chloroplasts and the case of the disappearing nucleus.Proc Natl Acad Sci USA9374327435CrossRefPubMedGoogle Scholar
  46. 46.
    Pan, J, Thirumalai, D, Woodson, SA 1997Folding of RNA involves parallel pathways.J Mol Biol273713PubMedGoogle Scholar
  47. 47.
    Paquin, B, Kathe, SD, Nierzwicki-Bauer, SA, Shub, DA 1997Origin and evolution of group-I introns in cyanobacterial tRNA genes.J Bacteriol17967986806PubMedGoogle Scholar
  48. 48.
    Potter, D, Saunders, GW, Andersen, RA 1997Phylogenetic relationships of the Raphidophyceae and Xanthophyceae as inferred from nucleotide sequences of the 18S ribosomal RNA gene.Am J Bot84966972Google Scholar
  49. 49.
    Price, JV, Kieft, GL, Kent, JR, Sievers, EL, Cech, TR 1985Sequence requirements for self-splicing of the Tetrahymena thermophila pre-ribosomal RNA.Nucleic Acids Res1318711889PubMedGoogle Scholar
  50. 50.
    Pryer, KM, Schneider, H, Smith, AR, Cranfill, R, Wolf, PG, Hunt, JS, Sipes, SD 2001Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants.Nature409618622CrossRefPubMedGoogle Scholar
  51. 51.
    Reith, M, Munholland, J 1993A high-resolution gene map of the chloroplast genome of the red alga Porphyra purpurea.Plant Cell5465475CrossRefPubMedGoogle Scholar
  52. 52.
    Rodriguez, F, Oliver, JL, Marin, A, Medina, JR 1990The general stochastic model of nucleotide substitution.J Theor Biol142485501PubMedGoogle Scholar
  53. 53.
    Rudi, K, Jakobsen, KS 1997Cyanobacterial tRNA(Leu)(UAA) group I introns have polyphyletic origin.FEMS Microbiol Lett156293298CrossRefPubMedGoogle Scholar
  54. 54.
    Rudi, K, Jakobsen, KS 1999Complex evolutionary patterns of tRNA Leu(UAA) group I introns in the cyanobacterial radiation.J Bacteriol18134453451PubMedGoogle Scholar
  55. 55.
    Rudi, K, Fossheim, T, Jakobsen, KS 2002Nested evolution of a tRNA(Leu)(UAA) group I intron by both horizontal intron transfer and recombination of the entire tRNA locus.J Bacteriol184666671PubMedGoogle Scholar
  56. 56.
    Schopf, JW 1993Microfossils of the early Archaen Apex chert: New evidence of the antiquity of life.Science260640646PubMedGoogle Scholar
  57. 57.
    Soliva, M, Kocyan, A, Widmer, A 2001Molecular phylogenetics of the sexually deceptive orchid genus Ophrys (Orchidaceae) based on nuclear and chloroplast DNA sequences.Mol Phylogenet Evol207888CrossRefPubMedGoogle Scholar
  58. 58.
    Summons, RE, Jahnke, LL, Hope, JM, Logan, GA 19992-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis.Nature400554557CrossRefPubMedGoogle Scholar
  59. 59.
    Swofford, DL 2002PAUP*: Phylogenetic analysis using parsimony (*and other methods) 4.0b8.Sinauer AssociatesSunderland, MAGoogle Scholar
  60. 60.
    Tajima, F, Nei, M 1984Estimation of evolutionary distance between nucleotide sequences.Mol Biol Evol1269285PubMedGoogle Scholar
  61. 61.
    Turner, S, Pryer, KM, Miao, VP, Palmer, JD 1999Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis.J Eukaryot Microbiol46327338PubMedGoogle Scholar
  62. 62.
    Uhlenbeck, OC 1995Keeping RNA happy.RNA146PubMedGoogle Scholar
  63. 63.
    Van der Horst, G, Christian, A, Inoue, T 1991Reconstitution of a group I intron self-splicing reaction with an activator RNA.Proc Natl Acad Sci USA66184188Google Scholar
  64. 64.
    Wallander, E, Albert, VA 2000Phylogeny and classification of Oleaceae based on rps16 and trnL-F sequence data.Am J Bot8718271841PubMedGoogle Scholar
  65. 65.
    Xu, M-Q, Kathe, SD, Goodrich-Blair, H, Nierzwicki-Bauer, SA, Shub, DA 1990Bacterial origin of a chloroplast intron: Conserved self-splicing group-I introns in cyanobacteria.Science25015661570PubMedGoogle Scholar
  66. 66.
    Yoon, HS, Hackett, JD, Pinto, G, Bhattacharya, D 2002The single, ancient origin of chromist plastids.Proc Natl Acad Sci USA991550715512CrossRefPubMedGoogle Scholar
  67. 67.
    Yoon, HS, Lee, JY, Boo, SM, Bhattacharya, D 2001Phylogeny of Alariaceae, Laminariaceae, and Lessoniaceae (Phaeophyceae) based on plastid-encoded RuBisCo spacer and nuclear-encoded ITS sequence comparisons.Mol Phylogenet Evol21231243CrossRefPubMedGoogle Scholar
  68. 68.
    Zaug, AJ, McEvoy, MM, Cech, TR 1993Self-splicing of the group I intron from Anabaena pre-tRNA. Requirement for base-pairing of the exons in the anticodon stem.Biochemistry3279467953PubMedGoogle Scholar

Copyright information

© Springer-Verlag New York Inc. 2003

Authors and Affiliations

  • Dawn Simon
    • 1
  • David Fewer
    • 2
  • Thomas Friedl
    • 2
  • Debashish Bhattacharya
    • 1
    Email author
  1. 1.Department of Biological Sciences and Center for Comparative GenomicsUniversity of Iowa, 210 Biology Building, Iowa City, IA 52242-1324USA
  2. 2.Albrecht-von-Haller-Institut für Pflanzenwissenschaften, Abteilung Experimentelle Phykologie und Sammlung von AlgenkulturenUniversität Göttingen, 37073 GöttingenGermany

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