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MBE Advance Access published online on March 19, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh126
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted February 17, 2004
© 2004 Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved.

Original Articles

Twelve Group I Introns in the Same Pre-rRNA Transcript of the Myxomycete Fuligo septica: RNA Processing and Evolution

Eirik W. Lundblad 1, Christer Einvik 1, Sissel Rønning 1, Kari Haugli 1, and Steinar Johansen 2*

1 Department of Molecular Biotechnology - RNA research group, Institute of Medical Biology, University of Tromsø, Tromsø, Norway
2 Department of Molecular Biotechnology - RNA research group, Institute of Medical Biology, University of Tromsø, Tromsø, Norway; Faculty of Fishery and Natural Sciences, Bodø Regional University, Bodø, Norway

* To whom correspondence should be addressed. E-mail: Steinar.Johansen{at}fagmed.uit.no.


  Abstract

The ribosomal DNA region of the myxomycete Fuligo septica was investigated and found to contain 12 group I introns (4 in the small subunit and 8 in the large subunit ribosomal RNAs). We have performed molecular and phylogenetic analyses in order 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 analysed 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.

Key Words: Fuligo, group I intron, myxomycete, ribosomal RNA, RNA splicing


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