MBE Advance Access published online on March 11, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp044
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Research Article |
Phylogenetically close group I introns with different positions among Paramecium bursaria photobionts imply a primitive stage of intron diversification
1 Department of Biomedical Science, College of Life Sciences, Ritsumeikan University
2 Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University
Corresponding author; N Imamura, imamura{at}ph.ritsumei.ac.jp Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Noji Higashi 1-1-1 Kusatsu Shiga, Japan 525-8577
Received for publication June 5, 2008. Revision received October 6, 2008. Revision received December 10, 2008. Revision received February 17, 2009. Accepted for publication February 27, 2009.
Group I introns are a distinct RNA group that catalyse their excision from precursor RNA transcripts, and ligate the exons. Group I introns have a sporadic and highly biased distribution, due to the two intron-transfer mechanisms of homing and reverse splicing. These transfer pathways recognise assigned sequences even when introns are transferred beyond the species level. Consequently, introns at homologous gene sites between different host organisms are more related than those at heterologous sites within an organism. We describe the subgroup IE introns of two Chlorella species that are symbiotic green algae (photobionts) of a ciliate, Paramecium bursaria. One strain Chlorella sp. SW1-ZK (Csw.) had two IE introns at S651 and L2449, and the other strain Chlorella sp. OK1-ZK (Cok.) had four IE introns at S943, L1688, L1926 and L2184 (numbering reflects their homologous position in Escherichia coli rRNA gene: S = SSU rRNA, L = LSU rRNA). Despite locating on six heterologous sites, the introns formed a monophyletic clade independent of other groups. Phylogenetic and structural analyses of the introns indicated that Csw.L2449 has an archaic state and the other introns are assumed to be originated from this intron. Some of the introns shared common internal guide sequences (IGS), which are necessary for misdirected transfer (i.e., transposition) via reverse splicing. Other introns, however, shared similar sequence fragments further upstream, after the insertions. We propose a hypothetical model to explain how these intron transpositions may have occurred in these photobionts; they transposed by a combination of homing-like event requiring relaxed sequence homology of recognition sequences and reverse splicing. This case study may represent a key to describe how group I intron explore new insertion sites.
Key Words: degenerative homing • intron diversification • intron transposition • Paramecium bursaria symbiotic algae • reverse splicing
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