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Nucleic Acids Research 2005 33(2):734-744; doi:10.1093/nar/gki199
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Published online 2 February 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms

Elias Seif1, Jessica Leigh2, Yu Liu1, Ingeborg Roewer3, Lise Forget1 and B. Franz Lang1,*

1 Program in Evolutionary Biology, Canadian Institute for Advanced Research; Centre Robert Cedergren, Département de Biochimie, Université de Montréal 2900 Boulevard Edouard-Montpetit, Montréal, Québec, Canada H3T 1J4 2 Department of Biochemistry and Molecular Biology, Dalhousie University Halifax (Nova Scotia), Canada B3H 4H7 3 National Research Council of Canada, Plant, Biotechnology Institute 110 Gymnasium Place, Saskatoon, SK, Canada S7N 0W9

*To whom correspondence should be addressed. Tel: +1 514 343 5842; Fax: +1 514 343 2210; Email: Franz.Lang{at}umontreal.ca

Received October 25, 2004. Revised December 29, 2004. Accepted December 29, 2004.

To generate data for comparative analyses of zygomycete mitochondrial gene expression, we sequenced mtDNAs of three distantly related zygomycetes, Rhizopus oryzae, Mortierella verticillata and Smittium culisetae. They all contain the standard fungal mitochondrial gene set, plus rnpB, the gene encoding the RNA subunit of the mitochondrial RNase P (mtP-RNA) and rps3, encoding ribosomal protein S3 (the latter lacking in R.oryzae). The mtP-RNAs of R.oryzae and of additional zygomycete relatives have the most eubacteria-like RNA structures among fungi. Precise mapping of the 5' and 3' termini of the R.oryzae and M.verticillata mtP-RNAs confirms their expression and processing at the exact sites predicted by secondary structure modeling. The 3' RNA processing of zygomycete mitochondrial mRNAs, SSU-rRNA and mtP-RNA occurs at the C-rich sequence motifs similar to those identified in fission yeast and basidiomycete mtDNAs. The C-rich motifs are included in the mature transcripts, and are likely generated by exonucleolytic trimming of RNA 3' termini. Zygomycete mtDNAs feature a variety of insertion elements: (i) mtDNAs of R.oryzae and M.verticillata were subject to invasions by double hairpin elements; (ii) genes of all three species contain numerous mobile group I introns, including one that is closest to an intron that invaded angiosperm mtDNAs; and (iii) at least one additional case of a mobile element, characterized by a homing endonuclease insertion between partially duplicated genes [Paquin,B., Laforest,M.J., Forget,L., Roewer,I., Wang,Z., Longcore,J. and Lang,B.F. (1997) Curr. Genet., 31, 380–395]. The combined mtDNA-encoded proteins contain insufficient phylogenetic signal to demonstrate monophyly of zygomycetes.

DDBJ/EMBL/GenBank accession nos+

+ AY863211, AY863212, AY8632133, AY861439–AY861442


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