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

Abstract

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.

The RNase P family

“…These secondary structures are highly variable in length, ranging from 188 nt to 982 nt. 41 The P12 and P15 regions . Representative eukaryotic nuclear RNase P RNAs.…”

“…20 of these RNAs contains remarkable variation in length, sequence and structure. 41 RNase P. Ascomycete mitochondrial RNase P RNAs are, on the other hand, highly reduced in size and lack most of the sequence and structural elements conserved in other RNase P RNAs. [42][43][44][45] The human (and presumably other metazoans) mitochondrial RNase P lacks the RNA subunit entirely; the RNase P catalytic function has been replaced by a Rube Goldberg triad of unrelated proteins.…”

Hybrid E. coli—Mitochondrial ribonuclease P RNAs are catalytically active

“…P-RNA genes (rnpB) have been identified in numerous species from all domains of life, also including plastids and mitochondria (Seif et al 2003(Seif et al , 2005. When present, the P-RNA subunit seems indispensable for the endonucleolytic activity of RNase P (e.g., Stark et al 1978;Gardiner and Pace 1980;Kline et al 1981;Hollingsworth and Martin 1986;Jayanthi and Van Tuyle 1992;Baum et al 1996;Lee et al 1996a;Han et al 1998;Vainauskas et al 1998;Thomas et al 2000;Stathopoulos et al 2001).…”

“…1A; Lang et al 1997), reflecting consecutive losses of structural elements from an ancestral a-proteobacteriumlike P-RNA (Seif et al 2003(Seif et al , 2005. In budding yeasts and in the zygomycete Smittium culisetae, secondary structures of mtP-RNAs are reduced to two elements only: P1 and P4 (Seif et al 2003(Seif et al , 2005Talla et al 2005).…”

“…Secondary structure models of bacteria-like mtP-RNAs. (A) Minimum bacterial consensus (Brown et al 1994) and mtP-RNA secondary structure models for R. americana #50394, N. olivacea (Turmel et al 1999) and Rhizopus oryzae (Seif et al 2005). The S-domain is shown in red, and the C-domain is in black.…”