As part of the Phycomyces genome project at JGI, the complete nucleotide sequence of the circular-mapping mitochondrial DNA (mtDNA) has been determined (62,082 bp; A+T content 62.1%). The identified genes that are typical for most fungal mitochondria include those for the large (rnl) and small subunit (rns) ribosomal RNAs, three ATPase subunits (atp6, atp8 and atp9), apocytochrome b (cob), three subunits of the cytochrome oxidase complex (cox1, cox2 and cox3), and seven subunits of the NADH dehydrogenase complex (nad1, nad2, nad3, nad4, nad4L, nad5 and nad6). A total of 19 introns are found, many of which containing open reading frames (ORFs) that code for potential endonucleases. All protein coding genes and ORFs can be translated with the standard translation code.
The reduced set of only 24 tRNAs genes in this mtDNA does not
include
trnI(cau), which would code for a tRNA recognizing AUA codons. Because
no AUA codons are found in mitochondrial protein coding genes of Phycomyces
(same situation in its close relative Rhizopus oryzae),
the 24 tRNAs are sufficient to translate all mitochondrial mRNAs. 5'
processing of tRNA precursors is most likely achieved by a
mitochondrial RNase P, whose RNA subunit is coded by a mitochondrial
gene (rnpB). Its structure is
highly conserved, resembling most that of Rhizopus, Mucor, and other zygomycetes (Seif
et al. 2005).
Like in several other fungal mtDNAs, highly structured and
conserved DNA
elements
are inserted in intergenic spacers, introns, and variable regions of
the
rnl and rns genes.
For further details and access to the primary, annotated
sequence, see the gene annotation page.
References:
Seif E, Leigh J, Liu Y, Roewer I, Forget L, and Lang BF (2005)
Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase
P RNAs, mobile elements, and a close source of the group I intron
invasion in angiosperms.
Nucleic
Acids Res 33:
734-744
Seif E, Cadieux
A and Lang BF (2006)
Hybrid E. coli -
mitochondrial ribonuclease P RNAs are catalytically
active
RNA
12: 1661-1670