Fungal Mitochondrial Genomes
| 1) Sequenced fungal mitochondrial genomes |
| 2) Mitochondrial genes and mutants in Neurospora crassa |
Completely sequenced fungal mitochondrial genomes
mtDNA Structure
Fungal mt genomes commonly map as single, circular DNA molecules; however, both linear mt genomes and segmented mtDNAs have been identified. Examples of these are found in Table, with Hyaloraphidium curvatum having a linear mtDNA and the Spizellomyces punctatus genome being composed of 3 circular molecules. The mt genomes of more than 10 fungi, including species of two other genera listed in the table (Candida and Pichia) have been shown to be linear (Fukuhara et al. 1993; Nosek et al. 1998). There is even evidence to support the idea that linear mtDNAs may represent the major form in vivo (Bendich 1996); however, true linear genomes appear to have specific telomeric structures that protect the ends from degradation and ensure that sequence information is not lost during replication (Nosek et al. 1998). For example, the H. curvatum genome has telomeres that consist of long (1.4 kb) inverted repeats (Forget et al. 2002) that are similar to structures associated with other fungal linear mtDNAs (Nosek et al. 1998).
The mitochondrial genome of S. punctatus is unusual in that it is divided into three circular molecules; a large 58.8 kb molecule and two molecules of approximately 1.2 kb. One of the smaller molecules codes for the atp9 gene, whereas the other has no identifiable genes (Laforest et al. 1997). Plant mitochondrial genomes are commonly divided into several molecules, called “subgenomic” mtDNAs, and this is the first report of a divided or segmented mitochondrial genome in fungi. Little is known about how subgenomic molecules are perpetuated in plants yet recombination between molecules can rapidly reorganize gene order and appears to be responsible for the generation of novel, chimeric genes (Hanson 1991).
Mitochondrial Genes
Mitochondrial DNAs generally contain genes encoding hydrophobic subunits of respiratory chain complexes, as well as genes for the large and small ribosomal RNAs and a full set of tRNAs (Gray et al. 1999). The standard repertoire of polypeptides encoded by animal mitochondrial genomes includes apocytochrome b; cytochrome oxidase subunits 1, 2, and 3; NADH dehydrogenase subunits 1, 2, 3, 4, 4L, 5 and 6; and ATPase subunits 6 and 8. Most fungal mitochondria contain the same set of genes plus atp9 which encodes subunit 9 of the ATPase complex. Interestingly, atp9 is encoded by both the nuclear and mitochondrial genomes in N. crassa and Aspergillus nidulans (van den Boogaart et al. 1982; Brown et al. 1985) and is absent from the largest genome (Podospora anserina) shown in Table. In addition, there are commonly intron-encoded ORFs as well as unidentified ORFs that potentially encode polypeptides greater than 100 amino acids. Many fungal mtDNAs also encode a ribosomal protein associated with the small rRNA. Initially identified in S. cerevisiae and called Var1, a second type (S5) was also found in N. crassa. More recently, a homologue to the bacterial small ribosomal subunit protein 3 (rps3) was found in Allomyces macrogynus. After re-examination of Var1 and S5 genes, it was shown they both contain homology to certain regions of rps3 and are all likely related (Bullerwell et al. 2000). The RNA component of RNase P has also been identified in several mtDNAs (rnpB gene).
Other notable differences among mtDNAs are the number of tRNA genes. Higher fungi encode a complete complement of tRNAs sufficient to read all codons, based on an extended wobble hypothesis (Bonitz et al. 1980). In contrast, all the members of the Chytridiales included in Table 1, except Allomyces macrogynus, have only seven or eight tRNA genes. It is likely that the remainder of tRNAs are nuclear-encoded and are imported into mitochondria (Forget et al. 2002). Most genes are encoded on the same strand and the order of genes within fungal mitochondrial genomes varies widely, a likely consequence of the high rate of mtDNA recombination. One common feature is that tRNA genes are often grouped together and these clusters tend to be dispersed throughout the genome and in some cases are involved in processing transcripts of flanking genes. A third-position codon bias of A and T is commonly observed among fungal mitochondrial genes (Gray et al. 1998), and there are many species that deviate from the universal code (Nobrega et al. 1980; Knight et al. 2001). The stop codon UGA is translated as tryptophan in many Ascomycetes, whereas some lower fungi translate the stop codon UAG as leucine (Paquin et al. 1997). In a number of Candida species the 'universal' leucine codon CUG is decoded as serine (O’Sullivan et al. 2001). Other deviations are listed in the footnotes of the Table.
