DNA sequence analysis of the mitochondrial ND4L-ND5 gene complex from Podospora anserina. Duplication of the ND4L gene within its intron

Mapping and characterization of polymorphism in mtDNA of Cryphonectria parasitica: evidence of the presence of an optional intron

The mitochondrial DNA (mtDNA) of the filamentous ascomycete Cryphonectria parasitica is large and polymorphic so, to better understand the nature of the polymorphisms within populations, a small collection of Italian strains of the fungus was examined. Known mtDNA polymorphisms were mapped and found to cluster in four regions of the mtDNA molecule, particularly in the RFLP region 2 where five different mtDNA haplotypes out of 13 strains were identified. This region included an area of 8.4kbp which was entirely sequenced in strain Ep155 showing the presence of two introns. An internal 3.2kbp portion was sequenced also in six additional strains. Sequence comparison of the C. parasitica mitochondrial intronic ORFs revealed similarities to known endonucleases such as those of Podospora anserina and Neurospora crassa. DNA sequence analysis showed that three polymorphisms of this mtDNA region within this population of 12 strains were due to the optional presence in the ND5 gene of an intron and of an intervening sequence within the intron. Evidence was also found within this population of mixed mitochondrial types within a single strain.

Requirements for alternative forms of the activator domain, P5abc, in the Tetrahymena ribozyme

The role of P5abc domain of the Tetrahymena LSU self-splicing Group I intron is to enhance the activity of the intron via tertiary interactions involving A-rich bulge and terminal loops L5b and L5c. We constructed and examined alternative forms of the domain that accelerate the ribozymatic reaction. The results indicate that the characteristic structure of P5c subdomain plays an important role by forming L2xL5c interaction (P14) and that the region flanking P5c subdomain can be significantly mutable without much affecting the activity of the ribozyme.

A robust fungal phytogeny using the mitochondrially encoded NAD5 protein sequence

We present a fungal phylogeny based on mitochondrial NAD5 (subunit of the NADH dehydrogenase) protein sequences. The tree topology is well supported by bootstrap analysis and mostly congruent with trees inferred from nuclear sequences, ultrastructural data, or mitochondrial COX1 and COX3 (subunits of the cytochrome oxidase) protein sequences. The NAD5 tree points to (i) an early divergence of the Chytridiomycetes, (ii) an appearance of Zygomycetes prior to the divergence of Ascomycetes and Basidiomycetes, and (iii) Oomycetes as clearly unrelated to fungi. In addition, this analysis predicts a common ancestor of fungi and animals, to the exclusion of green algae and plants. Our results reinforce the view that protein sequences are of high value in the reconstruction of the phylogenetic history of mitochondria. Key words: protein sequences, mitochondria, phylogeny, fungi, Oomycetes.

The Dictyostelium discoideum mitochondrial genome: a primordial system using the universal code and encoding hydrophilic proteins atypical of metazoan mitochondrial DNA

A 3,345-bp fragment of Dictyostelium discoideum mitochondrial DNA (mtDNA) has been sequenced. This fragment contained the 80-kDa subunit of complex I (NADH:ubiquinone oxidoreductase), encoding a predicted amino acid sequence of 688 residues and a molecular mass of 79,805 daltons which is nuclear encoded in other metazoa. The C-terminus of the D. discoideum complex I gene shared a 10-bp overlap with NADH:ubiquinone oxidoreductase chain 5 (ND5), while 21 bp 5' were three tRNA genes (two isoleucine and a histidine) and a further 25 bp 5' of these genes is the partial sequence (104 residues) of an unidentified open reading frame (ORF104). Both the 80-kDa subunit and the ORF104 were hydrophilic and highly charged, suggesting they are not membrane associated, unlike most mitochondrially encoded proteins in the metazoa. Sequence analysis of the 80-kDa subunit, its adjacent ND5 gene, and ORF104 indicates the universal stop codon TGA, which codes for tryptophan in nearly all nonplant mtDNA, is either unassigned or coding for a stop codon in D. discoideum. The large size of the mitochondrial genome (54 kb), the lack of intergenic sequence, and the apparent use of the universal code suggest D. discoideum mtDNA may encode many primitive genes that are nuclear encoded in higher organisms.

The mitochondrial genome of yeast Hansenula wingei encodes NADH dehydrogenase subunit genes ND4L and ND5

Genes homologous to those encoding mitochondrial NADH dehydrogenase subunits ND4L and ND5 in filamentous fungi were identified in the mitochondrial genome of a budding yeast, Hansenula wingei. The structure and expression of these genes were investigated. The H. wingei ND4L gene is 282 bp long, and potentially codes for a polypeptide of 94 amino acids. The putative ND4L protein sequence shares about 46% homology with the analogous mitochondrial proteins of filamentous fungi. The H. wingei ND5 gene is 1935 bp long, and encodes a 645-residue polypeptide. The derived ND5 protein shares about 38% sequence homology with the analogue in filamentous fungi. The ND4L and ND5 genes have no intervening sequence, and form a gene cluster in the order of 5'-ND4L-ND5-3'. A presumptive mature dicistronic or polycistronic transcript of these genes was detected by Northern blot hybridization. These results strongly indicate that these ND4L and ND5 genes are active. As far as we are aware, this is the first report on the identification of mitochondrially encoded ND genes in yeast.

P2 functions as a spacer in the Tetrahymena ribozyme

The function of the P2 stem-loop region in the group I catalytic intron from Tetrahymena thermophila has been investigated. A comprehensive mutation analysis suggests that the bottom base pair of the P2 stem and nucleotides in the loop L2 are involved in interactions elsewhere on the intron. In addition, the P2 stem can be varied only between 9 and 11 base pairs in length. Phylogenetic evidence (3) from a sub-class of group I introns supports a model in which the P1 and P2 stems are coaxially stacked. We found that variation of the length of P2 does not shift the sites of intron-catalyzed cleavage in P1 (9). This suggests that coaxial stacking of the P1 and P2 stems is unlikely in the Tetrahymena intron. A narrowing of the window for cleavage activity and a drop in cleavage efficiency are observed when substrates with an insertion in P2 are compared with those with a deletion. A possible explanation for this phenomenon is an unfavorable movement of P1 away from the active site as a result of the the lengthening of P2.

Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function

Many group II introns encode reverse transcriptase-like proteins that potentially function in intron mobility and RNA splicing. We compared 34 intron-encoded open reading frames and four related open reading frames that are not encoded in introns. Many of these open reading frames have a reverse transcriptase-like domain, followed by an additional conserved domain X, and a Zn(2+)-finger-like region. Some open reading frames have lost conserved sequence blocks or key amino acids characteristic of functional reverse transcriptases, and some lack the Zn(2+)-finger-like region. The open reading frames encoded by the chloroplast tRNA(Lys) genes and the related Epifagus virginiana matK open reading frame lack a Zn(2+)-finger-like region and have only remnants of a reverse transcriptase-like domain, but retain a readily identifiable domain X. Several findings lead us to speculate that domain X may function in binding of the intron RNA during reverse transcription and RNA splicing. Overall, our findings are consistent with the hypothesis that all of the known group II intron open reading frames evolved from an ancestral open reading frame, which contained reverse transcriptase, X, and Zn(2+)-finger-like domains, and that the reverse transcriptase and Zn(2+)-finger-like domains were lost in some cases. The retention of domain X in most proteins may reflect an essential function in RNA splicing, which is independent of the reverse transcriptase activity of these proteins.

The nad4L gene is encoded between exon c of nad5 and orf25 in the Arabidopsis mitochondrial genome

In the Arabidopsis thaliana mitochondrial genome the gene coding for subunit 4L of NADH dehydrogenase (nad4L) is located between exon c of the nad5 open reading frame and orf25. The physical proximity of these genes further supports the trans-splicing model for assembly of the nad5 mRNA. Some transcripts comprise the nad4L open reading frame cotranscribed with nad5 exon c and orf25, while other mRNAs contain only nad4L and orf25. Both open reading frames for nad4L and orf25 are edited in several positions with different frequencies.

Mitochondrial DNA sequence analysis of the cytochrome oxidase subunit I and II genes, the ATPase9 gene, the NADH dehydrogenase ND4L and ND5 gene complex, and the glutaminyl, methionyl and arginyl tRNA genes from Trichophyton rubrum

In this paper, we present the nucleotide sequence of a 5248 bp-long region of the mitochondrial (mt) genome of the dermatophyte Trichophyton rubrum. This region which represents about 1/4 of the total mt genome of this species reveals a compact organization of genes including: the glutaminyl tRNA, the methionyl tRNA, the cytochrome oxidase subunit I gene, the arginyl tRNA, the mitochondrial version of the ATPase subunit 9 gene, the cytochrome oxidase subunit II gene and a part of the NADH dehydrogenase ND4L and ND5 gene "complex". The main features of the part of mt DNA sequenced is the non-interrupted COXI gene and the presence in the mitochondrial version of the ATPase 9 gene of a small group IA intron. The extensive amino-acid sequence similarity with the equivalent gene in Aspergillus nidulans and Neuropora crassa indicates that this gene codes for a dicyclohexylcarbodiimide binding protein. The conserved arrangement of this portion of the mt genome and the presence of tRNAs between the protein-coding genes are compatible with a large polycistronic transcript processed by the excision of tRNAs, or similar secondary structures, as proposed for other fungal or mammalian mt DNAS.

The higher plant nad5 mitochondrial gene: a conserved discontinuous transcription pattern

The single copy nad5 gene has been identified in the mitochondrial genomes of cauliflower, chicory, potato, fennel, and common bean. In these five dicot species the same organization as in Oenothera, Arabidopsis, wheat, and maize has been found for the gene: it consists of five exons organized into three independent groups. The first group comprises exons I and II, separated by a highly conserved group II intron, while the second group consists of exon III only. In the third group exons IV and V are separated by a group II intron of variable, species-specific, length. Transcription analysis of the nad5 gene in chicory and in cauliflower shows that the five exons are assembled as a mature mRNA through intermolecular interactions and multiple splicing events. Comparison of transcription in the gene with that of wheat and maize suggests that a common mechanism exists in higher plants for nad5 transcript processing.

Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis

Alignment of the 87 available sequences of group I self-splicing introns reveals numerous instances of covariation between distant sites. Some of these covariations cannot be ascribed to historical coincidences or the known secondary structure of group I introns, and are, therefore, best explained as reflecting tertiary contacts. With the help of stereochemical modelling, we have taken advantage of these novel interactions to derive a three-dimensional model of the conserved core of group I introns. Two noteworthy features of that model are its extreme compactness and the fact that all of the most evolutionarily conserved residues happen to converge around the two helices that constitute the substrate of the core ribozyme and the site that binds the guanosine cofactor necessary for self-splicing. Specific functional implications are discussed, both with regard to the way the substrate helices are recognized by the core and possible rearrangements of the introns during the self-splicing process. Concerning potential long-range interactions, emphasis is put on the possible recognition of two consecutive purines in the minor groove of a helix by a GAAA or related terminal loop.

Mitochondrial DNA sequence analysis of the cytochrome oxidase subunit II gene from Podospora anserina. A group IA intron with a putative alternative splice site

A 5 kb region of the 95 kb mitochondrial genome of Podospora anserina race s has been mapped and sequenced (1 kb = 10(3) base-pairs). This DNA region is continuous with the sequence for the ND4L and ND5 gene complex in the accompanying paper. We show that this sequence contains the gene for cytochrome oxidase subunit II (COII). This gene is 4 kb in length and is interrupted by a subgroup IB intron (1267 base-pairs (bp) in length) and a subgroup IA intron (1992 bp in length). This group IA intron has a long open reading frame (ORF; 472 amino acid residues) discontinuous with the upstream exon sequence. A putative alternative splice site is present, which brings the ORF into phase with the 5' exon sequence. The 5'- and 3'-flanking regions of the COII gene contain G + C-rich palindromic sequences that resemble similar sequences flanking many Neurospora crassa mitochondrial genes.