Development of an in vitro transcription system for Neurospora crassa mitochondrial DNA and identification of transcription initiation sites

RNA-level unscrambling of fragmented genes in Diplonema mitochondria

We previously reported a unique genome with systematically fragmented genes and gene pieces dispersed across numerous circular chromosomes, occurring in mitochondria of diplonemids. Genes are split into up to 12 short fragments (modules), which are separately transcribed and joined in a way that differs from known trans-splicing. Further, cox1 mRNA includes six non-encoded uridines indicating RNA editing. In the absence of recognizable cis-elements, we postulated that trans-splicing and RNA editing are directed by trans-acting molecules. Here, we provide insight into the post-transcriptional processes by investigating transcription, RNA processing, trans-splicing and RNA editing in cox1 and at a newly discovered site in cob. We show that module precursor transcripts are up to several thousand nt long and processed accurately at their 5' and 3' termini to yield the short coding-only regions. Processing at 5' and 3' ends occurs independently, and a processed terminus engages in trans-splicing even if the module's other terminus is yet unprocessed. Moreover, only cognate module transcripts join, though without directionality. In contrast, module transcripts requiring RNA editing only trans-splice when editing is completed. Finally, experimental and computational analyses suggest the existence of RNA trans-factors with the potential for guiding both trans-splicing and RNA editing.

The Cryphonectria parasitica mitochondrial rns gene: plasmid-like elements, introns and homing endonucleases

The mt-rns gene of Cryphonectria parasitica is 9872bp long and includes two group I and two group II introns. An analysis of intronic protein-encoding sequences revealed that LAGLIDADG ORFs, which usually are associated with group I introns, were transferred at least twice into group II introns. A plasmid-like mitochondrial element (plME) that appears in high amounts in previously mutagen-induced mit1 and mit2 hypovirulent mutants of the Ep155 standard virulent strain of C. parasitica was found to be derived from a short region of the mt-rns gene, including the exon 1 and most of the first intron. The plME is a 4.2-kb circular, multimeric DNA and an autonomously-replicating mtDNA fragment. Although sexual transmission experiments indicate that the plME does not directly cause hypovirulence, its emergence is one manifestation of the many complex molecular and genetic events that appear to underlie this phenotype.

The complete mitochondrial genome of the vascular wilt fungus Verticillium dahliae: a novel gene order for Verticillium and a diagnostic tool for species identification

The complete sequence (27,184 bp) of the mitochondrial (mt) genome of the phytopathogenic fungus Verticillium dahliae has been determined. It contains 14 protein-coding genes related to oxidative phosphorylation, two rRNA genes and a set of 25 tRNA genes. A single intron, that harbors an intronic ORF coding for a putative ribosomal protein (rps), is located within the large rRNA gene (rnl). Gene order comparisons of V. dahliae mtDNA and complete mt genomes of Pezizomycotina revealed four units of synteny for Sordariomycetes, namely rnl-trn ((11-12))-nad2-nad3, nad4L-nad5-cob-cox1, nad1-nad4-atp8-atp6 and rns-trn ((1-5))-cox3-trn ((1-5))-nad6-trn ((2-5)). These four units, in different combinations, merged to single continuous unit in the orders of Hypocreales and Sordariales. V. dahliae (Phyllachorales) and all members of the genus showed a unique feature which is the translocation of the nad1-nad4-atp8-atp6-rns-cox3-nad6 region in between genes nad3 and atp9 of the Hypocreales mtDNA gene order. Analysis of mt intergenic sequences of Verticillium species permitted the design of a species-specific primer allowing the discrimination of V. longisporum against V. dahliae and V. albo-atrum. By considering the protein-coding gene sequences as one unit, a phylogenetic comparison with representatives of Ascomycota complete mtDNA was performed.

Biogenesis and replication of small plasmid-like derivatives of the mitochondrial DNA in Neurospora crassa

For reasons that are not obvious, sets of related, small, plasmid-like elements appear spontaneously and become amplified in the mitochondria of some cytochrome-deficient and/or UV-sensitive mutants of Neurospora crassa. These plasmid-like DNAs are multimeric series of circular molecules, each consisting of a finite number of identical tandem repeats of a relatively short mtDNA-derived nucleotide sequence (monomer). The plasmid-like elements that have been characterized in this study consist of monomers that vary in length from 125 to 296 base pairs, depending on the strain of origin. Each monomer includes a GC-rich palindrome that is followed by the promoter and a short section of the 5' terminal region of the mitochondrial large-subunit rRNA gene (rnl). Analyses of the nucleotide sequences of variants of this group of elements indicates that they are not generated by intra-molecular recombination, but are the result of single- or double-strand DNA breaks that are produced by a mismatch or base excision repair process. These elements do not appear to contain a defined origin of replication, but replicate by a recombination-dependent rolling-circle mechanism. One- and two-dimensional gel electrophoresis of the plasmid-like element derived Hind III and Pst I fragments combined with S1 nuclease treatments suggest that the intergenic GC-rich palindromes, which are ubiquitous in the mtDNA Neurospora, could be replication fork pausing points.

Transcripts and transcript-binding proteins in mitochondria of Neurospora crassa

We analyzed expression elements of three disparate groups of mitochondrial genes in Neurospora crassa, apocytochrome b (COB), cytochrome c oxidase 1 (COX1), and the clustered ATP8-ATP6-mtATP9-COX2. To identify promoter sequences we employed the published N. crassa consensus sequence for COB and rRNA genes, and we found closely related sequences within the 5'-regions of both COX1 and the ATP8-COX2 transcriptional units. We determined that the mature COX1 RNA includes two flanking unassigned reading frame (URF) sequences, but the 3'-flanking ND1 is not included in the COX1 mRNA. The ATP8-ATP6-mtATP9-COX2 polycistronic transcript does not include an adjacent 5'-URF sequence. Primer extension analysis showed one likely 5'-end for the COX1 transcript, which is 73 nucleotides downstream of the consensus promoter sequence and is the first nucleotide 3' of the sequence for the tRNA(cys). Primer extension analysis and S1 nuclease mapping of the ATP8-COX2 RNA showed that the 5'-end for this transcript is the first nucleotide 3' of the consensus promoter sequence. We performed gel-shift experiments to detect proteins in mitochondria that bind to transcripts as possible regulatory proteins. The 5'-untranslated region (UTR) RNAs of COB, COX1, and ATP8-COX2 appear to bind both unique proteins and an overlapping group of two to four proteins of approximately 155-45 M(r). We successively deleted regions of the RNA 5'-UTRs to identify sequences that bound these proteins. Similar predicted stem-loop secondary structures were detected in the protein-binding regions of all three UTRs.

Characterization of an unusual tRNA-like sequence found inserted in a Neurospora retroplasmid

We characterized an unusual tRNA-like sequence that had been found inserted in suppressive variants of the mitochondrial retroplasmid of Neurospora intermedia strain Varkud. We previously identified two forms of the tRNA-like sequence, one of 64 nt (TRL-64)and the other of 78 nt (TRL-78) containing a 14-nt internal insertion in the anticodon stem at a position expected for a nuclear tRNA intron. Here, we show that TRL-78 is encoded in Varkud mitochondrial (mt)DNA within a 7 kb sequence that is not present in Neurospora crassa wild-type 74A mtDNA. This 7-kb insertion also contains a perfectly duplicated tRNA(Trp)gene, segments of several mitochondrial plasmids and numerous GC-rich pallindromic sequences that are repeated elsewhere in the mtDNA. The mtDNA-encoded copy of TRL-78 is transcribed and apparently undergoes 5'- and 3'-end processing and 3' nucleotide addition by tRNA nucleotidyl transferase to yield a discrete tRNA-sized molecule. However, the 14 nt intron-like sequence in TRL-78, which is missing in the TRL-64 form, is not spliced detectably in vivo or in vitro. Our results show that TRL-78 is an unusual tRNA-like species that could be incorporated into suppressive retroplasmids by the same reverse transcription mechanism used to incorporate mt tRNAs. The tRNA-like sequence may have been derived from an intron-containing nuclear tRNA gene or it may serve some function, like tmRNA. Our results suggest that mtRNAs or tRNA-like species may be integrated into mtDNA via reverse transcription, analogous to SINE elements in animal cells.

Characterization of an unusual tRNA-like sequence found inserted in a Neurospora retroplasmid

We characterized an unusual tRNA-like sequence that had been found inserted in suppressive variants of the mitochondrial retroplasmid of Neurospora intermedia strain Varkud. We previously identified two forms of the tRNA-like sequence, one of 64 nt (TRL-64) and the other of 78 nt (TRL-78) containing a 14-nt internal insertion in the anticodon stem at a position expected for a nuclear tRNA intron. Here, we show that TRL-78 is encoded in Varkud mitochondrial (mt)DNA within a 7 kb sequence that is not present in Neurospora crassa wild-type 74 A mtDNA. This 7-kb insertion also contains a perfectly duplicated tRNA(Trp)gene, segments of several mitochondrial plasmids and numerous GC-rich palindromic sequences that are repeated elsewhere in the mtDNA. The mtDNA-encoded copy of TRL-78 is transcribed and apparently undergoes 5'- and 3'-end processing and 3' nucleotide addition by tRNA nucleotidyl transferase to yield a discrete tRNA-sized molecule. However, the 14 nt intron-like sequence in TRL-78, which is missing in the TRL-64 form, is not spliced detectably in vivo or in vitro. Our results show that TRL-78 is an unusual tRNA-like species that could be incorporated into suppressive retroplasmids by the same reverse transcription mechanism used to incorporate mt tRNAs. The tRNA-like sequence may have been derived from an intron-containing nuclear tRNA gene or it may serve some function, like mtRNA. Our results suggest that mt tRNAs or tRNA-like species may be integrated into mtDNA via reverse transcription, analogous to SINE elements in animal cells.

Recombinant mitochondrial plasmids in Neurospora composed of Varkud and a new multimeric mitochondrial plasmid

A mitochondrial plasmid, V5124, in Neurospora intermedia isolate 5124 has a deletion in its sequence relative to the highly similar Mauriceville and Varkud plasmids. These insertions in the latter plasmids are 28 bp in length and are positioned at sites that correspond to their major transcript 5' termini. The 28-bp sequence is nearly identical to a putative processing site upstream of the ND4L gene on the mitochondrial genome. The absence of this 28-bp sequence in V5124 apparently results in transcripts whose 5' termini correspond to an upstream consensus promoter sequence. Two variant forms of V5124 coexist with V5124 and have either of two similar 0.3-kb inserts positioned exactly as is the 28-bp insert in Varkud. These long inserts are chimeric, partly deriving from a newly discovered multimeric plasmid, MP. MP has significant similarity to a short region of the mitochondrial satellite plasmid VS. Another part of the 0.3-kb inserts in V5124 variants derives from the mitochondrial genome, within restriction fragment EcoRI-8. Neurospora mitochondria in many isolates can have several types of mitochondrial plasmids belonging to different homology groups. We propose that a common ancestral plasmid acquired insertions from either the mitochondrial genome or from other plasmids. The V5124 variants are the first instance of a chimeric mitochondrial plasmid in which distinct plasmids have recombined. This recombination proves that different plasmids coexist currently, or else did so at some point in their evolution, within a single mitochondrion.

A novel pea mitochondrial in vitro transcription system recognizes homologous and heterologous mRNA and tRNA promoters

To elucidate the mechanism involved in the transcription initiation process in mitochondria of dicotyledonous plants, an in vitro transcription system was established for pea (Pisum sativum L.). The partially purified mitochondrial protein extract initiates transcription on homologous pea templates as well as on heterologous mitochondrial DNA from other dicot plant species. In vitro transcription begins within the nonanucleotide 5'-(-7)CRTAAGAGA(+2)-3' (transcription start site is underlined) conserved at most of the identified transcription initiation sites in dicot plant mitochondria. The in vitro initiation at promoters of protein as well as of tRNA coding genes indicates a common mode of transcription initiation for different types of RNA. The competent recognition of different heterologous templates supports a general functional role of the conserved nonanucleotide within mitochondrial promoters of dicotyledonous plants. Initial studies of the promoter structure by deletion analysis in the 5' region of the pea atp9 promoter show that in addition to the conserved nonanucleotide, which is essential for transcription initiation in vitro, sequences up to 25 nucleotides upstream of the transcription start site are necessary for an efficient initiation event.

Senescence-specific mitochondrial DNA molecules in P. anserina: evidence for transcription and normal processing of the RNA

In Podospora anserina the phenomenon of senescence was previously shown to be correlated with the presence of senescence-specific circular DNAs (senDNAs), resulting from the amplification of distinct regions (alpha, beta, gamma and epsilon) of the mitochondrial chromosome. The beta region gives rise to senDNAs with variable sizes, but sharing a 1-kb common sequence. Here, we present a molecular analysis of five beta senDNAs. We have determined the nucleotide sequence around the circularization site of each senDNA monomer. In two cases, the presence of a tRNA gene, very close to the 3' end of the monomer, has been observed. This suggests that some beta senDNAs could be generated via a reverse transcription step. We have furthermore shown that the beta senDNAs produce specific transcripts which undergo normal processing of their introns. We propose that a transcription start site, located in the beta common region, is involved in mitochondrial replication allowing the amplification of the beta senDNAs.

Transcripts and translation products of a mitochondrial plasmid of Claviceps purpurea

Expression of the linear mitochondrial (mt) plasmid pClK1 of strain K of the ascomycete Claviceps purpurea was studied at the RNA and protein level. Using strand-specific probes two major transcripts were detected, corresponding to ORF1 and ORF2 of the plasmid, which most likely code for a DNA-polymerase and an RNA-polymerase, respectively. Primer extension experiments showed that both transcripts start at identical positions from opposite sides within the terminal inverted repeat (TIR). The initiation sequence corresponds to the proposed general mt initiation consensus-sequence. Conserved parts of the putative polymerase ORFs were expressed in an E. coli system and used to prepare antisera. In Western experiments the presence of corresponding proteins was demonstrated in a strain carrying plasmid pClK1, whereas a plasmid-free strain lacked these polypeptides. The sizes of these proteins are in good accordance with the sizes derived from the coding capacity of ORF1 and 2.

Sequence analysis of wheat mitochondrial transcripts capped in vitro: definitive identification of transcription initiation sites

To identify transcription initiation sites in wheat mitochondria, the nascent 5'-ends of transcripts were specifically labeled by incubation of wheat mitochondrial RNA with [alpha-32P]GTP in the presence of the enzyme guanylyltransferase. After separation of the resulting capped transcripts by electrophoresis in polyacrylamide gels, individual RNAs were recovered and directly sequenced. Four RNA sequences obtained in this way were localized upstream of the protein-coding genes atpA, coxII, coxIII and orf25. Comparison of mRNA and gene sequences allowed precise positioning of transcription initiation sites for these four genes. Sequence similarities immediately upstream of these sites define a conserved motif that we suggest as a candidate regulatory element in wheat mtDNA. The relationship between this motif and putative mitochondrial promoters in other plant species is discussed.