Identification of the reverse transcriptase encoded by the Mauriceville and Varkud mitochondrial plasmids of Neurospora

In vivo conformation and replication intermediates of circular mitochondrial plasmids in Neurospora and Cryphonectria parasitica

The in vivo conformation and replication intermediates of fungal circular mitochondrial plasmids and plasmid-like mitochondrial element (plMEs) were analyzed by two-dimensional gel electrophoresis and electron microscopy. Plasmids with circular restriction maps exist predominantly as circular molecules and were found to replicate by rolling circle mechanisms. However, the reverse transcriptase-encoding Mauriceville plasmid of Neurospora crassa was observed to replicate by two possible mechanisms: one that is consistent with a reverse transcriptase-mediated process and a second one might involve rolling circle DNA replication. Like the mtDNA-derived plasmid-like elements of N. crassa (Hausner et al. 2006a, b), a plasmid-like element of Cryphonectria parasitica (plME-C9), which consists predominantly of a 1.4 kb nucleotide sequence different from mitochondrial DNA, also was found to replicate by a rolling circle mechanism. Although the techniques used in this study were not suited for the establishment of the in vivo conformation and mode of replication of the mtDNAs of Neurospora or Cryphonectria, we surmise that the rolling circle mechanism might be the predominant mode of DNA replication in fungal mitochondria.

Evidence for the phenotypic neutrality of the Neurospora Varkud (V) and Varkud satellite (VS) plasmids

The Varkud satellite (VS) plasmid, which requires the Varkud (V) plasmid for replication, is found in the mitochondria of several natural isolates of Neurospora. The VS transcript is sufficiently abundant that it might be expected to alter the function of mitochondria; however, previous limited characterization revealed no effect. In this work we have used genetic, biochemical and proteomic approaches to search for effects of the V and VS plasmids. We observed differences in the relative abundance of several mitochondrial proteins between plasmid-containing and plasmid-lacking natural isolates, but subsequently found these not to be due to the plasmids. We constructed a pair of iso-nuclear and iso-mitochondrial strains that differed only by the presence or absence of V and VS, and observed only subtle differences in the abundance of several mitochondrial proteins. We further attempted to detect a cryptic plasmid-related phenotype by growing this pair of strains in the presence of a variety of inhibitors of mitochondrial function or other stress conditions: this also revealed no effect of the plasmids. These observations suggest that, despite the high concentration of VS RNA in the mitochondrion, the V and VS plasmids do not cause substantial changes in the host.

Origin of hepatitis delta virus

This article addresses some of the questions relating to how hepatitis delta virus (HDV), an agent so far unique in the animal world, might have arisen. HDV was discovered in patients infected with hepatitis B virus (HBV). It generally makes HBV infections more damaging to the liver. It is a subviral satellite agent that depends upon HBV envelope proteins for its assembly and ability to infect new cells. In other aspects of replication, HDV is both independent of and very different from HBV. In addition, the small single-stranded circular RNA genome of HDV, and its mechanism of replication, demonstrate an increasing number of similarities to the viroids - a large family of helper-independent subviral agents that cause pathogenesis in plants.

Expression and localization of the linear DNA plasmid-encoded protein (RS224) in Rhizoctonia solani AG2-2

Expression of the linear DNA plasmid-encoded protein (RS224) from the plant-pathogenic fungus Rhizoctonia solani isolate H-16, anastomosis group 2-2, and its localization were studied. Extracts from Escherichia coli cells expressing the open reading frame (ORF) of RS224 (RS224ORF in pRS224) contain a 92-kDa T7.Tag-RS224orf fusion protein. Antisera raised against the fusion protein obtained from E. coli cells cross-reacted with a 90-kDa protein in the mycelia. To analyze the subcellular localization of the 92-kDa protein, mycelia of R. solani were disrupted and fractionated. Antibodies against RS224 proteins specifically reacted to the mitochondrial fraction, suggesting that RS224 is localized in mitochondria.

Structural analysis of the plasmid pAAT56 of the filamentous fungus Alternaria alternata

The circular DNA plasmid, designated pAAT56, has been isolated from strain T88-56 of the Japanese pear pathotype of Alternaria alternata. We determined the complete nucleotide sequence (5354 bp) of pAAT56 and mapped its possible open reading frames (ORFs). Three long ORFs, ORF1 (1290 bp), ORF2 (1653 bp) and ORF3 (690 bp), and four smaller ORFs, ORF4 to ORF7 (> or = 300 bp), were predicted from the sequence. The potential peptides derived from the ORFs other than ORF2 show no homology to other known proteins from a database search. However, ORF2 has significant homology to the pol gene of retrotransposons. The polypeptide derived from ORF2 includes sequences homologous to the reverse transcriptase (RT) and ribonuclease H (RNase H) domains of the retrotransposon Pol peptide. Phylogenetic comparison of RT domains from the retroelements placed pAAT56 in the Ty3/gypsy group of long terminal repeat (LTR) retrotransposons, most closely linked with those of filamentous fungi. The PCR primers were designed on the basis of nucleotide sequences encoding the highly-conserved amino-acid sequences in RT domains among pAAT56 and fungal retrotransposons. The PCR amplified the DNA fragments that possibly encode RT from strains of filamentous fungi that have been reported to carry retrotransposons. These results suggest that pAAT56 has acquired the pol gene from a Ty3/gypsy-group retrotransposon.

A reverse transcriptase activity in potato mitochondria

A reverse transcriptase activity has been detected in potato mitochondria using special RNAs as templates: a bacterial RNA coding for neomycin phosphotransferase (neo pa RNA) and a Neurospora crassa mitochondrial RNA (184 nt RNA). Surprisingly, no exogenous primer addition was required. These RNA templates share a primary and secondary structure similar to the T psi CG loop of tRNAs that could constitute the recognition site for the enzyme. Reverse transcriptase activity was inhibited by ddTTP, ethidium bromide and aphidicolin, while potato mitochondrial DNA polymerase was not inhibited by aphidicolin indicating that these activities correspond to distinct enzymes. A conserved sequence of reverse transcriptases was detected in potato mitochondrial DNA suggesting that this enzyme could be mitochondrially encoded.

Rearrangements of mitochondrial DNA and the mitochondrial fusion-promoting plasmid (mF) are associated with defective mitochondrial fusion in Physarum polycephalum

A specific linear mitochondrial plasmid (mF) is genetically associated with the fusion of mitochondria in the true slime mould, Physarum polycephalum. In matings between mF+ and mF- strains, which respectively carry and do not carry the mF plasmid, mitochondrial fusion occurs in the zygote. Mitochondrial fusion induces recombination between specific sites in the mitochondrial DNA (mtDNA) and in the mF plasmid. To detect a region which is associated with the mitochondrial fusion in the mF plasmid, we isolated, by fluorescence microscopy, strains which showed defective mitochondrial fusion (delta mif-) from those which showed normal mitochondrial fusion (mif+). Analysis of the mitochondrial genomes of delta mif- strains showed only mtDNA which recombined with the mF plasmid in mitochondria. Comparison of this recombinant mtDNA in one delta mif- strain (NG 15) with that of a mif+ strain showed that a 2.2-kbp region, which included the integration site of the mF plasmid, was deleted in the delta mif- strain by recombination between the main mtDNA and the mF plasmid. In other strains, in addition to this deletion, a 6-kbp region which included both termini was deleted by recombination at six repeats of AAT sequences in the mF plasmid. Moreover, transcripts of the mF plasmid were not detected in NG15 by slot hybridization.

The Mauriceville and Varkud plasmids: primitive retroelements found inNeurosporamitochondria

The Mauriceville and closely related Varkud plasmids are small circular DNAs (3.6 and 3.7 kb, respectively) found in the mitochondria of certain Neurospora spp. strains isolated from nature. The plasmids replicate via reverse transcription and appear to be primitive retroelements that may be related to the early ancestors of retroviruses. Recent studies have shown that the plasmid reverse transcriptase closely resembles certain viral RNA-dependent RNA polymerases in initiating (−) strand cDNA synthesis de novo (i.e., without a primer) at a tRNA-like structure at the 3′ end of the plasmid transcript. The plasmid reverse transcriptase can also use DNA or RNA primers and can carry out template-switching reactions that lead to the generation of suppressive mutant plasmids or the integration of the plasmids into mitochondrial DNA. The characteristics of the plasmids and their reverse transcription mechanism suggest an evolutionary connection between RNA and DNA replication and raise the possibility that the plasmids are related to the earliest DNA-based life forms that emerged at the time of transition from an RNA to a DNA world. Key words: DNA synthesis, evolution, retrovirus, reverse transcriptase, RNA virus.

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 family of linear plasmids with homology to plasmid pAL2-1 of Podospora anserina

Three recently isolated wild-type strains of the ascomycete Podospora anserina were analyzed for the presence of linear mitochondrial plasmids. In one of these strains, designated Wat, at least 12 distinct plasmid-like elements were identified. From molecular analyses a minimum number of 78 individual linear molecules with proteins bound to their 5' ends was estimated. In addition, the different members of this family of typical linear plasmids were shown to possess a common central region and terminal sequences which differ from one plasmid to another due to the presence of different numbers of a 2.4 kb sequence module. Finally, the pWa6 plasmids share a high degree of sequence similarity with pAL2-1, a linear plasmid previously identified in mitochondria of a long-lived mutant of P.anserina. A mechanism is proposed which explains the generation of these distinct, closely related extra-chromosomal genetic traits.

The VS catalytic RNA replicates by reverse transcription as a satellite of a retroplasmid

The mitochondria of certain natural isolates of Neurospora contain both the Varkud plasmid, which encodes a reverse transcriptase, and a small unrelated RNA (VS RNA) that performs RNA-mediated self-cleavage and ligation reactions. Here, we show that VS RNA is transcribed from a VS plasmid DNA template by the Neurospora mitochondrial RNA polymerase using a promoter located immediately upstream of the RNA self-cleavage site that generates monomeric transcripts. VS RNA is then reverse transcribed by the Varkud plasmid reverse transcriptase to yield a full-length (-) strand cDNA, a predicted replication intermediate. Combined with previous genetic evidence, our results indicate that the VS plasmid replicates by reverse transcription as a satellite of the Varkud plasmid. This mode of replication, unprecedented for a satellite RNA, likely reflects the promiscuity of the Varkud plasmid reverse transcriptase, which does not require a specific primer to initiate cDNA synthesis. Our findings indicate how primitive reverse transcriptases with similar relaxed specificity could have facilitated the evolution of new retroelements.

tRNAs as primer of reverse transcriptases

Genetic elements coding for proteins that present amino acid identity with the conserved motifs of retroviral reverse transcriptases constitute the retroid family. With the exception of reverse transcriptases encoded by mitochondrial plasmids of Neurospora, all reverse transcriptases have an absolute requirement for a primer to initiate DNA synthesis. In retroviruses, plant pararetroviruses, and retrotransposons (transposons containing long terminal repeats), DNA synthesis is primed by specific tRNAs. All these retroelements contain a primer binding site presenting a Watson-Crick complementarity with the primer tRNA. The tRNAs most widely used as primers are tRNA(Trp), tRNA(Pro), tRNA(1,2Lys), tRNA(3Lys), tRNA(iMet). Other tRNAs such as tRNA(Gln), tRNA(Leu), tRNA(Ser), tRNA(Asn) and tRNA(Arg) are also occasionally used as primers. In the retroviruses and plant pararetroviruses, the primer binding site is complementary to the 3' end of the primer tRNA. In the case of retrotransposons, the primer binding site is either complementary to the 3' end or to an internal region of the primer tRNA. Additional interactions taking place between the primer tRNA and the retro-RNA outside of the primer binding site have been evidenced in the case of Rous sarcoma virus, human immunodeficiency virus type I, and yeast retrotransposon Ty1. A selective encapsidation of the primer tRNA, probably promoted by interactions with reverse transcriptase, occurs during the formation of virus or virus-like particles. Annealing of the primer tRNA to the primer binding site appears to be mediated by reverse transcriptase and/or the nucleocapsid protein. Modified nucleosides of the primer tRNA have been shown to be important for replication of the primer binding site, encapsidation of the primer (in the case of Rous sarcoma virus), and interaction with the genomic RNA (in the case of human immunodeficiency virus type I).

Distribution of seven homology groups of mitochondrial plasmids in Neurospora: evidence for widespread mobility between species in nature

A survey of mitochondrial DNAs from over 225 Neurospora and related fungal isolates from around the world uncovered three new homology groups of mitochondrial plasmids, two divergent subgroups of the Fiji plasmid family, and extended previous data about plasmid distribution patterns. Newly-discovered circular plasmids, Java and MB1, and the linear Moorea plasmids, were found in relatively-few isolates. A large proportion of isolates (51%) were found to have these or previously-discovered plasmids in the Varkud, kalilo, LaBelle, or Fiji families. Plasmids in most families were found in isolates worldwide and distributed nearly randomly with respect to species. As many as three types of plasmids were found in single isolates, and plasmids typically were found alone or in pairs in a random, independent pattern. The regional clustering of some plasmids was independent of species, providing a strong argument that horizontal transfer of plasmids occurs frequently in nature. Some plasmid families were much more diverse than others. The Fiji plasmids are a superfamily composed of distinct subgroups defined by degrees of cross-hybridization. Between some subgroups there were large regions of non-homology.

Evidence for a life span-prolonging effect of a linear plasmid in a longevity mutant of Podospora anserina

The linear mitochondrial plasmid pAL2-1 of the long-lived mutant AL2 of Podospora anserina was demonstrated to be able to integrate into the high molecular weight mitochondrial DNA (mtDNA). Hybridization analysis and densitometric evaluation of the mitochondrial genome isolated from cultures of different ages revealed that the mtDNA is highly stable during the whole life span of the mutant. In addition, and in sharp contrast to the situation in certain senescence-prone Neurospora strains, the mutated P. anserina mtDNA molecules containing integrated plasmid copies are not suppressive to wild-type genomes. As demonstrated by hybridization and polymerase chain reaction (PCR) analysis, the proportion of mtDNA molecules affected by the integration of pAL2-1 fluctuates between 10% and 50%. Comparative sequence analysis of free and integrated plasmid copies revealed four differences within the terminal inverted repeats (TIRs). These point mutations are not caused by the integration event since they occur subsequent to integration and at various ages. Interestingly, both repeats contain identical sequences indicating that the mechanism involved in the maintenance of perfect TIRs is active on both free and integrated plasmid copies. Finally, in reciprocal crosses between AL2 and the wild-type strain A, some abnormal progeny were obtained. One group of strains did not contain detectable amounts of plasmid pAL2-1, although the mtDNA was clearly of the type found in the long-lived mutant AL2. These strains exhibited a short-lived phenotype. In contrast, one strain was selected that was found to contain wild-type A-specific mitochondrial genomes and traces of pAL2-1. This strain was characterized by an increased life span. Altogether these data suggest that the linear plasmid pAL2-1 is involved in the expression of longevity in mutant AL2.

The Mauriceville plasmid reverse transcriptase can initiate cDNA synthesis de novo and may be related to reverse transcriptase and DNA polymerase progenitor

We show that the reverse transcriptase (RT) encoded by the Mauriceville mitochondrial plasmid of Neurospora closely resembles viral RNA-dependent RNA polymerases in initiating cDNA synthesis opposite the penultimate C residue of a 3' tRNA-like structure and has the unprecedented ability for a DNA polymerase to initiate DNA synthesis at a specific site in a natural template without a primer. The Mauriceville plasmid enzyme can also use DNA or RNA primers in a manner suggesting how a primitive RT could have evolved from an RNA-dependent RNA polymerase into retroviral and other types of RTs. The characteristics of the Mauriceville plasmid RT suggest that it may be related to the progenitor of present-day RTs and DNA polymerases.

Characterization of circular mitochondrial plasmids in three Pythium species

Four circular plasmids, with a monomer size ranging from 3.2 to 4.94 kb, have been identified in isolates of P. aphanidermatum (two different plasmids), P. torulosum, and an unidentified echinulate isolate. The mitochondrial location has been confirmed for three of the plasmids. Each fungal isolate contained a single plasmid, present in both monomeric and oligomeric forms; plasmid monomers were present as open circles and as supercoiled forms. Restriction maps of the plasmids were dissimilar. Hybridization studies using cloned plasmids revealed no DNA sequence similarity among the different plasmids or between the plasmids and the nuclear or mitochondrial genome of the isolates from which they were recovered. Hybridization of labeled plasmid DNA to Northern transfers of mitochondrial RNA for two isolates indicate that what appears to be the predominant RNA transcript is unit length in size. For three isolates, the plasmid was retained following subculturing and was present in all asexual and sexual single-spore progeny evaluated. For one isolate of P. aphanidermatum the plasmid was unstable and was lost during subculturing.

Analysis of large deletions in the Mauriceville and Varkud mitochondrial plasmids of Neurospora

The Mauriceville and Varkud mitochondrial plasmids are closely related, closed-circular DNAs (3.6 and 3.7 kb, respectively) that have characteristics of mtDNA introns and retroid elements. Both plasmids contain a 710 amino acid open reading frame (ORF) that encodes an 81 kDa protein having reverse transcriptase activity. Here, we analyzed two mutant plasmids, V5-36 and M3-24, that have undergone relatively large deletions (approximately 0.35 and 0.5 kb, respectively). Both deletions occur downstream of the long ORF in a non-coding region of the plasmids that contains a direct repeat of 160 bp and a cluster of five PstI-palindromes, a repetitive sequence element in Neurospora mtDNA. In V5-36, the deletion end points are at the bases of two hairpin structures that are centered around PstI-palindromes and flank the deleted region. In M3-24, the deletion junction contains an extra T-residue that is not encoded in the plasmid. In both plasmids, the deletion end points do not correspond to homologous or directly repeated sequences of more than one nucleotide, whose pairing could account for the deletion junction. The characteristics of the deletion end points can be accounted for either by illegitimate recombination, possibly following double strand breaks at cruciform structures, or by interruption of reverse transcription followed by reinitiation downstream. The finding that the deletions encompass the 160 bp direct repeat and all five PstI-palindromes indicates that neither are required for propagation of the plasmids and supports the hypothesis that PstI-palindromes are selfish DNA elements that inserted into a nonessential region of the plasmid.