The Mauriceville retroplasmid reverse transcriptase initiates cDNA synthesis de novo at the 3' end of tRNAs

Horizontal transfer of tRNA genes to mitochondrial plasmids facilitates gene loss from fungal mitochondrial DNA

Fungal and plant mitochondria are known to exchange DNA with retroviral plasmids. Transfer of plasmid DNA to the organellar genome is best known and occurs through wholesale insertion of the plasmid. Less well known is the transfer of organellar DNA to plasmids, in particular tRNA genes. Presently, it is unknown whether fungal plasmids can adopt mitochondrial functions such as tRNA production through horizontal gene transfer. In this paper, we studied the exchange of DNA between fungal linear plasmids and fungal mtDNA, mainly focusing on the basidiomycete family Lyophyllaceae. We report at least six independent transfers of complete tRNA genes to fungal plasmids. Furthermore, we discovered two independent cases of loss of a tRNA gene from a fungal mitochondrial genome following transfer of such a gene to a linear mitochondrial plasmid. We propose that loss of a tRNA gene from mtDNA following its transfer to a plasmid creates a mutualistic dependency of the host mtDNA on the plasmid. We also find that tRNA genes transferred to plasmids encode codons that occur at the lowest frequency in the host mitochondrial genomes, possibly due to a higher number of unused transcripts. We discuss the potential consequences of mtDNA transfer to plasmids for both the host mtDNA and the plasmid.

Template-switching mechanism of a group II intron-encoded reverse transcriptase and its implications for biological function and RNA-Seq

The reverse transcriptases (RTs) encoded by mobile group II introns and other non-LTR retroelements differ from retroviral RTs in being able to template-switch efficiently from the 5' end of one template to the 3' end of another with little or no complementarity between the donor and acceptor templates. Here, to establish a complete kinetic framework for the reaction and to identify conditions that more efficiently capture acceptor RNAs or DNAs, we used a thermostable group II intron RT (TGIRT; GsI-IIC RT) that can template switch directly from synthetic RNA template/DNA primer duplexes having either a blunt end or a 3'-DNA overhang end. We found that the rate and amplitude of template switching are optimal from starter duplexes with a single nucleotide 3'-DNA overhang complementary to the 3' nucleotide of the acceptor RNA, suggesting a role for nontemplated nucleotide addition of a complementary nucleotide to the 3' end of cDNAs synthesized from natural templates. Longer 3'-DNA overhangs progressively decreased the template-switching rate, even when complementary to the 3' end of the acceptor template. The reliance on only a single bp with the 3' nucleotide of the acceptor together with discrimination against mismatches and the high processivity of group II intron RTs enable synthesis of full-length DNA copies of nucleic acids beginning directly at their 3' end. We discuss the possible biological functions of the template-switching activity of group II intron- and other non-LTR retroelement-encoded RTs, as well as the optimization of this activity for adapter addition in RNA- and DNA-Seq protocols.

Virus world as an evolutionary network of viruses and capsidless selfish elements

Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus "self" that defines the identity of deep, ancient viral lineages. However, several other widespread viral "hallmark genes" encode key components of the viral replication apparatus (such as polymerases and helicases) and combine with different capsid proteins, given the inherently modular character of viral evolution. Furthermore, diverse, widespread, capsidless selfish genetic elements, such as plasmids and various types of transposons, share hallmark genes with viruses. Viruses appear to have evolved from capsidless selfish elements, and vice versa, on multiple occasions during evolution. At the earliest, precellular stage of life's evolution, capsidless genetic parasites most likely emerged first and subsequently gave rise to different classes of viruses. In this review, we develop the concept of a greater virus world which forms an evolutionary network that is held together by shared conserved genes and includes both bona fide capsid-encoding viruses and different classes of capsidless replicons. Theoretical studies indicate that selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators. Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host.

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.

Is tRNA only a translation factor or also a regulator of other processes?

tRNA has been discovered as a factor playing a central role in the translation of genetic information (encoded in DNA and transcribed to mRNA) into amino acid sequences of proteins. However, subsequent studies led to the hypothesis that during evolution, tRNA originated in replication, not translation. Indeed, there are many examples of tRNA-like molecules playing roles in reactions other than translation, including replication of various replicons. In this review, we have focused on functions of tRNA molecules (not tRNA-like structures) outside of their direct roles in translation as factors for a passive transportation of amino acids into a ribosome and deciphering triplets of nucleotides in codons of mRNA. Interestingly, it appears that such tRNA-dependent reactions are effective only when tRNA is uncharged. The most spectacular examples come from bacterial cells and include induction of the stringent control, regulation of transcription of some operons, and control of replication of ColE1-type plasmids. Recent studies indicated that tRNA (not only pre-tRNA, shown previously to be capable of self-excision of intron sequences) can be responsible for specific cleavage of another transcript, a ColE1 plasmid-encoded RNA I, which is involved in the regulation of plasmid DNA replication initiation. If this reaction is not restricted to RNA I but represents a more general phenomenon, one might suspect a potential role for uncharged tRNA molecules in regulation of various processes, whose efficiency depends on tRNA-cleavable RNAs. This kind of regulation would provide a possibility for a cell to respond to different nutrition conditions resulting in different levels of tRNA aminoacylation.

Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5' and 3' tRNA halves

The discovery of separate 5′ and 3′ halves of transfer RNA (tRNA) molecules—so-called split tRNA—in the archaeal parasite Nanoarchaeum equitans made us wonder whether ancestral tRNA was encoded on 1 or 2 genes. We performed a comprehensive phylogenetic analysis of tRNAs in 45 archaeal species to explore the relationship between the three types of tRNAs (nonintronic, intronic and split). We classified 1953 mature tRNA sequences into 22 clusters. All split tRNAs have shown phylogenetic relationships with other tRNAs possessing the same anticodon. We also mimicked split tRNA by artificially separating the tRNA sequences of 7 primitive archaeal species at the anticodon and analyzed the sequence similarity and diversity of the 5′ and 3′ tRNA halves. Network analysis revealed specific characteristics of and topological differences between the 5′ and 3′ tRNA halves: the 5′ half sequences were categorized into 6 distinct groups with a sequence similarity of >80%, while the 3′ half sequences were categorized into 9 groups with a higher sequence similarity of >88%, suggesting different evolutionary backgrounds of the 2 halves. Furthermore, the combinations of 5′ and 3′ halves corresponded with the variation of amino acids in the codon table. We found not only universally conserved combinations of 5′–3′ tRNA halves in tRNA^iMet, tRNA^Thr, tRNA^Ile, tRNA^Gly, tRNA^Gln, tRNA^Glu, tRNA^Asp, tRNA^Lys, tRNA^Arg and tRNA^Leu but also phylum-specific combinations in tRNA^Pro, tRNA^Ala, and tRNA^Trp. Our results support the idea that tRNA emerged through the combination of separate genes and explain the sequence diversity that arose during archaeal tRNA evolution.

Hybrid mitochondrial plasmids from senescence suppressor isolates of Neurospora intermedia

We analyzed several natural suppressor isolates of the pKalilo-based fungal senescence syndrome of Neurospora intermedia. The pKalilo plasmid did not increase in titer in these isolates. Nor did it show integration "de novo." In at least two of the senescence suppressor isolates, pKalilo had formed stable recombinants with other mitochondrial elements. pKalilo/mtDNA recombination junctions were complete and appeared to have been formed via a nonhomologous recombination mechanism. Further analysis revealed that pKalilo had recombined a novel, 2.6-kb cryptic mitochondrial retroplasmid, similar to the mitochondrial retroplasmid pTHR1 from Trichoderma harzianum and retroplasmids of the "Varkud" homology group. The recombinant molecules consisted of pKalilo, the novel element, and short intervening stretches of mtDNA. The latter stretches clearly corresponded to "in vivo" mitochondrial cDNA, suggesting that the molecules had formed via the action of a template-switching reverse transcriptase. We discuss how different types of mitochondrial plasmids interact and how their detrimental effect on the host may be suppressed.

Co-evolution of the genetic code and ribozyme replication

The origin of translation has stimulated much discussion since the basic processes involved were deciphered during the 1960s and 1970s. One strand of thought suggested that the process originated from RNA replication in the RNA world (Weiner & Maizels, 1987, 1994). In this paper I seek to extend this model. The mRNA originates as a replication intermediate of minus-strand ribozyme replication and thus contains all the genetic information contained in both the ribozyme portion and the putative tRNA-like portion of the RNA molecule. Qualitatively, this is similar to the model for the origin of chromosomes (Szathmary & Maynard-Smith, 1993, Maynard-Smith & Szathmary, 1993). This model explicitly describes the evolution of early chromosomes and the role replication played in generating the modern mRNA. Moreover, by pursuing this model, the START and STOP codons were derived and their original function with regard to the primitive 23S ribosomal RNA is suggested. Co-evolution of the genetic code (Wong, 1975) is also contained within the model. Lastly, I address some of the benefits and costs that the process may have for the organism in the context of autotrophy in the RNA world.

Duplication of a truncated paralog of the family B DNA polymerase gene Aa-polB in the Agrocybe aegerita mitochondrial genome

The Agrocybe aegerita mitochondrial genome contains a truncated family B DNA polymerase gene (Aa-polB P1) whose nucleotide sequence is 86% identical to the previously described and potentially functional Aa-polB gene. A tRNA(Met) gene occurs at the 3' end of the Aa-polB P1 gene. The Aa-polB P1 gene could result from reverse transcription of an Aa-polB mRNA primed by a tRNA(Met) followed by the integration of the cDNA after recombination at the mitochondrial tRNA locus. Two naturally occurring alleles of Aa-polB P1 carry one or two copies of the disrupted sequence. In strains with two copies of Aa-polB P1, these copies are inverted relative to one another and separated by a short sequence carrying the tRNA(Met) gene. Both A. aegerita mitochondrial family B DNA polymerases were found to be related to other family B DNA polymerases (36 to 53% amino acid similarity), including the three enzymes of the archaebacterium Sulfolobus solfataricus. If mitochondria originated from a fusion between a Clostridium-like eubacterium and a Sulfolobus-like archaebacterium, then the A. aegerita family B DNA polymerase genes could be remnants of the archaebacterial genes.

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.

De novo and DNA primer-mediated initiation of cDNA synthesis by the mauriceville retroplasmid reverse transcriptase involve recognition of a 3' CCA sequence

The Mauriceville mitochondrial retroplasmid of Neurospora encodes a novel reverse transcriptase that initiates cDNA synthesis at a 3' tRNA-like structure of the plasmid transcript, either de novo (i.e. without a primer) or by using the 3' OH group of a DNA primer. Both the de novo and primer-mediated initiations involve recognition of structural features at the 3' end of the retroplasmid transcript, which ends with a 3' CCACCA. Here, detailed biochemical characterization of the retroplasmid reverse transcriptase shows that the 3' CCA of the plasmid transcript is the major structural feature recognized by the reverse transcriptase for both the de novo and primer-mediated initiations. Complementarity between the DNA primer and RNA template is not required for the primer-mediated initiation, although short (1 to 3 nt) base-pairing interactions can influence both the efficiency and site of initiation near the 3' end of the transcript. Single nucleotide changes in the 3' CCA lead to less efficient initiation in the upstream CCA with an increased propensity to add extra "non-coded" nucleotides to the 5' end of the cDNA during de novo initiation or to the 3' end of the primer during primer-mediated initiation. Secondary structure features upstream of the 3' CCA also influence the efficiency of initiation, but are not stringently required in vitro. Finally, we find that the retroplasmid reverse transcriptase does not efficiently use DNA primers that are base-paired to internal positions in the RNA template, nor does it use analogs of natural substrates used by non-long terminal repeat retrotransposon or retroviral reverse transcriptases. Our results indicate that the retroplasmid reverse transcriptase is uniquely adapted to initiate cDNA synthesis by recognizing a 3' CCA sequence. The ability to recognize a specific template sequence is common for RNA polymerases, but unprecedented for a reverse transcriptase.