Origin, evolution, and mechanism of 5' tRNA editing in chytridiomycete fungi

Thg1 family 3'-5' RNA polymerases as tools for targeted RNA synthesis

Members of the 3'-5' RNA polymerase family, comprised of tRNAHis guanylyltransferase (Thg1) and Thg1-like proteins (TLPs), catalyze templated synthesis of RNA in the reverse direction to all other known 5'-3' RNA and DNA polymerases. The discovery of enzymes capable of this reaction raised the possibility of exploiting 3'-5' polymerases for posttranscriptional incorporation of nucleotides to the 5'-end of nucleic acids without ligation, and instead by templated polymerase addition. To date, studies of these enzymes have focused on nucleotide addition to highly structured RNAs, such as tRNA and other noncoding RNAs. Consequently, general principles of RNA substrate recognition and nucleotide preferences that might enable broader application of 3'-5' polymerases have not been elucidated. Here, we investigated the feasibility of using Thg1 or TLPs for multiple nucleotide incorporation to the 5'-end of a short duplex RNA substrate, using a templating RNA oligonucleotide provided in trans to guide 5'-end addition of specific sequences. Using optimized assay conditions, we demonstrated a remarkable capacity of certain TLPs to accommodate short RNA substrate-template duplexes of varying lengths with significantly high affinity, resulting in the ability to incorporate a desired nucleotide sequence of up to eight bases to 5'-ends of the model RNA substrates in a template-dependent manner. This work has further advanced our goals to develop this atypical enzyme family as a versatile nucleic acid 5'-end labeling tool.

The linear mitochondrial genome of the quarantine chytrid Synchytrium endobioticum; insights into the evolution and recent history of an obligate biotrophic plant pathogen

BACKGROUND

Chytridiomycota species (chytrids) belong to a basal lineage in the fungal kingdom. Inhabiting terrestrial and aquatic environments, most are free-living saprophytes but several species cause important diseases: e.g. Batrachochytrium dendrobatidis, responsible for worldwide amphibian decline; and Synchytrium endobioticum, causing potato wart disease. S. endobioticum has an obligate biotrophic lifestyle and isolates can be further characterized as pathotypes based on their virulence on a differential set of potato cultivars. Quarantine measures have been implemented globally to control the disease and prevent its spread. We used a comparative approach using chytrid mitogenomes to determine taxonomical relationships and to gain insights into the evolution and recent history of introductions of this plant pathogen.

RESULTS

We assembled and annotated the complete mitochondrial genome of 30 S. endobioticum isolates and generated mitochondrial genomes for five additional chytrid species. The mitochondrial genome of S. endobioticum is linear with terminal inverted repeats which was validated by tailing and PCR amplifying the telomeric ends. Surprisingly, no conservation in organisation and orientation of mitochondrial genes was observed among the Chytridiomycota except for S. endobioticum and its sister species Synchytrium microbalum. However, the mitochondrial genome of S. microbalum is circular and comprises only a third of the 72.9 Kbp found for S. endobioticum suggesting recent linearization and expansion. Four mitochondrial lineages were identified in the S. endobioticum mitochondrial genomes. Several pathotypes occur in different lineages, suggesting that these have emerged independently. In addition, variations for polymorphic sites in the mitochondrial genome of individual isolates were observed demonstrating that S. endobioticum isolates represent a community of different genotypes. Such communities were shown to be complex and stable over time, but we also demonstrate that the use of semi-resistant potato cultivars triggers a rapid shift in the mitochondrial haplotype associated with increased virulence.

CONCLUSIONS

Mitochondrial genomic variation shows that S. endobioticum has been introduced into Europe multiple times, that several pathotypes emerged multiple times, and that isolates represent communities of different genotypes. Our study represents the most comprehensive dataset of chytrid mitogenomes, which provides new insights into the extraordinary dynamics and evolution of mitochondrial genomes involving linearization, expansion and reshuffling.

Repairing tRNA termini: News from the 3' end

The removal of transcriptional 5' and 3' extensions is an essential step in tRNA biogenesis. In some bacteria, tRNA 5'- and 3'-end maturation require no further steps, because all their genes encode the full tRNA sequence. Often however, the ends are incomplete, and additional maturation, repair or editing steps are needed. In all Eukarya, but also many Archaea and Bacteria, e.g., the universal 3'-terminal CCA is not encoded and has to be added by the CCA-adding enzyme. Apart from such widespread "repair/maturation" processes, tRNA genes in some cases apparently cannot give rise to intact, functional tRNA molecules without further, more specific end repair or editing. Interestingly, the responsible enzymes as far as identified appear to be polymerases usually involved in regular tRNA repair after damage. Alternatively, enzymes are recruited from other non-tRNA pathways; e.g., in animal mitochondria, poly(A) polymerase plays a crucial role in the 3'-end repair/editing of tRNAs. While these repair/editing pathways apparently allowed peculiar tRNA-gene overlaps or mismatching mutations in the acceptor stem to become genetically fixed in some present-day organisms, they may have also driven some global changes in tRNA maturation on a greater evolutionary scale.

Identification of distinct biological functions for four 3'-5' RNA polymerases

The superfamily of 3'-5' polymerases synthesize RNA in the opposite direction to all other DNA/RNA polymerases, and its members include eukaryotic tRNA(His) guanylyltransferase (Thg1), as well as Thg1-like proteins (TLPs) of unknown function that are broadly distributed, with family members in all three domains of life. Dictyostelium discoideum encodes one Thg1 and three TLPs (DdiTLP2, DdiTLP3 and DdiTLP4). Here, we demonstrate that depletion of each of the genes results in a significant growth defect, and that each protein catalyzes a unique biological reaction, taking advantage of specialized biochemical properties. DdiTLP2 catalyzes a mitochondria-specific tRNA(His) maturation reaction, which is distinct from the tRNA(His) maturation reaction typically catalyzed by Thg1 enzymes on cytosolic tRNA. DdiTLP3 catalyzes tRNA repair during mitochondrial tRNA 5'-editing in vivo and in vitro, establishing template-dependent 3'-5' polymerase activity of TLPs as a bona fide biological activity for the first time since its unexpected discovery more than a decade ago. DdiTLP4 is cytosolic and, surprisingly, catalyzes robust 3'-5' polymerase activity on non-tRNA substrates, strongly implying further roles for TLP 3'-5' polymerases in eukaryotes.

In vitro substrate specificities of 3'-5' polymerases correlate with biological outcomes of tRNA 5'-editing reactions

Protozoan mitochondrial tRNAs (mt-tRNAs) are repaired by a process known as 5'-editing. Mt-tRNA sequencing revealed organism-specific patterns of editing G-U base pairs, wherein some species remove G-U base pairs during 5'-editing, while others retain G-U pairs in the edited tRNA. We tested whether 3'-5' polymerases that catalyze the repair step of 5'-editing exhibit organism-specific preferences that explain the treatment of G-U base pairs. Biochemical and kinetic approaches revealed that a 3'-5' polymerase from Acanthamoeba castellanii tolerates G-U wobble pairs in editing substrates much more readily than several other enzymes, consistent with its biological pattern of editing.

tRNA biology in mitochondria

Mitochondria are the powerhouses of eukaryotic cells. They are considered as semi-autonomous because they have retained genomes inherited from their prokaryotic ancestor and host fully functional gene expression machineries. These organelles have attracted considerable attention because they combine bacterial-like traits with novel features that evolved in the host cell. Among them, mitochondria use many specific pathways to obtain complete and functional sets of tRNAs as required for translation. In some instances, tRNA genes have been partially or entirely transferred to the nucleus and mitochondria require precise import systems to attain their pool of tRNAs. Still, tRNA genes have also often been maintained in mitochondria. Their genetic arrangement is more diverse than previously envisaged. The expression and maturation of mitochondrial tRNAs often use specific enzymes that evolved during eukaryote history. For instance many mitochondria use a eukaryote-specific RNase P enzyme devoid of RNA. The structure itself of mitochondrial encoded tRNAs is also very diverse, as e.g., in Metazoan, where tRNAs often show non canonical or truncated structures. As a result, the translational machinery in mitochondria evolved adapted strategies to accommodate the peculiarities of these tRNAs, in particular simplified identity rules for their aminoacylation. Here, we review the specific features of tRNA biology in mitochondria from model species representing the major eukaryotic groups, with an emphasis on recent research on tRNA import, maturation and aminoacylation.

From end to end: tRNA editing at 5'- and 3'-terminal positions

During maturation, tRNA molecules undergo a series of individual processing steps, ranging from exo- and endonucleolytic trimming reactions at their 5'- and 3'-ends, specific base modifications and intron removal to the addition of the conserved 3'-terminal CCA sequence. Especially in mitochondria, this plethora of processing steps is completed by various editing events, where base identities at internal positions are changed and/or nucleotides at 5'- and 3'-ends are replaced or incorporated. In this review, we will focus predominantly on the latter reactions, where a growing number of cases indicate that these editing events represent a rather frequent and widespread phenomenon. While the mechanistic basis for 5'- and 3'-end editing differs dramatically, both reactions represent an absolute requirement for generating a functional tRNA. Current in vivo and in vitro model systems support a scenario in which these highly specific maturation reactions might have evolved out of ancient promiscuous RNA polymerization or quality control systems.

Mitochondrial tRNA 5'-editing in Dictyostelium discoideum and Polysphondylium pallidum

Mitochondrial tRNA (mt-tRNA) 5'-editing was first described more than 20 years ago; however, the first candidates for 5'-editing enzymes were only recently identified in a eukaryotic microbe (protist), the slime mold Dictyostelium discoideum. In this organism, eight of 18 mt-tRNAs are predicted to be edited based on the presence of genomically encoded mismatched nucleotides in their aminoacyl-acceptor stem sequences. Here, we demonstrate that mt-tRNA 5'-editing occurs at all predicted sites in D. discoideum as evidenced by changes in the sequences of isolated mt-tRNAs compared with the expected sequences encoded by the mitochondrial genome. We also identify two previously unpredicted editing events in which G-U base pairs are edited in the absence of any other genomically encoded mismatches. A comparison of 5'-editing in D. discoideum with 5'-editing in another slime mold, Polysphondylium pallidum, suggests organism-specific idiosyncrasies in the treatment of U-G/G-U pairs. In vitro activities of putative D. discoideum editing enzymes are consistent with the observed editing reactions and suggest an overall lack of tRNA substrate specificity exhibited by the repair component of the editing enzyme. Although the presence of terminal mismatches in mt-tRNA sequences is highly predictive of the occurrence of mt-tRNA 5'-editing, the variability in treatment of U-G/G-U base pairs observed here indicates that direct experimental evidence of 5'-editing must be obtained to understand the complete spectrum of mt-tRNA editing events in any species.

Absence of a universal element for tRNAHis identity in Acanthamoeba castellanii

The additional G(-1) nucleotide on tRNA(His) is a nearly universal feature that specifies tRNA(His) identity in all three domains of life. In eukaryotes, the G(-1) identity element is obtained by a post-transcriptional pathway, through the unusual 3'-5' polymerase activity of the highly conserved tRNA(His) guanylyltransferase (Thg1) enzyme, and no examples of eukaryotic histidyl-tRNAs that lack this essential element have been identified. Here we report that the eukaryote Acanthamoeba castellanii lacks the G(-1) identity element on its tRNA(His), consistent with the lack of a gene encoding a bona fide Thg1 ortholog in the A. castellanii genome. Moreover, the cytosolic histidyl-tRNA synthetase in A. castellanii exhibits an unusual tRNA substrate specificity, efficiently aminoacylating tRNA(His) regardless of the presence of G(-1). A. castellanii does contain two Thg1-related genes (encoding Thg1-like proteins, TLPs), but the biochemical properties we associate here with these proteins are consistent with a function for these TLPs in separate pathways unrelated to tRNA(His) metabolism, such as mitochondrial tRNA repair during 5'-editing.

Evolutionary patterns of non-coding RNAs

A plethora of new functions of non-coding RNAs (ncRNAs) have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple regulatory layers from transcription, RNA maturation, and RNA modification to translational regulation. Nevertheless, very little is known about the evolution of this "Modern RNA World" and its components. In this contribution, we attempt to provide at least a cursory overview of the diversity of ncRNAs and functional RNA motifs in non-translated regions of regular messenger RNAs (mRNAs) with an emphasis on evolutionary questions. This survey is complemented by an in-depth analysis of examples from different classes of RNAs focusing mostly on their evolution in the vertebrate lineage. We present a survey of Y RNA genes in vertebrates and study the molecular evolution of the U7 snRNA, the snoRNAs E1/U17, E2, and E3, the Y RNA family, the let-7 microRNA (miRNA) family, and the mRNA-like evf-1 gene. We furthermore discuss the statistical distribution of miRNAs in metazoans, which suggests an explosive increase in the miRNA repertoire in vertebrates. The analysis of the transcription of ncRNAs suggests that small RNAs in general are genetically mobile in the sense that their association with a hostgene (e.g. when transcribed from introns of a mRNA) can change on evolutionary time scales. The let-7 family demonstrates, that even the mode of transcription (as intron or as exon) can change among paralogous ncRNA.

Doing it in reverse: 3'-to-5' polymerization by the Thg1 superfamily

The tRNA(His) guanylyltransferase (Thg1) family of enzymes comprises members from all three domains of life (Eucarya, Bacteria, Archaea). Although the initial activity associated with Thg1 enzymes was a single 3'-to-5' nucleotide addition reaction that specifies tRNA(His) identity in eukaryotes, the discovery of a generalized base pair-dependent 3'-to-5' polymerase reaction greatly expanded the scope of Thg1 family-catalyzed reactions to include tRNA repair and editing activities in bacteria, archaea, and organelles. While the identification of the 3'-to-5' polymerase activity associated with Thg1 enzymes is relatively recent, the roots of this discovery and its likely physiological relevance were described ≈ 30 yr ago. Here we review recent advances toward understanding diverse Thg1 family enzyme functions and mechanisms. We also discuss possible evolutionary origins of Thg1 family-catalyzed 3'-to-5' addition activities and their implications for the currently observed phylogenetic distribution of Thg1-related enzymes in biology.

A role for tRNA(His) guanylyltransferase (Thg1)-like proteins from Dictyostelium discoideum in mitochondrial 5'-tRNA editing

Genes with sequence similarity to the yeast tRNA(His) guanylyltransferase (Thg1) gene have been identified in all three domains of life, and Thg1 family enzymes are implicated in diverse processes, ranging from tRNA(His) maturation to 5'-end repair of tRNAs. All of these activities take advantage of the ability of Thg1 family enzymes to catalyze 3'-5' nucleotide addition reactions. Although many Thg1-containing organisms have a single Thg1-related gene, certain eukaryotic microbes possess multiple genes with sequence similarity to Thg1. Here we investigate the activities of four Thg1-like proteins (TLPs) encoded by the genome of the slime mold, Dictyostelium discoideum (a member of the eukaryotic supergroup Amoebozoa). We show that one of the four TLPs is a bona fide Thg1 ortholog, a cytoplasmic G(-1) addition enzyme likely to be responsible for tRNA(His) maturation in D. discoideum. Two other D. discoideum TLPs exhibit biochemical activities consistent with a role for these enzymes in mitochondrial 5'-tRNA editing, based on their ability to efficiently repair the 5' ends of mitochondrial tRNA editing substrates. Although 5'-tRNA editing was discovered nearly two decades ago, the identity of the protein(s) that catalyze this activity has remained elusive. This article provides the first identification of any purified protein that appears to play a role in the 5'-tRNA editing reaction. Moreover, the presence of multiple Thg1 family members in D. discoideum suggests that gene duplication and divergence during evolution has resulted in paralogous proteins that use 3'-5' nucleotide addition reactions for diverse biological functions in the same organism.

When you can't trust the DNA: RNA editing changes transcript sequences

RNA editing describes targeted sequence alterations in RNAs so that the transcript sequences differ from their DNA template. Since the original discovery of RNA editing in trypanosomes nearly 25 years ago more than a dozen such processes of nucleotide insertions, deletions, and exchanges have been identified in evolutionarily widely separated groups of the living world including plants, animals, fungi, protists, bacteria, and viruses. In many cases gene expression in mitochondria is affected, but RNA editing also takes place in chloroplasts and in nucleocytosolic genetic environments. While some RNA editing systems largely seem to repair defect genes (cryptogenes), others have obvious functions in modulating gene activities. The present review aims for an overview on the current states of research in the different systems of RNA editing by following a historic timeline along the respective original discoveries.

Organellar RNA editing

RNA editing is a term used for a number of mechanistically different processes that alter the nucleotide sequence of RNA molecules to differ from the gene sequence. RNA editing occurs in a wide variety of organisms and is particularly frequent in organelle transcripts of eukaryotes. The discontiguous phylogenetic distribution of mRNA editing, the mechanistic differences observed in different organisms, and the nonhomologous editing machinery described in different taxonomic groups all suggest that RNA editing has appeared independently several times. This raises questions about the selection pressures acting to maintain editing that are yet to be completely resolved. Editing tends to be frequent in organisms with atypical organelle genomes and acts to correct the effect of DNA mutations that would otherwise compromise the synthesis of functional proteins. Additional functions of editing in generating protein diversity or regulating gene expression have been proposed but so far lack widespread experimental evidence, at least in organelles.

tRNA 5'-end repair activities of tRNAHis guanylyltransferase (Thg1)-like proteins from Bacteria and Archaea

The tRNA^His guanylyltransferase (Thg1) family comprises a set of unique 3′–5′ nucleotide addition enzymes found ubiquitously in Eukaryotes, where they function in the critical G₋₁ addition reaction required for tRNA^His maturation. However, in most Bacteria and Archaea, G₋₁ is genomically encoded; thus post-transcriptional addition of G₋₁ to tRNA^His is not necessarily required. The presence of highly conserved Thg1-like proteins (TLPs) in more than 40 bacteria and archaea therefore suggests unappreciated roles for TLP-catalyzed 3′–5′ nucleotide addition. Here, we report that TLPs from Bacillus thuringiensis (BtTLP) and Methanosarcina acetivorans (MaTLP) display biochemical properties consistent with a prominent role in tRNA 5′-end repair. Unlike yeast Thg1, BtTLP strongly prefers addition of missing N₊₁ nucleotides to 5′-truncated tRNAs over analogous additions to full-length tRNA (k_cat/K_M enhanced 5–160-fold). Moreover, unlike for −1 addition, BtTLP-catalyzed additions to truncated tRNAs are not biased toward addition of G, and occur with tRNAs other than tRNA^His. Based on these distinct biochemical properties, we propose that rather than functioning solely in tRNA^His maturation, bacterial and archaeal TLPs are well-suited to participate in tRNA quality control pathways. These data support more widespread roles for 3′–5′ nucleotide addition reactions in biology than previously expected.

Template-dependent 3'-5' nucleotide addition is a shared feature of tRNAHis guanylyltransferase enzymes from multiple domains of life

The presence of an additional 5' guanosine residue (G(-1)) is a unique feature of tRNA(His). G(-1) is incorporated posttranscriptionally in eukarya via an unusual 3'-5' nucleotide addition reaction catalyzed by the tRNA(His) guanylyltransferase (Thg1). Yeast Thg1 catalyzes an unexpected second activity: Watson-Crick-dependent 3'-5' nucleotide addition that occurs in the opposite direction to nucleotide addition by all known DNA and RNA polymerases. This discovery led to the hypothesis that there are alternative roles for Thg1 family members that take advantage of this unusual enzymatic activity. Here we show that archaeal homologs of Thg1 catalyze G(-1) addition, in vitro and in vivo in yeast, but only in a templated reaction, i.e. with tRNA(His) substrates that contain a C(73) discriminator nucleotide. Because tRNA(His) from archaea contains C(73), these findings are consistent with a physiological function for templated nucleotide addition in archaeal tRNA(His) maturation. Moreover, unlike yeast Thg1, archaeal Thg1 enzymes also exhibit a preference for template-dependent U(-1) addition to A(73)-containing tRNA(His). Taken together, these results demonstrate that Watson-Crick template-dependent 3'-5' nucleotide addition is a shared catalytic activity exhibited by Thg1 family members from multiple domains of life, and therefore, that this unusual reaction may constitute an ancestral activity present in the earliest members of the Thg1 enzyme family.

Fungal evolution: the case of the vanishing mitochondrion

Mitochondria, the energy-producing organelles of the eukaryotic cell, are derived from an ancient endosymbiotic alpha-Proteobacterium. These organelles contain their own genetic system, a remnant of the endosymbiont's genome, which encodes only a fraction of the mitochondrial proteome. The majority of mitochondrial proteins are translated from nuclear genes and are imported into mitochondria. Recent studies of phylogenetically diverse representatives of Fungi reveal that their mitochondrial DNAs are among the most highly derived, encoding only a limited set of genes. Much of the reduction in the coding content of the mitochondrial genome probably occurred early in fungal evolution. Nevertheless, genome reduction is an ongoing process. Fungi in the chytridiomycete order Neocallimastigales and in the pathogenic Microsporidia have taken mitochondrial reduction to the extreme and have permanently lost a mitochondrial genome. These organisms have organelles derived from mitochondria that retain traces of their mitochondrial ancestry.

Mitochondria of Protists

Over the past several decades, our knowledge of the origin and evolution of mitochondria has been greatly advanced by determination of complete mitochondrial genome sequences. Among the most informative mitochondrial genomes have been those of protists (primarily unicellular eukaryotes), some of which harbor the most gene-rich and most eubacteria-like mitochondrial DNAs (mtDNAs) known. Comparison of mtDNA sequence data has provided insights into the radically diverse trends in mitochondrial genome evolution exhibited by different phylogenetically coherent groupings of eukaryotes, and has allowed us to pinpoint specific protist relatives of the multicellular eukaryotic lineages (animals, plants, and fungi). This comparative genomics approach has also revealed unique and fascinating aspects of mitochondrial gene expression, highlighting the mitochondrion as an evolutionary playground par excellence.

In vitro characterization of a tRNA editing activity in the mitochondria of Spizellomyces punctatus, a Chytridiomycete fungus

In the chytridiomycete fungus, Spizellomyces punctatus, all eight of the mitochondrially encoded tRNAs are predicted to have one or more base pair mismatches at the first three positions of their aminoacyl acceptor stems. These tRNAs are edited post-transcriptionally by replacement of the 5'-nucleotide in each mismatched pair with a nucleotide that can form a standard Watson-Crick base pair with its counterpart in the 3'-half of the stem. The type of mitochondrial tRNA editing found in S. punctatus also occurs in Acanthamoeba castellanii, a distantly related amoeboid protist. Using an S. punctatus mitochondrial extract, we have developed an in vitro assay of tRNA editing in which nucleotides are incorporated into various tRNA substrates. Experiments employing synthetic transcripts revealed that the S. punctatus tRNA editing activity incorporates nucleotides on the 5'-side of substrate tRNAs, uses the 3'-sequence as a template for incorporation, and adds nucleotides in a 3'-to-5' direction. This activity can add nucleotides to a triphosphorylated 5'-end in the absence of ATP but requires ATP to add nucleotides to a monophosphorylated 5'-end; moreover, it functions independently of the state of tRNA 3' processing. These data parallel results obtained in a previous in vitro study of A. castellanii tRNA editing, suggesting that remarkably similar activities function in the mitochondria of these two organisms. The evolutionary origins of these activities are discussed.