Bacteriophage T4-induced anticodon-loop nuclease detected in a host strain restrictive to RNA ligase mutants

RNA Repair: Hiding in Plain Sight

Enzymes that phosphorylate, dephosphorylate, and ligate RNA 5' and 3' ends were discovered more than half a century ago and were eventually shown to repair purposeful site-specific endonucleolytic breaks in the RNA phosphodiester backbone. The pace of discovery and characterization of new candidate RNA repair activities in taxa from all phylogenetic domains greatly exceeds our understanding of the biological pathways in which they act. The key questions anent RNA break repair in vivo are (a) identifying the triggers, agents, and targets of RNA cleavage and (b) determining whether RNA repair results in restoration of the original RNA, modification of the RNA (by loss or gain at the ends), or rearrangements of the broken RNA segments (i.e., RNA recombination). This review provides a perspective on the discovery, mechanisms, and physiology of purposeful RNA break repair, highlighting exemplary repair pathways (e.g., tRNA restriction-repair and tRNA splicing) for which genetics has figured prominently in their elucidation.

Nicked tRNAs are stable reservoirs of tRNA halves in cells and biofluids

Nonvesicular extracellular RNAs (nv-exRNAs) constitute the majority of the extracellular RNAome, but little is known about their stability, function, and potential use as disease biomarkers. Herein, we measured the stability of several naked RNAs when incubated in human serum, urine, and cerebrospinal fluid (CSF). We identified extracellularly produced tRNA-derived small RNAs (tDRs) with half-lives of several hours in CSF. Contrary to widespread assumptions, these intrinsically stable small RNAs are full-length tRNAs containing broken phosphodiester bonds (i.e., nicked tRNAs). Standard molecular biology protocols, including phenol-based RNA extraction and heat, induce the artifactual denaturation of nicked tRNAs and the consequent in vitro production of tDRs. Broken bonds are roadblocks for reverse transcriptases, preventing amplification and/or sequencing of nicked tRNAs in their native state. To solve this, we performed enzymatic repair of nicked tRNAs purified under native conditions, harnessing the intrinsic activity of phage and bacterial tRNA repair systems. Enzymatic repair regenerated an RNase R-resistant tRNA-sized band in northern blot and enabled RT-PCR amplification of full-length tRNAs. We also separated nicked tRNAs from tDRs by chromatographic methods under native conditions, identifying nicked tRNAs inside stressed cells and in vesicle-depleted human biofluids. Dissociation of nicked tRNAs produces single-stranded tDRs that can be spontaneously taken up by human epithelial cells, positioning stable nv-exRNAs as potentially relevant players in intercellular communication pathways.

tRNA-Derived Small RNAs: Biogenesis, Modification, Function and Potential Impact on Human Disease Development

Transfer RNAs (tRNAs) are abundant small non-coding RNAs that are crucially important for decoding genetic information. Besides fulfilling canonical roles as adaptor molecules during protein synthesis, tRNAs are also the source of a heterogeneous class of small RNAs, tRNA-derived small RNAs (tsRNAs). Occurrence and the relatively high abundance of tsRNAs has been noted in many high-throughput sequencing data sets, leading to largely correlative assumptions about their potential as biologically active entities. tRNAs are also the most modified RNAs in any cell type. Mutations in tRNA biogenesis factors including tRNA modification enzymes correlate with a variety of human disease syndromes. However, whether it is the lack of tRNAs or the activity of functionally relevant tsRNAs that are causative for human disease development remains to be elucidated. Here, we review the current knowledge in regard to tsRNAs biogenesis, including the impact of RNA modifications on tRNA stability and discuss the existing experimental evidence in support for the seemingly large functional spectrum being proposed for tsRNAs. We also argue that improved methodology allowing exact quantification and specific manipulation of tsRNAs will be necessary before developing these small RNAs into diagnostic biomarkers and when aiming to harness them for therapeutic purposes.

Tie-Break: Host and Retrotransposons Play tRNA

tRNA fragments (tRFs) are a class of small, regulatory RNAs with diverse functions. 3'-Derived tRFs perfectly match long terminal repeat (LTR)-retroelements which use the 3'-end of tRNAs to prime reverse transcription. Recent work has shown that tRFs target LTR-retroviruses and -transposons for the RNA interference (RNAi) pathway and also inhibit mobility by blocking reverse transcription. The highly conserved tRNA primer binding site (PBS) in LTR-retroelements is a unique target for 3'-tRFs to recognize and block abundant but diverse LTR-retrotransposons that become transcriptionally active during epigenetic reprogramming in development and disease. 3'-tRFs are processed from full-length tRNAs under so far unknown conditions and potentially protect many cell types. tRFs appear to be an ancient link between RNAi, transposons, and genome stability.

Surveillance and cleavage of eukaryotic tRNAs

Beyond their central role in protein synthesis, transfer RNAs (tRNAs) have many other crucial functions. This includes various roles in the regulation of gene expression, stress responses, metabolic processes and priming reverse transcription. In the RNA world, tRNAs are, with ribosomal RNAs, among the most stable molecules. Nevertheless, they are not eternal. As key elements of cell function, tRNAs need to be continuously quality-controlled. Two tRNA surveillance pathways have been identified. They act on hypo-modified or mis-processed pre-tRNAs and on mature tRNAs lacking modifications. A short overview of these two pathways will be presented here. Furthermore, while the exoribonucleases acting in these pathways ultimately lead to complete tRNA degradation, numerous tRNA-derived fragments (tRFs) are present within a cell. These cleavage products of tRNAs now potentially emerge as a new class of small non-coding RNAs (sncRNAs) and are suspected to have important regulatory functions. The tRFs are evolutionarily widespread and created by cleavage at different positions by various endonucleases. Here, we review our present knowledge on the biogenesis and function of tRFs in various organisms.

Type I restriction enzymes and their relatives

Type I restriction enzymes (REases) are large pentameric proteins with separate restriction (R), methylation (M) and DNA sequence-recognition (S) subunits. They were the first REases to be discovered and purified, but unlike the enormously useful Type II REases, they have yet to find a place in the enzymatic toolbox of molecular biologists. Type I enzymes have been difficult to characterize, but this is changing as genome analysis reveals their genes, and methylome analysis reveals their recognition sequences. Several Type I REases have been studied in detail and what has been learned about them invites greater attention. In this article, we discuss aspects of the biochemistry, biology and regulation of Type I REases, and of the mechanisms that bacteriophages and plasmids have evolved to evade them. Type I REases have a remarkable ability to change sequence specificity by domain shuffling and rearrangements. We summarize the classic experiments and observations that led to this discovery, and we discuss how this ability depends on the modular organizations of the enzymes and of their S subunits. Finally, we describe examples of Type II restriction-modification systems that have features in common with Type I enzymes, with emphasis on the varied Type IIG enzymes.

Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data

Prokaryotic transcripts constitute almost always uninterrupted intervals when mapped back to the genome. Split reads, i.e., RNA-seq reads consisting of parts that only map to discontiguous loci, are thus disregarded in most analysis pipelines. There are, however, some well-known exceptions, in particular, tRNA splicing and circularized small RNAs in Archaea as well as self-splicing introns. Here, we reanalyze a series of published RNA-seq data sets, screening them specifically for non-contiguously mapping reads. We recover most of the known cases together with several novel archaeal ncRNAs associated with circularized products. In Eubacteria, only a handful of interesting candidates were obtained beyond a few previously described group I and group II introns. Most of the atypically mapping reads do not appear to correspond to well-defined, specifically processed products. Whether this diffuse background is, at least in part, an incidental by-product of prokaryotic RNA processing or whether it consists entirely of technical artifacts of reverse transcription or amplification remains unknown.

The primary target of the killer toxin from Pichia acaciae is tRNA(Gln)

The Pichia acaciae killer toxin (PaT) arrests yeast cells in the S-phase of the cell cycle and induces DNA double-strand breaks (DSBs). Surprisingly, loss of the tRNA-methyltransferase Trm9 - along with the Elongator complex involved in synthesis of 5-methoxy-carbonyl-methyl (mcm(5)) modification in certain tRNAs - conferred resistance against PaT. Overexpression of mcm(5)-modified tRNAs identified tRNA(Gln)((UUG)) as the intracellular target. Consistently, toxin-challenged cells displayed reduced levels of tRNA(Gln) and in vitro the heterologously expressed active toxin subunit disrupts the integrity of tRNA(Gln)((UUG)). Other than Kluyveromyces lactis zymocin, an endonuclease specific for tRNA(Glu)((UUC)), affecting its target in a mcm(5)-dependent manner, PaT exerts activity also on tRNA(Gln) lacking such modification. As sensitivity is restored in trm9 elp3 double mutants, target tRNA cleavage is selectively inhibited by incomplete wobble uridine modification, as seen in trm9, but not in elp3 or trm9 elp3 cells. In addition to tRNA(Gln)((UUG)), tRNA(Gln)((CUG)) is also cleaved in vitro and overexpression of the corresponding gene increased resistance. Consistent with tRNA(Gln)((CUG)) as an additional TRM9-independent target, overexpression of PaT's tRNase subunit abolishes trm9 resistance. Most interestingly, a functional DSB repair pathway confers PaT but also zymocin resistance, suggesting DNA damage to occur generally concomitant with specific tRNA offence.

PrrC-anticodon nuclease: functional organization of a prototypical bacterial restriction RNase

The tRNA^Lys anticodon nuclease PrrC is associated in latent form with the type Ic DNA restriction endonuclease EcoprrI and activated by a phage T4-encoded inhibitor of EcoprrI. The activation also requires the hydrolysis of GTP and presence of dTTP and is inhibited by ATP. The N-proximal NTPase domain of PrrC has been implicated in relaying the activating signal to a C-proximal anticodon nuclease site by interacting with the requisite nucleotide cofactors [Amitsur et al. (2003) Mol. Microbiol., 50, 129–143]. Means described here to bypass PrrC's self-limiting translation and thermal instability allowed purifying an active mutant form of the protein, demonstrating its oligomeric structure and confirming its anticipated interactions with the nucleotide cofactors of the activation reaction. Mutagenesis and chemical rescue data shown implicate the C-proximal Arg³²⁰, Glu³²⁴ and, possibly, His³⁵⁶ in anticodon nuclease catalysis. This triad exists in all the known PrrC homologs but only some of them feature residues needed for tRNA^Lys recognition by the Escherichia coli prototype. The differential conservation and consistent genetic linkage of the PrrC proteins with EcoprrI homologs portray them as a family of restriction RNases of diverse substrate specificities that are mobilized when an associated DNA restriction nuclease is compromised.

Bacteriophage T4-encoded Stp can be replaced as activator of anticodon nuclease by a normal host cell metabolite

The bacterial tRNALys-specific anticodon nuclease is known as a phage T4 exclusion system. In the uninfected host cell anticodon nuclease is kept latent due to the association of its core protein PrrC with the DNA restriction-modification endonuclease EcoprrI. Stp, the T4-encoded peptide inhibitor of EcoprrI activates the latent enzyme. Previous in vitro work indicated that the activation by Stp is sensitive to DNase and requires added nucleotides. Biochemical and mutational data reported here suggest that Stp activates the latent holoenzyme when its EcoprrI component is tethered to a cognate DNA substrate. Moreover, the activation is driven by GTP hydrolysis, possibly mediated by the NTPase domain of PrrC. The data also reveal that Stp can be replaced as the activator of latent anticodon nuclease by certain pyrimidine nucleotides, the most potent of which is dTTP. The activation by dTTP likewise requires an EcoprrI DNA substrate and GTP hydrolysis but involves a different form of the latent holoenzyme/DNA complex. Moreover, whereas Stp relays its activating effect through EcoprrI, dTTP targets PrrC. The activation of the latent enzyme by a normal cell constituent hints that anticodon nuclease plays additional roles, other than warding off phage T4 infection.

The modes of action of colicins E5 and D, and related cytotoxic tRNases

Colicins E5 and D cleave the anticodon loops of distinct tRNAs of Escherichia coli both in vivo and in vitro, which accounts for their bactericidal actions through depletion of tRNAs and prevention of protein synthesis. The targets of colicin E5 are five tRNA species for four amino acids, tyrosine, histidine, asparagine and aspartic acid, and those of colicin D are four isoaccepting tRNAs for arginine. These two colicins represent a new class, the "tRNase-type", of the nuclease-type colicins, which previously comprised the DNase-type and ribotoxin-type (or rRNase-type). On the other hand, a certain clinical E. coli strain produces a potentially suicidal "anticodon-nuclease", PrrC, in response to phage T4 infection, which specifically cleaves its own lysine tRNA. For these three tRNases, i.e. colicins E5 and D, and PrrC, the substrates and reaction products, as well as their physiological consequences, are very similar to each other, but so many molecular features are different that these three proteins are assumed to have acquired similar functions through evolutionary convergence from different origins.

Anticodon nucleases

A tRNALys-specific anticodon nuclease is kept in a latent form in a rare Escherichia coli strain, complexed with a DNA restriction enzyme. A phage T4 inhibitor of DNA restriction activates anticodon nuclease, but other T4 proteins restore tRNALys. Detection of a homologous system in Neisseria and a different anticodon nuclease in colicin E5 suggest ubiquity and diversity of such tRNA toxins. Analysis of these systems could reveal novel RNA recognition and cleavage mechanisms.

Detection of anticodon nuclease residues involved in tRNALys cleavage specificity

The tRNALys-specific anticodon nuclease exists in latent form in Escherichia coli strains containing the optional prr locus. The latency is a result of a masking interaction between the anticodon nuclease core-polypeptide PrrC and the Type IC DNA restriction-modification enzyme EcoprrI. Activation of the latent enzyme by phage T4-infection elicits cleavage of tRNALys 5' to the wobble base, yielding 5'-OH and 2', 3'-cyclic phosphate termini. The N-proximal half of PrrC has been implicated with (A/G) TPase and EcoprrI interfacing activities. Therefore, residues involved in recognition and cleavage of tRNALys were searched for at the C-half. Random mutagenesis of the low-G+C portion encoding PrrC residues 200-313 was performed, followed by selection for loss of anticodon nuclease-dependent lethality and production of full-sized PrrC-like protein. This process yielded a cluster of missense mutations mapping to a region highly conserved between PrrC and two putative Neisseria meningitidis MC58 homologues. This cluster included two adjacent members that relaxed the inherent enzyme's cleavage specificity. We also describe another mode of relaxed specificity, due to mere overexpression of PrrC. This mode was shared by wild-type PrrC and the other mutant alleles. The additional substrates recognised under the promiscuous conditions had, in general, anticodons resembling that of tRNALys. Taken together, the data suggest that the anticodon of tRNALys harbours anticodon nuclease identity elements and implicates a conserved region in PrrC in their recognition.

Phage-exclusion enzymes: a bonanza of biochemical and cell biology reagents?

Many parasitic DNA elements including prophages and plasmids synthesize proteins that kill the cell after infection by other phages, thereby blocking the multiplication of the infecting phages and their spread to other nearby cells. The only known function of these proteins is to exclude the infecting phage, and therefore to protect their hosts, and thereby the DNA elements themselves, against phage contagion. Many of these exclusions have been studied extensively and some have long been used in molecular genetics, but their molecular basis was unknown. The most famous of the phage exclusions are those caused by the Rex proteins of lambda prophage. The Rex exclusions are still not completely understood, but recent evidence has begun to lead to more specific models for their action. One of the Rex proteins, RexA, may be activated by a DNA-protein complex, perhaps a recombination or replication intermediate, produced after phage infection. In the activated state, RexA may activate RexB, which has been proposed to be a membrane ion channel that allows the passage of monovalent cations, destroying the cellular membrane potential, and killing the cell. We now understand two other phage exclusions at the molecular level which use strategies that are remarkably similar to each other. The parasitic DNA elements responsible for the exclusions both constitutively synthesize enzymes that are inactive as synthesized by the DNA element but are activated after phage infection by a short peptide determinant encoded by the infecting phage. In the activated state, the enzymes cleave evolutionarily conserved components of the translation apparatus, in one case EF-Tu, and in the other case tRNALys.(ABSTRACT TRUNCATED AT 250 WORDS)

3' truncated tRNAArg is essential for in vitro specific cleavage of partially synthesized mouse 18S rRNA

In vitro synthesized 5' portions of mouse 18S rRNA are cleaved efficiently at a specific site in partially purified extracts of mouse FM3A cells and several mouse tissues. This activity is composed of both protein and RNA, and can be reconstituted with the protein component in micrococcal nuclease-treated extracts and the RNA component in phenol-treated ones. The RNA component of about 65 nucleotides with the complementing activity was purified from total RNA in the partially purified FM3A cell extracts by polyacrylamide gel electrophoreses. Chemical sequencing of this RNA elucidated that it is tRNAArg lacking nine nucleotides from its 3' terminus. Ribonuclease H treatment directed by deoxyoligonucleotides complementary to tRNAArg completely abolishes the cleavage activity, supporting the above conclusion.

Cleavage of tRNA within the mature tRNA sequence by the catalytic RNA of RNase P: implication for the formation of the primer tRNA fragment for reverse transcription in copia retrovirus-like particles

The retrovirus-like particles of Drosophila are intermediates of retrotransposition of the transposable element copia. In these particles, a 39-nucleotide-long fragment from the 5' region of Drosophila initiator methionine tRNA (tRNA(iMet) is used as the primer for copia minus-strand reverse transcription. To function as primer for this reverse transcription, the Drosophila tRNA(iMet) must be cleaved in vivo at the site between nucleotides 39 and 40. When a synthetic Drosophila tRNA(iMet) precursor was incubated with M1RNA, the catalytic RNA of Escherichia coli RNase P, other cleavages within the mature tRNA sequence were detected in addition to the efficient removal of the 5' leader sequence of this tRNA precursor. One of these cleavage sites is between nucleotides 39 and 40 of Drosophila tRNA(iMet). Based on this result, we propose a model for formation of the primer tRNA fragment for reverse transcription in copia retrovirus-like particles.

Host transfer RNA cleavage and reunion in T4-infected Escherichia coli CTr5x

T4 mutants lacking polynucleotide kinase (pnk-) or RNA ligase (rli-) do not grow on E. coli CTr5x. During the abortive infections there accumulate host tRNA fragments that match into two species severed 3' to the anticodon. The CTr5x-specific fragments appear only transiently with wt phage, implicating the affected enzymes in phosphoryl group rearrangement and religation [David et al. (1982) Virol. 123, 480]. In a search for the vulnerable host tRNAs and putative religation products, tRNA ensembles from uninfected E. coli CTr5x or cells infected with various phage strains were fractionated and compared. A tRNA species absent from rli- infected cells but present in uninfected cells or late in wt infection was thus detected. RNase T1 finger prints of this species, isolated before or after wt infection, were compared with that of an in vitro ligated pair of CTr5x-specific fragments. The results indicated that this tRNA is cleaved upon infection and later on restored to it's original or to a very similar form, by polynucleotide kinase and RNA ligase reactions. It is suggested that depletion of such vulnerable host tRNA species underlies the restriction of pnk- or rli- phage on E. coli CTr5x.

Genetic and physiological studies of an Escherichia coli locus that restricts polynucleotide kinase- and RNA ligase-deficient mutants of bacteriophage T4

The RNA ligase and polynucleotide kinase of bacteriophage T4 are nonessential enzymes in most laboratory Escherichia coli strains. However, T4 mutants which do not induce the enzymes are severely restricted in E. coli CTr5X, a strain derived from a clinical E. coli isolate. We have mapped the restricting locus in E. coli CTr5X and have transduced it into other E. coli strains. The restrictive locus seems to be a gene, or genes, unique to CTr5X or to be an altered form of a nonessential gene, since deleting the locus seems to cause loss of the phenotypes. In addition to restricting RNA ligase- and polynucleotide kinase-deficient T4, the locus also restricts bacteriophages lambda and T4 with cytosine DNA. When lambda or T4 with cytosine DNA infect strains with the prr locus, the phage DNA is injected, but phage genes are not expressed and the host cells survive. These phenotypes are unlike anything yet described for a phage-host interaction.