An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA

Maida, Yoshiko; Yasukawa, Mami; Furuuchi, Miho; Lassmann, Timo; Possemato, Richard; Okamoto, Nobuhiko; Kasim, Vivi; Hayashizaki, Yoshihide; Hahn, William C.; Masutomi, Kenkichi

doi:10.1038/nature08283

Cited by 339 publications

(372 citation statements)

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“…The ability of RVT to add NTPs and, to a lesser extent, dNTPs to 39-OH termini places it apart from conventional RTs and closer to TERTs, which are known to exhibit RdRP and template-independent terminal deoxynucleotidyltransferase (TdT) activity in addition to RT activity (24,25). The emergence of a unique type of RT-related genes raises questions about their relationship to other RT-like proteins.…”

Section: Resultsmentioning

confidence: 99%

A widespread class of reverse transcriptase-related cellular genes

Gladyshev

Arkhipova

2011

Proc. Natl. Acad. Sci. U.S.A.

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Reverse transcriptases (RTs) polymerize DNA on RNA templates. They fall into several structurally related but distinct classes and form an assemblage of RT-like enzymes that, in addition to RTs, also includes certain viral RNA-dependent RNA polymerases (RdRP) synthesizing RNA on RNA templates. It is generally believed that most RT-like enzymes originate from retrotransposons or viruses and have no specific function in the host cell, with telomerases being the only notable exception. Here we report on the discovery and properties of a unique class of RT-related cellular genes collectively named rvt. We present evidence that rvts are not components of retrotransposons or viruses, but single-copy genes with a characteristic domain structure that may contain introns in evolutionarily conserved positions, occur in syntenic regions, and evolve under purifying selection. These genes can be found in all major taxonomic groups including protists, fungi, animals, plants, and even bacteria, although they exhibit patchy phylogenetic distribution in each kingdom. We also show that the RVT protein purified from one of its natural hosts, Neurospora crassa, exists in a multimeric form and has the ability to polymerize NTPs as well as dNTPs in vitro, with a strong preference for NTPs, using Mn 2+ as a cofactor. The existence of a previously unknown class of single-copy RT-related genes calls for reevaluation of the current views on evolution and functional roles of RNA-dependent polymerases in living cells.D NA-dependent polymerases are essential for cellular function, as they mediate the flow of genetic information from DNA to RNA to proteins (1). In contrast, RNA-dependent polymerases have long been associated with replication of selfish and parasitic genetic elements, such as viruses or transposons. Although the discovery of reverse transcriptase (RT) challenged the concept of unidirectionality of the flow of genetic information, this reverse direction has been reserved for retroviruses, pararetroviruses (hepadna-and caulimoviruses), and other RT-containing multicopy entities such as non-LTR and LTR retrotransposons, group II introns, retrons, and retroplasmids, as well as occasional retro (pseudo)genes (2-4). Similarly, viral RNA-dependent RNA polymerases (RdRPs), enzymes structurally related to RTs, serve to replicate the genomes of viruses that use RNA as genetic material (5). These and certain other polymerases are unified by the architecture known as "right hand," composed of the three subdomains called fingers, palm, and thumb (6). Like all polymerases, they use two-metal-ion catalysis for phosphoryl transfer reactions resulting in nucleotide addition.In 1997, this diverse superfamily of enzymes was joined by the telomerase reverse transcriptase (TERT), a specialized RT that maintains the ends of eukaryotic linear chromosomes by addition of short G-rich repeated DNA sequences that are copied multiple times via reverse transcription of a specific region of the associated RNA template constituting part of the holoenzyme (...

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Section: Resultsmentioning

confidence: 99%

A widespread class of reverse transcriptase-related cellular genes

Gladyshev

Arkhipova

2011

Proc. Natl. Acad. Sci. U.S.A.

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“…RNA exosome sequencing suggests, however, that RNAdependent RNA polymerase activity is also present in mammals because AS transcripts, which cross splice junctions and contain non-encoded 5Ј stretches of polyuridine, have been detected (71,81). TERT, the protein subunit of telomerase, is reported to function as an RNA-dependent RNA polymerase (82). However, TERT is not expressed in the ALT-positive U2OS cell line (83,84), suggesting that it is not responsible for the AS transcription at the CMV promoter-regulated array.…”

Section: Discussionmentioning

confidence: 99%

Single Cell Analysis of RNA-mediated Histone H3.3 Recruitment to a Cytomegalovirus Promoter-regulated Transcription Site

Newhart

Rafalska-Metcalf

Yang

et al. 2013

Journal of Biological Chemistry

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Background: Replication-independent (RI) histone H3.3 chromatin assembly is a highly conserved but incompletely understood genome regulatory mechanism. Results: When RI H3.3 chromatin assembly is blocked, H3.3 accumulates at its incorporation site with sense and antisense RNA. Conclusion: H3.3 recruitment is RNA-mediated and chaperone-independent. Significance: Understanding the temporal and spatial organization of RI H3.3 chromatin assembly is crucial for understanding genome regulation.

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“…Interestingly, telomerase can also apparently reverse transcribe telomere RNA to internal chromosomal sites (75), suggesting that telomerase can "retrotranspose" its associated RNA to new chromosomal locations. Telomerase also may bind other mRNAs (76).…”

Section: Discussionmentioning

confidence: 99%

Similarities between long interspersed element-1 (LINE-1) reverse transcriptase and telomerase

Kopera¹,

Moldovan²,

Morrish³

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Long interspersed element-1 (LINE-1 or L1) retrotransposons encode two proteins (ORF1p and ORF2p) that contain activities required for conventional retrotransposition by a mechanism termed target-site primed reverse transcription. Previous experiments in XRCC4 or DNA protein kinase catalytic subunit-deficient CHO cell lines, which are defective for the nonhomologous endjoining DNA repair pathway, revealed an alternative endonuclease-independent (ENi) pathway for L1 retrotransposition. Interestingly, some ENi retrotransposition events in DNA protein kinase catalytic subunit-deficient cells are targeted to dysfunctional telomeres. Here we used an in vitro assay to detect L1 reverse transcriptase activity to demonstrate that wild-type or endonuclease-defective L1 ribonucleoprotein particles can use oligonucleotide adapters that mimic telomeric ends as primers to initiate the reverse transcription of L1 mRNA. Importantly, these ribonucleoprotein particles also contain a nuclease activity that can process the oligonucleotide adapters before the initiation of reverse transcription. Finally, we demonstrate that ORF1p is not strictly required for ENi retrotransposition at dysfunctional telomeres. Thus, these data further highlight similarities between the mechanism of ENi L1 retrotransposition and telomerase.L ong interspersed element-1 sequences (LINE-1s or L1s) are abundant non-long terminal repeat (non-LTR) retrotransposons that constitute approximately one-sixth (i.e., ≈17%) of human nuclear DNA (1). An estimated 80-100 full-length, retrotransposition competent L1s (RC-L1s) are present in a typical diploid human genome, and a small number, termed "hot L1s" exhibit high retrotransposition efficiencies in cultured human cells (2). Human RC-L1s are ≈6 kb (3, 4) and encode two proteins (ORF1p and ORF2p) required for retrotransposition (5). ORF1p is a 40-kDa protein (6) with RNA binding (7-12) and nucleic acid chaperone activities (13-15). ORF2p is a 150-kDa protein (16, 17) with endonuclease (EN) (18,19) and reverse transcriptase (RT) (20, 21) activities.The mobilization of RC-L1s can be mutagenic (22); germ line and, less often, somatic L1 insertions have led to ≈65 sporadic cases of disease in humans (reviewed in ref. 23). ORF1p and/or ORF2p also can act in trans to mobilize short interspersed elements [e.g., Alu (24) and SINE-VNTR-Alu (25) elements], certain noncoding RNAs [e.g., U6 snRNA and small nucleolar RNAs (24, 26-29)], and some cellular mRNAs, which leads to the formation of processed pseudogenes (30-32). In total, these trans retrotransposition events account for at least an additional 10% of human DNA (1). Moreover, several recent studies have further demonstrated that L1-mediated retrotransposition events are responsible for a significant proportion of interindividual genetic variation in the human population (33-39) and may cause intraindividual variation in the mammalian nervous system (40, 41). L1 retrotransposition likely occurs by a mechanism termed target-site primed reverse transcription (TPRT) (42)...

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An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA

Cited by 339 publications

References 50 publications

A widespread class of reverse transcriptase-related cellular genes

A widespread class of reverse transcriptase-related cellular genes

Single Cell Analysis of RNA-mediated Histone H3.3 Recruitment to a Cytomegalovirus Promoter-regulated Transcription Site

Similarities between long interspersed element-1 (LINE-1) reverse transcriptase and telomerase

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