An intact unfolded protein response in <i>Trpt1</i> knockout mice reveals phylogenic divergence in pathways for RNA ligation

Harding, Heather P.; Lackey, Jeremy G.; Hsu, Hao-Chi; Zhang, Yuhong; Deng, Jing; Xu, Rui-Ming; Damha, Masad J.; Ron, David

doi:10.1261/rna.859908

Cited by 53 publications

(53 citation statements)

References 42 publications

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“…If the yeast-type pathway is redundant, then other mammalian homologs of yeast-type tRNA repair proteins might also not be essential. This is the case for mammalian Tpt1, the ortholog of the yeast phosphotransferase that removes the 29-PO 4 from the tRNA splice junction (Harding et al 2007). The major challenge now is to identify the protein catalysts of the direct tRNA ligation pathway in mammalian cells (and archaea).…”

Section: Cnp Complementation Of New Conditional Mutations In the Trl1mentioning

confidence: 99%

Mammalian 2′,3′ cyclic nucleotide phosphodiesterase (CNP) can function as a tRNA splicing enzyme in vivo

Schwer¹,

Aronova²,

Ramı́rez³

et al. 2007

RNA

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Yeast and plant tRNA splicing entails discrete healing and sealing steps catalyzed by a tRNA ligase that converts the 29,39 cyclic phosphate and 59-OH termini of the broken tRNA exons to 39-OH/29-PO 4 and 59-PO 4 ends, respectively, then joins the ends to yield a 29-PO 4 , 39-59 phosphodiester splice junction. The junction 29-PO 4 is removed by a tRNA phosphotransferase, Tpt1. Animal cells have two potential tRNA repair pathways: a yeast-like system plus a distinctive mechanism, also present in archaea, in which the 29,39 cyclic phosphate and 59-OH termini are ligated directly. Here we report that a mammalian 29,39 cyclic nucleotide phosphodiesterase (CNP) can perform the essential 39 end-healing steps of tRNA splicing in yeast and thereby complement growth of strains bearing lethal or temperature-sensitive mutations in the tRNA ligase 39 end-healing domain. Although this is the first evidence of an RNA processing function in vivo for the mammalian CNP protein, it seems unlikely that the yeast-like pathway is responsible for animal tRNA splicing, insofar as neither CNP nor Tpt1 is essential in mice.

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Section: Cnp Complementation Of New Conditional Mutations In the Trl1mentioning

confidence: 99%

Mammalian 2′,3′ cyclic nucleotide phosphodiesterase (CNP) can function as a tRNA splicing enzyme in vivo

Schwer¹,

Aronova²,

Ramı́rez³

et al. 2007

RNA

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“…Since pre-tRNA splicing normally occurs in the cytoplasm, the nuclear Tpt1 pool presumably serves a role other than for tRNA splicing. Likewise, the 29 phosphotransferase is conserved in vertebrates that do not require this enzyme for pre-tRNA splicing (Spinelli et al 1998;Harding et al 2008) and in bacterial genomes that do not encode any tRNA genes with introns (Spinelli et al 1998;Steiger et al 2001). Thus, it seems very likely that each of the three enzymes required for splicing yeast pre-tRNAs moonlights in a process distinct from tRNA splicing.…”

Section: Removal Of 59 Leader and 39 Trailer Sequences From Pre-trnasmentioning

confidence: 99%

Transfer RNA Post-Transcriptional Processing, Turnover, and Subcellular Dynamics in the YeastSaccharomyces cerevisiae

2013

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Transfer RNAs (tRNAs) are essential for protein synthesis. In eukaryotes, tRNA biosynthesis employs a specialized RNA polymerase that generates initial transcripts that must be subsequently altered via a multitude of post-transcriptional steps before the tRNAs beome mature molecules that function in protein synthesis. Genetic, genomic, biochemical, and cell biological approaches possible in the powerful Saccharomyces cerevisiae system have led to exciting advances in our understandings of tRNA post-transcriptional processing as well as to novel insights into tRNA turnover and tRNA subcellular dynamics. tRNA processing steps include removal of transcribed leader and trailer sequences, addition of CCA to the 39 mature sequence and, for tRNA His , addition of a 59 G. About 20% of yeast tRNAs are encoded by intron-containing genes. The three-step splicing process to remove the introns surprisingly occurs in the cytoplasm in yeast and each of the splicing enzymes appears to moonlight in functions in addition to tRNA splicing. There are 25 different nucleoside modifications that are added post-transcriptionally, creating tRNAs in which 15% of the residues are nucleosides other than A, G, U, or C. These modified nucleosides serve numerous important functions including tRNA discrimination, translation fidelity, and tRNA quality control. Mature tRNAs are very stable, but nevertheless yeast cells possess multiple pathways to degrade inappropriately processed or folded tRNAs. Mature tRNAs are also dynamic in cells, moving from the cytoplasm to the nucleus and back again to the cytoplasm; the mechanism and function of this retrograde process is poorly understood. Here, the state of knowledge for tRNA post-transcriptional processing, turnover, and subcellular dynamics is addressed, highlighting the questions that remain. TABLE OF CONTENTS Abstract 43Introduction 44

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“…Genetic ablation of a murine homolog of a yeast-like pathway component Tpt1 (the enzyme that removes the 2Ј-phosphate at the splice junction; see Fig. 1) has no discernible phenotype (17), suggesting that the mammalian yeastlike pathway either is functionally redundant with direct ligation or is non-contributory to mammalian tRNA splicing. By contrast, siRNA-directed depletion of the mammalian RNA 5Ј-kinase (an ortholog of the kinase domain of yeast/plant tRNA ligase) elicited a defect in tRNA splicing in vitro (10).…”

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confidence: 99%

RtcB, a Novel RNA Ligase, Can Catalyze tRNA Splicing and HAC1 mRNA Splicing in Vivo

Tanaka

Meineke

Shuman

2011

Journal of Biological Chemistry

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RtcB enzymes are novel RNA ligases that join 2,3-cyclic phosphate and 5-OH ends. The phylogenetic distribution of RtcB points to its candidacy as a tRNA splicing/repair enzyme. Here we show that Escherichia coli RtcB is competent and sufficient for tRNA splicing in vivo by virtue of its ability to complement growth of yeast cells that lack the endogenous "healing/ sealing-type" tRNA ligase Trl1. RtcB also protects yeast trl1⌬ cells against a fungal ribotoxin that incises the anticodon loop of cellular tRNAs. Moreover, RtcB can replace Trl1 as the catalyst of HAC1 mRNA splicing during the unfolded protein response. Thus, RtcB is a bona fide RNA repair enzyme with broad physiological actions. Biochemical analysis of RtcB highlights the uniqueness of its active site and catalytic mechanism. Our findings draw attention to tRNA ligase as a promising drug target.Escherichia coli RtcB exemplifies a new family of RNA ligases that directly seal 2Ј,3Ј-cyclic phosphate and 5Ј-OH ends (1-3). Direct ligation is thought to be the main pathway of tRNA splicing in animals and archaea (4 -6). By contrast, yeast and plants rely on a different mechanism of tRNA splicing in which the broken 3Ј and 5Ј ends are healed (converted to a 3Ј-OH/2Ј-PO 4 and 5Ј-PO 4 , respectively) and then sealed by a classical ATPdependent RNA ligase (7) (see Fig. 1). RNA ligases of the RtcB family are present in metazoa and protozoa, but not in fungi and plants. RtcB homologs purified from archaeal and mammalian cells can seal broken tRNA halves and are thereby imputed to be the catalysts of archaeal and mammalian tRNA splicing (2, 3). However, this scenario is complicated by the existence of a yeast/plant-like tRNA splicing pathway in mammalian cells (8 -12) and of analogous yeast-like RNA repair enzymes in many archaeal taxa (13-16). Definitive genetic evidence that RtcB is the sole essential agent of the repair phase of mammalian or archaeal tRNA splicing is lacking, and the available genetic evidence concerning the healing-sealing pathway in animals is equivocal. Genetic ablation of a murine homolog of a yeast-like pathway component Tpt1 (the enzyme that removes the 2Ј-phosphate at the splice junction; see Fig. 1) has no discernible phenotype (17), suggesting that the mammalian yeastlike pathway either is functionally redundant with direct ligation or is non-contributory to mammalian tRNA splicing. By contrast, siRNA-directed depletion of the mammalian RNA 5Ј-kinase (an ortholog of the kinase domain of yeast/plant tRNA ligase) elicited a defect in tRNA splicing in vitro (10). However, siRNA-directed depletion of mammalian RtcB was also reported to inhibit ligation of tRNA halves in cell extracts and to delay tRNA splicing in living cells (3). These findings leave unresolved the following key issues: (i) whether RtcB can suffice for tRNA splicing as the only source of tRNA ligase activity in a eukaryal cell and (ii) whether RtcB can perform other RNA repair functions in vivo. Here we address these questions by using budding yeast as a surrogate geneti...

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An intact unfolded protein response in Trpt1 knockout mice reveals phylogenic divergence in pathways for RNA ligation

Cited by 53 publications

References 42 publications

Mammalian 2′,3′ cyclic nucleotide phosphodiesterase (CNP) can function as a tRNA splicing enzyme in vivo

Mammalian 2′,3′ cyclic nucleotide phosphodiesterase (CNP) can function as a tRNA splicing enzyme in vivo

Transfer RNA Post-Transcriptional Processing, Turnover, and Subcellular Dynamics in the YeastSaccharomyces cerevisiae

RtcB, a Novel RNA Ligase, Can Catalyze tRNA Splicing and HAC1 mRNA Splicing in Vivo

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