Structure of tRNA splicing enzyme Tpt1 illuminates the mechanism of RNA 2′-PO4 recognition and ADP-ribosylation

Banerjee, Ankan; Munir, Annum; Abdullahu, Leonora; Damha, Masad J.; Goldgur, Yehuda; Shuman, Stewart

doi:10.1038/s41467-018-08211-9

Cited by 25 publications

(41 citation statements)

References 31 publications

(51 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This final reaction occurs in three nucleotidyl transfer steps: (1) Trl1-LIG reacts with ATP to form a covalent LIG-(lysyl-N)-AMP intermediate; (2) the bound AMP is transferred to the 5’ phosphate end to form a 5’-to-5’ RNA-adenylate; (3) Trl1-LIG catalyzes the attack by the 3’-OH on the RNA-adenylate to form a phosphodiester bond, releasing AMP (Greer et al, 1983; Phizicky et al, 1986). The remaining 2’ phosphate at the splice junction is removed by an additional enzyme, Tpt1, which is a 2’ phosphotransferase that, like Trl1, is also essential for cell viability (Banerjee et al, 2019; Culver et al, 1997; Culver et al, 1993).…”

Section: Introductionmentioning

confidence: 99%

tRNA ligase structure reveals kinetic competition between non-conventional mRNA splicing and mRNA decay

Peschek

Walter

2019

eLife

View full text Add to dashboard Cite

Yeast tRNA ligase (Trl1) is an essential trifunctional enzyme that catalyzes exon-exon ligation during tRNA biogenesis and the non-conventional splicing of HAC1 mRNA during the unfolded protein response (UPR). The UPR regulates the protein folding capacity of the endoplasmic reticulum (ER). ER stress activates Ire1, an ER-resident kinase/RNase, which excises an intron from HAC1 mRNA followed by exon-exon ligation by Trl1. The spliced product encodes for a potent transcription factor that drives the UPR. Here we report the crystal structure of Trl1 RNA ligase domain from Chaetomium thermophilum at 1.9 Å resolution. Structure-based mutational analyses uncovered kinetic competition between RNA ligation and degradation during HAC1 mRNA splicing. Incompletely processed HAC1 mRNA is degraded by Xrn1 and the Ski/exosome complex. We establish cleaved HAC1 mRNA as endogenous substrate for ribosome-associated quality control. We conclude that mRNA decay and surveillance mechanisms collaborate in achieving fidelity of non-conventional mRNA splicing during the UPR.

show abstract

Section: Introductionmentioning

confidence: 99%

tRNA ligase structure reveals kinetic competition between non-conventional mRNA splicing and mRNA decay

Peschek

Walter

2019

eLife

View full text Add to dashboard Cite

show abstract

“…Our results here highlight RNA 2 ′ -PO 4 and 3 ′ -PO 4 ends as plausible endogenous substrates with which CthTpt1 reacted to form the ADP-ribose-1 ′′ -phosphate ligand retained in the NAD + site in the CthTpt1 crystal structure (Banerjee et al 2019). This is a more parsimonious scenario than invoking a hypothetical E. coli pathway for the formation of an internal RNA 2 ′ -PO 4 .…”

Section: Discussionmentioning

confidence: 67%

“…It will be of interest to understand why certain Tpt1 enzymes react with noncanonical phospho-substrates whereas others do not. The structure of CthTpt1 as a product complex mimetic with ADP-ribose-1 ′′ -phosphate in the NAD + site and pAp in the RNA site revealed that the essential active site amino acid chains (an Arg-His-Arg-Arg tetrad) form an elaborate network of contacts to the 1 ′′ -phosphate (equivalent to the splice junction 2 ′ -PO 4 prior to its transfer to NAD + ) and the vicinal 3 ′ -PO 4 of the splice junction (Banerjee et al 2019). The inference from the CthTpt1 structure that the junction 2 ′ -PO 4 and 3 ′ -PO 4 are the most critical determinants of substrate recognition accords with the biochemical insights of Steiger et al (2001) who showed that an RNA trinucleotide with a gem-diphospho 2 ′ -PO 4 ,3 ′ -PO 4 terminus sufficed for efficient 2 ′ -phosphotransferase activity of S. cerevisiae Tpt1.…”

Section: Discussionmentioning

confidence: 99%

“…The intrigue around Tpt1 was heightened by the 1.4 Å X-ray structure of Clostridium thermocellum Tpt1 (CthTpt1), produced as a recombinant protein in Escherichia coli and providentially crystallized with ADP-ribose-1 ′′ -phosphate in the NAD + site (Banerjee et al 2019). To our knowledge, there had been no prior description of ADPribose-1 ′′ -phosphate as a metabolite in E. coli.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

NAD⁺-dependent RNA terminal 2′ and 3′ phosphomonoesterase activity of a subset of Tpt1 enzymes

Munir

Abdullahu

Banerjee

et al. 2019

RNA

Self Cite

View full text Add to dashboard Cite

The enzyme Tpt1 removes the 2 ′ ′ ′ ′ ′-PO 4 at the splice junction generated by fungal tRNA ligase; it does so via a two-step reaction in which (i) the internal RNA 2 ′ ′ ′ ′ ′-PO 4 attacks NAD + to form an RNA-2 ′ ′ ′ ′ ′-phospho-ADP-ribosyl intermediate; and (ii) transesterification of the ribose O2 ′′ ′′ ′′ ′′ ′′ to the 2 ′ ′ ′ ′ ′-phosphodiester yields 2 ′ ′ ′ ′ ′-OH RNA and ADP-ribose-1 ′′ ′′ ′′ ′′ ′′ ,2 ′′ ′′ ′′ ′′ ′′-cyclic phosphate products. The role that Tpt1 enzymes play in taxa that have no fungal-type RNA ligase remains obscure. An attractive prospect is that Tpt1 enzymes might catalyze reactions other than internal RNA 2 ′ ′ ′ ′ ′-PO 4 removal, via their unique NAD +-dependent transferase mechanism. This study extends the repertoire of the Tpt1 enzyme family to include the NAD +-dependent conversion of RNA terminal 2 ′ ′ ′ ′ ′ and 3 ′ ′ ′ ′ ′ monophosphate ends to 2 ′ ′ ′ ′ ′-OH and 3 ′ ′ ′ ′ ′-OH ends, respectively. The salient finding is that different Tpt1 enzymes vary in their capacity and positional specificity for terminal phosphate removal. Clostridium thermocellum and Aeropyrum pernix Tpt1 proteins are active on 2 ′ ′ ′ ′ ′-PO 4 and 3 ′ ′ ′ ′ ′-PO 4 ends, with a 2.4-to 2.6-fold kinetic preference for the 2 ′ ′ ′ ′ ′-PO 4. The accumulation of a terminal 3 ′ ′ ′ ′ ′-phospho-ADP-ribosylated RNA intermediate during the 3 ′ ′ ′ ′ ′-phosphotransferase reaction suggests that the geometry of the 3 ′ ′ ′ ′ ′-p-ADPR adduct is not optimal for the ensuing transesterification step. Chaetomium thermophilum Tpt1 acts specifically on a terminal 2 ′ ′ ′ ′ ′-PO 4 end and not with a 3 ′ ′ ′ ′ ′-PO 4. In contrast, Runella slithyformis Tpt1 and human Tpt1 are ineffective in removing either a 2 ′ ′ ′ ′ ′-PO 4 or 3 ′ ′ ′ ′ ′-PO 4 end.

show abstract

“…Modification of RNAs by ADPr has been described for the divergent TpT1. Saccharomyces cerevisiae TpT1 is involved in RNA splicing by acting as tRNA 2′-phosphotransferase, catalysing the transfer of the 2′phosphate from ligated tRNA to NAD + , producing mature tRNA and ADP ribose-1″-2″-cyclic phosphate at the splice junction of tRNAs [5,[129][130][131]. Similarly, the bacterial homologue KptA, performs same reaction in vitro [132], though its physiological function in E. coli remains largely unknown since splicing is absent.…”

Section: Substrates Of Adprmentioning

confidence: 99%

Targeting ADP-ribosylation as an antimicrobial strategy

Catara

Corteggio

Valente

et al. 2019

Biochemical Pharmacology

View full text Add to dashboard Cite

A B S T R A C T ADP-ribosylation (ADPr) is an ancient reversible modification of cellular macromolecules controlling major biological processes as diverse as DNA damage repair, transcriptional regulation, intracellular transport, immune and stress responses, cell survival and proliferation. Furthermore, enzymatic reactions of ADPr are central in the pathogenesis of many human diseases, including infectious conditions. By providing a review of ADPr signalling in bacterial systems, we highlight the relevance of this chemical modification in the pathogenesis of human diseases depending on host-pathogen interactions. The post-antibiotic era has raised the need to find alternative approaches to antibiotic administration, as major pathogens becoming resistant to antibiotics. An in-depth understanding of ADPr reactions provides the rationale for designing novel antimicrobial strategies for treatment of infectious diseases. In addition, the understanding of mechanisms of ADPr by bacterial virulence factors offers important hints to improve our knowledge on cellular processes regulated by eukaryotic homologous enzymes, which are often involved in the pathogenesis of human diseases.T large number of worldwide spread diseases, affecting humans, insects and plants [31,[56][57][58], with a great impact on human health. In addition, infectious diseases strongly affect the world economy in terms of costs for the human health as well as food and agricultural economic losses [59]. The use of antibiotics to counteract the pathogen infections has represented the therapeutic strategy of choice in the last century, however the emergence of antibiotic resistance strains represents the major challenge of the 21st century [60][61][62]. Targeting bacterial pathogenic mechanisms by disarming pathogens of virulence factors, for instance by inhibiting the enzymatic activity of bART, represents a valid alternative intervention strategy to overcome antibiotic resistance [63][64][65][66]. In addition, because of the conservation of ADPr systems throughout the evolution, the understanding of bacterial pathogenic mechanisms may contribute to unveil novel and conserved cellular processes regulated by ADPr in high organisms [34,45,67,68]. The dysregulation of such processes can be either cause of human diseases or be target of therapeutic intervention [39,[69][70][71].Herein, we will provide a summary of bacterial ADPr systems describing their pathogenic mechanisms and highlighting the similarities with ADPr systems in mammals as well. Further, we discuss the potential of targeting ADPr for therapeutic strategies of infection diseases. ADP-ribosylation in pathophysiologyADPr was originally described in the 60s; two independent studies reported the identification of a new polymer, poly(ADP-ribose) (PAR) synthesised from NAD + in vertebrate cells [72] and, simultaneously, the finding that bacterial DTX activity from C. diphteriae is dependent on NAD + content [73]. In the following decades, research in the field has expanded the involvement of ADPr ...

show abstract

Structure of tRNA splicing enzyme Tpt1 illuminates the mechanism of RNA 2′-PO4 recognition and ADP-ribosylation

Cited by 25 publications

References 31 publications

tRNA ligase structure reveals kinetic competition between non-conventional mRNA splicing and mRNA decay

tRNA ligase structure reveals kinetic competition between non-conventional mRNA splicing and mRNA decay

NAD⁺-dependent RNA terminal 2′ and 3′ phosphomonoesterase activity of a subset of Tpt1 enzymes

Targeting ADP-ribosylation as an antimicrobial strategy

Contact Info

Product

Resources

About

Structure of tRNA splicing enzyme Tpt1 illuminates the mechanism of RNA 2′-PO4 recognition and ADP-ribosylation

Cited by 25 publications

References 31 publications

tRNA ligase structure reveals kinetic competition between non-conventional mRNA splicing and mRNA decay

tRNA ligase structure reveals kinetic competition between non-conventional mRNA splicing and mRNA decay

NAD+-dependent RNA terminal 2′ and 3′ phosphomonoesterase activity of a subset of Tpt1 enzymes

Targeting ADP-ribosylation as an antimicrobial strategy

Contact Info

Product

Resources

About

NAD⁺-dependent RNA terminal 2′ and 3′ phosphomonoesterase activity of a subset of Tpt1 enzymes