The tRNA Splicing Endonuclease Complex Cleaves the Mitochondria-localized CBP1 mRNA

Tsuboi, Tatsuhisa; Yamazaki, Reina; Nobuta, Risa; Ikeuchi, Ken; Makino, Shiho; Ohtaki, Ayumi; Suzuki, Yutaka; Yoshihisa, Tohru; Trotta, Christopher R.; Inada, Toshifumi

doi:10.1074/jbc.m114.634592

Cited by 26 publications

(30 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…1C), consistent with this complex having an essential function beyond splicing of pre-tRNA (Dhungel and Hopper 2012). The gene encoding the only other known substrate of the SEN complex, CBP1, is non-essential (Tsuboi et al 2015), suggesting that the SEN complex has another essential function, possibly to process unknown RNA substrates.…”

Section: Resultssupporting

confidence: 55%

Genetic bypass of essential RNA repair enzymes in budding yeast

Cherry

White

York

et al. 2017

RNA

View full text Add to dashboard Cite

RNA repair enzymes catalyze rejoining of an RNA molecule after cleavage of phosphodiester linkages. RNA repair in budding yeast is catalyzed by two separate enzymes that process tRNA exons during their splicing and mRNA exons during activation of the unfolded protein response (UPR). The RNA ligase Trl1 joins 2',3'-cyclic phosphate and 5'-hydroxyl RNA fragments, creating a phosphodiester linkage with a 2'-phosphate at the junction. The 2'-phosphate is removed by the 2'-phosphotransferase Tpt1. We bypassed the essential functions of and in budding yeast by expressing "prespliced," intronless versions of the 10 normally intron-containing tRNAs, indicating this repair pathway does not have additional essential functions. Consistent with previous studies, expression of intronless tRNAs failed to rescue the growth of cells with deletions in components of the SEN complex, implying an additional essential role for the splicing endonuclease. TheΔ and Δ mutants accumulate tRNA and splicing intermediates indicative of RNA repair defects and are hypersensitive to drugs that inhibit translation. Failure to induce the unfolded protein response in Δ cells grown with tunicamycin is lethal owing to their inability to ligate after its cleavage by Ire1. In contrast, Δ mutants grow in the presence of tunicamycin despite reduced accumulation of spliced mRNA. We optimized a PCR-based method to detect RNA 2'-phosphate modifications and show they are present on ligated mRNA. These RNA repair mutants enable new studies of the role of RNA repair in cellular physiology.

show abstract

Section: Resultssupporting

confidence: 55%

Genetic bypass of essential RNA repair enzymes in budding yeast

Cherry

White

York

et al. 2017

RNA

View full text Add to dashboard Cite

show abstract

“…Previous work suggests that the eukaryotic TSEN complex has broad specificity. For example, the Xenopus TSEN complex can cleave a bulge-helix-bulge (BHB) substrate, the universal substrate for archaeal TSENs (49), whereas recent work with the S. Cerevisiae TSEN complex identified the stem loop of CBP1 mRNA as a new TSEN substrate (54). To begin to address substrate recognition, we designed a synthetic mini intron construct with a 5′ fluorescent label ( Figure 3B), that includes only the anticodon stem loop (ASL) of tRNA-R1 ( Figure S1).…”

Section: Human Tsen Core Is Active On Pre-trna Substratesmentioning

confidence: 99%

Reconstitution of the Human tRNA Splicing Endonuclease Complex: insight into the regulation of pre-tRNA cleavage

Hayne

Schmidt²,

Matera³

et al. 2019

Preprint

View full text Add to dashboard Cite

The splicing of tRNA introns is a critical step in pre-tRNA maturation. In archaea and eukaryotes, tRNA intron removal is catalyzed by the tRNA splicing endonuclease (TSEN) complex. Eukaryotic TSEN is comprised of four core subunits (TSEN54, TSEN2, TSEN34, and TSEN15). The human TSEN complex additionally co-purifies with the polynucleotide kinase CLP1; however, CLP1's role in tRNA splicing remains unclear. Mutations in genes encoding all four TSEN subunits, as well as CLP1, are known to cause neurodegenerative disorders, yet the mechanisms underlying the pathogenesis of these disorders are unknown. Here, we developed a recombinant system that produces active TSEN complex. Co-expression of all four TSEN subunits is required for efficient formation and function of the complex. We show that human CLP1 associates with the active TSEN complex, but is not required for tRNA intron cleavage in vitro. Moreover, RNAi knockdown of the Drosophila CLP1 orthologue, cbc, promotes biogenesis of mature tRNAs and circularized tRNA introns (tricRNAs) in vivo. Collectively, these and other findings suggest that CLP1/cbc plays a regulatory role in tRNA splicing by serving as a negative modulator of the direct tRNA ligation pathway in animal cells.We thank Drs. Andrew Sikkema and Marcos Morgan as well as members of the Stanley Lab for their critical reading of this manuscript. We would like to acknowledge Robert Petrovich and the NIEHS Protein Expression Facility for assistance with protein expression in HEK293 suspension cultures and for supplying the anti-GFP resin. We also thank Robert Dutcher for his assistance with running SEC-MALS.

show abstract

“…The yeast tRNA splicing endonuclease also catalyzes a particular step in mRNA biogenesis on the mitochondrial surface. It cleaves the mitochondria-localized mRNA encoding Cbp1 (cytochrome b mRNA processing 1) [151]. Cleavage of this unessential CBP1 mRNA requires the mitochondrial localization of the SEN complex and two CBP1 mRNA cis-elements: the mitochondrial targeting signal and the stem-loop 652–726-nt region [151].…”

Section: Cytoplasmic Splicing Of Intron-containing Trnasmentioning

confidence: 99%

“…It cleaves the mitochondria-localized mRNA encoding Cbp1 (cytochrome b mRNA processing 1) [151]. Cleavage of this unessential CBP1 mRNA requires the mitochondrial localization of the SEN complex and two CBP1 mRNA cis-elements: the mitochondrial targeting signal and the stem-loop 652–726-nt region [151]. The authors proposed that endonucleolytic cleavage of Cbp1 mRNA occurs co-translationally, when CBP1 mRNA is localized to mitochondria via its mitochondrial targeting signal [151].…”

Section: Cytoplasmic Splicing Of Intron-containing Trnasmentioning

confidence: 99%

“…First, it is possible that the mitochondrial localization of the RNA processing enzymes evolved for moonlighting functions. For example, in addition to tRNA splicing, the SEN complex also splices CBP1 mRNA on the mitochondrial surface for the co-translational import of Cbp1 protein [151]. It is possible that the RNA processing enzymes located on the mitochondrial surface have unidentified moonlighting functions that may be involved in mitochondria composition and/or function.…”

Section: Cytoplasmic Splicing Of Intron-containing Trnasmentioning

confidence: 99%

See 1 more Smart Citation

tRNA dynamics between the nucleus, cytoplasm and mitochondrial surface: Location, location, location

Chatterjee

Nostramo

Wan

et al. 2018

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

View full text Add to dashboard Cite

Although tRNAs participate in the essential function of protein translation in the cytoplasm, tRNA transcription and numerous processing steps occur in the nucleus. This subcellular separation between tRNA biogenesis and function requires that tRNAs be efficiently delivered to the cytoplasm in a step termed "primary tRNA nuclear export". Surprisingly, tRNA nuclear-cytoplasmic traffic is not unidirectional, but, rather, movement is bidirectional. Cytoplasmic tRNAs are imported back to the nucleus by the "tRNA retrograde nuclear import" step which is conserved from budding yeast to vertebrate cells and has been hijacked by viruses, such as HIV, for nuclear import of the viral reverse transcription complex in human cells. Under appropriate environmental conditions cytoplasmic tRNAs that have been imported into the nucleus return to the cytoplasm via the 3rd nuclear-cytoplasmic shuttling step termed "tRNA nuclear re-export", that again is conserved from budding yeast to vertebrate cells. We describe the 3 steps of tRNA nuclear-cytoplasmic movements and their regulation. There are multiple tRNA nuclear export and import pathways. The different tRNA nuclear exporters appear to possess substrate specificity leading to the tantalizing possibility that the cellular proteome may be regulated at the level of tRNA nuclear export. Moreover, in some organisms, such as budding yeast, the pre-tRNA splicing heterotetrameric endonuclease (SEN), which removes introns from pre-tRNAs, resides on the cytoplasmic surface of the mitochondria. Therefore, we also describe the localization of the SEN complex to mitochondria and splicing of pre-tRNA on mitochondria, which occurs prior to the participation of tRNAs in protein translation. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.

show abstract

The tRNA Splicing Endonuclease Complex Cleaves the Mitochondria-localized CBP1 mRNA

Cited by 26 publications

References 31 publications

Genetic bypass of essential RNA repair enzymes in budding yeast

Genetic bypass of essential RNA repair enzymes in budding yeast

Reconstitution of the Human tRNA Splicing Endonuclease Complex: insight into the regulation of pre-tRNA cleavage

tRNA dynamics between the nucleus, cytoplasm and mitochondrial surface: Location, location, location

Contact Info

Product

Resources

About