tRNA processing in the nucleus (Homo sapiens)

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5, 7, 9, 10, 17...30, 37, 451, 15, 22, 24, 25, 31...27, 3328, 30, 37, 42, 454, 11-13, 38...6, 16, 20, 21, 29...41, 47nucleoplasmcytosolNUP62 Cleaved pre-tRNA (intronless) with 3' CCA GTP Spliced tRNA with 3' CCA Spliced tRNA with 3' CCA NUP214 GTP TSEN complexCPSF1 Cleaved pre-tRNA (intronless) with 3' CCA NUP133 POP1 NUP93 Cleaved pre-tRNA(intron-containing)with 3' CCANUPL1-2 RPP21 POP5 GDP TPR Nuclear Pore Complex(NPC)C2orf49 RPP14 POM121C PPiRAN RTCB RPP40 TSEN34 PiCleaved tRNA with 3'CCAAMPRANBP2 NUP54 RPP38 Ran-GTPNUP188 XPOT3' tRNA exon with 5'hydroxylRAN RAE1 5' cleaved pre-tRNA (intron-containing) CLP1 pre-tRNAtRNA intronRan:GDPRNase PNUP98-3 C14orf166 5' cleaved, 3' cleaved pre-tRNA (intron-containing) ZBTB8OS NUP155 NUP43 XPOTPOP7 NUPL2 NUP205 AAAS NUP107 POM121 Spliced tRNA with 3' CCA RPP30 tRNARAN CTP5' cleaved, 3' cleaved pre-tRNA (intronless) NUP160 TSEN54 5' cleaved pre-tRNACleaved pre-tRNA (intron-containing) with 3' CCA ATPtRNA:XPOT:RAN:GTPNDC1 NUP153 NUP35 NUP88 TSEN15 tRNAPPiDDX1 NUP210 CPSF4 ELAC25',3' cleavedpre-tRNACleaved pre-tRNA (intronless) with 3' CCA 5' tRNA exon with2',3' cyclicphosphate5' cleaved pre-tRNA (intronless) NUP50 CSTF2 NUP98-5 SEH1L-2 ATPSpliced tRNA with 3'CCANUP37 NUP98-4 XPOT POP4 Cleaved pre-tRNA (intronless) with 3' CCA FAM98B Nup45 NUP85 pre-tRNA (intronless) pre-tRNA (intron-containing) RPPH1 RNA TSEN2 tRNA ligase complexRPP25 TRNT12741, 471420, 4928, 30, 37, 452, 24, 25, 313, 8, 23, 44


Description

Genes encoding transfer RNAs are transcribed in the nucleus by RNA polymerase III. (Distinct processes of transcription and processing also occur in mitochondria.) The initial transcripts, pre-tRNAs, contain extra nucleotides at the 5' end and 3' end. 6.3% (32 of 509) of human tRNAs also contain introns, which are located in the anticodon loop, 3' to the anticodon. The additional nucleotides are removed and a non-templated CCA sequence is added to the resulting 3' terminus by processing reactions in the nucleus and cytosol (reviewed in Nakanishi and Nureki 2005, Phizicky and Hopper 2010).
The order of processing and nucleotide modification events may be different for different tRNAs and its analysis is complicated by a retrograde transport mechanism that can import tRNAs from the cytosol back to the nucleus (retrograde movement, Shaheen and Hopper 2005, reviewed in Phizicky 2005). Generally, the 5' leader of the pre-tRNA is removed first by endonucleolytic cleavage by the RNase P ribonucleoprotein complex, which contains a catalytic RNA (RNA H1 in humans) and at least 10 protein subunits (reviewed in Jarrous 2002, Xiao et al. 2002, Jarrous and Gopalan 2010).
The 3' trailer is then removed by RNase Z activity, a single protein in humans (reviewed in Maraia and Lamichhane 2011). ELAC2 is a RNase Z found in both nucleus and mitochondria. ELAC1 is found in the cytosol and may also act as an RNase Z. Human tRNA genes do not encode the universal acceptor 3' terminus CCA, instead it is added post-transcriptionally by TRNT1, an unusual polymerase that requires no nucleic acid template (reviewed in Xiong and Steitz 2006, Hou 2010, Tomita and Yamashita 2014).
In humans introns are spliced from intron-containing tRNAs in the nucleus by a two step mechanism that is distinct from mRNA splicing (reviewed in Popow et al. 2012, Lopes et al. 2015). The TSEN complex first cleaves 5' and 3' to the intron, generating a 2'3' cyclic phosphate on the 5' exon and a 5' hydroxyl group on the 3' exon. These two ends are ligated by a complex containing at least 6 proteins in a single reaction that both hydrolyzes the 2' phosphate bond and joins the 3' phosphate to the 5' hydroxyl. (In yeast the ligation and the hydrolysis of the 2' phosphate are separate reactions. The splicing reactions in yeast occur in the cytosol at the mitochondrial outer membrane.)
Mature transfer RNAs contain a large number of modified nucleotide residues that are produced by post-transcriptional modification reactions (reviewed in Li and Mason 2014). Depending on the specific tRNA these reactions may occur before or after splicing and before or after export from the nucleus to the cytosol. View original pathway at:Reactome.

Comments

Reactome-Converter 
Pathway is converted from Reactome ID: 6784531
Reactome-version 
Reactome version: 61
Reactome Author 
Reactome Author: May, Bruce

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Ontology Terms

 

Bibliography

View all...
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  21. Shaheen HH, Hopper AK.; ''Retrograde movement of tRNAs from the cytoplasm to the nucleus in Saccharomyces cerevisiae.''; PubMed
  22. Brzezniak LK, Bijata M, Szczesny RJ, Stepien PP.; ''Involvement of human ELAC2 gene product in 3' end processing of mitochondrial tRNAs.''; PubMed
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  47. Reichert AS, Thurlow DL, Mörl M.; ''A eubacterial origin for the human tRNA nucleotidyltransferase?''; PubMed
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History

View all...
CompareRevisionActionTimeUserComment
101566view11:43, 1 November 2018ReactomeTeamreactome version 66
101102view21:26, 31 October 2018ReactomeTeamreactome version 65
100631view20:01, 31 October 2018ReactomeTeamreactome version 64
100181view16:45, 31 October 2018ReactomeTeamreactome version 63
99731view15:12, 31 October 2018ReactomeTeamreactome version 62 (2nd attempt)
93908view13:44, 16 August 2017ReactomeTeamreactome version 61
93482view11:24, 9 August 2017ReactomeTeamreactome version 61
88354view16:26, 1 August 2016FehrhartOntology Term : 'tRNA maturation pathway' added !
86579view09:21, 11 July 2016ReactomeTeamreactome version 56
83442view12:25, 18 November 2015ReactomeTeamNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
3' tRNA exon with 5' hydroxylR-HSA-5696797 (Reactome)
5' cleaved pre-tRNA (intron-containing) R-HSA-5696775 (Reactome)
5' cleaved pre-tRNA (intronless) R-HSA-5696767 (Reactome)
5' cleaved pre-tRNAComplexR-HSA-6784537 (Reactome)
5' cleaved, 3' cleaved pre-tRNA (intron-containing) R-HSA-5696773 (Reactome)
5' cleaved, 3' cleaved pre-tRNA (intronless) R-HSA-5696763 (Reactome)
5' tRNA exon with

2',3' cyclic

phosphate
R-HSA-5696785 (Reactome)
5',3' cleaved pre-tRNAComplexR-HSA-6784544 (Reactome)
AAAS ProteinQ9NRG9 (Uniprot-TrEMBL)
AMPMetaboliteCHEBI:16027 (ChEBI)
ATPMetaboliteCHEBI:15422 (ChEBI)
C14orf166 ProteinQ9Y224 (Uniprot-TrEMBL)
C2orf49 ProteinQ9BVC5 (Uniprot-TrEMBL)
CLP1 ProteinQ92989 (Uniprot-TrEMBL)
CPSF1 ProteinQ10570 (Uniprot-TrEMBL)
CPSF4 ProteinO95639 (Uniprot-TrEMBL)
CSTF2 ProteinP33240 (Uniprot-TrEMBL)
CTPMetaboliteCHEBI:17677 (ChEBI)
Cleaved pre-tRNA

(intron-containing)

with 3' CCA
R-HSA-5696798 (Reactome)
Cleaved pre-tRNA (intron-containing) with 3' CCA R-HSA-5696798 (Reactome)
Cleaved pre-tRNA (intronless) with 3' CCA R-HSA-5696790 (Reactome)
Cleaved pre-tRNA (intronless) with 3' CCA R-HSA-6785481 (Reactome)
Cleaved tRNA with 3' CCAComplexR-HSA-6784557 (Reactome)
DDX1 ProteinQ92499 (Uniprot-TrEMBL)
ELAC2ProteinQ9BQ52 (Uniprot-TrEMBL)
FAM98B ProteinQ52LJ0 (Uniprot-TrEMBL)
GDP MetaboliteCHEBI:17552 (ChEBI)
GTP MetaboliteCHEBI:15996 (ChEBI)
NDC1 ProteinQ9BTX1 (Uniprot-TrEMBL)
NUP107 ProteinP57740 (Uniprot-TrEMBL)
NUP133 ProteinQ8WUM0 (Uniprot-TrEMBL)
NUP153 ProteinP49790 (Uniprot-TrEMBL)
NUP155 ProteinO75694 (Uniprot-TrEMBL)
NUP160 ProteinQ12769 (Uniprot-TrEMBL)
NUP188 ProteinQ5SRE5 (Uniprot-TrEMBL)
NUP205 ProteinQ92621 (Uniprot-TrEMBL)
NUP210 ProteinQ8TEM1 (Uniprot-TrEMBL)
NUP214 ProteinP35658 (Uniprot-TrEMBL)
NUP35 ProteinQ8NFH5 (Uniprot-TrEMBL)
NUP37 ProteinQ8NFH4 (Uniprot-TrEMBL)
NUP43 ProteinQ8NFH3 (Uniprot-TrEMBL)
NUP50 ProteinQ9UKX7 (Uniprot-TrEMBL)
NUP54 ProteinQ7Z3B4 (Uniprot-TrEMBL)
NUP62 ProteinP37198 (Uniprot-TrEMBL)
NUP85 ProteinQ9BW27 (Uniprot-TrEMBL)
NUP88 ProteinQ99567 (Uniprot-TrEMBL)
NUP93 ProteinQ8N1F7 (Uniprot-TrEMBL)
NUP98-3 ProteinP52948-3 (Uniprot-TrEMBL)
NUP98-4 ProteinP52948-4 (Uniprot-TrEMBL)
NUP98-5 ProteinP52948-5 (Uniprot-TrEMBL)
NUPL1-2 ProteinQ9BVL2-1 (Uniprot-TrEMBL)
NUPL2 ProteinO15504 (Uniprot-TrEMBL)
Nuclear Pore Complex (NPC)ComplexR-HSA-157689 (Reactome)
Nup45 ProteinQ9BVL2-2 (Uniprot-TrEMBL)
POM121 ProteinQ96HA1 (Uniprot-TrEMBL)
POM121C ProteinA8CG34 (Uniprot-TrEMBL)
POP1 ProteinQ99575 (Uniprot-TrEMBL)
POP4 ProteinO95707 (Uniprot-TrEMBL)
POP5 ProteinQ969H6 (Uniprot-TrEMBL)
POP7 ProteinO75817 (Uniprot-TrEMBL)
PPiMetaboliteCHEBI:29888 (ChEBI)
PiMetaboliteCHEBI:18367 (ChEBI)
RAE1 ProteinP78406 (Uniprot-TrEMBL)
RAN ProteinP62826 (Uniprot-TrEMBL)
RANBP2 ProteinP49792 (Uniprot-TrEMBL)
RNase PComplexR-HSA-5696795 (Reactome)
RPP14 ProteinO95059 (Uniprot-TrEMBL)
RPP21 ProteinQ9H633 (Uniprot-TrEMBL)
RPP25 ProteinQ9BUL9 (Uniprot-TrEMBL)
RPP30 ProteinP78346 (Uniprot-TrEMBL)
RPP38 ProteinP78345 (Uniprot-TrEMBL)
RPP40 ProteinO75818 (Uniprot-TrEMBL)
RPPH1 RNA ProteinENST00000516869 (Ensembl)
RTCB ProteinQ9Y3I0 (Uniprot-TrEMBL)
Ran-GTPComplexR-HSA-180738 (Reactome)
Ran:GDPComplexR-HSA-206617 (Reactome)
SEH1L-2 ProteinQ96EE3-2 (Uniprot-TrEMBL)
Spliced tRNA with 3' CCAR-HSA-5696762 (Reactome)
Spliced tRNA with 3' CCA R-HSA-5696762 (Reactome)
Spliced tRNA with 3' CCA R-HSA-6785475 (Reactome)
TPR ProteinP12270 (Uniprot-TrEMBL)
TRNT1ProteinQ96Q11 (Uniprot-TrEMBL)
TSEN complexComplexR-HSA-5696765 (Reactome)
TSEN15 ProteinQ8WW01 (Uniprot-TrEMBL)
TSEN2 ProteinQ8NCE0 (Uniprot-TrEMBL)
TSEN34 ProteinQ9BSV6 (Uniprot-TrEMBL)
TSEN54 ProteinQ7Z6J9 (Uniprot-TrEMBL)
XPOT ProteinO43592 (Uniprot-TrEMBL)
XPOTProteinO43592 (Uniprot-TrEMBL)
ZBTB8OS ProteinQ8IWT0 (Uniprot-TrEMBL)
pre-tRNA (intron-containing) R-HSA-5696768 (Reactome) 6.3% (32 of 509) of human tRNAs contain introns. Introns are always located one base 3' to the anticodon.
pre-tRNA (intronless) R-HSA-5696799 (Reactome) 93.7% (477 of 509) of human tRNAs do not have introns.
pre-tRNAComplexR-HSA-6784574 (Reactome)
tRNA intronR-HSA-5696774 (Reactome)
tRNA ligase complexComplexR-HSA-5696778 (Reactome)
tRNA:XPOT:RAN:GTPComplexR-HSA-6783450 (Reactome)
tRNAComplexR-HSA-6783491 (Reactome)
tRNAComplexR-HSA-6785476 (Reactome)

Annotated Interactions

View all...
SourceTargetTypeDatabase referenceComment
3' tRNA exon with 5' hydroxylArrowR-HSA-5696813 (Reactome)
3' tRNA exon with 5' hydroxylR-HSA-5696816 (Reactome)
5' cleaved pre-tRNAArrowR-HSA-5696810 (Reactome)
5' cleaved pre-tRNAR-HSA-5696815 (Reactome)
5' tRNA exon with

2',3' cyclic

phosphate
ArrowR-HSA-5696813 (Reactome)
5' tRNA exon with

2',3' cyclic

phosphate
R-HSA-5696816 (Reactome)
5',3' cleaved pre-tRNAArrowR-HSA-5696815 (Reactome)
5',3' cleaved pre-tRNAR-HSA-5696807 (Reactome)
AMPArrowR-HSA-5696816 (Reactome)
ATPR-HSA-5696807 (Reactome)
ATPR-HSA-5696816 (Reactome)
CTPR-HSA-5696807 (Reactome)
Cleaved pre-tRNA

(intron-containing)

with 3' CCA
R-HSA-5696813 (Reactome)
Cleaved tRNA with 3' CCAArrowR-HSA-5696807 (Reactome)
ELAC2mim-catalysisR-HSA-5696815 (Reactome)
Nuclear Pore Complex (NPC)mim-catalysisR-HSA-6783483 (Reactome)
PPiArrowR-HSA-5696807 (Reactome)
PPiArrowR-HSA-5696816 (Reactome)
PiArrowR-HSA-6783483 (Reactome)
R-HSA-5696807 (Reactome) TRNT1 (CCA-adding enzyme) polymerizes the non-templated nucleotides CCA onto the 3' end (acceptor arm) of tRNAs (Reichert et al. 2001, Lizano et al. 2007, Lizano et al. 2008). In contrast to some eubacterial tRNA genes, eukaryotic tRNA genes do not encode CCA at the 3' end. The added CCA sequence is determined by the structural properties of the TRNT1 protein itself rather than by any nucleic acid template (Augustin et al. 2003, Ernst et al. 2015, Kuhn et al. 2015, see also the structure of the bacterial enzyme in Li et al. 2002). After polymerization of a single CCA motif, conformational change of the enzyme ejects the tRNA before additional nucleotides can be polymerized (Kuhn et al. 2015). Aberrant RNA with two CCA motifs is targeted for destruction.
R-HSA-5696810 (Reactome) The RNase P RNA-protein complex located in the nucleus endonucleolytically cleaves near the 5' end of pre-tRNAs, generating the mature 5' end (Ferrari et al. 1980, Bartkiewicz et al. 1989, Jiang et al. 2001, Reiner et al. 2011, reviewed in Jarrous 2002). The site of cleavage is determined by the length of the helices in the acceptor and T stems of the tRNA (Yuan and Altman 1995). Human cells contain distinct nuclear and mitochondrial RNase P activities (Rossmanith et al. 1995), with nuclear RNase P localized in the nucleolus (Jarrous et al. 1999). The nuclear RNase P is similar to bacterial enzymes in having a catalytic RNA component. The mitochondrial RNase P is unusual in containing only protein subunits (Holzmann et al. 2008).
R-HSA-5696813 (Reactome) The TSEN complex endonucleolytically cleaves 5' and 3' of introns in tRNAs, leaving a 2',3' cyclic phosphate on the 5' exon and a 5' hydroxyl on the 3' exon (Paushkin et al. 2004, Trotta et al. 2006).
R-HSA-5696815 (Reactome) ELAC2, a RNaseZ activity in humans, endonucleolytically cleaves pre-tRNAs near the 3' end, generating a 3' hydroxyl group to which the nucleotides CCA will be polymerized (Takaku et al. 2004, Yan et al. 2006, Elbarbary et al. 2008). ELAC2 is located in both the nucleus and mitochondria (Brzezniak et al. 2011). ELAC1, a homologue of ELAC2, is located in the cytosol (Rossmanith 2011) and cleaves 3' ends of tRNAs in vitro (Takaku et al. 2003).
R-HSA-5696816 (Reactome) The RNA ligase complex ligates tRNA exons yielding intact, spliced tRNAs (Popow et al. 2011, Popow et al. 2014). The reaction apparently occurs in one step with no residual 2' phosphate that requires removal, as in yeast.
R-HSA-6783483 (Reactome) The nuclear export receptor XPOT (Exportin-t) interacts with both tRNA (Li and Sprinzl 2006) and RAN:GTP and the complex is translocated from the nucleus to the cytosol through the nuclear pore (Arts et al. 1998, Kutay et al. 1998, Kuersten et al. 2002, reviewed in Leisegang et al. 2012). RAN:GTP-dependent interactions of XPOT with components of the nuclear pore may increase the efficiency of the transport cycle (Kuersten et al. 2002).
R-HSA-6785478 (Reactome) XPOT binds processed tRNA together with RAN:GTP in the nucleus (Arts et al. 1998, Kutay et al. 1998, Li and Sprinzl 2006).
RNase Pmim-catalysisR-HSA-5696810 (Reactome)
Ran-GTPR-HSA-6785478 (Reactome)
Ran:GDPArrowR-HSA-6783483 (Reactome)
Spliced tRNA with 3' CCAArrowR-HSA-5696816 (Reactome)
TRNT1mim-catalysisR-HSA-5696807 (Reactome)
TSEN complexmim-catalysisR-HSA-5696813 (Reactome)
XPOTArrowR-HSA-6783483 (Reactome)
XPOTR-HSA-6785478 (Reactome)
pre-tRNAR-HSA-5696810 (Reactome)
tRNA intronArrowR-HSA-5696813 (Reactome)
tRNA ligase complexmim-catalysisR-HSA-5696816 (Reactome)
tRNA:XPOT:RAN:GTPArrowR-HSA-6785478 (Reactome)
tRNA:XPOT:RAN:GTPR-HSA-6783483 (Reactome)
tRNAArrowR-HSA-6783483 (Reactome)
tRNAR-HSA-6785478 (Reactome)
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