rRNA processing (Homo sapiens)

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7, 15, 28, 33, 35...2, 3, 10-12, 14...cytosolmitochondrial matrixmitochondrionnucleoplasmMT-CO1 mRNAMT-CO2 mRNApre-MT-TRMT-CYB mRNAMT-ND4 mRNApre-MT-TKpre-MT-TImtRNase Ppre-MT-TW12S rRNApre-MT-TVMT-ND3 mRNArRNA modification inthe nucleusMT-ND5 mRNApre-MT-TFpre-MT-TL2H strand transcriptMT-ND1 mRNAELAC2pre-MT-TMpre-MT-TS2MT-ATP8 mRNApre-MT-TTpre-MT-TDMT-ND4L mRNATRMT10C Major pathway ofrRNA processing inthe nucleoluspre-MT-THMT-ATP6 mRNAMT-ND2 mRNApre-MT-TL1KIAA0391 HSD17B10 pre-MT-TG16S rRNAMT-CO3 mRNA141, 4-7, 9...8, 20, 22, 24, 25, 35...4217, 37


Each eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 28S rRNA are produced by endonucleolytic and exonucleolytic processing of a single 47S precursor (pre-rRNA) (reviewed in Henras et al. 2015). Transcription of ribosomal RNA genes, processing of pre-rRNA, and assembly of precursor 60S and 40S subunits occurs in the nucleolus (reviewed in Hernandez-Verdun et al. 2010). Within the nucleolus non-transcribed DNA and inactive polymerase complexes are located in the fibrillar center, active DNA polymerase I transcription occurs at the interface between the fibrillar center and the dense fibrillar component, early processing of pre-rRNA occurs in the dense fibrillar component, and late processing of pre-rRNA occurs in the granular component (Stanek et al. 2001).
Processed ribosomal RNA contains many modified nucleotides which are generated by enzymes acting on encoded nucleotides contained in the precursor rRNA (reviewed in Boschi-Muller and Motorin et al.2013). The most numerous modifications are pseudouridine residues and 2'-O-methylribonucleotides. Pseudouridylation is guided by base pairing between the precursor rRNA and a small nucleolar RNA (snoRNA) in a Box C/D snoRNP (reviewed in Henras et al 2004, Yu and Meier 2014). Similarly, 2'-O-methylation is guided by base pairing between the precursor rRNA and a snoRNA in a Box H/ACA snoRNP (reviewed in Henras et al. 2004, Hamma and Ferre-D'Amare 2010). Other modifications include N(1)-methylpseudouridine, 5-methylcytosine, 7-methylguanosine, 6-dimethyladenosine, and 4-acetylcytidine. Modification of nucleotides occur as the pre-rRNA is being cleaved. However, the order of cleavage and modification steps is not clear so these two processes are presented separately here. Defects in ribosome biogenesis factors can cause disease (reviewed in Freed et al. 2010) View original pathway at:Reactome.


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  1. Howard MJ, Lim WH, Fierke CA, Koutmos M.; ''Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5' processing.''; PubMed Europe PMC Scholia
  2. Freed EF, Bleichert F, Dutca LM, Baserga SJ.; ''When ribosomes go bad: diseases of ribosome biogenesis.''; PubMed Europe PMC Scholia
  3. Holzmann J, Frank P, Löffler E, Bennett KL, Gerner C, Rossmanith W.; ''RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme.''; PubMed Europe PMC Scholia
  4. Brzezniak LK, Bijata M, Szczesny RJ, Stepien PP.; ''Involvement of human ELAC2 gene product in 3' end processing of mitochondrial tRNAs.''; PubMed Europe PMC Scholia
  5. Henras AK, Dez C, Henry Y.; ''RNA structure and function in C/D and H/ACA s(no)RNPs.''; PubMed Europe PMC Scholia
  6. Van Haute L, Pearce SF, Powell CA, D'Souza AR, Nicholls TJ, Minczuk M.; ''Mitochondrial transcript maturation and its disorders.''; PubMed Europe PMC Scholia
  7. Levinger L, Serjanov D.; ''Pathogenesis-related mutations in the T-loops of human mitochondrial tRNAs affect 3' end processing and tRNA structure.''; PubMed Europe PMC Scholia
  8. Ofman R, Ruiter JP, Feenstra M, Duran M, Poll-The BT, Zschocke J, Ensenauer R, Lehnert W, Sass JO, Sperl W, Wanders RJ.; ''2-Methyl-3-hydroxybutyryl-CoA dehydrogenase deficiency is caused by mutations in the HADH2 gene.''; PubMed Europe PMC Scholia
  9. Henras AK, Plisson-Chastang C, O'Donohue MF, Chakraborty A, Gleizes PE.; ''An overview of pre-ribosomal RNA processing in eukaryotes.''; PubMed Europe PMC Scholia
  10. Haack TB, Kopajtich R, Freisinger P, Wieland T, Rorbach J, Nicholls TJ, Baruffini E, Walther A, Danhauser K, Zimmermann FA, Husain RA, Schum J, Mundy H, Ferrero I, Strom TM, Meitinger T, Taylor RW, Minczuk M, Mayr JA, Prokisch H.; ''ELAC2 mutations cause a mitochondrial RNA processing defect associated with hypertrophic cardiomyopathy.''; PubMed Europe PMC Scholia
  11. Hernandez-Verdun D, Roussel P, Thiry M, Sirri V, Lafontaine DL.; ''The nucleolus: structure/function relationship in RNA metabolism.''; PubMed Europe PMC Scholia
  12. Rossmanith W.; ''Localization of human RNase Z isoforms: dual nuclear/mitochondrial targeting of the ELAC2 gene product by alternative translation initiation.''; PubMed Europe PMC Scholia
  13. Stanek D, Koberna K, Pliss A, Malínský J, Masata M, Vecerová J, Risueño MC, Raska I.; ''Non-isotopic mapping of ribosomal RNA synthesis and processing in the nucleolus.''; PubMed Europe PMC Scholia
  14. Boschi-Muller S, Motorin Y.; ''Chemistry enters nucleic acids biology: enzymatic mechanisms of RNA modification.''; PubMed Europe PMC Scholia
  15. Reinhard L, Sridhara S, Hällberg BM.; ''Structure of the nuclease subunit of human mitochondrial RNase P.''; PubMed Europe PMC Scholia
  16. Sanchez MI, Mercer TR, Davies SM, Shearwood AM, Nygård KK, Richman TR, Mattick JS, Rackham O, Filipovska A.; ''RNA processing in human mitochondria.''; PubMed Europe PMC Scholia
  17. Yu YT, Meier UT.; ''RNA-guided isomerization of uridine to pseudouridine--pseudouridylation.''; PubMed Europe PMC Scholia
  18. Rorbach J, Minczuk M.; ''The post-transcriptional life of mammalian mitochondrial RNA.''; PubMed Europe PMC Scholia
  19. Vilardo E, Rossmanith W.; ''Molecular insights into HSD10 disease: impact of SDR5C1 mutations on the human mitochondrial RNase P complex.''; PubMed Europe PMC Scholia
  20. Li F, Liu X, Zhou W, Yang X, Shen Y.; ''Auto-inhibitory Mechanism of the Human Mitochondrial RNase P Protein Complex.''; PubMed Europe PMC Scholia
  21. Hamma T, Ferré-D'Amaré AR.; ''The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification.''; PubMed Europe PMC Scholia
  22. Vilardo E, Nachbagauer C, Buzet A, Taschner A, Holzmann J, Rossmanith W.; ''A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase--extensive moonlighting in mitochondrial tRNA biogenesis.''; PubMed Europe PMC Scholia


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101630view11:49, 1 November 2018ReactomeTeamreactome version 66
101166view21:36, 31 October 2018ReactomeTeamreactome version 65
100692view20:08, 31 October 2018ReactomeTeamreactome version 64
100242view16:54, 31 October 2018ReactomeTeamreactome version 63
99794view15:19, 31 October 2018ReactomeTeamreactome version 62 (2nd attempt)
93586view11:28, 9 August 2017ReactomeTeamreactome version 61
86693view09:24, 11 July 2016ReactomeTeamNew pathway

External references


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NameTypeDatabase referenceComment
12S rRNARnaENST00000389680 (Ensembl)
16S rRNARnaENST00000387347 (Ensembl)
ELAC2ProteinQ9BQ52 (Uniprot-TrEMBL)
H strand transcriptR-HSA-6786802 (Reactome)
HSD17B10 ProteinQ99714 (Uniprot-TrEMBL)
KIAA0391 ProteinO15091 (Uniprot-TrEMBL)
MT-ATP6 mRNARnaENST00000361899 (Ensembl)
MT-ATP8 mRNARnaENST00000361851 (Ensembl)
MT-CO1 mRNARnaENST00000361624 (Ensembl)
MT-CO2 mRNARnaENST00000361739 (Ensembl)
MT-CO3 mRNARnaENST00000362079 (Ensembl)
MT-CYB mRNARnaENST00000361789 (Ensembl)
MT-ND1 mRNARnaENST00000361390 (Ensembl)
MT-ND2 mRNARnaENST00000361453 (Ensembl)
MT-ND3 mRNARnaENST00000361227 (Ensembl)
MT-ND4 mRNARnaENST00000361381 (Ensembl)
MT-ND4L mRNARnaENST00000361335 (Ensembl)
MT-ND5 mRNARnaENST00000361567 (Ensembl)
Major pathway of

rRNA processing in

the nucleolus
PathwayR-HSA-6791226 (Reactome) In humans, a 47S precursor rRNA (pre-rRNA) is transcribed by RNA polymerase I from rRNA-encoding genes (rDNA) at the boundary of the fibrillar center and the dense fibrillar components of the nucleolus (Stanek et al. 2001). The 47S precursor is processed over the course of about 5-8 minutes (Popov et al. 2013) by endoribonucleases and exoribonucleases to yield the 28S rRNA and 5.8S rRNA of the 60S subunit and the 18S rRNA of the 40S subunit (reviewed in Mullineus and Lafontaine 2012, Henras et al. 2015). As the pre-rRNA is being transcribed, a large protein complex, the small subunit (SSU) processome, assembles in the region of the 18S rRNA sequence, forming terminal knobs on the pre-rRNA (reviewed in Phipps et al. 2011, inferred from yeast in Dragon et al. 2002). The SSU processome contains both ribosomal proteins of the small subunit and processing factors which process the pre-rRNA and modify nucleotides. Through addition of subunits the SSU processome appears to be converted into the larger 90S pre-ribosome (inferred from yeast in Grandi et al. 2002). An analogous large subunit processome (LSU) assembles in the region of the 28S rRNA, however the LSU is less well characterized (inferred from yeast in McCann et al. 2015).
Following cleavage of the pre-rRNA within internal transcribed spacer 1 (ITS1), the pre-ribosomal particle separates into a pre-60S subunit and a pre-40S subunit in the nucleolus (reviewed in Hernandez-Verdun et al. 2010, Phipps et al. 2011). The pre-60S and pre-40S ribosomal particles are then exported from the nucleus to the cytoplasm where the processing factors dissociate and recycle back to the nucleus
Nuclease digestions of the 47S pre-rRNA can follow several paths. In the major pathway, the ends of the 47S pre-rRNA are trimmed to yield the 45S pre-rRNA. Digestion at site 2 (also called site 2b in mouse, see Henras et al. 2015 for nomenclature) cleaves the 45S pre-rRNA to yield the 30S pre-rRNA containing the 18S rRNA of the small subunit and the 32S pre-rRNA containing the 5.8S rRNA and the 28S rRNA of the large subunit. The 32S pre-rRNA is digested in the nucleus to yield the 5.8S rRNA and the 28S rRNA while the 30S pre-rRNA is digested in the nucleus to yield the 18SE pre-rRNA which is then processed in the nucleus and cytosol to yield the 18S rRNA. At least 286 human proteins, 74 of which have no yeast homolog, are required for efficient processing of pre-rRNA in the nucleus (Tafforeau et al. 2013)
TRMT10C ProteinQ7L0Y3 (Uniprot-TrEMBL)
mtRNase PComplexR-HSA-6785726 (Reactome)
pre-MT-TDRnaENST00000387419 (Ensembl)
pre-MT-TFRnaENST00000387314 (Ensembl)
pre-MT-TGRnaENST00000387429 (Ensembl)
pre-MT-THRnaENST00000387441 (Ensembl)
pre-MT-TIRnaENST00000387365 (Ensembl)
pre-MT-TKRnaENST00000387421 (Ensembl)
pre-MT-TL1RnaENST00000386347 (Ensembl)
pre-MT-TL2RnaENST00000387456 (Ensembl)
pre-MT-TMRnaENST00000387377 (Ensembl)
pre-MT-TRRnaENST00000387439 (Ensembl)
pre-MT-TS2RnaENST00000387449 (Ensembl)
pre-MT-TTRnaENST00000387460 (Ensembl)
pre-MT-TVRnaENST00000387342 (Ensembl)
pre-MT-TWRnaENST00000387382 (Ensembl)
rRNA modification in the nucleusPathwayR-HSA-6790901 (Reactome) Human ribosomal RNAs (rRNAs) contain about 200 residues that are enzymatically modified after transcription in the nucleolus (Maden and Khan 1977, Maden 1988, Maden and Hughes 1997, reviewed in Hernandez-Verdun et al. 2010, Boschi-Muller and Motorin 2013). The modified residues occur in regions of the rRNAs that are located in functionally important parts of the ribosome, notably in the A and P peptidyl transfer sites, the polypeptide exit tunnel, and intersubunit contacts (Polikanov et al. 2015, reviewed in Decatur and Fournier 2002, Chow et al. 2007, Sharma and Lafontaine 2015). The two most common modifications are pseudouridines and 2'-O-methylribonucleotides. Formation of pseudouridine from encoded uridine is catalyzed by box H/ACA small nucleolar ribonucleoprotein (snoRNP) complexes (reviewed in Hamma and Ferre-D'Amare 2010, Watkins and Bohnsack 2011, Ge and Yu 2013, Kierzek et al. 2014, Yu and Meier 2014) and methylation of the hydroxyl group of the 2' carbon is catalyzed by box C/D snoRNPs (Kiss-Laszlo et al. 1996, Lapinaite et al. 2013, reviewed in Watkins and Bohnsack 2011). The snoRNP complexes contain common sets of protein subunits and unique snoRNAs that guide each complex to its target nucleotide of the rRNA by base-pairing between the snoRNA and the rRNA (reviewed in Henras et al. 2004, Watkins and Bohnsack 2011). Other modifications of rRNA include 5-methylcytidine (reviewed in Squires and Preiss 2010), 1-methylpseudouridine, 7-methylguanosine, 6-dimethyladenosine, and 4-acetylcytidine (reviewed in Sharma and Lafontaine 2015). In yeast most modifications are introduced co-transcriptionally (Kos and Tollervey 2010, reviewed in Turowski and Tollervey 2015), however the order of modification events and pre-rRNA cleavage events is not well characterized.

Annotated Interactions

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SourceTargetTypeDatabase referenceComment
12S rRNAArrowR-HSA-6785722 (Reactome)
16S rRNAArrowR-HSA-6785722 (Reactome)
ELAC2mim-catalysisR-HSA-6785722 (Reactome)
H strand transcriptR-HSA-6785722 (Reactome)
MT-ATP6 mRNAArrowR-HSA-6785722 (Reactome)
MT-ATP8 mRNAArrowR-HSA-6785722 (Reactome)
MT-CO1 mRNAArrowR-HSA-6785722 (Reactome)
MT-CO2 mRNAArrowR-HSA-6785722 (Reactome)
MT-CO3 mRNAArrowR-HSA-6785722 (Reactome)
MT-CYB mRNAArrowR-HSA-6785722 (Reactome)
MT-ND1 mRNAArrowR-HSA-6785722 (Reactome)
MT-ND2 mRNAArrowR-HSA-6785722 (Reactome)
MT-ND3 mRNAArrowR-HSA-6785722 (Reactome)
MT-ND4 mRNAArrowR-HSA-6785722 (Reactome)
MT-ND4L mRNAArrowR-HSA-6785722 (Reactome)
MT-ND5 mRNAArrowR-HSA-6785722 (Reactome)
R-HSA-6785722 (Reactome) RNase P, ELAC2, and additional unknown nucleases cleave H strand transcripts to release the various tRNAs, rRNAs, and mRNAs contained in the long polycistronic transcripts.
Mitochondrial RNase P, comprising 3 protein subunits and no RNA moiety (Holzmann et al. 2008), endonucleolytically cleaves polycistronic mitochondrial transcripts at the 5' ends of the tRNA sequences (Sanchez et al. 2011, Howard et al. 2012, Vilardo et al. 2012, Li et al. 2015, Reinhard et al. 2015, Vilardo and Rossmanith 2015). A subcomplex of RNase P also functions as a tRNA methyltransferase and the SDR5C1 subunit is an amino acid and fatty acid dehydrogenase. Mutations in the SDR5C1 subunit of RNase P cause HSD10 disease, which is characterized by progressive neurodegeneration and cardiomyopathy (Vilardo and Rossmanith 2015)
ELAC2 cleaves polycistronic mitochondrial transcripts at the 3' ends of the tRNA sequences (Brzezniak et al. 2011, Sanchez et al. 2011). Different isoforms of ELAC2 are present in the nucleus and mitochondria (Rossmanith 2011). Mutations in ELAC2 cause cardiac hypertrophy (Haack et al. 2013) and disorders of oxidative phosphorylation (reviewed in Van Haute et al. 2015).
Unknown nucleases also cleave the H strand transcript at sites 5' to MT-CO3, 5' to MT-CO1, and 5' to MT-CYB (reviewed in Van Haute et al. 2015).
mtRNase Pmim-catalysisR-HSA-6785722 (Reactome)
pre-MT-TDArrowR-HSA-6785722 (Reactome)
pre-MT-TFArrowR-HSA-6785722 (Reactome)
pre-MT-TGArrowR-HSA-6785722 (Reactome)
pre-MT-THArrowR-HSA-6785722 (Reactome)
pre-MT-TIArrowR-HSA-6785722 (Reactome)
pre-MT-TKArrowR-HSA-6785722 (Reactome)
pre-MT-TL1ArrowR-HSA-6785722 (Reactome)
pre-MT-TL2ArrowR-HSA-6785722 (Reactome)
pre-MT-TMArrowR-HSA-6785722 (Reactome)
pre-MT-TRArrowR-HSA-6785722 (Reactome)
pre-MT-TS2ArrowR-HSA-6785722 (Reactome)
pre-MT-TTArrowR-HSA-6785722 (Reactome)
pre-MT-TVArrowR-HSA-6785722 (Reactome)
pre-MT-TWArrowR-HSA-6785722 (Reactome)
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