KEGG   PATHWAY: plop03008
Entry
plop03008                   Pathway                                
Name
Ribosome biogenesis in eukaryotes - Perognathus longimembris pacificus (Pacific pocket mouse)
Description
Ribosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It requires hundreds of factors not present in the mature particle. In the absence of these proteins, ribosome biogenesis is stalled and cell growth is terminated even under optimal growth conditions. The primary pre-rRNA transcript is assembled into the 90S pre-ribosome, which contains both 40S and 60S assembly factors. Within this complex, the pre-rRNA is cleaved. pre-60S ribosomes are subjected to several sequential processing steps in the nucleoplasm involving numerous assembly intermediates before it is exported to the cytoplasm and matured into the 60S ribosomal subunit. The pre-40S ribosome is matured to the small ribosomal subunit in the cytoplasm by cleavage.
Class
Genetic Information Processing; Translation
Pathway map
plop03008  Ribosome biogenesis in eukaryotes
plop03008

Organism
Perognathus longimembris pacificus (Pacific pocket mouse) [GN:plop]
Gene
125338635  Mphosph10; U3 small nucleolar ribonucleoprotein protein MPP10 [KO:K14559]
125338709  Pop4; ribonuclease P protein subunit p29 isoform X1 [KO:K03538] [EC:3.1.26.5]
125338715  Fbl; rRNA 2'-O-methyltransferase fibrillarin [KO:K14563] [EC:2.1.1.-]
125338737  Sbds; ribosome maturation protein SBDS [KO:K14574]
125339892  Wdr36; WD repeat-containing protein 36 [KO:K14554]
125339984  Riok2; serine/threonine-protein kinase RIO2 [KO:K07179] [EC:2.7.11.1]
125340171  Tcof1; treacle protein [KO:K14562]
125340618  Nop10; H/ACA ribonucleoprotein complex subunit 3 [KO:K11130]
125340916  Tbl3; transducin beta-like protein 3 [KO:K14555]
125341648  Spata5; ATPase family protein 2 homolog isoform X1 [KO:K14575]
125341723  Gar1; H/ACA ribonucleoprotein complex subunit 1 [KO:K11128]
125342024  Fbll1; rRNA/tRNA 2'-O-methyltransferase fibrillarin-like protein 1 [KO:K14563] [EC:2.1.1.-]
125342203  Nhp2; H/ACA ribonucleoprotein complex subunit 2 [KO:K11129]
125342253  [KO:K01986]
125342264  [KO:K01986]
125342265  [KO:K01979]
125342266  [KO:K01979]
125342267  [KO:K01979]
125342269  [KO:K01982]
125342270  [KO:K01986]
125342405  [KO:K18532] [EC:2.7.4.3]
125342647  Xrn1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
125343006  [KO:K14284]
125343011  [KO:K14284]
125343012  [KO:K14284]
125343292  Dkc1; H/ACA ribonucleoprotein complex subunit DKC1 [KO:K11131] [EC:5.4.99.-]
125343547  Gnl3l; guanine nucleotide-binding protein-like 3-like protein [KO:K14538]
125343692  Utp14a; U3 small nucleolar RNA-associated protein 14 homolog A isoform X1 [KO:K14567]
125344149  Nxt2; NTF2-related export protein 2 isoform X1 [KO:K14285]
125344300  Nxf3; nuclear RNA export factor 3 [KO:K14284]
125344616  [KO:K01986]
125344618  [KO:K01982]
125344619  [KO:K01986]
125344620  [KO:K01979]
125344621  [KO:K01979]
125344622  [KO:K01982]
125344623  [KO:K01986]
125344625  [KO:K01986]
125344626  [KO:K01979]
125344627  [KO:K01979]
125344628  [KO:K01982]
125344678  [KO:K01981]
125344779  [KO:K01981]
125344780  [KO:K01981]
125344781  [KO:K01981]
125344782  [KO:K01981]
125344783  [KO:K01981]
125344784  [KO:K01981]
125344785  [KO:K01981]
125344787  [KO:K01981]
125344788  [KO:K01981]
125344789  [KO:K01981]
125344796  [KO:K01986]
125344797  [KO:K01979]
125344798  [KO:K01982]
125344845  [KO:K01986]
125344847  [KO:K01979]
125344848  [KO:K01982]
125344949  [KO:K01986]
125344968  [KO:K01986]
125344969  [KO:K01979]
125344970  [KO:K01982]
125345103  [KO:K14563] [EC:2.1.1.-]
125345180  [KO:K01986]
125345181  [KO:K01982]
125345329  [KO:K14284]
125345543  [KO:K01986]
125345544  [KO:K01982]
125345545  [KO:K01982]
125345546  [KO:K01986]
125345547  [KO:K01979]
125345549  [KO:K01979]
125345550  [KO:K01979]
125345624  [KO:K01986]
125345625  [KO:K01979]
125345626  [KO:K01979]
125345627  [KO:K01982]
125345634  [KO:K01986]
125345635  [KO:K01979]
125345636  [KO:K01982]
125345638  [KO:K01982]
125345639  [KO:K01982]
125345640  [KO:K01986]
125345641  [KO:K01986]
125345642  [KO:K01979]
125345643  [KO:K01979]
125346288  Rpp30; ribonuclease P protein subunit p30 [KO:K03539] [EC:3.1.26.5]
125346561  Bms1; ribosome biogenesis protein BMS1 homolog [KO:K14569]
125346857  [KO:K14561]
125347108  Rbm28; RNA-binding protein 28 [KO:K14573]
125347367  [KO:K01981]
125347476  [KO:K01981]
125347482  [KO:K01981]
125347494  [KO:K01981]
125347505  [KO:K01981]
125347875  [KO:K07936]
125347969  Pop5; ribonuclease P/MRP protein subunit POP5 [KO:K03537] [EC:3.1.26.5]
125348399  [KO:K14567]
125348487  Rexo1; RNA exonuclease 1 homolog [KO:K14570] [EC:3.1.-.-]
125349228  Ran; GTP-binding nuclear protein Ran [KO:K07936]
125349591  Rexo2; oligoribonuclease, mitochondrial [KO:K13288] [EC:3.1.-.-]
125350390  Nop58; nucleolar protein 58 isoform X1 [KO:K14565]
125350476  Wdr75; WD repeat-containing protein 75 [KO:K14552]
125350811  Imp4; U3 small nucleolar ribonucleoprotein protein IMP4 [KO:K14561]
125351414  Pwp2; periodic tryptophan protein 2 homolog [KO:K14558]
125351514  [KO:K14285]
125351855  Lsg1; large subunit GTPase 1 homolog [KO:K14539] [EC:3.6.1.-]
125352008  Nmd3; 60S ribosomal export protein NMD3 [KO:K07562]
125352123  [KO:K14483]
125352124  [KO:K14483]
125352809  Csnk2b; casein kinase II subunit beta [KO:K03115]
125353088  Riok1; serine/threonine-protein kinase RIO1 [KO:K07178] [EC:2.7.11.1]
125353111  Rpp40; ribonuclease P protein subunit p40 [KO:K14530] [EC:3.1.26.5]
125353193  Nxt1; NTF2-related export protein 1 [KO:K14285]
125353196  Xrn2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
125353326  Nop56; nucleolar protein 56 [KO:K14564]
125353343  Csnk2a1; casein kinase II subunit alpha [KO:K03097] [EC:2.7.11.1]
125353411  Eif6; eukaryotic translation initiation factor 6 [KO:K03264]
125354934  Gnl2; nucleolar GTP-binding protein 2 [KO:K14537]
125355055  Pop7; ribonuclease P protein subunit p20 [KO:K14527] [EC:3.1.26.5]
125355473  Wdr3; WD repeat-containing protein 3 isoform X1 [KO:K14556]
125355848  [KO:K14483]
125355849  [KO:K14483]
125355850  [KO:K14483]
125356409  Xpo1; exportin-1 [KO:K14290]
125356601  Wdr43; WD repeat-containing protein 43 isoform X1 [KO:K14546]
125356938  [KO:K01981]
125357132  Mdn1; midasin isoform X1 [KO:K14572]
125357445  Rrp7a; ribosomal RNA-processing protein 7 homolog A [KO:K14545]
125357755  Snu13; NHP2-like protein 1 isoform X1 [KO:K12845]
125358232  Nob1; RNA-binding protein NOB1 [KO:K11883]
125358239  Utp4; U3 small nucleolar RNA-associated protein 4 homolog isoform X1 [KO:K14548]
125358386  Csnk2a2; casein kinase II subunit alpha' [KO:K03097] [EC:2.7.11.1]
125358602  Gnl3; guanine nucleotide-binding protein-like 3 isoform X1 [KO:K14538]
125360243  Nvl; nuclear valosin-containing protein-like [KO:K14571]
125360490  Pop1; ribonucleases P/MRP protein subunit POP1 [KO:K01164] [EC:3.1.26.5]
125361650  Nat10; RNA cytidine acetyltransferase [KO:K14521] [EC:2.3.1.-]
125362107  Nxf1; nuclear RNA export factor 1 [KO:K14284]
125363246  Fcf1; rRNA-processing protein FCF1 homolog isoform X1 [KO:K14566]
125364106  Nol6; nucleolar protein 6 [KO:K14544]
125364353  [KO:K14483]
125364460  [KO:K14557]
125365654  Utp6; U3 small nucleolar RNA-associated protein 6 homolog [KO:K14557]
125366117  Utp18; U3 small nucleolar RNA-associated protein 18 homolog [KO:K14553]
125366172  Rpp25l; ribonuclease P protein subunit p25-like protein [KO:K14525] [EC:3.1.26.5]
125366639  [KO:K14483]
125366640  [KO:K14483]
125366792  Heatr1; HEAT repeat-containing protein 1 [KO:K14550]
125367137  Rpp38; ribonuclease P protein subunit p38 [KO:K14523] [EC:3.1.26.5]
125367283  Gtpbp4; GTP-binding protein 4 [KO:K06943]
125367384  [KO:K01979]
125367492  Utp15; U3 small nucleolar RNA-associated protein 15 homolog [KO:K14549]
125367763  Drosha; LOW QUALITY PROTEIN: ribonuclease 3 [KO:K03685] [EC:3.1.26.3]
125367832  Ak6; adenylate kinase isoenzyme 6 [KO:K18532] [EC:2.7.4.3]
125368047  Efl1; LOW QUALITY PROTEIN: elongation factor-like GTPase 1 [KO:K14536] [EC:3.6.5.-]
125368287  Rcl1; RNA 3'-terminal phosphate cyclase-like protein isoform X1 [KO:K11108]
125368343  Imp3; LOW QUALITY PROTEIN: U3 small nucleolar ribonucleoprotein protein IMP3 [KO:K14560]
125368498  Rpp25; ribonuclease P protein subunit p25 [KO:K14525] [EC:3.1.26.5]
Reference
  Authors
Freed EF, Bleichert F, Dutca LM, Baserga SJ
  Title
When ribosomes go bad: diseases of ribosome biogenesis.
  Journal
Mol Biosyst 6:481-93 (2010)
DOI:10.1039/b919670f
Reference
  Authors
Perez-Fernandez J, Roman A, De Las Rivas J, Bustelo XR, Dosil M
  Title
The 90S preribosome is a multimodular structure that is assembled through a hierarchical mechanism.
  Journal
Mol Cell Biol 27:5414-29 (2007)
DOI:10.1128/MCB.00380-07
Reference
  Authors
Strunk BS, Karbstein K
  Title
Powering through ribosome assembly.
  Journal
RNA 15:2083-104 (2009)
DOI:10.1261/rna.1792109
Reference
  Authors
Granneman S, Baserga SJ
  Title
Ribosome biogenesis: of knobs and RNA processing.
  Journal
Exp Cell Res 296:43-50 (2004)
DOI:10.1016/j.yexcr.2004.03.016
Reference
  Authors
Kressler D, Hurt E, Bassler J
  Title
Driving ribosome assembly.
  Journal
Biochim Biophys Acta 1803:673-83 (2010)
DOI:10.1016/j.bbamcr.2009.10.009
Related
pathway
plop03010  Ribosome
KO pathway
ko03008   

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