KEGG   PATHWAY: omy03008
Entry
omy03008                    Pathway                                
Name
Ribosome biogenesis in eukaryotes - Oncorhynchus mykiss (rainbow trout)
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
omy03008  Ribosome biogenesis in eukaryotes
omy03008

Organism
Oncorhynchus mykiss (rainbow trout) [GN:omy]
Gene
110488421  casein kinase II subunit beta [KO:K03115]
110535231  casein kinase II subunit beta [KO:K03115]
110496050  casein kinase II subunit beta isoform X1 [KO:K03115]
110506718  casein kinase II subunit beta [KO:K03115]
110528522  casein kinase II subunit alpha [KO:K03097] [EC:2.7.11.1]
110496662  casein kinase II subunit alpha [KO:K03097] [EC:2.7.11.1]
110513011  casein kinase II subunit alpha' [KO:K03097] [EC:2.7.11.1]
110516628  casein kinase II subunit alpha'-like [KO:K03097] [EC:2.7.11.1]
110517756  casein kinase II subunit alpha' [KO:K03097] [EC:2.7.11.1]
118936609  casein kinase II subunit alpha-like [KO:K03097] [EC:2.7.11.1]
110493916  casein kinase II subunit alpha isoform X1 [KO:K03097] [EC:2.7.11.1]
110493986  casein kinase II subunit alpha' isoform X1 [KO:K03097] [EC:2.7.11.1]
110488044  zgc:86598; casein kinase II subunit alpha isoform X1 [KO:K03097] [EC:2.7.11.1]
110520732  casein kinase II subunit alpha [KO:K03097] [EC:2.7.11.1]
110525289  nol6; nucleolar protein 6 [KO:K14544]
110486452  rrp7a; ribosomal RNA-processing protein 7 homolog A [KO:K14545]
110505246  WD repeat-containing protein 43 [KO:K14546]
110506265  wdr43; WD repeat-containing protein 43 [KO:K14546]
110519996  U3 small nucleolar RNA-associated protein 4 homolog [KO:K14548]
110494472  U3 small nucleolar RNA-associated protein 4 homolog [KO:K14548]
110526053  utp15; U3 small nucleolar RNA-associated protein 15 homolog [KO:K14549]
110498747  heatr1; HEAT repeat-containing protein 1 isoform X1 [KO:K14550]
110501551  WD repeat-containing protein 75 isoform X1 [KO:K14552]
110520019  WD repeat-containing protein 75 isoform X1 [KO:K14552]
110538122  U3 small nucleolar RNA-associated protein 18 homolog [KO:K14553]
110538132  U3 small nucleolar RNA-associated protein 18 homolog [KO:K14553]
110486195  U3 small nucleolar RNA-associated protein 18 homolog [KO:K14553]
110523881  wdr36; WD repeat-containing protein 36 [KO:K14554]
110486873  transducin beta-like protein 3 [KO:K14555]
110486894  transducin beta-like protein 3 [KO:K14555]
110501664  wdr3; WD repeat-containing protein 3 [KO:K14556]
110493574  utp6; U3 small nucleolar RNA-associated protein 6 homolog [KO:K14557]
110497020  periodic tryptophan protein 2 homolog [KO:K14558]
110497022  periodic tryptophan protein 2 homolog [KO:K14558]
110506430  mphosph10; U3 small nucleolar ribonucleoprotein protein MPP10 [KO:K14559]
100305178  imp3; U3 small nucleolar ribonucleoprotein protein IMP3 [KO:K14560]
100305199  imp4; U3 small nucleolar ribonucleoprotein protein IMP4 [KO:K14561]
110525905  U3 small nucleolar ribonucleoprotein protein IMP4 [KO:K14561]
110512218  fbl; rRNA 2'-O-methyltransferase fibrillarin [KO:K14563] [EC:2.1.1.-]
110538837  rRNA 2'-O-methyltransferase fibrillarin [KO:K14563] [EC:2.1.1.-]
110494006  nop56; nucleolar protein 56 [KO:K14564]
118947557  nucleolar protein 58-like isoform X1 [KO:K14565]
110513518  LOW QUALITY PROTEIN: nucleolar protein 58 [KO:K14565]
110517259  nucleolar protein 58 isoform X1 [KO:K14565]
110502939  NHP2-like protein 1 [KO:K12845]
110515633  NHP2-like protein 1 [KO:K12845]
110499221  NHP2-like protein 1 [KO:K12845]
118937766  NHP2-like protein 1 [KO:K12845]
110509933  H/ACA ribonucleoprotein complex subunit DKC1 isoform X1 [KO:K11131] [EC:5.4.99.-]
110533950  H/ACA ribonucleoprotein complex subunit DKC1 isoform X1 [KO:K11131] [EC:5.4.99.-]
110537797  H/ACA ribonucleoprotein complex subunit 2-like protein [KO:K11129]
110533406  nhp2; H/ACA ribonucleoprotein complex subunit 2-like protein [KO:K11129]
110488920  H/ACA ribonucleoprotein complex subunit 1 [KO:K11128]
110505115  H/ACA ribonucleoprotein complex subunit 1 [KO:K11128]
100301851  nola3; H/ACA ribonucleoprotein complex subunit 3 [KO:K11130]
110500396  H/ACA ribonucleoprotein complex subunit 3 [KO:K11130]
110497930  rRNA-processing protein FCF1 homolog [KO:K14566]
110505535  rRNA-processing protein FCF1 homolog [KO:K14566]
110510095  si:dkey-251i10.3; U3 small nucleolar RNA-associated protein 14 homolog A [KO:K14567]
110535567  drosha; ribonuclease 3 isoform X1 [KO:K03685] [EC:3.1.26.3]
110509324  ribosomal RNA small subunit methyltransferase NEP1 [KO:K14568] [EC:2.1.1.260]
110537348  ribosomal RNA small subunit methyltransferase NEP1 isoform X1 [KO:K14568] [EC:2.1.1.260]
110534710  LOW QUALITY PROTEIN: ribosome biogenesis protein BMS1 homolog [KO:K14569]
110514095  ribosome biogenesis protein BMS1 homolog [KO:K14569]
110525389  nat10; RNA cytidine acetyltransferase [KO:K14521] [EC:2.3.1.-]
100301792  rcl1; RNA 3'-terminal phosphate cyclase-like protein [KO:K11108]
110512205  pop1; ribonucleases P/MRP protein subunit POP1 isoform X1 [KO:K01164] [EC:3.1.26.5]
110535793  ribonuclease P protein subunit p38 isoform X1 [KO:K14523] [EC:3.1.26.5]
110507876  ribonuclease P protein subunit p38 [KO:K14523] [EC:3.1.26.5]
110526259  pop4; ribonuclease P protein subunit p29 isoform X1 [KO:K03538] [EC:3.1.26.5]
100301805  pop5; ribonuclease P/MRP protein subunit POP5 [KO:K03537] [EC:3.1.26.5]
110535382  ribonuclease P protein subunit p25-like protein [KO:K14525] [EC:3.1.26.5]
110515205  ribonuclease P protein subunit p25-like protein [KO:K14525] [EC:3.1.26.5]
110506475  ribonuclease P protein subunit p25-like [KO:K14525] [EC:3.1.26.5]
110526358  uncharacterized protein LOC110526358 [KO:K14525] [EC:3.1.26.5]
110500748  uncharacterized protein LOC110500748 [KO:K14525] [EC:3.1.26.5]
110531656  ribonuclease P protein subunit p20 isoform X1 [KO:K14527] [EC:3.1.26.5]
110500518  pop7; ribonuclease P protein subunit p20 isoform X1 [KO:K14527] [EC:3.1.26.5]
110498997  ribonuclease P protein subunit p30 isoform X1 [KO:K03539] [EC:3.1.26.5]
110498998  rpp30; ribonuclease P protein subunit p30 isoform X2 [KO:K03539] [EC:3.1.26.5]
110509095  rpp40; ribonuclease P protein subunit p40 isoform X1 [KO:K14530] [EC:3.1.26.5]
110521513  RNA exonuclease 1 homolog [KO:K14570] [EC:3.1.-.-]
110511854  RNA exonuclease 5 isoform X1 [KO:K14570] [EC:3.1.-.-]
110524379  rexo1; RNA exonuclease 1 homolog [KO:K14570] [EC:3.1.-.-]
110525426  zgc:152968; RNA exonuclease 1 homolog isoform X1 [KO:K14570] [EC:3.1.-.-]
110517154  RNA exonuclease 5-like isoform X1 [KO:K14570] [EC:3.1.-.-]
110533424  smfn; small fragment nuclease [KO:K13288] [EC:3.1.-.-]
110508810  xrn1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
110530214  5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
110522080  5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
110529465  5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
110530259  gtpbp4; nucleolar GTP-binding protein 1 [KO:K06943]
110488984  gnl2; nucleolar GTP-binding protein 2 [KO:K14537]
110527980  gnl3; guanine nucleotide-binding protein-like 3 isoform X1 [KO:K14538]
110494479  guanine nucleotide-binding protein-like 3 [KO:K14538]
110494569  gnl3l; guanine nucleotide-binding protein-like 3-like protein [KO:K14538]
110528362  nvl; nuclear valosin-containing protein-like isoform X1 [KO:K14571]
110503089  nuclear valosin-containing protein-like [KO:K14571]
110522101  midasin isoform X1 [KO:K14572]
110529504  midasin isoform X1 [KO:K14572]
110521593  rbm28; RNA-binding protein 28 isoform X1 [KO:K14573]
110512298  RNA-binding protein NOB1 [KO:K11883]
110526880  RNA-binding protein NOB1 [KO:K11883]
110534440  GTP-binding nuclear protein Ran isoform X3 [KO:K07936]
110488823  ran; GTP-binding nuclear protein Ran [KO:K07936]
110497439  GTP-binding nuclear protein Ran [KO:K07936]
110505029  GTP-binding nuclear protein Ran [KO:K07936]
110485112  exportin-1 [KO:K14290]
110513996  exportin-1 isoform X1 [KO:K14290]
110517253  exportin-1 isoform X1 [KO:K14290]
110493719  exportin-1 [KO:K14290]
110503792  nmd3; 60S ribosomal export protein NMD3 isoform X1 [KO:K07562]
110507634  60S ribosomal export protein NMD3 isoform X1 [KO:K07562]
110489078  zgc:153681; nuclear RNA export factor 1 isoform X1 [KO:K14284]
110509974  nuclear RNA export factor 1 [KO:K14284]
110533985  nuclear RNA export factor 1 [KO:K14284]
100301754  nxt2; NTF2-related export protein 2 [KO:K14285]
110527666  eukaryotic translation initiation factor 6 [KO:K03264]
100301763  if6; Eukaryotic translation initiation factor 6 [KO:K03264]
110503890  ribosome maturation protein SBDS isoform X2 [KO:K14574]
110507728  ribosome maturation protein SBDS [KO:K14574]
110515557  elongation factor-like GTPase 1 [KO:K14536] [EC:3.6.5.-]
110506168  elongation factor-like GTPase 1 [KO:K14536] [EC:3.6.5.-]
110524176  lsg1; large subunit GTPase 1 homolog [KO:K14539] [EC:3.6.1.-]
110505085  spata5; ATPase family protein 2 homolog [KO:K14575]
110536429  ak6; adenylate kinase isoenzyme 6 isoform X1 [KO:K18532] [EC:2.7.4.3]
110509098  riok1; serine/threonine-protein kinase RIO1 [KO:K07178] [EC:2.7.11.1]
110536149  riok2; serine/threonine-protein kinase RIO2 [KO:K07179] [EC:2.7.11.1]
118951575  18S ribosomal RNA [KO:K01979]
118955579  18S ribosomal RNA [KO:K01979]
118948691  18S ribosomal RNA [KO:K01979]
118946658  18S ribosomal RNA [KO:K01979]
118948692  18S ribosomal RNA [KO:K01979]
118946659  18S ribosomal RNA [KO:K01979]
118938640  18S ribosomal RNA [KO:K01979]
110528711  18S ribosomal RNA [KO:K01979]
118965427  18S ribosomal RNA [KO:K01979]
118947156  5.8S ribosomal RNA [KO:K01986]
118946666  28S ribosomal RNA [KO:K01982]
118948648  28S ribosomal RNA [KO:K01982]
118947804  28S ribosomal RNA [KO:K01982]
118961091  28S ribosomal RNA [KO:K01982]
118947850  28S ribosomal RNA [KO:K01982]
118937054  small nucleolar RNA U3 [KO:K14483]
118941551  small nucleolar RNA U3 [KO:K14483]
118937055  small nucleolar RNA U3 [KO:K14483]
118937058  small nucleolar RNA U3 [KO:K14483]
118945876  small nucleolar RNA U3 [KO:K14483]
118945925  small nucleolar RNA U3 [KO:K14483]
118952811  small nucleolar RNA U3 [KO:K14483]
118937059  small nucleolar RNA U3 [KO:K14483]
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
omy03010  Ribosome
KO pathway
ko03008   
LinkDB

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