KEGG   PATHWAY: oke03008
Entry
oke03008                    Pathway                                
Name
Ribosome biogenesis in eukaryotes - Oncorhynchus keta (chum salmon)
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
oke03008  Ribosome biogenesis in eukaryotes
oke03008

Organism
Oncorhynchus keta (chum salmon) [GN:oke]
Gene
127927552  casein kinase II subunit beta-like [KO:K03115]
118375632  casein kinase II subunit beta-like [KO:K03115]
118398303  casein kinase II subunit beta [KO:K03115]
118399157  casein kinase II subunit beta isoform X1 [KO:K03115]
118401354  casein kinase II subunit alpha' [KO:K03097] [EC:2.7.11.1]
127927547  casein kinase II subunit alpha-like [KO:K03097] [EC:2.7.11.1]
118375239  casein kinase II subunit alpha-like [KO:K03097] [EC:2.7.11.1]
118396584  csnk2a2b; casein kinase II subunit alpha' isoform X1 [KO:K03097] [EC:2.7.11.1]
118397974  zgc:86598; STKc_CK2_alpha domain-containing protein [KO:K03097] [EC:2.7.11.1]
127918077  casein kinase II subunit alpha'-like [KO:K03097] [EC:2.7.11.1]
127919167  casein kinase II subunit alpha'-like [KO:K03097] [EC:2.7.11.1]
118399644  casein kinase II subunit alpha-like [KO:K03097] [EC:2.7.11.1]
118400589  casein kinase II subunit alpha-like [KO:K03097] [EC:2.7.11.1]
118392889  nucleolar protein 6 [KO:K14544]
118365489  ribosomal RNA-processing protein 7 homolog A isoform X1 [KO:K14545]
118368556  WD repeat-containing protein 43-like [KO:K14546]
118402809  wdr43; WD repeat-containing protein 43 [KO:K14546]
118401307  U3 small nucleolar RNA-associated protein 4 homolog isoform X1 [KO:K14548]
118396625  U3 small nucleolar RNA-associated protein 4 homolog isoform X1 [KO:K14548]
118376495  utp15; U3 small nucleolar RNA-associated protein 15 homolog [KO:K14549]
118357518  heatr1; HEAT repeat-containing protein 1 isoform X1 [KO:K14550]
118385954  wdr75; WD repeat-containing protein 75 isoform X1 [KO:K14552]
118367157  WD repeat-containing protein 75-like isoform X1 [KO:K14552]
118365220  U3 small nucleolar RNA-associated protein 18 homolog [KO:K14553]
118384463  U3 small nucleolar RNA-associated protein 18 homolog [KO:K14553]
118387853  wdr36; WD repeat-containing protein 36 [KO:K14554]
118380896  tbl3; transducin beta-like protein 3 [KO:K14555]
118386236  wdr3; WD repeat-containing protein 3 [KO:K14556]
118376076  utp6; U3 small nucleolar RNA-associated protein 6 homolog isoform X1 [KO:K14557]
118375310  pwp2h; PWP2 small subunit processome component [KO:K14558]
118358878  U3 small nucleolar ribonucleoprotein protein MPP10-like [KO:K14559]
118402355  imp3; U3 small nucleolar ribonucleoprotein protein IMP3 [KO:K14560]
118358513  U3 small nucleolar ribonucleoprotein protein IMP4-like isoform X1 [KO:K14561]
118374535  rRNA 2'-O-methyltransferase fibrillarin-like [KO:K14563] [EC:2.1.1.-]
118380105  rRNA 2'-O-methyltransferase fibrillarin-like [KO:K14563] [EC:2.1.1.-]
118389036  nucleolar protein 56-like [KO:K14564]
127925426  snu13a; LOW QUALITY PROTEIN: SNU13 homolog, small nuclear ribonucleoprotein a (U4/U6.U5) [KO:K12845]
118402922  NHP2-like protein 1 [KO:K12845]
118372951  NHP2-like protein 1 [KO:K12845]
118385153  H/ACA ribonucleoprotein complex subunit DKC1-like [KO:K11131] [EC:5.4.99.-]
118390326  H/ACA ribonucleoprotein complex subunit DKC1-like isoform X1 [KO:K11131] [EC:5.4.99.-]
118370387  H/ACA ribonucleoprotein complex subunit 2-like protein [KO:K11129]
118389791  nhp2; H/ACA ribonucleoprotein complex subunit 2-like protein [KO:K11129]
118363585  H/ACA ribonucleoprotein complex subunit 1-like [KO:K11128]
118379422  H/ACA ribonucleoprotein complex subunit 1-like [KO:K11128]
118368950  H/ACA ribonucleoprotein complex subunit 3-like [KO:K11130]
118392171  H/ACA ribonucleoprotein complex subunit 3 [KO:K11130]
118362480  rRNA-processing protein FCF1 homolog isoform X1 [KO:K14566]
118368318  rRNA-processing protein FCF1 homolog [KO:K14566]
118385017  si:dkey-251i10.3; U3 small nucleolar RNA-associated protein 14 homolog A [KO:K14567]
118361554  drosha; ribonuclease 3 isoform X1 [KO:K03685] [EC:3.1.26.3]
118379505  ribosomal RNA small subunit methyltransferase NEP1-like [KO:K14568] [EC:2.1.1.260]
118367907  ribosomal RNA small subunit methyltransferase NEP1-like isoform X1 [KO:K14568] [EC:2.1.1.260]
118367529  bms1; ribosome biogenesis protein BMS1 homolog [KO:K14569]
118400929  nat10; RNA cytidine acetyltransferase [KO:K14521] [EC:2.3.1.-]
118387923  rcl1; RNA 3'-terminal phosphate cyclase-like protein [KO:K11108]
118382893  ribonucleases P/MRP protein subunit POP1 [KO:K01164] [EC:3.1.26.5]
118382670  LOW QUALITY PROTEIN: ribonucleases P/MRP protein subunit POP1-like [KO:K01164] [EC:3.1.26.5]
118367932  ribonuclease P protein subunit p38 [KO:K14523] [EC:3.1.26.5]
118376269  ribonuclease P protein subunit p38-like isoform X1 [KO:K14523] [EC:3.1.26.5]
118393739  pop4; ribonuclease P protein subunit p29 [KO:K03538] [EC:3.1.26.5]
118358232  pop5; ribonuclease P/MRP protein subunit POP5 isoform X1 [KO:K03537] [EC:3.1.26.5]
118394308  uncharacterized protein LOC118394308 [KO:K14525] [EC:3.1.26.5]
118362832  ribonuclease P protein subunit p25-like [KO:K14525] [EC:3.1.26.5]
118372781  rpp25l; LOW QUALITY PROTEIN: ribonuclease P protein subunit p25-like protein [KO:K14525] [EC:3.1.26.5]
118373855  uncharacterized protein LOC118373855 isoform X1 [KO:K14525] [EC:3.1.26.5]
118368851  ribonuclease P protein subunit p20-like isoform X1 [KO:K14527] [EC:3.1.26.5]
118392062  ribonuclease P protein subunit p20-like [KO:K14527] [EC:3.1.26.5]
118357487  rpp30; ribonuclease P protein subunit p30 [KO:K03539] [EC:3.1.26.5]
118394390  rpp40; ribonuclease P protein subunit p40 [KO:K14530] [EC:3.1.26.5]
118392992  zgc:152968; RNA exonuclease 1 homolog [KO:K14570] [EC:3.1.-.-]
118390495  RNA exonuclease 1 homolog [KO:K14570] [EC:3.1.-.-]
118359175  RNA exonuclease 1 homolog [KO:K14570] [EC:3.1.-.-]
118389854  smfn; small fragment nuclease [KO:K13288] [EC:3.1.-.-]
118402197  5'-3' exoribonuclease 1-like isoform X1 [KO:K12618] [EC:3.1.13.-]
118376609  xrn1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
118386692  5'-3' exoribonuclease 2-like isoform X1 [KO:K12619] [EC:3.1.13.-]
118398792  5'-3' exoribonuclease 2-like isoform X1 [KO:K12619] [EC:3.1.13.-]
118402161  gtpbp4; nucleolar GTP-binding protein 1 [KO:K06943]
118364283  nucleolar GTP-binding protein 2-like [KO:K14537]
118367357  nucleolar GTP-binding protein 2 [KO:K14537]
118388365  gnl3l; guanine nucleotide-binding protein-like 3-like protein [KO:K14538]
118388449  guanine nucleotide-binding protein-like 3 [KO:K14538]
118400177  gnl3; guanine nucleotide-binding protein-like 3 [KO:K14538]
118369671  nuclear valosin-containing protein-like isoform X1 [KO:K14571]
118386725  midasin-like isoform X1 [KO:K14572]
118398759  midasin-like isoform X1 [KO:K14572]
118401176  rbm28; RNA-binding protein 28 isoform X1 [KO:K14573]
118382601  LOW QUALITY PROTEIN: RNA-binding protein NOB1 [KO:K11883]
127921642  RNA-binding protein NOB1-like [KO:K11883]
118362978  GTP-binding nuclear protein Ran-like [KO:K07936]
118363499  GTP-binding nuclear protein Ran isoform X1 [KO:K07936]
118395453  GTP-binding nuclear protein Ran-like [KO:K07936]
118375701  ran; GTP-binding nuclear protein Ran [KO:K07936]
118381297  exportin-1-like [KO:K14290]
118364996  exportin-1 [KO:K14290]
118389179  exportin-1 [KO:K14290]
118378074  60S ribosomal export protein NMD3 isoform X1 [KO:K07562]
118397352  60S ribosomal export protein NMD3-like [KO:K07562]
118385113  nuclear RNA export factor 1-like [KO:K14284]
118390365  nuclear RNA export factor 1-like isoform X1 [KO:K14284]
118381071  nxf1a; nuclear RNA export factor 1 isoform X1 [KO:K14284]
118375488  nxt2; NTF2-related export protein 2 isoform X1 [KO:K14285]
118370041  eukaryotic translation initiation factor 6-like isoform X1 [KO:K03264]
118388883  eif6; eukaryotic translation initiation factor 6 [KO:K03264]
118397419  ribosome maturation protein SBDS [KO:K14574]
118367551  ribosome maturation protein SBDS-like isoform X1 [KO:K14574]
118375946  efl1; elongation factor-like GTPase 1 isoform X1 [KO:K14536] [EC:3.6.5.-]
118388585  lsg1; large subunit GTPase 1 homolog [KO:K14539] [EC:3.6.1.-]
118400665  LOW QUALITY PROTEIN: large subunit GTPase 1 homolog [KO:K14539] [EC:3.6.1.-]
118363557  spata5; ribosome biogenesis protein SPATA5 isoform X1 [KO:K14575]
118374740  ak6; adenylate kinase isoenzyme 6 [KO:K18532] [EC:2.7.4.3]
118394388  riok1; serine/threonine-protein kinase RIO1 [KO:K07178] [EC:2.7.11.1]
118377429  riok2; serine/threonine-protein kinase RIO2 [KO:K07179] [EC:2.7.11.1]
127911508  18S ribosomal RNA [KO:K01979]
127906263  18S ribosomal RNA [KO:K01979]
127909764  18S ribosomal RNA [KO:K01979]
127923727  28S ribosomal RNA [KO:K01982]
127920971  28S ribosomal RNA [KO:K01982]
118383036  28S ribosomal RNA [KO:K01982]
118374440  small nucleolar RNA U3 [KO:K14483]
118374442  small nucleolar RNA U3 [KO:K14483]
118374441  small nucleolar RNA U3 [KO:K14483]
118374445  small nucleolar RNA U3 [KO:K14483]
Reference
PMID:20174677
  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
PMID:17515605
  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
PMID:19850913
  Authors
Strunk BS, Karbstein K
  Title
Powering through ribosome assembly.
  Journal
RNA 15:2083-104 (2009)
DOI:10.1261/rna.1792109
Reference
PMID:15120992
  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
PMID:19879902
  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
oke03010  Ribosome
KO pathway
ko03008   
LinkDB

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