KEGG   PATHWAY: phyp03008
Entry
phyp03008                   Pathway                                
Name
Ribosome biogenesis in eukaryotes - Pangasianodon hypophthalmus (striped catfish)
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
phyp03008  Ribosome biogenesis in eukaryotes
phyp03008

Organism
Pangasianodon hypophthalmus (striped catfish) [GN:phyp]
Gene
113543702  csnk2b; casein kinase II subunit beta [KO:K03115]
113534013  casein kinase II subunit alpha-like [KO:K03097] [EC:2.7.11.1]
113546565  csnk2a2; casein kinase II subunit alpha' isoform X1 [KO:K03097] [EC:2.7.11.1]
113536707  casein kinase II subunit alpha'-like [KO:K03097] [EC:2.7.11.1]
113538109  casein kinase II subunit alpha [KO:K03097] [EC:2.7.11.1]
113536012  casein kinase II subunit alpha-like [KO:K03097] [EC:2.7.11.1]
113536865  nol6; nucleolar protein 6 [KO:K14544]
113545074  wdr43; WD repeat-containing protein 43 [KO:K14546]
113534305  utp4; U3 small nucleolar RNA-associated protein 4 homolog [KO:K14548]
113526337  U3 small nucleolar RNA-associated protein 15 homolog [KO:K14549]
113539205  heatr1; HEAT repeat-containing protein 1 [KO:K14550]
113526186  wdr75; WD repeat-containing protein 75 [KO:K14552]
113529041  utp18; U3 small nucleolar RNA-associated protein 18 homolog [KO:K14553]
113531351  wdr36; LOW QUALITY PROTEIN: WD repeat-containing protein 36 [KO:K14554]
113528313  tbl3; transducin beta-like protein 3 [KO:K14555]
113546390  wdr3; WD repeat-containing protein 3 [KO:K14556]
113523661  utp6; U3 small nucleolar RNA-associated protein 6 homolog [KO:K14557]
113537611  pwp2; periodic tryptophan protein 2 homolog [KO:K14558]
113546755  mphosph10; U3 small nucleolar ribonucleoprotein protein MPP10 [KO:K14559]
113540679  imp3; U3 small nucleolar ribonucleoprotein protein IMP3 [KO:K14560]
113537073  imp4; U3 small nucleolar ribonucleoprotein protein IMP4 [KO:K14561]
113524790  fbl; rRNA 2'-O-methyltransferase fibrillarin [KO:K14563] [EC:2.1.1.-]
113535390  nop56; nucleolar protein 56 [KO:K14564]
113538145  nop58; nucleolar protein 58 [KO:K14565]
113527529  NHP2-like protein 1 [KO:K12845]
113528352  NHP2-like protein 1 [KO:K12845]
113541627  dkc1; H/ACA ribonucleoprotein complex subunit DKC1 isoform X1 [KO:K11131] [EC:5.4.99.-]
113541640  nhp2; H/ACA ribonucleoprotein complex subunit 2 [KO:K11129]
113547196  gar1; H/ACA ribonucleoprotein complex subunit 1 [KO:K11128]
113544395  nop10; H/ACA ribonucleoprotein complex subunit 3 [KO:K11130]
113538752  fcf1; rRNA-processing protein FCF1 homolog [KO:K14566]
113531421  U3 small nucleolar RNA-associated protein 14 homolog A-like [KO:K14567]
113535287  drosha; ribonuclease 3 [KO:K03685] [EC:3.1.26.3]
113533958  emg1; ribosomal RNA small subunit methyltransferase NEP1 [KO:K14568] [EC:2.1.1.260]
113527540  bms1; ribosome biogenesis protein BMS1 homolog isoform X1 [KO:K14569]
113535819  nat10; RNA cytidine acetyltransferase [KO:K14521] [EC:2.3.1.-]
113531441  rcl1; RNA 3'-terminal phosphate cyclase-like protein isoform X1 [KO:K11108]
113532989  pop1; ribonucleases P/MRP protein subunit POP1 [KO:K01164] [EC:3.1.26.5]
113532686  rpp38; ribonuclease P protein subunit p38 [KO:K14523] [EC:3.1.26.5]
113525111  pop4; ribonuclease P protein subunit p29 [KO:K03538] [EC:3.1.26.5]
113546048  pop5; ribonuclease P/MRP protein subunit POP5 [KO:K03537] [EC:3.1.26.5]
113526836  ribonuclease P protein subunit p25-like protein [KO:K14525] [EC:3.1.26.5]
113525069  ribonuclease P protein subunit p25-like protein [KO:K14525] [EC:3.1.26.5]
113540440  pop7; ribonuclease P protein subunit p20 [KO:K14527] [EC:3.1.26.5]
113527165  rpp30; ribonuclease P protein subunit p30 [KO:K03539] [EC:3.1.26.5]
113543190  rpp40; ribonuclease P protein subunit p40 [KO:K14530] [EC:3.1.26.5]
113535096  rexo1; RNA exonuclease 1 homolog [KO:K14570] [EC:3.1.-.-]
113542582  RNA exonuclease 1 homolog isoform X1 [KO:K14570] [EC:3.1.-.-]
113544743  rexo2; oligoribonuclease, mitochondrial [KO:K13288] [EC:3.1.-.-]
113531933  xrn2; LOW QUALITY PROTEIN: 5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
113543097  gtpbp4; nucleolar GTP-binding protein 1 [KO:K06943]
113526535  gnl2; nucleolar GTP-binding protein 2 [KO:K14537]
113539596  gnl3; guanine nucleotide-binding protein-like 3 [KO:K14538]
113539653  gnl3l; guanine nucleotide-binding protein-like 3-like protein [KO:K14538]
113544348  nvl; nuclear valosin-containing protein-like isoform X1 [KO:K14571]
113529262  mdn1; midasin [KO:K14572]
113534828  rbm28; RNA-binding protein 28 [KO:K14573]
113526775  nob1; RNA-binding protein NOB1 [KO:K11883]
113542941  ran; GTP-binding nuclear protein Ran [KO:K07936]
113545047  exportin-1 isoform X1 [KO:K14290]
113537708  exportin-1-like [KO:K14290]
113543360  nmd3; 60S ribosomal export protein NMD3 [KO:K07562]
113529362  nuclear RNA export factor 1-like isoform X1 [KO:K14284]
113541528  nxf1; nuclear RNA export factor 1 [KO:K14284]
113528933  nxt2; NTF2-related export protein 2 [KO:K14285]
113527757  eif6; eukaryotic translation initiation factor 6 [KO:K03264]
113543324  sbds; ribosome maturation protein SBDS [KO:K14574]
113536619  efl1; elongation factor-like GTPase 1 [KO:K14536] [EC:3.6.5.-]
113527371  lsg1; large subunit GTPase 1 homolog [KO:K14539] [EC:3.6.1.-]
113528166  ATPase family protein 2 homolog [KO:K14575]
113542408  ak6; adenylate kinase isoenzyme 6 [KO:K18532] [EC:2.7.4.3]
113543313  riok1; serine/threonine-protein kinase RIO1 [KO:K07178] [EC:2.7.11.1]
113536871  riok2; serine/threonine-protein kinase RIO2 [KO:K07179] [EC:2.7.11.1]
113525262  5.8S ribosomal RNA [KO:K01986]
113528658  5S ribosomal RNA [KO:K01981]
113528647  5S ribosomal RNA [KO:K01981]
113540706  small nucleolar RNA U3 [KO:K14483]
113540704  small nucleolar RNA U3 [KO:K14483]
113540712  small nucleolar RNA U3 [KO:K14483]
113540700  small nucleolar RNA U3 [KO:K14483]
113540715  small nucleolar RNA U3 [KO:K14483]
113540709  small nucleolar RNA U3 [KO:K14483]
113540707  small nucleolar RNA U3 [KO:K14483]
113540719  small nucleolar RNA U3 [KO:K14483]
113540708  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
phyp03010  Ribosome
KO pathway
ko03008   
LinkDB

DBGET integrated database retrieval system