KEGG   PATHWAY: efo03008
Entry
efo03008                    Pathway                                
Name
Ribosome biogenesis in eukaryotes - Epinephelus fuscoguttatus (brown-marbled grouper)
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
efo03008  Ribosome biogenesis in eukaryotes
efo03008

Organism
Epinephelus fuscoguttatus (brown-marbled grouper) [GN:efo]
Gene
125904711  csnk2b; casein kinase II subunit beta [KO:K03115]
125893950  casein kinase II subunit beta [KO:K03115]
125885777  csnk2a4; casein kinase II subunit alpha [KO:K03097] [EC:2.7.11.1]
125893542  casein kinase II subunit alpha-like [KO:K03097] [EC:2.7.11.1]
125887766  csnk2a2b; casein kinase II subunit alpha' isoform X1 [KO:K03097] [EC:2.7.11.1]
125881111  casein kinase II subunit alpha'-like [KO:K03097] [EC:2.7.11.1]
125890555  nol6; nucleolar protein 6 [KO:K14544]
125879936  rrp7a; ribosomal RNA-processing protein 7 homolog A [KO:K14545]
125901261  wdr43; WD repeat-containing protein 43 [KO:K14546]
125888141  utp4; U3 small nucleolar RNA-associated protein 4 homolog [KO:K14548]
125890338  utp15; U3 small nucleolar RNA-associated protein 15 homolog [KO:K14549]
125881355  heatr1; HEAT repeat-containing protein 1 isoform X1 [KO:K14550]
125899273  wdr75; WD repeat-containing protein 75 isoform X1 [KO:K14552]
125879964  utp18; U3 small nucleolar RNA-associated protein 18 homolog [KO:K14553]
125906296  wdr36; WD repeat-containing protein 36 [KO:K14554]
125880128  tbl3; transducin beta-like protein 3 [KO:K14555]
125900188  wdr3; WD repeat-containing protein 3 isoform X1 [KO:K14556]
125886029  utp6; U3 small nucleolar RNA-associated protein 6 homolog [KO:K14557]
125884968  pwp2h; PWP2 small subunit processome component [KO:K14558]
125900580  mphosph10; U3 small nucleolar ribonucleoprotein protein MPP10 [KO:K14559]
125902205  imp3; U3 small nucleolar ribonucleoprotein protein IMP3 isoform X1 [KO:K14560]
125890270  imp4; U3 small nucleolar ribonucleoprotein protein IMP4 [KO:K14561]
125892876  fbl; rRNA 2'-O-methyltransferase fibrillarin [KO:K14563] [EC:2.1.1.-]
125892436  nop56; nucleolar protein 56 [KO:K14564]
125884712  LOW QUALITY PROTEIN: nucleolar protein 58-like [KO:K14565]
125880591  snu13b; SNU13 homolog, small nuclear ribonucleoprotein b (U4/U6.U5) [KO:K12845]
125900732  dkc1; H/ACA ribonucleoprotein complex subunit DKC1 [KO:K11131] [EC:5.4.99.-]
125898167  nhp2; H/ACA ribonucleoprotein complex subunit 2-like protein [KO:K11129]
125894050  gar1; H/ACA ribonucleoprotein complex subunit 1 [KO:K11128]
125883695  nop10; H/ACA ribonucleoprotein complex subunit 3 [KO:K11130]
125900745  fcf1; rRNA-processing protein FCF1 homolog [KO:K14566]
125900075  si:dkey-251i10.3; U3 small nucleolar RNA-associated protein 14 homolog A [KO:K14567]
125881505  drosha; ribonuclease 3 [KO:K03685] [EC:3.1.26.3]
125893165  emg1; ribosomal RNA small subunit methyltransferase NEP1 [KO:K14568] [EC:2.1.1.260]
125880985  bms1; ribosome biogenesis protein BMS1 homolog isoform X1 [KO:K14569]
125887702  nat10; RNA cytidine acetyltransferase [KO:K14521] [EC:2.3.1.-]
125906379  rcl1; RNA 3'-terminal phosphate cyclase-like protein [KO:K11108]
125892832  pop1; ribonucleases P/MRP protein subunit POP1 isoform X1 [KO:K01164] [EC:3.1.26.5]
125892803  rpp38; ribonuclease P protein subunit p38 [KO:K14523] [EC:3.1.26.5]
125879938  pop4; ribonuclease P protein subunit p29 [KO:K03538] [EC:3.1.26.5]
125890049  pop5; ribonuclease P/MRP protein subunit POP5 [KO:K03537] [EC:3.1.26.5]
125882257  uncharacterized protein LOC125882257 [KO:K14525] [EC:3.1.26.5]
125893006  rpp25l; ribonuclease P protein subunit p25-like protein [KO:K14525] [EC:3.1.26.5]
125887834  rpp25a; ribonuclease P protein subunit p25a [KO:K14525] [EC:3.1.26.5]
125883884  pop7; ribonuclease P protein subunit p20 [KO:K14527] [EC:3.1.26.5]
125880343  rpp30; ribonuclease P protein subunit p30 [KO:K03539] [EC:3.1.26.5]
125902749  rpp40; ribonuclease P protein subunit p40 [KO:K14530] [EC:3.1.26.5]
125889673  zgc:152968; RNA exonuclease 1 homolog [KO:K14570] [EC:3.1.-.-]
125896465  rexo1; RNA exonuclease 1 homolog [KO:K14570] [EC:3.1.-.-]
125885676  RNA exonuclease 5-like [KO:K14570] [EC:3.1.-.-]
125899035  smfn; small fragment nuclease [KO:K13288] [EC:3.1.-.-]
125901903  xrn1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
125897227  xrn2; 5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
125901615  gtpbp4; nucleolar GTP-binding protein 1 [KO:K06943]
125892784  gnl2; nucleolar GTP-binding protein 2 [KO:K14537]
125895936  gnl3l; guanine nucleotide-binding protein-like 3-like protein [KO:K14538]
125894514  gnl3; guanine nucleotide-binding protein-like 3 [KO:K14538]
125903953  nvl; nuclear valosin-containing protein-like isoform X1 [KO:K14571]
125897247  mdn1; midasin [KO:K14572]
125888013  rbm28; RNA-binding protein 28 isoform X1 [KO:K14573]
125881022  nob1; RNA-binding protein NOB1 [KO:K11883]
125894681  ran; GTP-binding nuclear protein Ran [KO:K07936]
125904069  xpo1b; exportin-1 [KO:K14290]
125886027  xpo1a; exportin-1 [KO:K14290]
125889276  nmd3; 60S ribosomal export protein NMD3 [KO:K07562]
125894339  nxf1a; nuclear RNA export factor 1 isoform X1 [KO:K14284]
125894076  nxt2; NTF2-related export protein 2 [KO:K14285]
125894952  eif6; eukaryotic translation initiation factor 6 [KO:K03264]
125889338  sbds; ribosome maturation protein SBDS [KO:K14574]
125905041  efl1; elongation factor-like GTPase 1 [KO:K14536] [EC:3.6.5.-]
125896235  lsg1; large subunit GTPase 1 homolog [KO:K14539] [EC:3.6.1.-]
125894179  spata5; ATPase family protein 2 homolog [KO:K14575]
125890977  ak6; adenylate kinase isoenzyme 6 [KO:K18532] [EC:2.7.4.3]
125902736  riok1; serine/threonine-protein kinase RIO1 [KO:K07178] [EC:2.7.11.1]
125890760  riok2; serine/threonine-protein kinase RIO2 [KO:K07179] [EC:2.7.11.1]
125885280  18S ribosomal RNA [KO:K01979]
125885270  5.8S ribosomal RNA [KO:K01986]
125885283  28S ribosomal RNA [KO:K01982]
125885284  28S ribosomal RNA [KO:K01982]
125881381  5S ribosomal RNA [KO:K01981]
125886658  small nucleolar RNA U3 [KO:K14483]
125884524  small nucleolar RNA U3 [KO:K14483]
125886663  small nucleolar RNA U3 [KO:K14483]
125886664  small nucleolar RNA U3 [KO:K14483]
125886665  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
efo03010  Ribosome
KO pathway
ko03008   
LinkDB

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