KEGG   PATHWAY: gat03008
Entry
gat03008                    Pathway                                
Name
Ribosome biogenesis in eukaryotes - Gasterosteus aculeatus (three-spined stickleback)
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
gat03008  Ribosome biogenesis in eukaryotes
gat03008

Organism
Gasterosteus aculeatus (three-spined stickleback) [GN:gat]
Gene
120810757  casein kinase II subunit beta [KO:K03115]
120826462  csnk2b; casein kinase II subunit beta [KO:K03115]
120834612  casein kinase II subunit alpha [KO:K03097] [EC:2.7.11.1]
120809138  csnk2a2b; LOW QUALITY PROTEIN: casein kinase II subunit alpha' [KO:K03097] [EC:2.7.11.1]
120810606  casein kinase II subunit alpha-like [KO:K03097] [EC:2.7.11.1]
120812217  casein kinase II subunit alpha' isoform X1 [KO:K03097] [EC:2.7.11.1]
120815004  casein kinase II subunit alpha'-like [KO:K03097] [EC:2.7.11.1]
120830888  nol6; nucleolar protein 6 [KO:K14544]
120827920  rrp7a; ribosomal RNA-processing protein 7 homolog A [KO:K14545]
120832862  wdr43; WD repeat-containing protein 43 [KO:K14546]
120809382  U3 small nucleolar RNA-associated protein 4 homolog [KO:K14548]
120812803  U3 small nucleolar RNA-associated protein 4 homolog isoform X1 [KO:K14548]
120830415  utp15; U3 small nucleolar RNA-associated protein 15 homolog [KO:K14549]
120819359  heatr1; HEAT repeat-containing protein 1 [KO:K14550]
120834086  wdr75; WD repeat-containing protein 75 isoform X1 [KO:K14552]
120828044  utp18; U3 small nucleolar RNA-associated protein 18 homolog isoform X1 [KO:K14553]
120831699  wdr36; WD repeat-containing protein 36 [KO:K14554]
120828486  tbl3; transducin beta-like protein 3 [KO:K14555]
120834340  wdr3; LOW QUALITY PROTEIN: WD repeat-containing protein 3 [KO:K14556]
120825551  utp6; U3 small nucleolar RNA-associated protein 6 homolog [KO:K14557]
120821936  pwp2h; PWP2 small subunit processome component [KO:K14558]
120831184  mphosph10; U3 small nucleolar ribonucleoprotein protein MPP10 [KO:K14559]
120815856  imp3; U3 small nucleolar ribonucleoprotein protein IMP3 [KO:K14560]
120830983  imp4; U3 small nucleolar ribonucleoprotein protein IMP4 [KO:K14561]
120810072  fbl; rRNA 2'-O-methyltransferase fibrillarin [KO:K14563] [EC:2.1.1.-]
120834595  nop56; nucleolar protein 56 [KO:K14564]
120824874  nop58; nucleolar protein 58 [KO:K14565]
120818923  NHP2-like protein 1 [KO:K12845]
120832673  dkc1; H/ACA ribonucleoprotein complex subunit DKC1 [KO:K11131] [EC:5.4.99.-]
120822007  nhp2; H/ACA ribonucleoprotein complex subunit 2-like protein [KO:K11129]
120817580  gar1; H/ACA ribonucleoprotein complex subunit 1 [KO:K11128]
120821334  nop10; H/ACA ribonucleoprotein complex subunit 3 [KO:K11130]
120832590  fcf1; rRNA-processing protein FCF1 homolog [KO:K14566]
120833906  si:dkey-251i10.3; U3 small nucleolar RNA-associated protein 14 homolog A [KO:K14567]
120811926  drosha; ribonuclease 3 [KO:K03685] [EC:3.1.26.3]
120810868  emg1; ribosomal RNA small subunit methyltransferase NEP1 [KO:K14568] [EC:2.1.1.260]
120819554  bms1; ribosome biogenesis protein BMS1 homolog isoform X1 [KO:K14569]
120809836  nat10; RNA cytidine acetyltransferase [KO:K14521] [EC:2.3.1.-]
120832267  rcl1; RNA 3'-terminal phosphate cyclase-like protein [KO:K11108]
120810954  pop1; ribonucleases P/MRP protein subunit POP1 isoform X1 [KO:K01164] [EC:3.1.26.5]
120810344  rpp38; ribonuclease P protein subunit p38 [KO:K14523] [EC:3.1.26.5]
120808047  pop4; ribonuclease P protein subunit p29 isoform X1 [KO:K03538] [EC:3.1.26.5]
120830842  pop5; ribonuclease P/MRP protein subunit POP5 [KO:K03537] [EC:3.1.26.5]
120834601  ribonuclease P protein subunit p25-like [KO:K14525] [EC:3.1.26.5]
120809286  rpp25a; ribonuclease P protein subunit p25a [KO:K14525] [EC:3.1.26.5]
120810455  rpp25l; ribonuclease P protein subunit p25-like protein [KO:K14525] [EC:3.1.26.5]
120821322  pop7; ribonuclease P protein subunit p20 [KO:K14527] [EC:3.1.26.5]
120819660  rpp30; ribonuclease P protein subunit p30 isoform X1 [KO:K03539] [EC:3.1.26.5]
120816629  rpp40; ribonuclease P protein subunit p40 [KO:K14530] [EC:3.1.26.5]
120830376  zgc:152968; RNA exonuclease 1 homolog isoform X1 [KO:K14570] [EC:3.1.-.-]
120824034  rexo1; RNA exonuclease 1 homolog isoform X1 [KO:K14570] [EC:3.1.-.-]
120825476  RNA exonuclease 5-like isoform X1 [KO:K14570] [EC:3.1.-.-]
120821435  smfn; small fragment nuclease [KO:K13288] [EC:3.1.-.-]
120815802  xrn1; LOW QUALITY PROTEIN: 5'-3' exoribonuclease 1 [KO:K12618] [EC:3.1.13.-]
120808248  xrn2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
120815646  gtpbp4; nucleolar GTP-binding protein 1 [KO:K06943]
120810584  gnl2; nucleolar GTP-binding protein 2 [KO:K14537]
120835474  gnl3l; guanine nucleotide-binding protein-like 3-like protein isoform X1 [KO:K14538]
120834625  gnl3; guanine nucleotide-binding protein-like 3 [KO:K14538]
120820592  nvl; nuclear valosin-containing protein-like isoform X1 [KO:K14571]
120807761  mdn1; midasin [KO:K14572]
120808777  RNA-binding protein 28-like [KO:K14573]
120812606  RNA-binding protein 28-like [KO:K14573]
120807699  nob1; RNA-binding protein NOB1 [KO:K11883]
120817455  ran; GTP-binding nuclear protein Ran [KO:K07936]
120825832  xpo1a; exportin-1 [KO:K14290]
120820987  xpo1b; exportin-1 isoform X1 [KO:K14290]
120826307  nmd3; 60S ribosomal export protein NMD3 [KO:K07562]
120816933  nxf1a; nuclear RNA export factor 1 isoform X1 [KO:K14284]
120818486  nxt2; NTF2-related export protein 2 [KO:K14285]
120834909  eif6; eukaryotic translation initiation factor 6 [KO:K03264]
120815889  sbds; ribosome maturation protein SBDS [KO:K14574]
120834610  efl1; elongation factor-like GTPase 1 [KO:K14536] [EC:3.6.5.-]
120823908  lsg1; large subunit GTPase 1 homolog [KO:K14539] [EC:3.6.1.-]
120817424  spata5; ATPase family protein 2 homolog isoform X1 [KO:K14575]
120830445  ak6; adenylate kinase isoenzyme 6 [KO:K18532] [EC:2.7.4.3]
120816627  riok1; serine/threonine-protein kinase RIO1 isoform X1 [KO:K07178] [EC:2.7.11.1]
120831007  riok2; serine/threonine-protein kinase RIO2 [KO:K07179] [EC:2.7.11.1]
120813882  18S ribosomal RNA [KO:K01979]
120813364  5.8S ribosomal RNA [KO:K01986]
120813495  28S ribosomal RNA [KO:K01982]
120813366  28S ribosomal RNA [KO:K01982]
120814626  5S ribosomal RNA [KO:K01981]
120823173  small nucleolar RNA U3 [KO:K14483]
120825894  small nucleolar RNA U3 [KO:K14483]
120823185  small nucleolar RNA U3 [KO:K14483]
120825903  small nucleolar RNA U3 [KO:K14483]
120812957  small nucleolar RNA U3 [KO:K14483]
120825902  small nucleolar RNA U3 [KO:K14483]
120823162  small nucleolar RNA U3 [KO:K14483]
120813847  small nucleolar RNA U3 [KO:K14483]
120812956  small nucleolar RNA U3 [KO:K14483]
120813848  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
gat03010  Ribosome
KO pathway
ko03008   
LinkDB

DBGET integrated database retrieval system