KEGG   PATHWAY: lcf03008
Entry
lcf03008                    Pathway                                
Name
Ribosome biogenesis in eukaryotes - Lates calcarifer (barramundi perch)
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
lcf03008  Ribosome biogenesis in eukaryotes
lcf03008

Organism
Lates calcarifer (barramundi perch) [GN:lcf]
Gene
108890309  csnk2b; casein kinase II subunit beta [KO:K03115]
108891052  casein kinase II subunit beta isoform X2 [KO:K03115]
108890849  casein kinase II subunit alpha [KO:K03097] [EC:2.7.11.1]
108886571  casein kinase II subunit alpha isoform X1 [KO:K03097] [EC:2.7.11.1]
108894169  csnk2a2a; casein kinase II subunit alpha' [KO:K03097] [EC:2.7.11.1]
108902286  csnk2a2b; casein kinase II subunit alpha' [KO:K03097] [EC:2.7.11.1]
108878229  nucleolar protein 6 [KO:K14544]
108877571  ribosomal RNA-processing protein 7 homolog A [KO:K14545]
108896166  LOW QUALITY PROTEIN: WD repeat-containing protein 43 [KO:K14546]
108902275  U3 small nucleolar RNA-associated protein 4 homolog [KO:K14548]
108881166  U3 small nucleolar RNA-associated protein 15 homolog [KO:K14549]
108886123  LOW QUALITY PROTEIN: HEAT repeat-containing protein 1 [KO:K14550]
108897212  WD repeat-containing protein 75 [KO:K14552]
108891031  U3 small nucleolar RNA-associated protein 18 homolog isoform X1 [KO:K14553]
108874617  LOW QUALITY PROTEIN: WD repeat-containing protein 36 [KO:K14554]
108879853  transducin beta-like protein 3 [KO:K14555]
108872822  LOW QUALITY PROTEIN: WD repeat-containing protein 3 [KO:K14556]
108875892  U3 small nucleolar RNA-associated protein 6 homolog [KO:K14557]
108873066  pwp2h; PWP2 small subunit processome component [KO:K14558]
108889696  U3 small nucleolar ribonucleoprotein protein MPP10 [KO:K14559]
108883746  U3 small nucleolar ribonucleoprotein protein IMP3 [KO:K14560]
108878155  U3 small nucleolar ribonucleoprotein protein IMP4 [KO:K14561]
108886109  rRNA 2'-O-methyltransferase fibrillarin [KO:K14563] [EC:2.1.1.-]
108899655  LOW QUALITY PROTEIN: nucleolar protein 56 [KO:K14564]
108880218  LOW QUALITY PROTEIN: nucleolar protein 58 [KO:K14565]
108880776  snu13b; SNU13 homolog, small nuclear ribonucleoprotein b (U4/U6.U5) [KO:K12845]
108891603  H/ACA ribonucleoprotein complex subunit DKC1 isoform X1 [KO:K11131] [EC:5.4.99.-]
108884078  H/ACA ribonucleoprotein complex subunit 2-like protein isoform X1 [KO:K11129]
108885169  H/ACA ribonucleoprotein complex subunit 1 [KO:K11128]
108890750  H/ACA ribonucleoprotein complex subunit 3 [KO:K11130]
108892492  rRNA-processing protein FCF1 homolog [KO:K14566]
108897145  si:dkey-251i10.3; U3 small nucleolar RNA-associated protein 14 homolog A [KO:K14567]
108885078  LOW QUALITY PROTEIN: ribonuclease 3 [KO:K03685] [EC:3.1.26.3]
108887348  ribosomal RNA small subunit methyltransferase NEP1 [KO:K14568] [EC:2.1.1.260]
108876778  LOW QUALITY PROTEIN: ribosome biogenesis protein BMS1 homolog [KO:K14569]
108876693  RNA cytidine acetyltransferase [KO:K14521] [EC:2.3.1.-]
108879209  RNA 3'-terminal phosphate cyclase-like protein [KO:K11108]
108876305  LOW QUALITY PROTEIN: ribonucleases P/MRP protein subunit POP1 [KO:K01164] [EC:3.1.26.5]
108889591  ribonuclease P protein subunit p38 [KO:K14523] [EC:3.1.26.5]
108880512  ribonuclease P protein subunit p29 isoform X2 [KO:K03538] [EC:3.1.26.5]
108878259  ribonuclease P/MRP protein subunit POP5 [KO:K03537] [EC:3.1.26.5]
108876967  uncharacterized protein LOC108876967 [KO:K14525] [EC:3.1.26.5]
108881855  rpp25l; ribonuclease P protein subunit p25-like protein [KO:K14525] [EC:3.1.26.5]
108876658  ribonuclease P protein subunit p25-like protein [KO:K14525] [EC:3.1.26.5]
108902167  ribonuclease P protein subunit p20 [KO:K14527] [EC:3.1.26.5]
108891545  ribonuclease P protein subunit p30 [KO:K03539] [EC:3.1.26.5]
108884959  ribonuclease P protein subunit p40 [KO:K14530] [EC:3.1.26.5]
108895911  zgc:152968; LOW QUALITY PROTEIN: RNA exonuclease 1 homolog [KO:K14570] [EC:3.1.-.-]
108896577  RNA exonuclease 1 homolog isoform X1 [KO:K14570] [EC:3.1.-.-]
108901169  rexo5; RNA exonuclease 5 [KO:K14570] [EC:3.1.-.-]
108900082  smfn; small fragment nuclease [KO:K13288] [EC:3.1.-.-]
108896664  LOW QUALITY PROTEIN: 5'-3' exoribonuclease 1 [KO:K12618] [EC:3.1.13.-]
108872468  5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
108884784  nucleolar GTP-binding protein 1 [KO:K06943]
108899500  nucleolar GTP-binding protein 2 [KO:K14537]
108889419  guanine nucleotide-binding protein-like 3 [KO:K14538]
108885578  guanine nucleotide-binding protein-like 3-like protein [KO:K14538]
108894846  nuclear valosin-containing protein-like isoform X1 [KO:K14571]
108899283  LOW QUALITY PROTEIN: midasin [KO:K14572]
108901787  midasin [KO:K14572]
108875152  RNA-binding protein 28 isoform X1 [KO:K14573]
108894223  RNA-binding protein NOB1 [KO:K11883]
108878285  GTP-binding nuclear protein Ran [KO:K07936]
108895727  xpo1b; exportin-1 isoform X1 [KO:K14290]
108882517  xpo1a; exportin-1 [KO:K14290]
108900928  60S ribosomal export protein NMD3 [KO:K07562]
108872558  nxf1a; nuclear RNA export factor 1 isoform X1 [KO:K14284]
108882777  NTF2-related export protein 2 [KO:K14285]
108889738  LOW QUALITY PROTEIN: eukaryotic translation initiation factor 6 [KO:K03264]
108876232  ribosome maturation protein SBDS [KO:K14574]
108880523  elongation factor-like GTPase 1 [KO:K14536] [EC:3.6.5.-]
108881253  large subunit GTPase 1 homolog [KO:K14539] [EC:3.6.1.-]
108901520  ribosome biogenesis protein SPATA5 [KO:K14575]
108898757  adenylate kinase isoenzyme 6 [KO:K18532] [EC:2.7.4.3]
108889248  adenylate kinase isoenzyme 6 [KO:K18532] [EC:2.7.4.3]
108884952  serine/threonine-protein kinase RIO1 isoform X1 [KO:K07178] [EC:2.7.11.1]
108878168  serine/threonine-protein kinase RIO2 [KO:K07179] [EC:2.7.11.1]
127141904  18S ribosomal RNA [KO:K01979]
127142056  18S ribosomal RNA [KO:K01979]
127142024  18S ribosomal RNA [KO:K01979]
127140081  18S ribosomal RNA [KO:K01979]
127140080  5.8S ribosomal RNA [KO:K01986]
127140076  28S ribosomal RNA [KO:K01982]
127140078  28S ribosomal RNA [KO:K01982]
127142035  28S ribosomal RNA [KO:K01982]
127141943  28S ribosomal RNA [KO:K01982]
127142527  small nucleolar RNA U3 [KO:K14483]
127143278  small nucleolar RNA U3 [KO:K14483]
127142536  small nucleolar RNA U3 [KO:K14483]
127142538  small nucleolar RNA U3 [KO:K14483]
127142537  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
lcf03010  Ribosome
KO pathway
ko03008   
LinkDB

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