KEGG   PATHWAY: dmk03008
Entry
dmk03008                    Pathway                                
Name
Ribosome biogenesis in eukaryotes - Daphnia magna (water flea)
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
dmk03008  Ribosome biogenesis in eukaryotes
dmk03008

Organism
Daphnia magna (water flea) [GN:dmk]
Gene
116932331  casein kinase II subunit beta [KO:K03115]
116921215  casein kinase II subunit alpha isoform X1 [KO:K03097] [EC:2.7.11.1]
116917224  LOW QUALITY PROTEIN: nucleolar protein 6 [KO:K14544]
116926570  ribosomal RNA-processing protein 7 homolog A [KO:K14545]
116924202  WD repeat-containing protein 43 [KO:K14546]
116920056  U3 small nucleolar RNA-associated protein 4 homolog [KO:K14548]
116928575  U3 small nucleolar RNA-associated protein 15 homolog [KO:K14549]
116919982  LOW QUALITY PROTEIN: HEAT repeat-containing protein 1 [KO:K14550]
116922646  WD repeat-containing protein 75 [KO:K14552]
116923406  U3 small nucleolar RNA-associated protein 18 homolog [KO:K14553]
116925175  WD repeat-containing protein 36 [KO:K14554]
116923944  transducin beta-like protein 3 [KO:K14555]
116929822  LOW QUALITY PROTEIN: WD repeat-containing protein 3 [KO:K14556]
116926757  U3 small nucleolar RNA-associated protein 6 homolog [KO:K14557]
116921675  periodic tryptophan protein 2 homolog isoform X1 [KO:K14558]
116928941  U3 small nucleolar ribonucleoprotein protein MPP10 [KO:K14559]
116925447  U3 small nucleolar ribonucleoprotein protein IMP4 [KO:K14561]
123473871  U3 small nucleolar ribonucleoprotein protein IMP4-like [KO:K14561]
116927987  nucleolar protein 56 [KO:K14564]
116929973  nucleolar protein 58 [KO:K14565]
116927347  NHP2-like protein 1 [KO:K12845]
116922306  H/ACA ribonucleoprotein complex subunit 4 [KO:K11131] [EC:5.4.99.-]
123476842  LOW QUALITY PROTEIN: H/ACA ribonucleoprotein complex subunit 4-like [KO:K11131] [EC:5.4.99.-]
116921977  H/ACA ribonucleoprotein complex subunit 2-like protein [KO:K11129]
116932203  probable H/ACA ribonucleoprotein complex subunit 1 [KO:K11128]
116924367  rRNA-processing protein FCF1 homolog [KO:K14566]
116916417  U3 small nucleolar RNA-associated protein 14 homolog A isoform X1 [KO:K14567]
123470127  LOW QUALITY PROTEIN: U3 small nucleolar RNA-associated protein 14 homolog A-like [KO:K14567]
116917509  ribonuclease 3 [KO:K03685] [EC:3.1.26.3]
116930654  ribosomal RNA small subunit methyltransferase NEP1 [KO:K14568] [EC:2.1.1.260]
116936510  ribosome biogenesis protein BMS1 homolog [KO:K14569]
116926114  RNA cytidine acetyltransferase [KO:K14521] [EC:2.3.1.-]
116921913  ribonucleases P/MRP protein subunit POP1 [KO:K01164] [EC:3.1.26.5]
116925816  ribonuclease P protein subunit p29 [KO:K03538] [EC:3.1.26.5]
116917566  ribonuclease P/MRP protein subunit POP5 [KO:K03537] [EC:3.1.26.5]
116916786  ribonuclease P protein subunit p25-like protein [KO:K14525] [EC:3.1.26.5]
116919861  ribonuclease P protein subunit p20 [KO:K14527] [EC:3.1.26.5]
116918665  ribonuclease P protein subunit p30 isoform X1 [KO:K03539] [EC:3.1.26.5]
116920289  ribonuclease P protein subunit p40 [KO:K14530] [EC:3.1.26.5]
116918423  LOW QUALITY PROTEIN: RNA exonuclease 1 homolog [KO:K14570] [EC:3.1.-.-]
116925677  uncharacterized protein LOC116925677 [KO:K14570] [EC:3.1.-.-]
116925687  small RNA degrading nuclease 5 [KO:K14570] [EC:3.1.-.-]
116928988  oligoribonuclease, mitochondrial [KO:K13288] [EC:3.1.-.-]
116920786  5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
116934378  5'-3' exoribonuclease 2 homolog isoform X1 [KO:K12619] [EC:3.1.13.-]
116935234  GTP-binding protein 4 [KO:K06943]
116931392  nucleolar GTP-binding protein 2 [KO:K14537]
116925527  guanine nucleotide-binding protein-like 3 homolog [KO:K14538]
116927042  nuclear valosin-containing protein-like [KO:K14571]
116930235  midasin [KO:K14572]
116918879  RNA-binding protein 28 [KO:K14573]
116921542  RNA-binding protein NOB1 [KO:K11883]
116932489  GTP-binding nuclear protein Ran [KO:K07936]
116926705  exportin-1 [KO:K14290]
116928843  60S ribosomal export protein NMD3 [KO:K07562]
116924864  nuclear RNA export factor 1 [KO:K14284]
116923035  NTF2-related export protein 1 [KO:K14285]
116932341  eukaryotic translation initiation factor 6 [KO:K03264]
123474747  eukaryotic translation initiation factor 6-like [KO:K03264]
123474761  eukaryotic translation initiation factor 6-like [KO:K03264]
123474781  eukaryotic translation initiation factor 6-like [KO:K03264]
123474875  eukaryotic translation initiation factor 6-like [KO:K03264]
116934916  eukaryotic translation initiation factor 6-like [KO:K03264]
123477437  eukaryotic translation initiation factor 6-like [KO:K03264]
116917965  ribosome maturation protein SBDS [KO:K14574]
116917446  elongation factor-like GTPase 1 isoform X1 [KO:K14536] [EC:3.6.5.-]
116919004  large subunit GTPase 1 homolog [KO:K14539] [EC:3.6.1.-]
116925340  ATPase family protein 2 homolog [KO:K14575]
116930707  uncharacterized protein LOC116930707 isoform X1 [KO:K18532] [EC:2.7.4.3]
116921009  adenylate kinase isoenzyme 6 [KO:K18532] [EC:2.7.4.3]
123477579  uncharacterized protein LOC123477579 isoform X1 [KO:K18532] [EC:2.7.4.3]
116917801  serine/threonine-protein kinase RIO1 [KO:K07178] [EC:2.7.11.1]
116920249  serine/threonine-protein kinase rio2 [KO:K07179] [EC:2.7.11.1]
123469326  large subunit ribosomal RNA [KO:K01982]
116924093  5S ribosomal RNA [KO:K01981]
116922204  small nucleolar RNA U3 [KO:K14483]
123472814  small nucleolar RNA U3 [KO:K14483]
116922203  small nucleolar RNA U3 [KO:K14483]
123472815  small nucleolar RNA U3 [KO:K14483]
123472857  small nucleolar RNA U3 [KO:K14483]
123472816  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
dmk03010  Ribosome
KO pathway
ko03008   
LinkDB

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