KEGG   PATHWAY: ath03008
Entry
ath03008                    Pathway                                
Name
Ribosome biogenesis in eukaryotes - Arabidopsis thaliana (thale cress)
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
ath03008  Ribosome biogenesis in eukaryotes
ath03008

Organism
Arabidopsis thaliana (thale cress) [GN:ath]
Gene
AT3G60250  CKB3; casein kinase II beta chain 3 [KO:K03115]
AT4G17640  CKB2; casein kinase II beta chain 2 [KO:K03115]
AT2G44680  CKB4; casein kinase II beta subunit 4 [KO:K03115]
AT5G47080  CKB1; casein kinase II beta chain 1 [KO:K03115]
AT2G23070  Protein kinase superfamily protein [KO:K03097] [EC:2.7.11.1]
AT2G23080  CKA3; Protein kinase superfamily protein [KO:K03097] [EC:2.7.11.1]
AT3G50000  CKA2; casein kinase II, alpha chain 2 [KO:K03097] [EC:2.7.11.1]
AT5G67380  CKA1; casein kinase alpha 1 [KO:K03097] [EC:2.7.11.1]
AT1G63810  nucleolar protein [KO:K14544]
AT5G38720  ribosomal RNA-processing 7 protein [KO:K14545]
AT1G15420  WD repeat protein [KO:K14546]
AT5G11240  transducin family protein / WD-40 repeat family protein [KO:K14546]
AT1G27470  transducin family protein / WD-40 repeat family protein [KO:K14548]
AT4G07410  PCN; Transducin family protein / WD-40 repeat family protein [KO:K14548]
AT2G47990  SWA1; transducin family protein / WD-40 repeat family protein [KO:K14549]
AT3G06530  ARM repeat superfamily protein [KO:K14550]
AT3G26480  Transducin family protein / WD-40 repeat family protein [KO:K14552]
AT2G18900  Transducin/WD40 repeat-like superfamily protein [KO:K14552]
AT5G14050  Transducin/WD40 repeat-like superfamily protein [KO:K14553]
AT4G04940  transducin family protein / WD-40 repeat family protein [KO:K14554]
AT5G16750  TOZ; Transducin family protein / WD-40 repeat family protein [KO:K14555]
AT3G21540  transducin family protein / WD-40 repeat family protein [KO:K14556]
AT4G28200  U3 small nucleolar RNA-associated-like protein [KO:K14557]
AT1G15440  PWP2; periodic tryptophan protein 2 [KO:K14558]
AT2G25420  transducin family protein / WD-40 repeat family protein [KO:K14558]
AT5G66540  U3 small nucleolar ribonucleoprotein [KO:K14559]
AT5G15750  Alpha-L RNA-binding motif/Ribosomal protein S4 family protein [KO:K14560]
AT1G63780  IMP4; Ribosomal RNA processing Brix domain protein [KO:K14561]
AT4G25630  FIB2; fibrillarin 2 [KO:K14563] [EC:2.1.1.-]
AT5G52490  Fibrillarin family protein [KO:K14563] [EC:2.1.1.-]
AT5G52470  FIB1; fibrillarin 1 [KO:K14563] [EC:2.1.1.-]
AT1G56110  NOP56; NOP56-like pre RNA processing ribonucleoprotein [KO:K14564]
AT3G12860  NOP56-like pre RNA processing ribonucleoprotein [KO:K14564]
AT5G27120  NOP56-like pre RNA processing ribonucleoprotein [KO:K14565]
AT3G05060  NOP56-like pre RNA processing ribonucleoprotein [KO:K14565]
AT5G27140  NOP56-like pre RNA processing ribonucleoprotein [KO:K14565]
AT4G22380  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein [KO:K12845]
AT4G12600  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein [KO:K12845]
AT5G20160  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein [KO:K12845]
AT3G57150  NAP57; homologue of NAP57 [KO:K11131] [EC:5.4.99.-]
AT5G08180  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein [KO:K11129]
AT3G03920  H/ACA ribonucleoprotein complex, subunit Gar1/Naf1 protein [KO:K11128]
AT5G18180  H/ACA ribonucleoprotein complex, subunit Gar1/Naf1 protein [KO:K11128]
AT2G20490  NOP10; nucleolar RNA-binding Nop10p family protein [KO:K11130]
AT2G46230  PIN domain-like family protein [KO:K14566]
AT1G26530  PIN domain-like family protein [KO:K14566]
AT4G02400  U3 ribonucleoprotein (Utp) family protein [KO:K14567]
AT5G08600  U3 ribonucleoprotein (Utp) family protein [KO:K14567]
AT3G57000  nucleolar essential protein-like protein [KO:K14568] [EC:2.1.1.260]
AT1G06720  P-loop containing nucleoside triphosphate hydrolases superfamily protein [KO:K14569]
AT3G57940  GNAT acetyltransferase (DUF699) [KO:K14521] [EC:2.3.1.-]
AT1G10490  GNAT acetyltransferase (DUF699) [KO:K14521] [EC:2.3.1.-]
AT5G22100  RNA cyclase family protein [KO:K11108]
AT2G47300  POP1; ribonuclease Ps [KO:K01164] [EC:3.1.26.5]
AT2G43190  POP4; ribonuclease P family protein [KO:K03538] [EC:3.1.26.5]
AT1G04635  EMB1687; ribonuclease P family protein / Rpp14 family protein [KO:K03537] [EC:3.1.26.5]
AT5G59980  GAF1; Polymerase/histidinol phosphatase-like protein [KO:K03539] [EC:3.1.26.5]
AT5G25800  Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K14570] [EC:3.1.-.-]
AT5G67240  SDN3; small RNA degrading nuclease 3 [KO:K14570] [EC:3.1.-.-]
AT3G50100  SDN1; small RNA degrading nuclease 1 [KO:K14570] [EC:3.1.-.-]
AT3G50090  Exonuclease family protein [KO:K14570] [EC:3.1.-.-]
AT5G05540  SDN2; small RNA degrading nuclease 2 [KO:K14570] [EC:3.1.-.-]
AT2G26970  Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K13288] [EC:3.1.-.-]
AT5G42540  XRN2; exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
AT1G75660  XRN3; 5'-3' exoribonuclease 3 [KO:K12619] [EC:3.1.13.-]
AT1G50920  Nucleolar GTP-binding protein [KO:K06943]
AT1G10300  Nucleolar GTP-binding protein [KO:K06943]
AT1G80770  PDE318; P-loop containing nucleoside triphosphate hydrolases superfamily protein [KO:K06943]
AT3G23860  GTP-binding protein-like protein [KO:K06943]
AT1G52980  AtNug2; GTP-binding family protein [KO:K14537]
AT3G07050  NSN1; GTP-binding family protein [KO:K14538]
AT3G01610  CDC48C; cell division cycle 48C [KO:K14571]
AT1G67120  midasin-like protein [KO:K14572]
AT2G21440  RNA-binding (RRM/RBD/RNP motifs) family protein [KO:K14573]
AT5G41190  RNA-binding NOB1-like protein [KO:K11883]
AT5G20010  RAN-1; RAS-related nuclear protein-1 [KO:K07936]
AT5G20020  RAN2; RAS-related GTP-binding nuclear protein 2 [KO:K07936]
AT5G55080  RAN4; ras-related nuclear protein 4 [KO:K07936]
AT5G55190  RAN3; RAN GTPase 3 [KO:K07936]
AT3G03110  XPO1B; exportin 1B [KO:K14290]
AT5G17020  XPO1A; exportin 1A [KO:K14290]
AT2G03820  NMD3; nonsense-mediated mRNA decay NMD3 family protein [KO:K07562]
AT2G39820  eIF6B; Translation initiation factor IF6 [KO:K03264]
AT3G55620  eIF6A; Translation initiation factor IF6 [KO:K03264]
AT1G43860  sequence-specific DNA binding transcription factor [KO:K14574]
AT3G22980  Ribosomal protein S5/Elongation factor G/III/V family protein [KO:K14536] [EC:3.6.5.-]
AT2G27200  P-loop containing nucleoside triphosphate hydrolases superfamily protein [KO:K14539] [EC:3.6.1.-]
AT1G08410  P-loop containing nucleoside triphosphate hydrolases superfamily protein [KO:K14539] [EC:3.6.1.-]
AT5G60340  AAK6; P-loop containing nucleoside triphosphate hydrolases superfamily protein [KO:K18532] [EC:2.7.4.3]
AT2G24990  Serine/threonine-protein kinase Rio1 [KO:K07178] [EC:2.7.11.1]
AT5G37350  Serine/threonine-protein kinase Rio1 [KO:K07178] [EC:2.7.11.1]
AT3G51270  protein serine/threonine kinase [KO:K07179] [EC:2.7.11.1]
ArthCr088  16S ribosomal RNA [KO:K01979]
AT3G41768  18S ribosomal RNA [KO:K01979]
AT2G01010  18S ribosomal RNA [KO:K01979]
ArthCr091  5S ribosomal RNA [KO:K01981]
AT5G54075  U3D; U3D; snoRNA [KO:K14483]
AT5G53902  U3B; U3B; snoRNA [KO:K14483]
Reference
PMID:20174677
  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
PMID:17515605
  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
PMID:19850913
  Authors
Strunk BS, Karbstein K
  Title
Powering through ribosome assembly.
  Journal
RNA 15:2083-104 (2009)
DOI:10.1261/rna.1792109
Reference
PMID:15120992
  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
PMID:19879902
  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
ath03010  Ribosome
KO pathway
ko03008   
LinkDB

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