KEGG   PATHWAY: gmx03008
Entry
gmx03008                    Pathway                                
Name
Ribosome biogenesis in eukaryotes - Glycine max (soybean)
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
gmx03008  Ribosome biogenesis in eukaryotes
gmx03008

Organism
Glycine max (soybean) [GN:gmx]
Gene
100799304  putative casein kinase II subunit beta [KO:K03115]
100789357  putative casein kinase II subunit beta isoform 1 [KO:K03115]
100780095  putative casein kinase II subunit beta [KO:K03115]
100784315  putative casein kinase II subunit beta [KO:K03115]
100793573  putative casein kinase II subunit beta-4 [KO:K03115]
100784848  putative casein kinase II subunit beta [KO:K03115]
100813528  casein kinase II subunit alpha-2 [KO:K03097] [EC:2.7.11.1]
100810748  casein kinase II subunit alpha-2 [KO:K03097] [EC:2.7.11.1]
100819679  casein kinase II subunit alpha-2 [KO:K03097] [EC:2.7.11.1]
100776388  casein kinase II subunit alpha [KO:K03097] [EC:2.7.11.1]
100820471  uncharacterized protein LOC100820471 precursor [KO:K03097] [EC:2.7.11.1]
100817795  casein kinase II subunit alpha-4, chloroplastic [KO:K03097] [EC:2.7.11.1]
100779287  nucleolar protein 6 [KO:K14544]
100776157  nucleolar protein 6 [KO:K14544]
100802650  ribosomal RNA-processing protein 7 homolog A isoform X1 [KO:K14545]
100776399  ribosomal RNA-processing protein 7 homolog A [KO:K14545]
100792757  WD repeat-containing protein 43 isoform X2 [KO:K14546]
100815458  WD repeat-containing protein 43 [KO:K14546]
100796828  WD repeat-containing protein 43 isoform X3 [KO:K14546]
100799236  WD repeat-containing protein 43 isoform X1 [KO:K14546]
102667004  WD repeat-containing protein 43 [KO:K14546]
100784148  WD repeat-containing protein 43 [KO:K14546]
100797494  WD repeat-containing protein PCN isoform X2 [KO:K14548]
100776641  WD repeat-containing protein PCN isoform X3 [KO:K14548]
100806066  protein SLOW WALKER 1 [KO:K14549]
102668105  protein SLOW WALKER 1 isoform X2 [KO:K14549]
100798087  uncharacterized protein At3g06530 isoform X1 [KO:K14550]
100796965  uncharacterized protein At3g06530 isoform X1 [KO:K14550]
100807740  WD repeat-containing protein 75 [KO:K14552]
100777699  WD repeat-containing protein 75 [KO:K14552]
100806692  U3 small nucleolar RNA-associated protein 18 homolog [KO:K14553]
100806023  U3 small nucleolar RNA-associated protein 18 homolog [KO:K14553]
100795420  WD repeat-containing protein 36 [KO:K14554]
100798946  WD repeat-containing protein 36 [KO:K14554]
100783244  transducin beta-like protein 3 [KO:K14555]
100800955  WD repeat-containing protein 3 [KO:K14556]
100775810  WD repeat-containing protein 3 [KO:K14556]
100820428  U3 small nucleolar RNA-associated protein 6 homolog [KO:K14557]
100817094  U3 small nucleolar RNA-associated protein 6 homolog [KO:K14557]
100526905  periodic tryptophan protein 2 [KO:K14558]
100793629  periodic tryptophan protein 2 [KO:K14558]
100817724  U3 small nucleolar ribonucleoprotein protein MPP10 [KO:K14559]
100781093  U3 small nucleolar ribonucleoprotein protein MPP10 [KO:K14559]
100782389  U3 small nucleolar ribonucleoprotein protein IMP3 [KO:K14560]
100798516  U3 small nucleolar ribonucleoprotein protein IMP3 [KO:K14560]
102661153  U3 small nucleolar ribonucleoprotein protein IMP3 [KO:K14560]
100817428  U3 small nucleolar ribonucleoprotein protein IMP3 [KO:K14560]
100803810  U3 small nucleolar ribonucleoprotein protein IMP4-like [KO:K14561]
100814677  uncharacterized protein LOC100814677 [KO:K14561]
102670478  uncharacterized protein LOC102670478 isoform X1 [KO:K14561]
100788688  rRNA 2'-O-methyltransferase fibrillarin 2 [KO:K14563] [EC:2.1.1.-]
100814656  rRNA 2'-O-methyltransferase fibrillarin 2 [KO:K14563] [EC:2.1.1.-]
100797625  rRNA 2'-O-methyltransferase fibrillarin 2 [KO:K14563] [EC:2.1.1.-]
100789137  rRNA 2'-O-methyltransferase fibrillarin 2 [KO:K14563] [EC:2.1.1.-]
100794470  nucleolar protein 56 [KO:K14564]
100815506  nucleolar protein 56 [KO:K14564]
100779446  nucleolar protein 56 isoform X1 [KO:K14564]
100783434  nucleolar protein 56 [KO:K14564]
100784721  probable nucleolar protein 5-2 [KO:K14565]
100775301  probable nucleolar protein 5-2 [KO:K14565]
100305817  uncharacterized protein LOC100305817 [KO:K12845]
100527424  uncharacterized protein LOC100527424 [KO:K12845]
100798912  NHP2-like protein 1 [KO:K12845]
100817627  NHP2-like protein 1 [KO:K12845]
100780706  H/ACA ribonucleoprotein complex subunit 4 [KO:K11131] [EC:5.4.99.-]
100806355  H/ACA ribonucleoprotein complex subunit 4 [KO:K11131] [EC:5.4.99.-]
100810689  H/ACA ribonucleoprotein complex subunit 2-like protein isoform X1 [KO:K11129]
100305515  uncharacterized protein LOC100305515 [KO:K11129]
100804186  H/ACA ribonucleoprotein complex subunit 2-like protein [KO:K11129]
100499993  uncharacterized protein LOC100499993 [KO:K11129]
100788981  putative H/ACA ribonucleoprotein complex subunit 1-like protein 1 [KO:K11128]
100799823  putative H/ACA ribonucleoprotein complex subunit 1-like protein 1 [KO:K11128]
100306376  H/ACA ribonucleoprotein complex subunit 3-like protein [KO:K11130]
100500467  H/ACA ribonucleoprotein complex subunit 3-like protein [KO:K11130]
100782798  rRNA-processing protein FCF1 homolog [KO:K14566]
100792488  rRNA-processing protein FCF1 homolog [KO:K14566]
100813838  rRNA-processing protein FCF1 homolog [KO:K14566]
100784007  uncharacterized protein C57A7.06 isoform X2 [KO:K14567]
100811431  U3 small nucleolar RNA-associated protein 14 isoform X1 [KO:K14567]
100788480  uncharacterized protein LOC100788480 [KO:K14568] [EC:2.1.1.260]
100778294  uncharacterized protein LOC100778294 [KO:K14568] [EC:2.1.1.260]
100810906  ribosome biogenesis protein BMS1 homolog isoform X1 [KO:K14569]
100792176  ribosome biogenesis protein BMS1 homolog isoform X1 [KO:K14569]
100788187  RNA cytidine acetyltransferase 1 [KO:K14521] [EC:2.3.1.-]
100798712  RNA cytidine acetyltransferase 1 [KO:K14521] [EC:2.3.1.-]
100812924  RNA cytidine acetyltransferase 1 isoform X1 [KO:K14521] [EC:2.3.1.-]
100778883  uncharacterized protein LOC100778883 [KO:K11108]
100797356  probable RNA 3'-terminal phosphate cyclase-like protein [KO:K11108]
100788705  uncharacterized protein LOC100788705 [KO:K01164] [EC:3.1.26.5]
100798058  uncharacterized protein LOC100798058 [KO:K01164] [EC:3.1.26.5]
100802747  LOW QUALITY PROTEIN: ribonuclease P protein subunit p29 [KO:K03538] [EC:3.1.26.5]
100527772  uncharacterized protein LOC100527772 [KO:K03537] [EC:3.1.26.5]
100779855  probable ribonuclease P/MRP protein subunit POP5 [KO:K03537] [EC:3.1.26.5]
100776746  protein GAMETOPHYTE DEFECTIVE 1 [KO:K03539] [EC:3.1.26.5]
100796963  small RNA degrading nuclease 5 [KO:K14570] [EC:3.1.-.-]
100802793  small RNA degrading nuclease 5 isoform X1 [KO:K14570] [EC:3.1.-.-]
100785565  small RNA degrading nuclease 3 [KO:K14570] [EC:3.1.-.-]
112998160  LOW QUALITY PROTEIN: small RNA degrading nuclease 3 [KO:K14570] [EC:3.1.-.-]
100795445  oligoribonuclease [KO:K13288] [EC:3.1.-.-]
100527858  Orn domain-containing protein [KO:K13288] [EC:3.1.-.-]
100783068  5'-3' exoribonuclease 3 isoform X2 [KO:K12619] [EC:3.1.13.-]
100794359  nucleolar GTP-binding protein 1 isoform X2 [KO:K06943]
100795311  nucleolar GTP-binding protein 1 [KO:K06943]
100784033  nucleolar GTP-binding protein 1 [KO:K06943]
100788649  nuclear/nucleolar GTPase 2 [KO:K14537]
100781028  nuclear/nucleolar GTPase 2 [KO:K14537]
100777028  guanine nucleotide-binding protein-like NSN1 isoform X2 [KO:K14538]
100799557  guanine nucleotide-binding protein-like NSN1 [KO:K14538]
100809594  cell division control protein 48 homolog C [KO:K14571]
100800513  LOW QUALITY PROTEIN: cell division control protein 48 homolog C [KO:K14571]
102663906  midasin [KO:K14572]
102669841  midasin [KO:K14572]
100791823  RNA-binding protein 28 [KO:K14573]
100794821  RNA-binding protein 28 [KO:K14573]
100785714  RNA-binding NOB1-like protein [KO:K11883]
100800291  RNA-binding NOB1-like protein [KO:K11883]
100500437  RAN GTPase 3 [KO:K07936]
100813067  GTP-binding nuclear protein Ran-3 [KO:K07936]
100813605  GTP-binding nuclear protein Ran-3 [KO:K07936]
100814146  GTP-binding nuclear protein Ran-3 [KO:K07936]
100801379  GTP-binding nuclear protein Ran-3 [KO:K07936]
100775298  uncharacterized protein LOC100775298 [KO:K07936]
100305680  uncharacterized protein LOC100305680 [KO:K07936]
100802384  protein EXPORTIN 1A [KO:K14290]
100813443  protein EXPORTIN 1A [KO:K14290]
100783433  protein EXPORTIN 1A isoform X1 [KO:K14290]
100787912  protein EXPORTIN 1A [KO:K14290]
100799026  60S ribosomal export protein NMD3 [KO:K07562]
100306262  eukaryotic translation initiation factor 6 [KO:K03264]
100813909  eukaryotic translation initiation factor 6-2 isoform X2 [KO:K03264]
100777602  eukaryotic translation initiation factor 6-2 [KO:K03264]
100800352  eukaryotic translation initiation factor 6-2 [KO:K03264]
100776352  uncharacterized protein LOC100776352 [KO:K14574]
100797497  ribosome maturation protein SBDS [KO:K14574]
100775257  elongation factor-like GTPase 1 [KO:K14536] [EC:3.6.5.-]
100793676  elongation factor-like GTPase 1 [KO:K14536] [EC:3.6.5.-]
100815023  GTPase LSG1-2 [KO:K14539] [EC:3.6.1.-]
100817523  GTPase LSG1-2 [KO:K14539] [EC:3.6.1.-]
100775499  GTPase LSG1-2 [KO:K14539] [EC:3.6.1.-]
100778137  GTPase LSG1-2 [KO:K14539] [EC:3.6.1.-]
100810701  adenylate kinase isoenzyme 6 homolog [KO:K18532] [EC:2.7.4.3]
100306226  putative adenylate kinase [KO:K18532] [EC:2.7.4.3]
100817637  serine/threonine-protein kinase RIO1 [KO:K07178] [EC:2.7.11.1]
100799345  serine/threonine-protein kinase rio1 [KO:K07178] [EC:2.7.11.1]
100797607  serine/threonine-protein kinase rio2 isoform X2 [KO:K07179] [EC:2.7.11.1]
100789490  serine/threonine-protein kinase rio2 [KO:K07179] [EC:2.7.11.1]
3989374  rrn16; 16S ribosomal RNA [KO:K01979]
112999052  18S ribosomal RNA [KO:K01979]
112999051  18S ribosomal RNA [KO:K01979]
112998970  18S ribosomal RNA [KO:K01979]
121174421  18S ribosomal RNA [KO:K01979]
112999058  18S ribosomal RNA [KO:K01979]
121174454  18S ribosomal RNA [KO:K01979]
112998968  18S ribosomal RNA [KO:K01979]
3989371  rrn23; 23S ribosomal RNA [KO:K01982]
112999102  28S ribosomal RNA [KO:K01982]
112999124  28S ribosomal RNA [KO:K01982]
112999178  28S ribosomal RNA [KO:K01982]
112999123  28S ribosomal RNA [KO:K01982]
121174461  28S ribosomal RNA [KO:K01982]
112999150  28S ribosomal RNA [KO:K01982]
112999196  28S ribosomal RNA [KO:K01982]
112999167  28S ribosomal RNA [KO:K01982]
112999179  28S ribosomal RNA [KO:K01982]
3989350  rrn5; 5S ribosomal RNA [KO:K01981]
3989369  rrn5; 5S ribosomal RNA [KO:K01981]
15308615  rrn5; 5S ribosomal RNA [KO:K01981]
112997706  small nucleolar RNA U3 [KO:K14483]
113001319  small nucleolar RNA U3 [KO:K14483]
113001320  small nucleolar RNA U3 [KO:K14483]
113000612  small nucleolar RNA U3 [KO:K14483]
100783829  60S ribosomal export protein NMD3-like [KO:K07562]
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
gmx03010  Ribosome
KO pathway
ko03008   
LinkDB

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