Entry Name RNA degradation - Oryza sativa japonica (Japanese rice) (RAPDB)
Description The correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay exist and both pathways are initiated by poly(A) shortening of the mRNA. In the 5' to 3' pathway, this is followed by decapping which then permits the 5' to 3' exonucleolytic degradation of transcripts. In the 3' to 5' pathway, the exosome, a large multisubunit complex, plays a key role. The exosome exists in archaeal cells, too. In bacteria, endoribonuclease E, a key enzyme involved in RNA decay and processing, organizes a protein complex called degradosome. RNase E or R interacts with the phosphate-dependent exoribonuclease polynucleotide phosphorylase, DEAD-box helicases, and additional factors in the RNA-degrading complex.
Class Genetic Information Processing; Folding, sorting and degradationBRITE hierarchy
Pathway map Ortholog table Other DBs Organism Oryza sativa japonica (Japanese rice) (RAPDB) [GN:
dosa ]
Gene Os03t0844450-01 (RAP-DB) Os03g0844450; Similar to 3' exoribonuclease family domain 1-containing protein. [KO:K12587 ]
Os10t0548200-01 (RAP-DB) Os10g0548200; Tetratricopeptide-like helical domain containing protein. [KO:K12600 ]
Os03t0652100-01 (RAP-DB) Os03g0652100; Not CCR4-Not complex component, N-terminal domain containing protein. [KO:K12580 ]
Os10t0123900-00 (RAP-DB) Os10g0123900; Similar to CAF1 family ribonuclease containing protein. [KO:K12581 ]
Os02t0796300-01 (RAP-DB) Os02g0796300; Similar to CCR4-NOT transcription complex subunit 7 (CCR4-associated factor 1) (CAF1) (BTG1 binding factor 1). [KO:K12581 ]
Os09t0416800-01 (RAP-DB) Os09g0416800; Similar to CCR4-NOT transcription complex subunit 7 (CCR4-associated factor 1) (CAF1) (BTG1 binding factor 1). [KO:K12581 ]
Os03t0784800-01 (RAP-DB) Os03g0784800; Homo sapiens protein involved in sexual development, complete cds. [KO:K12606 ]
Os09t0123100-01 (RAP-DB) Os09g0123100; Tetratricopeptide-like helical domain containing protein. [KO:K12607 ]
Os09t0279500-01 (RAP-DB) Os09g0279500; Similar to Plastid-specific 30S ribosomal protein 2, chloroplast precursor (PSRP- 2). [KO:K13126 ]
Os03t0278500-01 (RAP-DB) Os03g0278500; Nucleotide-binding, alpha-beta plait domain containing protein. [KO:K13126 ]
Os01t0769000-01 (RAP-DB) Os01g0769000; Topoisomerase II-associated protein PAT1 domain containing protein. [KO:K12617 ]
Os02t0517300-01 (RAP-DB) Os02g0517300; Topoisomerase II-associated protein PAT1 domain containing protein. [KO:K12617 ]
Os02t0294700-01 (RAP-DB) Os02g0294700; Topoisomerase II-associated protein PAT1 domain containing protein. [KO:K12617 ]
Os02t0295700-01 (RAP-DB) Os02g0295700; Aldehyde dehydrogenase, conserved site domain containing protein. [KO:K12617 ]
Os01t0872700-01 (RAP-DB) Os01g0872700; Zinc finger, CCHC-type domain containing protein. [KO:K12619 ] [EC:3.1.13.-]
Os04t0445800-01 (RAP-DB) Os04g0445800; Like-Sm ribonucleoprotein, core domain containing protein. [KO:K12620 ]
Os08t0154700-01 (RAP-DB) Os08g0154700; U6 snRNA-associated Sm-like protein LSm2 domain containing protein. [KO:K12621 ]
Os02t0510100-01 (RAP-DB) Os02g0510100; Similar to U6 snRNA-associated Sm-like protein LSm6 (Sm protein F). [KO:K12625 ]
Os04t0388900-01 (RAP-DB) Os04g0388900; Similar to U6 snRNA-associated Sm-like protein LSm6 (Sm protein F). [KO:K12625 ]
Os03t0248600-01 (RAP-DB) Os03g0248600; Similar to Enolase 2 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 2) (2-phospho- D-glycerate hydro-lyase 2). [KO:K01689 ] [EC:4.2.1.11 ]
Os06t0136600-01 (RAP-DB) Os06g0136600; Similar to Enolase 1 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 1) (2-phospho- D-glycerate hydro-lyase 1). [KO:K01689 ] [EC:4.2.1.11 ]
Os10t0167300-01 (RAP-DB) Os10g0167300; Similar to Enolase 2 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 2) (2-phospho- D-glycerate hydro-lyase 2). [KO:K01689 ] [EC:4.2.1.11 ]
Os01t0191700-01 (RAP-DB) Os01g0191700; Similar to Pyrophosphate-fructose-6-phosphate 1-phosphotransferase-like protein (Pyrophosphate-dependent phosphofructo-1-kinase-like protein). [KO:K00850 ] [EC:2.7.1.11 ]
Os05t0194900-01 (RAP-DB) Os05g0194900; Similar to Pyrophosphate-fructose-6-phosphate 1-phosphotransferase-like protein (Pyrophosphate-dependent phosphofructo-1-kinase-like protein). [KO:K00850 ] [EC:2.7.1.11 ]
Os02t0774300-01 (RAP-DB) Os02g0774300; Similar to Heat shock 70 kDa protein, mitochondrial precursor. [KO:K04043 ]
Os03t0113700-01 (RAP-DB) Os03g0113700; Similar to Heat shock 70 kDa protein, mitochondrial precursor. [KO:K04043 ]
Os04t0443900-01 (RAP-DB) Os04g0443900; Similar to RuBisCO large subunit-binding protein subunit beta, chloroplastic. [KO:K04077 ] [EC:5.6.1.7 ]
Os03t0143400-01 (RAP-DB) Os03g0143400; Similar to mitochondrial chaperonin-60 [Oryza sativa (japonica cultivar-group)]. [KO:K04077 ] [EC:5.6.1.7 ]
Os02t0102900-01 (RAP-DB) Os02g0102900; Similar to RuBisCO subunit binding-protein beta subunit, chloroplast (60 kDa chaperonin beta subunit) (CPN-60 beta) (Fragment). [KO:K04077 ] [EC:5.6.1.7 ]
Reference Authors Houseley J, Tollervey D
Title The many pathways of RNA degradation.
Journal Reference Authors Buttner K, Wenig K, Hopfner KP
Title The exosome: a macromolecular cage for controlled RNA degradation.
Journal Reference Authors Schilders G, van Dijk E, Raijmakers R, Pruijn GJ
Title Cell and molecular biology of the exosome: how to make or break an RNA.
Journal Reference Authors Hartung S, Hopfner KP
Title The exosome, plugged.
Journal Reference Authors Carpousis AJ
Title The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E.
Journal Reference Authors Marcaida MJ, DePristo MA, Chandran V, Carpousis AJ, Luisi BF
Title The RNA degradosome: life in the fast lane of adaptive molecular evolution.
Journal Reference Authors Condon C
Title Maturation and degradation of RNA in bacteria.
Journal Related KO pathway LinkDB All DBs
