Process_RNAProcessing – RNA processing

Name
WID Process_RNAProcessing
Name RNA processing
 
Implementation
Initialization order 25 View in model
 
Reactions
Chemical reactions View in model
 
Parameters
Parameters View in model
 
Comments
Comments Following transcription rRNA, tRNA, and tmRNA transcripts are cleaved, modified, and aminoacylated. First, 45S rRNA transcripts are cleaved by ribonuclease III (MG_367_DIMER) into 5S, 16S, and 23S rRNA precursors [PUB_0038, PUB_0039]. Next these precursors are cleaved at their 3' and 5' ends by ribonuclease J and RgsA [PUB_0038]. Similarly the 5' ends of each tRNA and tmRNA species are cleaved by ribonuclease P [PUB_0039, PUB_0649]. Ribonuclease III also cleaves scRNA at two sites [PUB_0039]. Second, 13 enzymes formylate, lysidinate, methylate, pseudouridylate, and thiolate 86 specific rRNA and tRNA bases. Third 19 tRNA synthetases conjugate 19 amino acids to 37 tRNA and tmRNA species, and 2 tRNA transferases complete the aminoacylation of the formylmethionine and glutamine tRNAs. rRNA, tRNA, and tmRNA cleavage, modification, and aminoacylation are modeled motivated by mass-action kinetics. First, the maximum rate of maturation of each RNA species is calculated based on (1) the abundance of immature transcripts, (2) the abundance of substrates and enzymes required to cleave or modify each RNA species, and (3) the experimentally measured kinetic rate of each enzyme required to cleave or modify each RNA species. Second, RNA maturations are randomly selected according to the calculated maximum rates. Finally, steps (1) and (2) are repeated until insufficient resources are available to mature additional RNAs. precusor r/s/t RNA cleavage Substrate Enzyme Kinetics Cofactors 30S RNA ⇒ pre 16/17S RNA, p23S RNA, 9s RNA RNAseIII, MG_367 pre 16/17S RNA ⇒ 16S RNA 5' end:rnjA, MG_139; 3' end:rgsA, MG_110 p23S RNA ⇒ 23S RNA 5' end:rnjA, MG_139 9 S RNA ⇒ 5S RNA 3' end tRNA precursors RNAseIII, MG_367 5' end tRNA precursors RNaseP, MG_0003, MG_465 0.027 1/s [PUB_0013] Mg2+ [PUB_0013] scRNA (MG_0001) precusors RNAseIII, MG_367
References
  1. Deutscher MP. Maturation and degradation of ribosomal RNA in bacteria. Prog Mol Biol Transl Sci 85, 369-91 (2009). WholeCell: PUB_0038, PubMed: 19215777

  2. Hsieh J, Andrews AJ, Fierke CA. Roles of protein subunits in RNA-protein complexes: lessons from ribonuclease P. Biopolymers 73, 79-89 (2004). WholeCell: PUB_0013, PubMed: 14691942

  3. Nakanishi K, Nureki O. Recent progress of structural biology of tRNA processing and modification. Mol Cells 19, 157-66 (2005). WholeCell: PUB_0649, PubMed: 15879697

  4. Nicholson AW. Function, mechanism and regulation of bacterial ribonucleases. FEMS Microbiol Rev 23, 371-90 (1999). WholeCell: PUB_0039, PubMed: 10371039

 
Metadata
Created 2012-10-01 15:07:35
Last updated 2012-10-01 15:14:00