Note_RNAProcessing – RNAProcessing

WID Note_RNAProcessing
Name RNAProcessing
Comments Ribonuclease P Ribonuclease P removes 5' leader sequence from pre-tRNA by hydrolyzing phosphodiester bond immediately 5' of first nucleotide of mature tRNA. Ribonuclease P is a ribonucleoprotein contain 1 protein subunit (MG_465, rpnA) and 1 RNA subunit (MG_0003, P RNA, MCS5). Ribonuclease P kinetics were investigated by Hsieh et al [PUB_0013]: ParameterValue (Mg2+)Value (Ca2+) kcat0.27 ±0.02 s-1 KM0.08 ± 0.02 μM k20.3 ± 0.01 s-11.8 ± 0.3 × 10-5 s-1 KDpretRNA4 ± 2 × 10-4 μM KDtRNA1.2 ± 0.1 μM0.2 ± 0.06 μM Network reconstruction rRNA, sRNA, and tRNA cleavage was reconstructed from the primary literature [PUB_0038, PUB_0039, PUB_0042, PUB_0061, PUB_0068, PUB_0069, PUB_0070, PUB_0101, PUB_0102, PUB_0104, PUB_0110, PUB_0163, PUB_0166]. Specific parameters were obtained from the following sources: Kinetics: [PUB_0013, PUB_0069, PUB_0103] Complex composition: [PUB_0011] Cofactors: [PUB_0006, PUB_0012, PUB_0013, PUB_0039, PUB_0043, PUB_0071, PUB_0096, PUB_0165]
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  8. Deutscher MP. Maturation and degradation of ribosomal RNA in bacteria. Prog Mol Biol Transl Sci 85, 369-91 (2009). WholeCell: PUB_0038, PubMed: 19215777

  9. Hase Y, Yokoyama S, Muto A, Himeno H. Removal of a ribosome small subunit-dependent GTPase confers salt resistance on Escherichia coli cells. RNA 15, 1766-74 (2009). WholeCell: PUB_0101, PubMed: 19620234

  10. Himeno H, Hanawa-Suetsugu K, Kimura T, Takagi K, Sugiyama W, Shirata S, Mikami T, Odagiri F, Osanai Y, Watanabe D, Goto S, Kalachnyuk L, Ushida C, Muto A. A novel GTPase activated by the small subunit of ribosome. Nucleic Acids Res 32, 5303-9 (2004). WholeCell: PUB_0103, PubMed: 15466596

  11. 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

  12. Keseler IM, Bonavides-Martínez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, Peralta-Gil M, Santos-Zavaleta A, Shearer AG, Karp PD. EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res 37, D464-70 (2009). WholeCell: PUB_0006, PubMed: 18974181

  13. Kimura T, Takagi K, Hirata Y, Hase Y, Muto A, Himeno H. Ribosome-small-subunit-dependent GTPase interacts with tRNA-binding sites on the ribosome. J Mol Biol 381, 467-77 (2008). WholeCell: PUB_0102, PubMed: 18588897

  14. Madhugiri R, Evguenieva-Hackenberg E. RNase J is involved in the 5'-end maturation of 16S rRNA and 23S rRNA in Sinorhizobium meliloti. FEBS Lett 583, 2339-42 (2009). WholeCell: PUB_0166, PubMed: 19540834

  15. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 39, D52-7 (2011). WholeCell: PUB_0061, PubMed: 21115458, URL:

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

  17. Py B, Higgins CF, Krisch HM, Carpousis AJ. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 381, 169-72 (1996). WholeCell: PUB_0068, PubMed: 8610017

  18. Rauhut R, Klug G. mRNA degradation in bacteria. FEMS Microbiol Rev 23, 353-70 (1999). WholeCell: PUB_0071, PubMed: 10371038

  19. Torres-Larios A, Swinger KK, Pan T, Mondragón A. Structure of ribonuclease P--a universal ribozyme. Curr Opin Struct Biol 16, 327-35 (2006). WholeCell: PUB_0011, PubMed: 16650980

  20. UniProt Consortium. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 37, D169-74 (2009). WholeCell: PUB_0096, PubMed: 18836194, URL:

  21. Wu Q, Huang L, Zhang Y. The structure and function of catalytic RNAs. Sci China C Life Sci 52, 232-44 (2009). WholeCell: PUB_0043, PubMed: 19294348

  22. Yao S, Blaustein JB, Bechhofer DH. Processing of Bacillus subtilis small cytoplasmic RNA: evidence for an additional endonuclease cleavage site. Nucleic Acids Res 35, 4464-73 (2007). WholeCell: PUB_0042, PubMed: 17576666

  23. de la Sierra-Gallay IL, Zig L, Jamalli A, Putzer H. Structural insights into the dual activity of RNase J. Nat Struct Mol Biol 15, 206-12 (2008). WholeCell: PUB_0165, PubMed: 18204464

Created 2012-10-01 15:07:34
Last updated 2012-10-01 15:13:58