RNase J1 endonuclease activity as a probe of RNA secondary structure

RNA

Volumn 15, Issue 7, 2009, Pages 1417-1425

  Daou Chabo, Roula ^a   Condon, Ciarán ^a  

^a INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

Author keywords

Bacillus subtilis; Endoribonuclease; RNA secondary structure; RNase J1

Indexed keywords

DOUBLE STRANDED RNA; ENDONUCLEASE; RIBONUCLEASE J1; SINGLE STRANDED RNA; THREONINE TRANSFER RNA; UNCLASSIFIED DRUG;

5' UNTRANSLATED REGION; ALGORITHM; ARTICLE; BACILLUS SUBTILIS; ENZYME ACTIVITY; FEASIBILITY STUDY; GENE; HBS GENE; IN VITRO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN CLEAVAGE; RIBOSOME SUBUNIT; RNA CONFORMATION; RNA PROBE; RNA STRUCTURE;

BACILLUS SUBTILIS; BACTERIAL PROTEINS; BASE SEQUENCE; DNA FOOTPRINTING; DNA-BINDING PROTEINS; GUANOSINE TRIPHOSPHATE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RIBONUCLEASES; RNA, BACTERIAL; RNA, TRANSFER; SUBSTRATE SPECIFICITY;

BACILLUS SUBTILIS;

EID: 67649366350     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1574309     Document Type: Article

References (19)

1. Boguski MS, Hieter PA, Levy CC. 1980. Identification of a cytidine-specific ribonuclease from chicken liver. J Biol Chem 255: 2160-2163.
2. Choonee N, Even S, Zig L, Putzer H. 2007. Ribosomal protein L20 controls expression of the Bacillus subtilis infC operon via a transcription attenuation mechanism. Nucleic Acids Res 35: 1578-1588. (Pubitemid 46592878)
3. Condon C, Putzer H, Luo D, Grunberg-Manago M. 1997. Processing of the Bacillus subtilis thrS leader mRNA is RNase E- dependent in Escherichia coli. J Mol Biol 268: 235-242. (Pubitemid 27208050)
4. Condon C, Pellegrini O, Mathy N, Benard L, Redko Y, Oussenko IA, Deikus G, Bechhofer DH. 2008. Assay of Bacillus subtilis ribonucleases in vitro. Methods Enzymol 447: 277-308.
5. Daou-Chabo R, Mathy N, Benard L, Condon C. 2009. Ribosomes initiating translation of the hbs mRNA protect it from 5′-to-3′ exoribonucleolytic degradation by RNase J1. Mol Microbiol 71: 1538-1550.
6. Deikus G, Condon C, Bechhofer DH. 2008. Role of Bacillus subtilis RNase J1 endonuclease and 5′-exonuclease activities in trp leader RNA turnover. J Biol Chem 283: 17158-17167.
7. Even S, Pellegrini O, Zig L, Labas V, Vinh J, Brechemmier-Baey D, Putzer H. 2005. Ribonucleases J1 and J2: Two novel endoribonucleases in B. subtilis with functional homology to E. coli RNase E. Nucleic Acids Res 33: 2141-2152. (Pubitemid 41439882)
8. Irie M, Ohgi K. 2001. Ribonuclease T2. Methods Enzymol 341: 42-55.
9. Li de la Sierra-Gallay I, Mathy N, Pellegrini O, Condon C. 2006. Structure of the ubiquitous 3′ processing enzyme RNase Z bound to transfer RNA. Nat Struct Mol Biol 13: 376-377. (Pubitemid 43873512)
10. Li de la Sierra-Gallay I, Zig L, Jamalli A, Putzer H. 2008. Structural insights into the dual activity of RNase J. Nat Struct Mol Biol 15: 206-212. (Pubitemid 351207513)
11. Mathy N, Benard L, Pellegrini O, Daou R, Wen T, Condon C. 2007. 5′-to-3′ exoribonuclease activity in bacteria: Role of RNase J1 in rRNA maturation and 5′ stability of mRNA. Cell 129: 681-692. (Pubitemid 46802375)
12. Merino EJ, Wilkinson KA, Coughlan JL, Weeks KM. 2005. RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE). J Am Chem Soc 127: 4223-4231. (Pubitemid 40463047)
13. Mortimer SA, Weeks KM. 2007. A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J Am Chem Soc 129: 4144-4145. (Pubitemid 46595421)
14. Nichols NM, Yue D. 2008. Ribonucleases. In Current Protocols in Molecular Biology, Chapter 3, Unit 3.13, Wiley, New York.
15. Oshima T, Uenishi N, Imahori K. 1976. Simple assay methods for ribonuclease T1, T2, and nuclease P1. Anal Biochem 71: 632-634.
16. Redko Y, Bechhofer DH, Condon C. 2008. Mini-III, an unusual member of the RNase III family of enzymes, catalyses 23S ribosomal RNA maturation in B. subtilis. Mol Microbiol 68: 1096-1106. (Pubitemid 351670191)
17. Richards FM, Wyckoff HW. 1971. Bovine pancreatic ribonuclease. In The enzymes (ed. PD Boyer), pp 647-806. Academic Press, New York.
18. Uchida T, Egami F. 1966. Procedures in nucleic acids research. I (eds. GL Cantoni, DR Davis), pp 3-13. Harper and Row, New York.
19. Yao S, Blaustein JB, Bechhofer DH. 2007. Processing of Bacillus subtilis small cytoplasmic RNA: Evidence for an additional endonuclease cleavage site. Nucleic Acids Res 35: 4464-4473. (Pubitemid 47244597)