Chapter 14 Analysis of mRNA Decay in Bacillus subtilis

Methods in Enzymology

Volumn 447, Issue , 2008, Pages 259-276

  Bechhofer, David H ^a   Oussenko, Irina A ^a   Deikus, Gintaras ^a   Yao, Shiyi ^a   Mathy, Nathalie ^b   Condon, Ciarán ^b  

^a NEW YORK UNIVERSITY   (United States)

^b INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RIBONUCLEASE; RNA 5S; MESSENGER RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; BACILLUS SUBTILIS; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM MUTANT; CULTURE MEDIUM; GEL ELECTROPHORESIS; GENE MAPPING; GENE SEQUENCE; MARKER GENE; NONHUMAN; NORTHERN BLOTTING; OLIGONUCLEOTIDE PROBE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVIEW; RNA ANALYSIS; RNA DEGRADATION; RNA ISOLATION; RNA PROBE; RNA PROCESSING; RNA TRANSCRIPTION; ARTICLE; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; POLYACRYLAMIDE GEL ELECTROPHORESIS;

BACILLUS SUBTILIS; POSIBACTERIA;

BACILLUS SUBTILIS; BASE SEQUENCE; BLOTTING, NORTHERN; ELECTROPHORESIS, POLYACRYLAMIDE GEL; OLIGONUCLEOTIDE PROBES; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

EID: 58249094402     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(08)02214-3     Document Type: Review

References (30)

1. Bechhofer D.H., and Wang W. Decay of ermC mRNA in a polynucleotide phosphorylase mutant of Bacillus subtilis. J. Bacteriol. 180 (1998) 5968-5977
2. Brenner S., Jacob F., and Meselson M. An unstable intermediate carrying information from genes to ribosomes for protein synthesis. Nature. 190 (1961) 576-581
3. Brosius J. Compilation of superlinker vectors. Methods Enzymol. 216 (1992) 469-483
4. Carpousis A.J., Vanzo N.F., and Raynal L.C. mRNA degradation: A tale of poly(A) and multiprotein machines. Trends Genet. 15 (1999) 24-28
5. Celesnik H., Deana A., and Belasco J.G. Initiation of RNA decay in Escherichia coli by 5′-pyrophosphate removal. Mol. Cell 27 (2007) 79-90
6. Coburn G.A., and Mackie G.A. Degradation of mRNA in Escherichia coli: An old problem with some new twists. Prog. Nucleic Acid Res. Mol. Biol. 62 (1999) 55-108
7. Condon C. RNA processing and degradation in Bacillus subtilis. Microbiol. Mol. Biol. Rev. 67 (2003) 157-174
8. Condon C., Brechemier-Baey D., Beltchev B., Grunberg-Manago M., and Putzer H. Identification of the gene encoding the 5S ribosomal RNA maturase in Bacillus subtilis: Mature 5S rRNA is dispensable for ribosome function. RNA 7 (2001) 242-253
9. Craven M.G., Henner D.J., Alessi D., Schauer A.T., Ost K.A., Deutscher M.P., and Friedman D.I. Identification of the rph (RNase PH) gene of Bacillus subtilis: Evidence for suppression of cold-sensitive mutations in Escherichia coli. J. Bacteriol. 174 (1992) 4727-4735
10. Deikus G., Condon C., and Bechhofer D.H. Role of Bacillus subtilis RNase J1 endonuclease and 5′-exonuclease activities in trp leader RNA turnover. J. Biol. Chem. 238 (2008) 17158-17167
11. Deutscher M.P., and Reuven N.B. Enzymatic basis for hydrolytic versus phosphorolytic mRNA degradation in Escherichia coli and Bacillus subtilis. Proc. Natl. Acad. Sci. USA 88 (1991) 3277-3280
12. Dubnau D., and Lovett Jr. C.M. Transformation and recombination. In: Hoch J.A., Losick R., and Sonenshein A.L. (Eds). Bacillus subtilis and its relatives: From genes to cells (2001), American Society for Microbiology, Washington, DC 453-471
13. Even S., Pellegrini O., Zig L., Labas V., Vinh J., Brechemmier-Baey D., and Putzer H. Ribonucleases J1 and J2: Two novel endoribonucleases in B. subtilis with functional homology to E. coli RNase E. Nucleic Acids Res. 33 (2005) 2141-2152
14. Gros F., Hiatt H., Gilbert W., Kurland C.G., Risebrough R.W., and Watson J.D. Unstable ribonucleic acid revealed by pulse labelling of Escherichia coli. Nature 190 (1961) 581-585
15. Herskovitz M.A., and Bechhofer D.H. Endoribonuclease RNase III is essential in Bacillus subtilis. Mol. Microbiol. 38 (2000) 1027-1033
16. Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390 (1997) 249-256
17. Kushner S.R. mRNA decay in Escherichia coli comes of age. J. Bacteriol. 184 (2002) 4658-4665
18. Luttinger A., Hahn J., and Dubnau D. Polynucleotide phosphorylase is necessary for competence development in Bacillus subtilis. Mol. Microbiol. 19 (1996) 343-356
19. Mathy N., Benard L., Pellegrini O., Daou R., Wen T., and Condon C. 5′ to 3′-exoribonuclease activity in bacteria: Role of RNase J1 in rRNA maturation and 5′-stability of mRNA. Cell 129 (2007) 681-692
20. Mitra S., Hue K., and Bechhofer D.H. In vitro processing activity of Bacillus subtilis polynucleotide phosphorylase. Mol. Microbiol. 19 (1996) 329-342
21. Oussenko I.A., Abe T., Ujiie H., Muto A., and Bechhofer D.H. Participation of 3′ to 5′-exoribonucleases in the turnover of Bacillus subtilis mRNA. J. Bacteriol. 187 (2005) 2758-2767
22. Oussenko I.A., and Bechhofer D.H. The yvaJ gene of Bacillus subtilis encodes a 3′ to 5′-exoribonuclease and is not essential in a strain lacking polynucleotide phosphorylase. J. Bacteriol. 182 (2000) 2639-2642
23. Oussenko I.A., Sanchez R., and Bechhofer D.H. Bacillus subtilis YhaM, a member of a new family of 3′ to 5′-exonucleases in gram-positive bacteria. J. Bacteriol. 184 (2002) 6250-6259
24. Oussenko I.A., Sanchez R., and Bechhofer D.H. Bacillus subtilis YhcR, a high-molecular-weight, nonspecific endonuclease with a unique domain structure. J. Bacteriol. 186 (2004) 5376-5383
25. Petit M.-A., Dervyn E., Rose M., Entian K.-D., McGovern S., Ehrlich D.S., and Bruand C. PcrA is an essential DNA helicase of Bacillus subtilis fulfilling functions both in repair and rolling-circle replication. Mol. Microbiol. 29 (1998) 261-273
26. Piggot P.J., and Losick R. Sporulation genes and intercompartmental regulation. In: Hoch J.A., Losick R., and Sonenshein A.L. (Eds). Bacillus subtilis and its relatives: from genes to cells (2001), American Society for Microbiology, Washington, DC 483-517
27. Ulmanen I., Lundstrom K., Lehtovaara P., Sarvas M., Ruohonen M., and Palva I. Transcription and translation of foreign genes in Bacillus subtilis by the aid of a secretion vector. J. Bacteriol. 162 (1985) 176-182
28. Wang W., and Bechhofer D.H. Properties of a Bacillus subtilis polynucleotide phosphorylase deletion strain. J. Bacteriol. 178 (1996) 2375-2382
29. Wen T., Oussenko I.A., Pellegrini O., Bechhofer D.H., and Condon C. Ribonuclease PH plays a major role in the exonucleolytic maturation of CCA-containing tRNA precursors in Bacillus subtilis. Nucleic Acids Res. 33 (2005) 3636-3643
30. Yao S., Blaustein J.B., and Bechhofer D.H. Processing of Bacillus subtilis small cytoplasmic RNA: Evidence for an additional endonuclease cleavage site. Nucleic Acids Res. 35 (2007) 4464-4473