Bacillus subtilis RNase Y Activity In Vivo Analysed by Tiling Microarrays

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Laalami, Soumaya ^a   Bessières, Philippe ^b   Rocca, Anna ^a   Zig, Léna ^a   Nicolas, Pierre ^b   Putzer, Harald ^a  

^a UNIVERSITÉ PARIS DESCARTES   (France)

^b INRA Institut National de la Recherche Agronomique   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RIBONUCLEASE; RIBONUCLEASE Y; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

ACCURACY; ARTICLE; BACILLUS SUBTILIS; ENZYME ACTIVITY; ENZYME DEFICIENCY; GENETIC TRANSCRIPTION; GENOME ANALYSIS; IN VIVO STUDY; MICROARRAY ANALYSIS; NONHUMAN; REPRODUCIBILITY; RNA CLEAVAGE; TILING MICROARRAY; UPREGULATION;

BACILLUS SUBTILIS; ENDORIBONUCLEASES; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; RIBONUCLEASES; RNA STABILITY; RNA, MESSENGER; RNA, UNTRANSLATED;

BACILLUS SUBTILIS; ESCHERICHIA COLI;

EID: 84872244472     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0054062     Document Type: Article

References (47)

1. Carpousis AJ, Luisi BF, McDowall KJ, (2009) Endonucleolytic initiation of mRNA decay in Escherichia coli. Prog Mol Biol Transl Sci 85: 91-135.
2. Garrey SM, Mackie GA, (2011) Roles of the 5′-phosphate sensor domain in RNase E. Mol Microbiol. 80: 1613-1624.
3. Kime L, Jourdan SS, Stead JA, Hidalgo-Sastre A, McDowall KJ, (2010) Rapid cleavage of RNA by RNase E in the absence of 5′ monophosphate stimulation. Mol Microbiol 76: 590-604.
4. Deana A, Celesnik H, Belasco JG, (2008) The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal. Nature 451: 355-358.
5. Even S, Pellegrini O, Zig L, Labas V, Vinh J, et al. (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.
6. Mathy N, Benard L, Pellegrini O, Daou R, Wen T, et al. (2007) 5′-to-3′ Exoribonuclease Activity in Bacteria: Role of RNase J1 in rRNA Maturation and 5′ Stability of mRNA. Cell 129: 681-692.
7. 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.
8. Richards J, Liu Q, Pellegrini O, Celesnik H, Yao S, et al. (2011) An RNA pyrophosphohydrolase triggers 5′-exonucleolytic degradation of mRNA in Bacillus subtilis. Mol Cell 43: 940-949.
9. Mathy N, Hebert A, Mervelet P, Benard L, Dorleans A, et al. (2010) Bacillus subtilis ribonucleases J1 and J2 form a complex with altered enzyme behaviour. Mol Microbiol 75: 489-498.
10. Mäder U, Zig L, Kretschmer J, Homuth G, Putzer H, (2008) mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene expression on a global scale. Mol Microbiol 70: 183-196.
11. Durand S, Gilet L, Bessieres P, Nicolas P, Condon C, (2012) Three Essential Ribonucleases-RNase Y, J1, and III-Control the Abundance of a Majority of Bacillus subtilis mRNAs. PLoS Genet 8: e1002520.
12. Shahbabian K, Jamalli A, Zig L, Putzer H, (2009) RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis. EMBO J 28: 3523-3533.
13. Hunt A, Rawlins JP, Thomaides HB, Errington J, (2006) Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology 152: 2895-2907.
14. Commichau FM, Rothe FM, Herzberg C, Wagner E, Hellwig D, et al. (2009) Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing. Mol Cell Proteomics 8: 1350-1360.
15. Lehnik-Habrink M, Newman J, Rothe FM, Solovyova AS, Rodrigues C, et al. (2011) RNase Y in Bacillus subtilis: a Natively disordered protein that is the functional equivalent of RNase E from Escherichia coli. J Bacteriol 193: 5431-5441.
16. Newman JA, Hewitt L, Rodrigues C, Solovyova AS, Harwood CR, et al. (2012) Dissection of the network of interactions that links RNA processing with glycolysis in the Bacillus subtilis degradosome. J Mol Biol 416: 121-136.
17. Laalami S, Putzer H, (2011) mRNA degradation and maturation in prokaryotes: the global players. Biomolecular Concepts 2: 491-506.
18. Naville M, Gautheret D, (2010) Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation. Genome Biol 11: R97.
19. Yao S, Bechhofer DH, (2010) Initiation of decay of Bacillus subtilis rpsO mRNA by endoribonuclease RNase Y. J Bacteriol. 192: 3279-3286.
20. Bruscella P, Shahbabian K, Laalami S, Putzer H, (2011) RNase Y is responsible for uncoupling the expression of translation factor IF3 from that of the ribosomal proteins L35 and L20 in Bacillus subtilis. Mol Microbiol 81: 1526-1541.
21. Marincola G, Schafer T, Behler J, Bernhardt J, Ohlsen K, et al. (2012) RNase Y of Staphylococcus aureus and its role in the activation of virulence genes. Mol Microbiol 85: 817-832.
22. Rasmussen S, Nielsen HB, Jarmer H, (2009) The transcriptionally active regions in the genome of Bacillus subtilis. Mol Microbiol 73: 1043-1057.
23. Lehnik-Habrink M, Schaffer M, Mader U, Diethmaier C, Herzberg C, et al. (2011) RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y. Mol Microbiol. 81: 1459-1473.
24. Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, et al. (2011) A novel factor controlling bistability in Bacillus subtilis: the YmdB protein affects flagellin expression and biofilm formation. J Bacteriol 193: 5997-6007.
25. Petit MA, Dervyn E, Rose M, Entian KD, McGovern S, et al. (1998) PcrA is an essential DNA helicase of Bacillus subtilis fulfilling functions both in repair and rolling-circle replication. Mol Microbiol 29: 261-273.
26. Antelmann H, Towe S, Albrecht D, Hecker M, (2007) The phosphorus source phytate changes the composition of the cell wall proteome in Bacillus subtilis. J Proteome Res 6: 897-903.
27. Tanner A, Bowater L, Fairhurst SA, Bornemann S, (2001) Oxalate decarboxylase requires manganese and dioxygen for activity. Overexpression and characterization of Bacillus subtilis YvrK and YoaN. J Biol Chem 276: 43627-43634.
28. MacLellan SR, Helmann JD, Antelmann H, (2009) The YvrI alternative sigma factor is essential for acid stress induction of oxalate decarboxylase in Bacillus subtilis. J Bacteriol 191: 931-939.
29. MacLellan SR, Wecke T, Helmann JD, (2008) A previously unidentified sigma factor and two accessory proteins regulate oxalate decarboxylase expression in Bacillus subtilis. Mol Microbiol 69: 954-967.
30. Irnov I, Sharma CM, Vogel J, Winkler WC, (2010) Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res 38: 6637-6651.
31. Nicolas P, Mader U, Dervyn E, Rochat T, Leduc A, et al. (2012) Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 335: 1103-1106.
32. Silvaggi JM, Perkins JB, Losick R, (2005) Small untranslated RNA antitoxin in Bacillus subtilis. J Bacteriol 187: 6641-6650.
33. Christensen QH, Martin N, Mansilla MC, de Mendoza D, Cronan JE, (2011) A novel amidotransferase required for lipoic acid cofactor assembly in Bacillus subtilis. Mol Microbiol 80: 350-363.
34. Guillouard I, Auger S, Hullo MF, Chetouani F, Danchin A, et al. (2002) Identification of Bacillus subtilis CysL, a regulator of the cysJI operon, which encodes sulfite reductase. J Bacteriol 184: 4681-4689.
35. Gaballa A, Wang T, Ye RW, Helmann JD, (2002) Functional analysis of the Bacillus subtilis Zur regulon. J Bacteriol 184: 6508-6514.
36. Bayle L, Chimalapati S, Schoehn G, Brown J, Vernet T, et al. (2011) Zinc uptake by Streptococcus pneumoniae depends on both AdcA and AdcAII and is essential for normal bacterial morphology and virulence. Mol Microbiol 82: 904-916.
37. Ogura Y, Imai Y, Ogasawara N, Moriya S, (2001) Autoregulation of the dnaA-dnaN operon and effects of DnaA protein levels on replication initiation in Bacillus subtilis. J Bacteriol 183: 3833-3841.
38. Bhavsar AP, Brown ED, (2006) Cell wall assembly in Bacillus subtilis: how spirals and spaces challenge paradigms. Mol Microbiol 60: 1077-1090.
39. Vollmer W, Blanot D, de Pedro MA, (2008) Peptidoglycan structure and architecture. FEMS Microbiol Rev 32: 149-167.
40. Spizizen J, (1958) Transformation of biochemically deficient strains of Bacillus subtilis by deoxyribonucleate. Proc Natl Acad Sci U S A 44: 407-408.
41. Nicolas P, Leduc A, Robin S, Rasmussen S, Jarmer H, et al. (2009) Transcriptional landscape estimation from tiling array data using a model of signal shift and drift. Bioinformatics 25: 2341-2347.
42. Strimmer K, (2008) A unified approach to false discovery rate estimation. BMC Bioinformatics 9: 303.
43. Putzer H, Gendron N, Grunberg-Manago M, (1992) Co-ordinate expression of the two threonyl-tRNA synthetase genes in Bacillus subtilis: control by transcriptional antitermination involving a conserved regulatory sequence. EMBO J 11: 3117-3127.
44. Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, et al. (2004) New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc Natl Acad Sci U S A 101: 6421-6426.
45. Ibrahim M, Nicolas P, Bessieres P, Bolotin A, Monnet V, et al. (2007) A genome-wide survey of short coding sequences in streptococci. Microbiology 153: 3631-3644.
46. Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, et al. (2011) Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res 39: D141-145.
47. Sterk P, Kersey PJ, Apweiler R, (2006) Genome reviews: Standardizing content and representation of information about complete genomes. OMICS 10: 114.