Bacillus subtilis possesses three essential enzymes thought to be involved in mRNA decay to varying degrees, namely RNase Y, RNase J1, and RNase III. Using recently developed high-resolution tiling arrays, we examined the effect of depletion of each of these enzymes on RNA abundance over the whole genome. The data are consistent with a model in which the degradation of a significant number of transcripts is dependent on endonucleolytic cleavage by RNase Y, followed by degradation of the downstream fragment by the 5′–3′ exoribonuclease RNase J1. However, many full-size transcripts also accumulate under conditions of RNase J1 insufficiency, compatible with a model whereby RNase J1 degrades transcripts either directly from the 5′ end or very close to it. Although the abundance of a large number of transcripts was altered by depletion of RNase III, this appears to result primarily from indirect transcriptional effects. Lastly, RNase depletion led to the stabilization of many low-abundance potential regulatory RNAs, both in intergenic regions and in the antisense orientation to known transcripts.
Vyšlo v časopise: Three Essential Ribonucleases—RNase Y, J1, and III—Control the Abundance of a Majority of mRNAs. PLoS Genet 8(3): e32767. doi:10.1371/journal.pgen.1002520 Kategorie: Research Article prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1002520
1. CarpousisAJLuisiBFMcDowallKJ 2009 Endonucleolytic initiation of mRNA decay in Escherichia coli. Prog Mol Biol Transl Sci 85 91 135
2. GarreySMMackieGA 2011 Roles of the 5′-phosphate sensor domain in RNase E. Mol Microbiol 80 1613 1624
3. DeanaACelesnikHBelascoJG 2008 The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal. Nature 451 355 358
4. HouseleyJTollerveyD 2009 The many pathways of RNA degradation. Cell 136 763 776
5. TomeckiRDziembowskiA 2010 Novel endoribonucleases as central players in various pathways of eukaryotic RNA metabolism. RNA 16 1692 1724
6. CondonC 2010 What is the role of RNase J in mRNA turnover? RNA Biol 7 316 321
7. CommichauFMRotheFMHerzbergCWagnerEHellwigD 2009 Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing. Mol Cell Proteomics 8 1350 1360
8. ShahbabianKJamalliAZigLPutzerH 2009 RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis. EMBO J 28 3523 3533
9. YaoSBechhoferDH 2010 Initiation of decay of Bacillus subtilis rpsO mRNA by endoribonuclease RNase Y. J Bacteriol 192 3279 3286
10. DiMariJFBechhoferDH 1993 Initiation of mRNA decay in Bacillus subtilis. Mol Microbiol 7 705 717
11. OguroAKakeshitaHNakamuraKYamaneKWangW 1998 Bacillus subtilis RNase III cleaves both 5′ - and 3′-sites of the small cytoplasmic RNA precursor. J Biol Chem 273 19542 19547
12. DeutscherMPReuvenNB 1991 Enzymatic basis for hydrolytic versus phosphorolytic mRNA degradation in Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci U S A 88 3277 3280
13. DeikusGBabitzkePBechhoferDH 2004 Recycling of a regulatory protein by degradation of the RNA to which it binds. Proc Natl Acad Sci U S A 101 2747 2751
14. MathyNBenardLPellegriniODaouRWenT 2007 5′-to-3′ exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5′ stability of mRNA. Cell 129 681 692
15. MathyNHebertAMerveletPBenardLDorleansA 2010 Bacillus subtilis ribonucleases J1 and J2 form a complex with altered enzyme behaviour. Mol Microbiol 75 489 498
16. RichardsJLiuQPellegriniOCelesnikHYaoS 2011 An RNA pyrophosphohydrolase triggers 5′-exonucleolytic degradation of mRNA in Bacillus subtilis. Mol Cell 43 940 949
17. GopalakrishnaYSarkarN 1982 Characterization of polyadenylate-containing ribonucleic acid from Bacillus subtilis. Biochemistry 21 2724 2729
18. Campos-GuillenJBralleyPJonesGHBechhoferDHOlmedo-AlvarezG 2005 Addition of poly(A) and heteropolymeric 3′ ends in Bacillus subtilis wild-type and polynucleotide phosphorylase-deficient strains. J Bacteriol 187 4698 4706
19. MaderUZigLKretschmerJHomuthGPutzerH 2008 mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene expression on a global scale. Mol Microbiol 70 183 196
20. RasmussenSNielsenHBJarmerH 2009 The transcriptionally active regions in the genome of Bacillus subtilis. Mol Microbiol 73 1043 1057
21. BrittonRAWenTSchaeferLPellegriniOUickerWC 2007 Maturation of the 5′ end of Bacillus subtilis 16S rRNA by the essential ribonuclease YkqC/RNase J1. Mol Microbiol 63 127 138
22. DiethmaierCPietackNGunkaKWredeCLehnik-HabrinkM 2011 A novel factor controlling bistability in Bacillus subtilis: the YmdB protein affects flagellin expression and biofilm formation. J Bacteriol 193 5997 6007
23. SteadMBMarshburnSMohantyBKMitraJCastilloLP 2011 Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays. Nucleic Acids Res 39 3188 3203
24. Lehnik-HabrinkMSchafferMMaderUDiethmaierCHerzbergC 2011 RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y. Mol Microbiol 81 1459 1473
25. IrnovISharmaCMVogelJWinklerWC 2010 Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res 38 6637 6651
26. AdlerEBarakIStragierP 2001 Bacillus subtilis locus encoding a killer protein and its antidote. J Bacteriol 183 3574 3581
27. BrillJHoffmannTPutzerHBremerE 2011 T-box-mediated control of the anabolic proline biosynthetic genes of Bacillus subtilis. Microbiology 157 977 987
28. KotschwarMDiermeierSSchumannW 2004 The yjoB gene of Bacillus subtilis encodes a protein that is a novel member of the AAA family. FEMS Microbiol Lett 230 241 249
29. ButcherBGHelmannJD 2006 Identification of Bacillus subtilis sigma-dependent genes that provide intrinsic resistance to antimicrobial compounds produced by Bacilli. Mol Microbiol 60 765 782
30. CaoMBernatBAWangZArmstrongRNHelmannJD 2001 FosB, a cysteine-dependent fosfomycin resistance protein under the control of sigma(W), an extracytoplasmic-function sigma factor in Bacillus subtilis. J Bacteriol 183 2380 2383
31. CaoMKobelPAMorshediMMWuMFPaddonC 2002 Defining the Bacillus subtilis sigma(W) regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches. J Mol Biol 316 443 457
32. SierroNMakitaYde HoonMNakaiK 2008 DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 36 D93 96
33. DeikusGBechhoferDH 2011 5′-end-independent RNase J1 endonuclease cleavage of a Bacillus subtilis model RNA. J Biol Chem 286 34932 34940
34. KolbFAEngdahlHMSlagter-JagerJGEhresmannBEhresmannC 2000 Progression of a loop-loop complex to a four-way junction is crucial for the activity of a regulatory antisense RNA. EMBO J 19 5905 5915
35. KolbFAWesthofEEhresmannBEhresmannCWagnerEG 2001 Four-way junctions in antisense RNA-mRNA complexes involved in plasmid replication control: a common theme? J Mol Biol 309 605 614
36. StragierPBonamyCKarmazyn-CampelliC 1988 Processing of a sporulation sigma factor in Bacillus subtilis: how morphological structure could control gene expression. Cell 52 697 704
37. Guerout-FleuryAMFrandsenNStragierP 1996 Plasmids for ectopic integration in Bacillus subtilis. Gene 180 57 61
38. HerskovitzMABechhoferDH 2000 Endoribonuclease RNase III is essential in Bacillus subtilis. Mol Microbiol 38 1027 1033
39. BechhoferDHOussenkoIADeikusGYaoSMathyN 2008 Analysis of mRNA decay in Bacillus subtilis. Methods Enzymol 447 259 276
40. NicolasPLeducARobinSRasmussenSJarmerH 2009 Transcriptional landscape estimation from tiling array data using a model of signal shift and drift. Bioinformatics 25 2341 2347
41. CalzaSValentiniDPawitanY 2008 Normalization of oligonucleotide arrays based on the least-variant set of genes. BMC Bioinformatics 9 140
42. BenjaminiYHochbergY 1995 Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B 57 289 300
43. HoebekeMNicolasPBessieresP 2003 MuGeN: simultaneous exploration of multiple genomes and computer analysis results. Bioinformatics 19 859 864
Zvýšte si kvalifikáciu online z pohodlia domova
Nemáte účet? Registrujte sa
Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.
