An effort to make sense of antisense transcription in bacteria

RNA Biology

Volumn 9, Issue 8, 2012, Pages 1039-1044

  Lasa, Iñigo ^a   Toledo Arana, Alejandro ^a   Gingeras, Thomas R ^b  

^a INSTITUTO DE AGROBIOTECNOLOGÍA   (Spain)

^b Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

Bacteria; Overlapping transcription; RNA processing; RNase III; Transcriptome

Indexed keywords

COMPLEMENTARY RNA; DNA DIRECTED DNA POLYMERASE; RIBONUCLEASE III;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ANABAENA; BACILLUS SUBTILIS; BACTERIAL CELL; BACTERIAL GENETICS; ENTEROCOCCUS FAECALIS; ENZYME ACTIVITY; GENE CONTROL; GENETIC TRANSCRIPTION; HELICOBACTER PYLORI; LISTERIA MONOCYTOGENES; NONHUMAN; OPERON; REVIEW; RNA DEGRADATION; RNA STABILITY; SALMONELLA ENTERICA; STAPHYLOCOCCUS AUREUS; SYNECHOCYSTIS; TRANSCRIPTION INITIATION;

BACTERIA (MICROORGANISMS); POSIBACTERIA; STAPHYLOCOCCUS AUREUS;

EID: 84866623270     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.21167     Document Type: Review

References (39)

1. Güell M, van Noort V, Yus E, Chen W-H, Leigh-Bell J, Michalodimitrakis K, et al. Transcriptome complexity in a genome-reduced bacterium. Science 2009; 326:1268-71; PMID:19965477; http://dx.doi.org/10.1126/ science.1176951.
2. Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, et al. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 2010; 464:250-5; PMID:20164839; http://dx.doi.org/10.1038/nature08756.
3. Wurtzel O, Sapra R, Chen F, Zhu Y, Simmons BA, Sorek R. A single-base resolution map of an archaeal transcriptome. Genome Res 2010; 20:133-41; PMID:19884261; http://dx.doi.org/10.1101/gr.100396.109.
4. Nicolas P, Mäder U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, et al. Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 2012; 335:1103-6; PMID:22383849; http://dx.doi.org/10.1126/science.1206848.
5. Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, et al. Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS One 2009; 4:e7526; PMID:19838305; http://dx.doi.org/10.1371/journal.pone.0007526.
6. Dornenburg JE, Devita AM, Palumbo MJ, Wade JT. Widespread antisense transcription in Escherichia coli. MBio 2010; 1; PMID:20689751; http://dx.doi.org/10.1128/mBio.00024-10.
7. Filiatrault MJ, Stodghill PV, Bronstein PA, Moll S, Lindeberg M, Grills G, et al. Transcriptome analysis of Pseudomonas syringae identifies new genes, non-coding RNAs, and antisense activity. J Bacteriol 2010; 192:2359-72; PMID:20190049; http://dx.doi.org/10.1128/JB.01445-09.
8. Vijayan V, Jain IH, O'Shea EK. A high resolution map of a cyanobacterial transcriptome. Genome Biol 2011; 12:R47; PMID:21612627; http://dx.doi.org/10. 1186/gb-2011-12-5-r47.
9. Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J, et al. Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res 2012; 40:2020-31; PMID:22080557; http://dx.doi.org/10.1093/nar/gkr904.
10. Mitschke J, Georg J, Scholz I, Sharma CM, Dienst D, Bantscheff J, et al. An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci U S A 2011; 108:2124-9; PMID:21245330; http://dx.doi.org/10.1073/pnas.1015154108.
11. Mitschke J, Vioque A, Haas F, Hess WR, Muro-Pastor AM. Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120. Proc Natl Acad Sci U S A 2011; 108:20130-5; PMID:22135468; http://dx.doi.org/10.1073/pnas.1112724108.
12. Lasa I, Toledo-Arana A, Dobin A, Villanueva M, de los Mozos IR, Vergara-Irigaray M, et al. Genomewide antisense transcription drives mRNA processing in bacteria. Proc Natl Acad Sci U S A 2011; 108:20172-7; PMID:22123973; http://dx.doi.org/10.1073/pnas.1113521108.
13. Wilms I, Overlöper A, Nowrousian M, Sharma CM, Narberhaus F. Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens. RNA Biol 2012; 9:9; PMID:22336765; http://dx.doi.org/10.4161/rna.17212.
14. Høvik H, Yu W-H, Olsen I, Chen T. Comprehensive transcriptome analysis of the periodontopathogenic bacterium Porphyromonas gingivalis W83. J Bacteriol 2012; 194:100-14; PMID:22037400; http://dx.doi.org/10.1128/JB.06385- 11.
15. Georg J, Voss B, Scholz I, Mitschke J, Wilde A, Hess WR. Evidence for a major role of antisense RNAs in cyanobacterial gene regulation. Mol Syst Biol 2009; 5:305; PMID:19756044; http://dx.doi.org/10.1038/msb.2009.63.
16. Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H, Balestrino D, et al. The Listeria transcriptional landscape from saprophytism to virulence. Nature 2009; 459:950-6; PMID:19448609; http://dx.doi.org/10.1038/ nature08080.
17. Johnson JM, Edwards S, Shoemaker D, Schadt EE. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet 2005; 21:93-102; PMID:15661355; http://dx.doi.org/10.1016/j.tig. 2004.12.009.
18. Perocchi F, Xu Z, Clauder-Münster S, Steinmetz LM. Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res 2007; 35:e128; PMID:17897965; http://dx.doi.org/10.1093/nar/ gkm683.
19. Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, Dus M, et al. An endogenous small interfering RNA pathway in Drosophila. Nature 2008; 453:798-802; PMID:18463631; http://dx.doi.org/10.1038/nature07007.
20. Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, et al. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 2009; 37:e123; PMID:19620212; http://dx.doi.org/10.1093/ nar/gkp596.
21. Arraiano CM, Andrade JM, Domingues S, Guinote IB, Malecki M, Matos RG, et al. The critical role of RNA processing and degradation in the control of gene expression. FEMS Microbiol Rev 2010; 34:883-923; PMID:20659169.
22. Carpousis AJ. The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annu Rev Microbiol 2007; 61:71-87; PMID:17447862; http://dx.doi.org/10.1146/annurev.micro.61.080706.093440.
23. Condon C. Maturation and degradation of RNA in bacteria. Curr Opin Microbiol 2007; 10:271- 8; PMID:17560162; http://dx.doi.org/10.1016/j.mib.2007. 05.008.
24. Krinke L, Wulff DL. RNase III-dependent hydrolysis of lambda cII-O gene mRNA mediated by lambda OOP antisense RNA. Genes Dev 1990; 4(12A):2223-33; PMID:2148537; http://dx.doi.org/10.1101/gad.4.12a.2223.
25. Lee E-J, Groisman EA. An antisense RNA that governs the expression kinetics of a multifunctional virulence gene. Mol Microbiol 2010; 76:1020-33; PMID:20398218; http://dx.doi.org/10.1111/j.1365-2958.2010.07161.x.
26. Storz G, Vogel J, Wassarman KM. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 2011; 43:880-91; PMID:21925377; http://dx.doi.org/10.1016/j.molcel.2011.08.022.
27. Stazic D, Lindell D, Steglich C. Antisense RNA protects mRNA from RNase E degradation by RNA-RNA duplex formation during phage infection. Nucleic Acids Res 2011; 39:4890-9; PMID:21325266; http://dx.doi.org/10.1093/nar/gkr037.
28. Kawano M, Aravind L, Storz G. An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin. Mol Microbiol 2007; 64:738-54; PMID:17462020; http://dx.doi.org/10.1111/j.1365-2958.2007.05688.x.
29. Dubnau D, Losick R. Bistability in bacteria. Mol Microbiol 2006; 61:564-72; PMID:16879639; http://dx.doi.org/10.1111/j.1365-2958.2006.05249.x.
30. Lawrence JG. Gene organization: selection, selfishness, and serendipity. Annu Rev Microbiol 2003; 57:419-40; PMID:14527286; http://dx.doi.org/10.1146/ annurev.micro.57.030502.090816.
31. Filipowicz W, Bhattacharyya SN, Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 2008; 9:102-14; PMID:18197166; http://dx.doi.org/10.1038/nrg2290.
32. Moazed D. Small RNAs in transcriptional gene silencing and genome defence. Nature 2009; 457:413-20; PMID:19158787; http://dx.doi.org/10.1038/ nature07756.
33. Cernilogar FM, Onorati MC, Kothe GO, Burroughs AM, Parsi KM, Breiling A, et al. Chromatinassociated RNA interference components contribute to transcriptional regulation in Drosophila. Nature 2011; 480:391-5; PMID:22056986; http://dx.doi.org/10.1038/nature10492.
34. Nakama M, Kawakami K, Kajitani T, Urano T, Murakami Y. DNA-RNA hybrid formation mediates RNAi-directed heterochromatin formation. Genes Cells 2012; 17:218-33; PMID:22280061; http://dx.doi.org/10.1111/j.1365-2443.2012.01583.x.
35. Pandey SP, Minesinger BK, Kumar J, Walker GC. A highly conserved protein of unknown function in Sinorhizobium meliloti affects sRNA regulation similar to Hfq. Nucleic Acids Res 2011; 39:4691-708; PMID:21325267; http://dx.doi.org/10. 1093/nar/gkr060.
36. Davies BW, Köhrer C, Jacob AI, Simmons LA, Zhu J, Aleman LM, et al. Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing. Mol Microbiol 2010; 78:506-18; PMID:20807199; http://dx.doi.org/10.1111/j.1365- 2958.2010.07351.x.
37. Shearwin KE, Callen BP, Egan JB. Transcriptional interference - a crash course. Trends Genet 2005; 21:339-45; PMID:15922833; http://dx.doi.org/10.1016/ j.tig.2005.04.009.
38. Thomason MK, Storz G. Bacterial antisense RNAs: how many are there, and what are they doing? Annu Rev Genet 2010; 44:167-88; PMID:20707673; http://dx.doi.org/10.1146/annurev-genet-102209-163523.
39. Georg J, Hess WR. cis-antisense RNA, another level of gene regulation in bacteria. Microbiol Mol Biol Rev 2011; 75:286-300; PMID:21646430; http://dx.doi.org/10.1128/MMBR.00032-10.