Genome-wide antisense transcription drives mRNA processing in bacteria

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 50, 2011, Pages 20172-20177

  Lasa, Iñigo ^a   Toledo Arana, Alejandro ^a   Dobin, Alexander ^b   Villanueva, Maite ^a   De Los Mozos, Igor Ruiz ^a   Vergara Irigaray, Marta ^a   Segura, Víctor ^c   Fagegaltier, Delphine ^b   Penadés, José R ^d   Valle, Jaione ^a   Solano, Cristina ^a   Gingeras, Thomas R ^b  

^a PUBLIC UNIVERSITY OF NAVARRE   (Spain)

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

^c UNIVERSITY OF NAVARRA   (Spain)

^d CSIC   (Spain)

Author keywords

Antisense RNA; MicroRNA; Overlapping transcription; Posttranscriptional regulation; RNA processing

Indexed keywords

COMPLEMENTARY RNA; MESSENGER RNA; RIBONUCLEASE III; RNA;

ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENE; ENTEROCOCCUS FAECALIS; ENZYME ACTIVITY; ENZYME SYNTHESIS; GENETIC ASSOCIATION; GRAM POSITIVE BACTERIUM; LISTERIA MONOCYTOGENES; NONHUMAN; PRIORITY JOURNAL; RNA PROCESSING; RNA SEQUENCE; STAPHYLOCOCCUS AUREUS;

GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; HUMANS; OPEN READING FRAMES; RIBONUCLEASE III; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, ANTISENSE; RNA, BACTERIAL; RNA, DOUBLE-STRANDED; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; SPECIES SPECIFICITY; STAPHYLOCOCCUS AUREUS; TRANSCRIPTION, GENETIC;

EID: 84055200530     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1113521108     Document Type: Article

References (37)

1. Selinger DW, et al. (2000) RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol 18:1262-1268.
2. Cho BK, et al. (2009) The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol 27:1043-1049.
3. Güell M, et al. (2009) Transcriptome complexity in a genome-reduced bacterium. Science 326:1268-1271.
4. Liu JM, et al. (2009) Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res 37:e46.
5. Toledo-Arana A, et al. (2009) The Listeria transcriptional landscape from saprophytism to virulence. Nature 459:950-956.
6. Mendoza-Vargas A, et al. (2009) Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS ONE 4:e7526.
7. Sharma CM, et al. (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464:250-255.
8. Filiatrault MJ, et al. (2010) Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity. J Bacteriol 192:2359-2372.
9. Wurtzel O, et al. (2010) A single-base resolution map of an archaeal transcriptome. Genome Res 20:133-141.
10. Beaume M, et al. (2010) Cartography of methicillin-resistant S. aureus transcripts: Detection, orientation and temporal expression during growth phase and stress conditions. PLoS ONE 5:e10725.
11. Jäger D, et al. (2009) Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability. Proc Natl Acad Sci USA 106:21878-21882.
12. Albrecht M, Sharma CM, Reinhardt R, Vogel J, Rudel T (2010) Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome. Nucleic Acids Res 38:868-877.
13. Martin J, Zhu W, Passalacqua KD, Bergman N, Borodovsky M (2010) Bacillus anthracis genome organization in light of whole transcriptome sequencing. BMC Bioinformatics 11(Suppl 3):S10.
14. Georg J, et al. (2009) Evidence for a major role of antisense RNAs in cyanobacterial gene regulation. Mol Syst Biol 5:305.
15. Mitschke J, et al. (2011) An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci USA 108:2124-2129.
16. Dornenburg JE, Devita AM, Palumbo MJ, Wade JT (2010) Widespread antisense transcription in Escherichia coli. MBio 1:e00024-10.
17. Rasmussen S, Nielsen HB, Jarmer H (2009) The transcriptionally active regions in the genome of Bacillus subtilis. Mol Microbiol 73:1043-1057.
18. Thomason MK, Storz G (2010) Bacterial antisense RNAs: How many are there, and what are they doing? Annu Rev Genet 44:167-188.
19. Wagner EG, Flärdh K (2002) Antisense RNAs everywhere? Trends Genet 18:223-226. (Pubitemid 34607127)
20. Brantl S (2007) Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr Opin Microbiol 10:102-109.
21. Faghihi MA, Wahlestedt C (2009) Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol 10:637-643.
22. Sorek R, Cossart P (2010) Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet 11:9-16.
23. Gripenland J, et al. (2010) RNAs: Regulators of bacterial virulence. Nat Rev Microbiol 8:857-866.
24. Toledo-Arana A, Solano C (2010) Deciphering the physiological blueprint of a bacterial cell: revelations of unanticipated complexity in transcriptome and proteome. Bioessays 32:461-467.
25. Klevens RM, et al.; Active Bacterial Core Surveillance of the Emerging Infections Program Network (2006) Community-associated methicillin-resistant Staphylococcus aureus and healthcare risk factors. Emerg Infect Dis 12:1991-1993. (Pubitemid 44904946)
26. Novick RP, et al. (1993) Synthesis of staphylococcal virulence factors is controlled by a regulatory RNA molecule. EMBO J 12:3967-3975. (Pubitemid 23282772)
27. Boisset S, et al. (2007) Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism. Genes Dev 21:1353-1366. (Pubitemid 46871039)
28. Pichon C, Felden B (2005) Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. Proc Natl Acad Sci USA 102:14249-14254. (Pubitemid 41429684)
29. Geissmann T, et al. (2009) A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Res 37:7239-7257.
30. Abu-Qatouseh LF, et al. (2010) Identification of differentially expressed small non-protein-coding RNAs in Staphylococcus aureus displaying both the normal and the small-colony variant phenotype. J Mol Med (Berl) 88:565-575.
31. Bohn C, et al. (2010) Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism. Nucleic Acids Res 38:6620-6636.
32. Anderson KL, Dunman PM (2009) Messenger RNA Turnover Processes in Escherichia coli, Bacillus subtilis, and Emerging Studies in Staphylococcus aureus. Int J Microbiol 2009:525491.
33. Parkhomchuk D, et al. (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37:e123.
34. Czech B, et al. (2008) An endogenous small interfering RNA pathway in Drosophila. Nature 453:798-802. (Pubitemid 351793787)
35. Nicol JW, Helt GA, Blanchard SG, Jr., Raja A, Loraine AE (2009) The Integrated Genome Browser: Free software for distribution and exploration of genome-scale datasets. Bioinformatics 25:2730-2731.
36. Huntzinger E, et al. (2005) Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression. EMBO J 24:824-835. (Pubitemid 40396111)
37. Fouquier d'Hérouel A, et al. (2011) A simple and efficient method to search for selected primary transcripts: Non-coding and antisense RNAs in the human pathogen Enterococcus faecalis. Nucleic Acids Res 39:e46.