Ultra deep sequencing of Listeria monocytogenes sRNA transcriptome revealed new antisense RNAs

PLoS ONE

Volumn 9, Issue 2, 2014, Pages

  Behrens, Sebastian ^a,b   Widder, Stefanie ^a   Mannala, Gopala Krishna ^b   Qing, Xiaoxing ^b   Madhugiri, Ramakanth ^b   Kefer, Nathalie ^c,d   Mraheil, Mobarak Abu ^b   Rattei, Thomas ^a   Hain, Torsten ^b  

^a UNIVERSITY OF VIENNA   (Austria)

^b JUSTUS LIEBIG UNIVERSITY   (Germany)

^c Febit Biomed Gmbh   (Germany)

^d Life Technologies   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY RNA; TRANSCRIPTOME; TRANSFER RNA; BACTERIAL RNA; SMALL UNTRANSLATED RNA;

ARTICLE; BIOLOGICAL FUNCTIONS; CONTROLLED STUDY; EXTRACELLULAR SPACE; FUMC GENE; GENE; GENE CONTROL; GENE EXPRESSION; HIGH THROUGHPUT SEQUENCING; INTRACELLULAR SPACE; LISTERIA MONOCYTOGENES; NONHUMAN; NUCLEOTIDE SEQUENCE; PGI GENE; PURA GENE; RNA ANALYSIS; RNA SEQUENCE; ANIMAL; CELL LINE; CHEMISTRY; GENETICS; MACROPHAGE; MICROBIOLOGY; MOUSE; NORTHERN BLOTTING; PROCEDURES; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; TRANSCRIPTION INITIATION SITE;

ANIMALS; BLOTTING, NORTHERN; CELL LINE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LISTERIA MONOCYTOGENES; MACROPHAGES; MICE; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, ANTISENSE; RNA, BACTERIAL; RNA, SMALL UNTRANSLATED; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION INITIATION SITE; TRANSCRIPTOME;

EID: 84895468353     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0083979     Document Type: Article

References (39)

1. Fuchs TM, Eisenreich W, Kern T, Dandekar T (2012) Toward a Systemic Understanding of Listeria monocytogenes Metabolism during Infection. Front Microbiol 3: 23.
2. Mraheil MA, Billion A, Mohamed W, Mukherjee K, Kuenne C, et al. (2011) The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages. Nucleic Acids Res 39: 4235-4248.
3. Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H, et al. (2009) The Listeria transcriptional landscape from saprophytism to virulence. Nature 459: 950-956.
4. Wurtzel O, Sesto N, Mellin JR, Karunker I, Edelheit S, et al. (2012) Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Mol Syst Biol 8: 583.
5. Guell M, Yus E, Lluch-Senar M, Serrano L (2011) Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nat Rev Microbiol 9: 658-669.
6. Siezen RJ, Wilson G, Todt T (2010) Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays. Microb Biotechnol 3: 125-130.
7. Sorek R, Cossart P (2010) Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet 11: 9-16.
8. Gottesman S (2005) Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genet 21: 399-404.
9. Livny J, Waldor MK (2010) Mining regulatory 5′UTRs from cDNA deep sequencing datasets. Nucleic Acids Res 38: 1504-1514.
10. Storz G, Altuvia S, Wassarman KM (2005) An abundance of RNA regulators. Annu Rev Biochem 74: 199-217. (Pubitemid 40995506)
11. Waters LS, Storz G (2009) Regulatory RNAs in bacteria. Cell 136: 615-628.
12. Albrecht M, Sharma CM, Dittrich MT, Muller T, Reinhardt R, et al. (2011) The transcriptional landscape of Chlamydia pneumoniae. Genome Biol 12: R98.
13. Vogel J, Luisi BF (2011) Hfq and its constellation of RNA. Nat Rev Microbiol 9: 578-589.
14. Irnov I, Sharma CM, Vogel J, Winkler WC (2010) Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res 38: 6637-6651.
15. Pischimarov J, Kuenne C, Billion A, Hemberger J, Cemic F, et al. (2012) sRNAdb: a small non-coding RNA database for gram-positive bacteria. BMC Genomics 13: 384.
16. Camejo A, Buchrieser C, Couve E, Carvalho F, Reis O, et al. (2009) In vivo transcriptional profiling of Listeria monocytogenes and mutagenesis identify new virulence factors involved in infection. PLoS Pathog 5: e1000449.
17. Hain T, Ghai R, Billion A, Kuenne CT, Steinweg C, et al. (2012) Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. BMC Genomics 13: 144.
18. Mandin P, Repoila F, Vergassola M, Geissmann T, Cossart P (2007) Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets. Nucleic Acids Res 35: 962-974. (Pubitemid 46344721)
19. Milohanic E, Glaser P, Coppee JY, Frangeul L, Vega Y, et al. (2003) Transcriptome analysis of Listeria monocytogenes identifies three groups of genes differently regulated by PrfA. Mol Microbiol 47: 1613-1625. (Pubitemid 36363343)
20. Oliver HF, Orsi RH, Ponnala L, Keich U, Wang W, et al. (2009) Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs. BMC Genomics 10: 641.
21. Metzker ML (2010) Sequencing technologies - the next generation. Nat Rev Genet 11: 31-46.
22. Glaser P, Frangeul L, Buchrieser C, Rusniok C, Amend A, et al. (2001) Comparative genomics of Listeria species. Science 294: 849-852. (Pubitemid 33032102)
23. Chatterjee SS, Hossain H, Otten S, Kuenne C, Kuchmina K, et al. (2006) Intracellular gene expression profile of Listeria monocytogenes . Infect Immun 74: 1323-1338. (Pubitemid 43185572)
24. Basineni SR, Madhugiri R, Kolmsee T, Hengge R, Klug G (2009) The influence of Hfq and ribonucleases on the stability of the small non-coding RNA OxyS and its target rpoS in E. coli is growth phase dependent. RNA Biol 6: 584-594.
25. Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5: e11147.
26. Faith NG, Kim JW, Azizoglu R, Kathariou S, Czuprynski C (2012) Purine biosynthesis mutants (purA and purB) of serotype 4b Listeria monocytogenes are severely attenuated for systemic infection in intragastrically inoculated A/J Mice. Foodborne Pathog Dis 9: 480-486.
27. Schauer K, Geginat G, Liang C, Goebel W, Dandekar T, et al. (2010) Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling. BMC Genomics 11: 573.
28. Loessner MJ, Inman RB, Lauer P, Calendar R (2000) Complete nucleotide sequence, molecular analysis and genome structure of bacteriophage A118 of Listeria monocytogenes: implications for phage evolution. Mol Microbiol 35: 324-340. (Pubitemid 30055229)
29. Wagner EG, Simons RW (1994) Antisense RNA control in bacteria, phages, and plasmids. Annu Rev Microbiol 48: 713-742.
30. Mehta P, Goyal S, Wingreen NS (2008) A quantitative comparison of sRNA-based and protein-based gene regulation. Mol Syst Biol 4: 221.
31. Storz G, Vogel J, Wassarman KM (2011) Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 43: 880-891.
32. Xiao B, Li W, Guo G, Li B, Liu Z, et al. (2009) Identification of small noncoding RNAs in Helicobacter pylori by a bioinformatics-based approach. Curr Microbiol 58: 258-263.
33. Georg J, Voss B, Scholz I, Mitschke J, Wilde A, et al. (2009) Evidence for a major role of antisense RNAs in cyanobacterial gene regulation. Mol Syst Biol 5: 305.
34. Eisenreich W, Dandekar T, Heesemann J, Goebel W (2010) Carbon metabolism of intracellular bacterial pathogens and possible links to virulence. Nat Rev Microbiol 8: 401-412.
35. Huynen MA, Dandekar T, Bork P (1999) Variation and evolution of the citricacid cycle: a genomic perspective. Trends Microbiol 7: 281-291. (Pubitemid 29304564)
36. Chatterjee SS, Hossain H, Otten S, Kuenne C, Kuchmina K, et al. (2006) Intracellular gene expression profile of Listeria monocytogenes . Infect Immun 74: 1323-1338. (Pubitemid 43185572)
37. Garcia-del Portillo F, Calvo E, D'Orazio V, Pucciarelli MG (2011) Association of ActA to peptidoglycan revealed by cell wall proteomics of intracellular Listeria monocytogenes. J Biol Chem 286: 34675-34689.
38. Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, et al. (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464: 250-255.
39. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, et al. (2000) Artemis: sequence visualization and annotation. Bioinformatics 16: 944-945.