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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
BMC Genomics. 2009; 10: 641.
Published online Dec 30, 2009. doi:  10.1186/1471-2164-10-641
PMCID: PMC2813243
Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
Haley F Oliver,#1 Renato H Orsi,#1 Lalit Ponnala,2 Uri Keich,3,4 Wei Wang,5 Qi Sun,2 Samuel W Cartinhour,6,7 Melanie J Filiatrault,6,7 Martin Wiedmann,1 and Kathryn J Boorcorresponding author1
1Department of Food Science, Cornell University, Ithaca, NY, USA
2Computational Biology Service Unit, Cornell University, Ithaca, NY, USA
3Department of Computer Science, Cornell University, Ithaca, NY, USA
4School of Mathematics and Statistics, University of Sydney, NSW, Australia
5Life Sciences Core Laboratories Center, Cornell University, Ithaca, NY, USA
6United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA
7Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
corresponding authorCorresponding author.
#Contributed equally.
Haley F Oliver: haf9/at/; Renato H Orsi: rho2/at/; Lalit Ponnala: ponnala/at/; Uri Keich: uri/at/; Wei Wang: ww77/at/; Qi Sun: qisun/at/; Samuel W Cartinhour: sam.cartinhour/at/; Melanie J Filiatrault: melanie.filiatrault/at/; Martin Wiedmann: mw16/at/; Kathryn J Boor: kjb4/at/
Received June 1, 2009; Accepted December 30, 2009.
Identification of specific genes and gene expression patterns important for bacterial survival, transmission and pathogenesis is critically needed to enable development of more effective pathogen control strategies. The stationary phase stress response transcriptome, including many σB-dependent genes, was defined for the human bacterial pathogen Listeria monocytogenes using RNA sequencing (RNA-Seq) with the Illumina Genome Analyzer. Specifically, bacterial transcriptomes were compared between stationary phase cells of L. monocytogenes 10403S and an otherwise isogenic ΔsigB mutant, which does not express the alternative σ factor σB, a major regulator of genes contributing to stress response, including stresses encountered upon entry into stationary phase.
Overall, 83% of all L. monocytogenes genes were transcribed in stationary phase cells; 42% of currently annotated L. monocytogenes genes showed medium to high transcript levels under these conditions. A total of 96 genes had significantly higher transcript levels in 10403S than in ΔsigB, indicating σB-dependent transcription of these genes. RNA-Seq analyses indicate that a total of 67 noncoding RNA molecules (ncRNAs) are transcribed in stationary phase L. monocytogenes, including 7 previously unrecognized putative ncRNAs. Application of a dynamically trained Hidden Markov Model, in combination with RNA-Seq data, identified 65 putative σB promoters upstream of 82 of the 96 σB-dependent genes and upstream of the one σB-dependent ncRNA. The RNA-Seq data also enabled annotation of putative operons as well as visualization of 5'- and 3'-UTR regions.
The results from these studies provide powerful evidence that RNA-Seq data combined with appropriate bioinformatics tools allow quantitative characterization of prokaryotic transcriptomes, thus providing exciting new strategies for exploring transcriptional regulatory networks in bacteria.
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