E-MTAB-329 - non-coding RNA-Seq of Listeria monocytogenes from bacteria growing extracellularly and in macrophages

Status
Released on 21 July 2011, last updated on 25 January 2012
Organism
Listeria monocytogenes EGD-e
Samples (2)
Protocols (6)
Description
Small non-coding RNAs (sRNAs) are widespread effectors of post-transcriptional gene regulation in bacteria. Currently extensive information exists on the sRNAs of Listeria monocytogenes (Lm) expressed during growth in extracellular environments. We used deep sequencing of cDNAs obtained from fractioned RNA (<500nt) isolated from extracellularly growing bacteria and from Lm-infected macrophages to catalog the sRNA repertoire during intracellular bacterial growth. Here we report on the discovery of 150 regulatory RNAs of which 71 have never been previously described. A total of 29 regulatory RNAs, including small non-coding antisense RNAs, are specifically expressed intracellularly. We validated highly expressed sRNAs by Northern blotting and demonstrated by the construction and characterization of isogenic mutants of rli31, rli33-1 and rli50 for intracellular expressed sRNA candidates, that their expression is required for efficient growth of bacteria in macrophages. All three mutants were attenuated when assessed for growth in mouse and insect models of infection. Comparative genomic analysis revealed the presence of lineage specific sRNAs and the absence of sRNA loci in genomes of naturally-occurring infection-attenuated bacteria, with additional loss in non-pathogenic listerial genomes. Our analyses reveal extensive sRNA expression as an important feature of bacterial regulation during intracellular growth.
Experiment types
 RNA-seq of non coding RNA, growth condition, transcript identification
Contact
Citation
The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages. Mraheil MA, Billion A, Mohamed W, Mukherjee K, Kuenne C, Pischimarov J, Krawitz C, Retey J, Hartsch T, Chakraborty T, Hain T. Nucleic Acids Res 39(10):4235-4248 (2011), PMID:21278422
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-MTAB-329.idf.txt
Sample and data relationshipE-MTAB-329.sdrf.txt
Processed data (1)E-MTAB-329.processed.1.zip
Links