Sequencing Illustrates the Transcriptional Response of Legionella pneumophila during Infection and Identifies Seventy Novel Small Non-Coding RNAs

Second generation sequencing has prompted a number of groups to re-interrogate the transcriptomes of several bacterial and archaeal species. One of the central findings has been the identification of complex networks of small non-coding RNAs that play central roles in transcriptional regulation in a...

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Bibliographic Details
Published in:PloS one Vol. 6; no. 3; p. e17570
Main Authors: Weissenmayer, Barbara A., Prendergast, James G. D., Lohan, Amanda J., Loftus, Brendan J.
Format: Journal Article
Language:English
Published: United States Public Library of Science 03.03.2011
Public Library of Science (PLoS)
Subjects:
Acanthamoeba castellanii
Acanthamoeba castellanii - microbiology
Amoeba
Analysis
Antisense RNA
Bacteria
Base Sequence
Biology
Biomedical research
Biosynthesis
Cell survival
Conserved Sequence - genetics
Culture Media
DNA microarrays
Gene expression
Gene Expression Profiling
Gene Expression Regulation, Bacterial
Gene regulation
Genes, Bacterial - genetics
Genetic aspects
Genomes
Genomics
Growth conditions
Health aspects
Humans
Infection
Infections
Intracellular
Intracellular Space - microbiology
Legionella
Legionella pneumophila
Legionella pneumophila - genetics
Legionella pneumophila - growth & development
Legionnaires disease
Legionnaires' Disease - genetics
Legionnaires' Disease - microbiology
Legionnaires' disease bacterium
Macrophages
Medicine
Metabolism
Molecular Sequence Data
Motility
Nucleic Acid Conformation
Pathogens
Physiology
Proteins
Ribonucleic acid
RNA
RNA, Antisense - genetics
RNA, Bacterial - genetics
RNA, Small Untranslated - chemistry
RNA, Small Untranslated - genetics
Sequence Analysis, DNA - methods
Sequences
Signal transduction
Species Specificity
Strain
Studies
Time Factors
Transcription
Transcription (Genetics)
Transcription, Genetic
Up-Regulation - genetics
Vibrio cholerae
Vibrio harveyi
Ireland
ISSN:1932-6203, 1932-6203
Online Access:Get full text
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Summary:Second generation sequencing has prompted a number of groups to re-interrogate the transcriptomes of several bacterial and archaeal species. One of the central findings has been the identification of complex networks of small non-coding RNAs that play central roles in transcriptional regulation in all growth conditions and for the pathogen's interaction with and survival within host cells. Legionella pneumophila is a gram-negative facultative intracellular human pathogen with a distinct biphasic lifestyle. One of its primary environmental hosts in the free-living amoeba Acanthamoeba castellanii and its infection by L. pneumophila mimics that seen in human macrophages. Here we present analysis of strand specific sequencing of the transcriptional response of L. pneumophila during exponential and post-exponential broth growth and during the replicative and transmissive phase of infection inside A. castellanii. We extend previous microarray based studies as well as uncovering evidence of a complex regulatory architecture underpinned by numerous non-coding RNAs. Over seventy new non-coding RNAs could be identified; many of them appear to be strain specific and in configurations not previously reported. We discover a family of non-coding RNAs preferentially expressed during infection conditions and identify a second copy of 6S RNA in L. pneumophila. We show that the newly discovered putative 6S RNA as well as a number of other non-coding RNAs show evidence for antisense transcription. The nature and extent of the non-coding RNAs and their expression patterns suggests that these may well play central roles in the regulation of Legionella spp. specific traits and offer clues as to how L. pneumophila adapts to its intracellular niche. The expression profiles outlined in the study have been deposited into Genbank's Gene Expression Omnibus (GEO) database under the series accession GSE27232.
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Conceived and designed the experiments: BAW BJL. Performed the experiments: BAW AJL. Analyzed the data: BAW JGDP BJL. Contributed reagents/materials/analysis tools: JGDP AJL. Wrote the paper: BAW JGDP BJL. Critical reading of the manuscript: AJL.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0017570