Molecular phenotyping of infection-associated small non-coding RNAs.
Infection is a complicated balance, with both pathogen and host struggling to tilt the result in their favour. Bacterial infection biology has relied on forward genetics for many of its advances, defining phenotype in terms of replication in model systems. However, many known virulence factors fail to produce robust phenotypes, particularly in the systems most amenable to genetic manipulation, such as cell-culture models. This has particularly been limiting for the study of the bacterial regulatory small RNAs (sRNAs) in infection. We argue that new sequencing-based technologies can work around this problem by providing a 'molecular phenotype', defined in terms of the specific transcriptional dysregulation in the infection system induced by gene deletion. We illustrate this using the example of our recent study of the PinT sRNA using dual RNA-seq, that is, simultaneous RNA sequencing of host and pathogen during infection. We additionally discuss how other high-throughput technologies, in particular genetic interaction mapping using transposon insertion sequencing, may be used to further dissect molecular phenotypes. We propose a strategy for how high-throughput technologies can be integrated in the study of non-coding regulators as well as bacterial virulence factors, enhancing our ability to rapidly generate hypotheses with regards to their function.This article is part of the themed issue 'The new bacteriology'.
RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany.
Lars
0000-0003-4732-2667
L
Barquist
RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany.
Alexander J
0000-0003-3236-0169
AJ
Westermann
RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany Research Centre for Infectious Diseases (ZINF), University of Würzburg, 97070 Würzburg, Germany joerg.vogel@uni-wuerzburg.de.
Jörg
0000-0003-2220-1404
J
Vogel
D002874:Chromosome Mapping / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012329:RNA, Bacterial / Q000235:genetics*; D058727:RNA, Small Untranslated / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
D012329:RNA, Bacterial; D058727:RNA, Small Untranslated
PinT; Tn-seq; dual RNA-seq; host–pathogen interaction; infection; small non-coding RNA
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