Abstract
The genus Yersinia includes three human pathogenic species, Yersinia pestis, the causative agent of the bubonic and pneumonic plague, and enteric pathogens Y. enterocolitica and Y. pseudotuberculosis that cause a number of gut-associated diseases. Over the past years a large repertoire of RNA-based regulatory systems has been discovered in these pathogens using different RNA-seq based approaches. Among them are several conserved or species-specific RNA-binding proteins, regulatory and sensory RNAs as well as various RNA-degrading enzymes. Many of them were shown to control the expression of important virulence-relevant factors and have a very strong impact on Yersinia virulence. The precise targets, the molecular mechanism and their role for Yersinia pathogenicity is only known for a small subset of identified genus- or species-specific RNA-based control elements. However, the ongoing development of new RNA-seq based methods and data analysis methods to investigate the synthesis, composition, translation, decay, and modification of RNAs in the bacterial cell will help us to generate a more comprehensive view of Yersinia RNA biology in the near future.
Highlights
For a long time it was thought that the RNA make-up and biology of bacteria is rather simple and constitutes mainly of mRNAs, tRNAs, and rRNAs and a few specific RNAs such as the tmRNA/SsrA of the ribosome rescue system
Multiple structured RNA elements have been identified in the 5′-untranslated regions of mRNAs sensing temperatures (RNA thermometers) or metabolites in order to modulate mRNA translation and/or stability (Kortmann and Narberhaus, 2012; Sherwood and Henkin, 2016; McCown et al, 2017)
We identified a massive remodeling of the CRP-controlled network in response to temperature and discovered CRP as a transcriptional master regulator of numerous conserved and newly identified non-coding RNAs which participate in this process (Nuss et al, 2015)
Summary
For a long time it was thought that the RNA make-up and biology of bacteria is rather simple and constitutes mainly of mRNAs, tRNAs, and rRNAs and a few specific RNAs such as the tmRNA/SsrA of the ribosome rescue system. Our findings suggest a life-style model for Y. pseudotuberculosis in which the bacteria change their gene expression profile from a virulent to an adapted phenotype, capable of persisting and spreading by fecal shedding This further illustrates that the developed Tissue Dual RNA-seq approach is well suited to decipher the complexity of hostpathogen interactions during different stages of the infection. Comparative analysis between the transcriptomes obtained with or without TEX treatment, called differential RNA-seq (dRNA-seq, Sharma and Vogel, 2014, Figures 1, 2), allowed global mapping of the transcription start sites of all transcripts This led to the identification of promoter elements and the definition of operon structures, and improved the annotation of the Yersinia genome and virulence plasmid (Nuss et al, 2015)
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