RNA-based mechanisms of virulence control in Enterobacteriaceae

Abstract

Enteric pathogens of the family Enterobacteriaceae colonize various niches within animals and humans in which they compete with intestinal commensals and are attacked by the host immune system. To survive these hostile environments they possess complex, multilayer regulatory networks that coordinate the control of virulence factors, host-adapted metabolic functions and stress resistance. An important part of these intricate control networks are RNA-based control systems that enable the pathogen to fine-tune its responses. Recent next-generation sequencing approaches revealed a large repertoire of conserved and species-specific riboregulators, including numerous cis-and trans-acting non-coding RNAs, sensory RNA elements (RNA thermometers, riboswitches), regulatory RNA-binding proteins and RNA degrading enzymes which regulate colonization factors, toxins, host defense processes and virulence-relevant physiological and metabolic processes. All of which are important cues for pathogens to sense and respond to fluctuating conditions during the infection. This review covers infection-relevant riboregulators of E. coli, Salmonella, Shigella and Yersinia, highlights their versatile regulatory mechanisms, complex target regulons and functions, and discusses emerging topics and future challenges to fully understand and exploit RNA-based control to combat bacterial infections.

Pulmonary Surfactant Promotes Virulence Gene Expression and Biofilm Formation in Klebsiella pneumoniae

“…Transcription of the genes for the glycine betaine ABC transporter, proVWX (43), also increased 4-fold, suggesting that the lipid-rich environment of lung surfactant invokes osmotic stress in K. pneumoniae. Two tRNA nucleotide modification enzymes were also induced under these conditions, with queC and gidA exhibiting 5.4-and 2.8-fold increases in transcript abundance, respectively (44,45). Finally, transcription of genes associated with antibiotic resistance were also upregulated, including the genes for the 23S rRNA methylation enzyme (yfgB) and aminoglycoside 3=-phosphotransferase (strB) (2.6-to 2.7-fold increase) (46,47).…”

Genome-Wide Identification of Dickeya solani Transcriptional Units Up-Regulated in Response to Plant Tissues From a Crop-Host Solanum tuberosum and a Weed-Host Solanum dulcamara

“…Thus, the observed result in the GUS quantitative assay was based on enzyme accumulation during bacterial growth, while qRT-PCR result reflected an instantaneous bacterial state at a given assay time. Likewise, it is possible that many plant-regulated genes in D. solani are controlled by so-called short lived transcripts ( Heroven et al, 2017 ) and, again, these genes could be found differentially induced as measured by both methods (GUS expression and qRT-PCR).…”

Tissue dual RNA-seq allows fast discovery of infection-specific functions and riboregulators shaping host–pathogen transcriptomes

“…Moreover, RNA-seq has permitted the identification of sensory RNA elements and numerous noncoding RNAs (ncRNAs) in pathogenic bacteria. A small subset of the few already characterized riboregulators was found to contribute to pathogenesis (1)(2)(3).…”