Wisdom of the crowds: A suggested polygenic plan for small-RNA-mediated regulation in bacteria

Abstract

Summary The omnigenic/polygenic theory, which states that complex traits are not shaped by single/few genes, but by situation-specific large networks, offers an explanation for a major enigma in microbiology: deletion of specific small RNAs (sRNAs) playing key roles in various aspects of bacterial physiology, including virulence and antibiotic resistance, results in surprisingly subtle phenotypes. A recent study uncovered polar accumulation of most sRNAs upon osmotic stress, the majority not known to be involved in the applied stress. Here we show that cells deleted for a handful of pole-enriched sRNAs exhibit fitness defect in several stress conditions, as opposed to single, double, or triple sRNA-knockouts, implying that regulation by sRNA relies on sets of genes. Moreover, analysis of RNA-seq data of Escherichia coli and Salmonella typhimurium exposed to antibiotics and/or infection-relevant conditions reveals the involvement of multiple sRNAs in all cases, in line with the existence of a polygenic plan for sRNA-mediated regulation.

TRS: a method for determining transcript termini from RNAtag-seq sequencing data

“…Finally, we verified that TRS identifies 3’ termini in RNAtag-seq datasets published by other research groups for E. coli 7 , 15 , 17 , 18 . Comparative analysis of E. coli primary 3’ termini identified in other RNAtag-seq datasets have shown high consistency with the previously identified ones (Supplementary Information and Supplementary Fig.…”

SRSF6 balances mitochondrial-driven innate immune outcomes through alternative splicing of BAX

“…S1A). Because it is well established that several members of the SR protein family are essential genes across multiple cell types (Feng et al, 2009; Goldberger et al, 2021; Ortiz-Sanchez et al, 2019; Wang et al, 2001; Xu et al, 2005) and because high-quality transcriptomics analyses have been carried out successfully for SR family members using shRNA or siRNA gene silencing (Consortium, 2004; Van Nostrand et al, 2020), we opted to stably knockdown these factors, instead of relying on CRISPR-mediated gene editing. To identify major transcriptomic changes due to loss of SR proteins, we isolated total RNA from each of these KD cell lines and a scramble (SCR) control that was selected alongside the SR KDs, performed RNA-seq, and measured differential gene expression using the CLC Genomics Workbench, as in (Wagner et al, 2021).…”

The Acinetobacter baumannii model can explain the role of small non-coding RNAs as potential mediators of host-pathogen interactions

“…Nowadays, thanks to the development of RNA sequencing, it is known that production and regulation of bacterial sRNAs is coordinated through other components, including others sRNAs, mRNAs, and remarkably sRNA-binding proteins (sRBPs) ( Adams & Storz, 2020 ; Goldberger et al, 2021 ). Several sRBPs (e.g., Hfq, ProQ, and CsrA) are involved in facilitating sRNA-mRNA base-pairing in Enterobacteriaceae , mainly investigated in E. coli and Salmonella enterica serovar Typhimurium ( Storz et al, 2011 ; Kim & Kwon, 2013 ; Klein & Raina, 2017 ; Goldberger et al, 2021 ). In E. coli , the Hfq protein, an RNA chaperone, enhances base pairing between a specific sRNA and its mRNA target ( Waters & Storz, 2009 ; De Lay et al, 2013 ; Vazquez-Anderson & Contreras, 2013 ).…”