A systematic analysis of the RNA-targeting potential of secreted bacterial effector proteins

Abstract

Many pathogenic bacteria utilize specialized secretion systems to deliver proteins called effectors into eukaryotic cells for manipulation of host pathways. The vast majority of known effector targets are host proteins, whereas a potential targeting of host nucleic acids remains little explored. There is only one family of effectors known to target DNA directly, and effectors binding host RNA are unknown. Here, we take a two-pronged approach to search for RNA-binding effectors, combining biocomputational prediction of RNA-binding domains (RBDs) in a newly assembled comprehensive dataset of bacterial secreted proteins, and experimental screening for RNA binding in mammalian cells. Only a small subset of effectors were predicted to carry an RBD, indicating that if RNA targeting was common, it would likely involve new types of RBDs. Our experimental evaluation of effectors with predicted RBDs further argues for a general paucity of RNA binding activities amongst bacterial effectors. We obtained evidence that PipB2 and Lpg2844, effector proteins of Salmonella and Legionella species, respectively, may harbor novel biochemical activities. Our study presenting the first systematic evaluation of the RNA-targeting potential of bacterial effectors offers a basis for discussion of whether or not host RNA is a prominent target of secreted bacterial proteins.

Purification of cross-linked RNA-protein complexes by phenol-toluol extraction

“…Using mutant strains carrying FLAG-tags fused to the C-terminus of PTex candidate RNA-interactors, we performed UV cross-linking, immunoprecipitation and radioactive labelling of co-purified RNA (known as PNK assay as described in ref. 55 ), validating that YihI, SipA and AhpC are indeed associated to RNA in vivo (Fig. 6d, Supplementary Figs.…”

Arabidopsis thaliana responds to colonisation of Piriformospora indica by secretion of symbiosis-specific proteins

“…Exudate proteins are often identified by bioinformatic tools based on the prediction of their N-terminal secretion sequence which directs them into the endoplasmic reticulum (ER) from where they are secreted via vesicle fusion with the plasma membrane [16, 27, 28]. However, only ~ 50% of the known secreted plant proteins possess such a signal [11, 22] whereas others utilise unconventional mechanisms of secretion, which resemble those of animal exosomes [29] or include exocyst-like structures [30].…”

Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein

“…Salmonella being a well-characterized pathogen, potential RBPs among its virulence factors are of special interest. While previous RNA-binding domain based searches failed to predict RBPs among Salmonella's secreted virulence factors (Sharan et al 2017;Tawk et al 2017), we note that the virulence-associated protein YopD of the related pathogen Yersinia pestis is well-known to moonlight as an RBP (Chen and Anderson 2011). In addition, Listeria monocytogenes has just been shown to secret an RBP to manipulate infected host cells (Gerovac and Vogel 2019;Pagliuso et al 2019).…”