Extracellular RNAs in Bacterial Infections: From Emerging Key Players on Host-Pathogen Interactions to Exploitable Biomarkers and Therapeutic Targets

Abstract

Non-coding RNAs (ncRNAs) are key regulators of post-transcriptional gene expression in prokaryotic and eukaryotic organisms. These molecules can interact with mRNAs or proteins, affecting a variety of cellular functions. Emerging evidence shows that intra/inter-species and trans-kingdom regulation can also be achieved with exogenous RNAs, which are exported to the extracellular medium, mainly through vesicles. In bacteria, membrane vesicles (MVs) seem to be the more common way of extracellular communication. In several bacterial pathogens, MVs have been described as a delivery system of ncRNAs that upon entry into the host cell, regulate their immune response. The aim of the present work is to review this recently described mode of host-pathogen communication and to foster further research on this topic envisaging their exploitation in the design of novel therapeutic and diagnostic strategies to fight bacterial infections.

Keywords: extracellular RNAs; host-pathogen interactions; membrane vesicles.

Figure 1

Modes of extracellular miRNA packaging in eukaryotic cells and routes leading to the formation of different membrane vesicle types in bacteria. Extracellular miRNAs can be cargo in membranous vesicles or can be vesicle free and associated with either Argonaute (Ago) proteins alone or incorporated into HDL particles. Apoptotic bodies, shedding vesicles, and exosomes are three types of membranous vesicles that contain these extracellular miRNAs. Apoptotic bodies can also contain various cellular organelles including mitochondria and nucleic acids [28]. In bacteria, distinct membrane vesicles are formed by Gram-negative and Gram-positive bacteria. Blebbing of the outer membrane and explosive cell lysis are the two main routes for vesicle formation in Gram-negative bacteria. The membrane vesicles from these bacteria can be divided into outer-inner membrane vesicles (OIMVs), explosive outer membrane vesicles (EOMVs), and traditional OMVs according to their formation routes, structures, and compositions [45]. In Gram-positive bacteria, membrane vesicles are formed by a mechanism involving the prophage-encoded endolysin that generates holes in the peptidoglycan cell wall, allowing the cytoplasmic membrane material to protrude into the extracellular space and release the cytoplasmic membrane vesicles (CMVs). CMVs can contain membrane and cytoplasmic components [46].

Figure 2

Activation of innate immune receptors by bacterial membrane vesicles and their RNA content. When bacterial EVs released by extracellular or intracellular bacteria reach the target cells, the sensing of these vesicles and/or its RNA content could occur at different intracellular locations. The pathogen-associated molecular patterns (PAMP) on the outside of these vesicles can induce the host innate immune response by activating the toll-like receptor and MAP-kinase (TLR/MAPK) signaling pathway, leading to the activation of transcription factors that induce the production of inflammatory mediators. The RNA cargo of EVs internalized by endocytosis can also be released and sensed by endosomal receptors. These receptors signal through the adaptor molecules MyD88 or TRIF, resulting in the activation and nuclear translocation of transcription factors that will induce production of inflammatory mediators and type I interferons. RNAs delivered into the cytoplasm after fusion of EVs with the host cell plasma membrane might be sensed by cytoplasmic RNA sensors such as RIG-I and MDA-5. Engagement of these receptors triggers signaling through the adaptor protein MAVS, which signals to induce the production of inflammatory mediators and type I interferon. On the other hand, some bacterial sRNAs delivered into receptor cells can target mRNAs from components of the mentioned signaling pathways, leading to the reduction of the inflammatory mediators, showing how complex the infection process can be.