Small RNAs in Bacterial Outer Membrane Vesicles
DOI:
https://doi.org/10.61173/3ptg1n22Keywords:
outer membrane vesicles, small RNAs, tRNA fragments, TLR7/8 sensing, Argonaute-mediated silencingAbstract
Outer membrane vesicles (OMVs) from Gram-negative bacteria exhibit selective enrichment for small RNAs (sRNAs), including tRNA fragments, as opposed to randomly reflecting cellular RNA pools. Building on well-established RNase-detergent controls and ddRTPCR quantification, we summarise delivery stoichiometry (≈1% of vesicle RNA reaching recipient cytoplasm) and propose reporting standards (vesicles per cell, RNA copies per vesicle, delivery per cell). Functionally, OMV RNAs signal via two main routes: cytosolic Argonaute-dependent silencing and endosomal TLR7/8 sensing in both pathogenic and commensal bacterial species. We highlight evidence that OMVs can travel along the gut–brain axis and activate astrocytic NF-κB, thereby exacerbating amyloidassociated pathology, and we outline the experimental controls needed to attribute these effects specifically to RNA cargo. Finally, we consider how these principles could guide the engineering of probiotic-derived OMVs to tune immune tone within a quantitative mechanistic framework. This review identifies key methodological gaps and puts forth quantitative frameworks for studying RNA delivery.
References
[1] Gilmore, W. J., Johnston, E. L., Bitto, N. J., Zavan, L., O’Brien-Simpson, N., Hill, A. F., & Kaparakis-Liaskos, M. (2022). Bacteroides fragilis outer membrane vesicles preferentially activate innate immune receptors compared to their parent bacteria. Frontiers in Immunology, 13, 970725.
[2] Ghosal, A., Upadhyaya, B. B., Fritz, J. V., Heintz‐Buschart, A., Desai, M. S., Yusuf, D., Huang, D., Baumuratov, A., Wang, K., Galas, D., & Wilmes, P. (2015). The extracellular RNA complement of Escherichia coli. MicrobiologyOpen, 4(2), 252– 266. https://doi.org/10.1002/mbo3.235
[3] Malabirade, A., Habier, J., et al. (2018). The RNA Complement of Outer Membrane Vesicles From Salmonella enterica Serovar Typhimurium Under Distinct Culture Conditions. Frontiers in Microbiology, 9, 2015. https://doi. org/10.3389/fmicb.2018.02015
[4] Koeppen, K., Hampton, T. H., et al. (2016). A Novel Mechanism of Host-Pathogen Interaction through sRNA in Bacterial Outer Membrane Vesicles. PLOS Pathogens, 12(6), e1005672.
[5] Blenkiron, C., Simonov, D., et al. (2016). Uropathogenic Escherichia coli Releases Extracellular Vesicles That Are Associated with RNA. PLOS ONE, 11(8), e0160440.
[6] Meng, D., Lai, Y., Zhang, L., et al. (2024). Helicobacter pylori outer membrane vesicles directly promote Aβ aggregation and enhance Aβ toxicity in APP/PS1 mice. Communications Biology, 7(1), 1474. https://doi.org/10.1038/s42003-024-07125-
[7] Palacios, E., Lobos-González, L., Guerrero, S., Kogan, M. J., Shao, B., Heinecke, J. W., Quest, A. F. G., Leyton, L., & Valenzuela-Valderrama, M. (2023). Helicobacter pylori outer membrane vesicles induce astrocyte reactivity through nuclear factor-κappa B activation and cause neuronal damage in vivo in a murine model. Journal of Neuroinflammation, 20(1), 66. https://doi.org/10.1186/s12974-023-02728-7
[8] Choi, J.-W., Kim, S.-C., Hong, S.-H., & Lee, H.-J. (2017). Secretable Small RNAs via Outer Membrane Vesicles in Periodontal Pathogens. Journal of Dental Research, 96(4), 458– 466.
[9] Shen, Y., Torchia, M. L. G., Lawson, G. W., Karp, C. L., Ashwell, J. D., & Mazmanian, S. K. (2012). Outer Membrane Vesicles of a Human Commensal Mediate Immune Regulation and Disease Protection. Cell Host & Microbe, 12(4), 509–520. https://doi.org/10.1016/j.chom.2012.08.004
[10] Kulp, A., & Kuehn, M. J. (2010). Biological Functions and Biogenesis of Secreted Bacterial Outer Membrane Vesicles. Annual Review of Microbiology, 64(1), 163–184.
[11] Tsatsaronis, J. A., Franch-Arroyo, S., Resch, U., & Charpentier, E. (2018). Extracellular Vesicle RNA: A Universal Mediator of Microbial Communication? Trends in Microbiology, 26(5), 401–410.
[12] Stein, E. V., et al. (2017). Steps to achieve quantitative measurements of microRNA using two step droplet digital PCR. PLOS ONE, 12(11), e0188085.
[13] Welsh, J. A., Goberdhan, D. C. I., et al. (2024). Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches. Journal of Extracellular Vesicles, 13(2), e12404.
[14] Han, E., Choi, S., Lee, Y., Park, J., Hong, S., & Lee, H. (2019). Extracellular RNAs in periodontopathogenic outer membrane vesicles promote TNF‐α production in human macrophages and cross the blood‐brain barrier in mice. The FASEB Journal, 33(12), 13412–13422.
[15] Krüger, A., Oldenburg, M., Chebrolu, C., Beisser, D., Kolter, J., Sigmund, A. M., Steinmann, J., Schäfer, S., Hochrein, H., Rahmann, S., Wagner, H., Henneke, P., Hornung, V., Buer, J., & Kirschning, C. J. (2015). Human TLR 8 senses UR / URR motifs in bacterial and mitochondrial RNA. EMBO Reports, 16(12), 1656–1663. https://doi.org/10.15252/embr.201540861
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