Unravelling the DNA sequences carried by Streptomyces coelicolor membrane vesicles

Abstract

Membrane vesicles (MVs) are spherical particles with nanoscale dimensions and characterized by the presence of diverse cargos, such as nucleic acids, proteins, lipids, and cellular metabolites. Many examples of (micro)organisms producing MVs are reported in literature. Among them, bacterial MVs are of particular interest because they are now considered as the fourth mechanism of horizontal gene transfer. Streptomyces bacteria are well-known for their ecological roles and ability to synthesize bioactive compounds, with Streptomyces coelicolor being the model organism. It was previously demonstrated that it can produce distinct populations of MVs characterized by different protein and metabolite cargos. In this work we demonstrated for the first time that MVs of S. coelicolor carry both DNA and RNA and that their DNA content represents the entire chromosome of the bacterium. These findings suggest that MV DNA could have a role in the evolution of Streptomyces genomes and that MVs could be exploited in new strain engineering strategies.

DNA characterization reveals potential operon-unit packaging of extracellular vesicle cargo from a gut bacterial symbiont

“…Our study reveals that the genomic packaging of EVs is a non-random process and potentially functionally selective of specific gene sets. We also find that EVs are capable of packaging DNA from any region of the genome, which supports the findings of recent studies 8,19 . Importantly, our study proposes a novel potential mechanism suggesting selective EV-DNA packaging.…”

“…Contrasting to the findings of Sartorio et al 48 and Elhenawy et al 16 identifying EV's specialized role as a glycan-degrader, we find a significant presence of DNA copies in EVs associated with coding for proteins in glycosyltransferase domains, particularly those from the membrane-associated GT-B family hinting at EV's potential role in altering the surface glycans of recipient cells. However, as studies have shown the strain-specificity and the dependencies of EV cargo content on the experimental growth condition, we limit our interpretation and findings to the particular bacterial strain and experimental condition used in this study 8,19,63 .…”

“…Here, we suggest a novel hypothesis of selective EV-DNA packaging, potentially arranged in operon units, hence providing new insights into our understanding of its genetic makeup and its potential role, underlining the importance of our findings in microbial community dynamics.Recent work has identified the function of EVs in facilitating horizontal gene transfer (HGT), with evidence showing their ability to mediate gene exchange both within and across bacterial species, even extending to different genera 13 . EVs have been shown to provide a safeguarded milieu for genetic material and facilitate intercellular gene transfer 14 and have been reported to contribute to bacterial genome evolution and potential antibiotic resistance gene transfer 8,15 . Environmental stressors have also been shown to escalate EV production and gene transfer rates 14 .…”

The Operon as a Conundrum of Gene Dynamics and Biochemical Constraints: What We Have Learned from Histidine Biosynthesis

“…Other mechanisms contemplate gene transfer agents, membrane vesicles (MV), nanotubes, and cell fusion [ 87 , 90 , 94 ]. The finding that MV are embedded with DNA fragments representing the entire genome of S. coelicolor slightly suggests that also vesicles might be responsible for the introgression of foreign DNA into recipient cells [ 95 ].…”

Application of Cloning-Free Genome Engineering to Escherichia coli

“…Gene transfer among and within bacterial populations is predominantly mediated by conjugation, transduction, and transformation [ 5 ]. Other mechanisms involve gene transfer agents, nanotubes, membrane vesicles, and cell fusion [ 6 , 7 , 8 , 9 ]. The natural transformation consists of the stable uptake, integration, and functional expression of extracellular DNA that can occur under natural bacterial growth conditions; prerequisites for natural transformation include the release and persistence of extracellular DNA, the presence of competent bacterial cells, and the ability of uptaken DNA to be stabilized by integration into the bacterial genome or, in the case of plasmids, the ability to integrate or re-circularize into self-replicating plasmids [ 1 ].…”