Introducing the extrabiome and its classification: a new view on extracellular nucleic acids

Abstract

Future MicrobiologyAhead of Print EditorialOpen AccessIntroducing the extrabiome and its classification: a new view on extracellular nucleic acidsGeorge Tetz & Victor TetzGeorge Tetz *Author for correspondence: E-mail Address: g.tetz@hmi-us.comhttps://orcid.org/0000-0003-3205-9018Human Microbiology Institute, New York, NY 10014, USASearch for more papers by this author & Victor Tetz https://orcid.org/0000-0001-9047-6763Human Microbiology Institute, New York, NY 10014, USASearch for more papers by this authorPublished Online:4 Apr 2023https://doi.org/10.2217/fmb-2023-0003AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinkedInReddit Keywords: autoimmune diseasescancercfDNADNaseextrabiomeextracellular DNAextracellular RNAextracellular vesiclesneutrophil extracellular trapsprotein misfoldingRNaseTeazeled receptorsTetz-proteinsThe first description of the extracellular DNA and RNA, bound together by the term ‘extracellular nucleic acids’, as free molecules identified in microbial communities that are also widespread in natural aquatic and terrestrial environments dates back to the 1950s [1,2]. Extracellular nucleic acids are released through multiple mechanisms, such as through active secretion, autolysis and their association with membrane vesicles [3].Since then, researchers have reported numerous different functions of extracellular nucleic acids in both prokaryotes and eukaryotes, starting from the single cell to multicellular humans. Although a common biological role has not yet been proposed, until recently, the most well-known functions have been attributed to their role in gene transfer or as structural and nutritional sources [3–5].Today the ongoing evolution of scientific knowledge has led to extracellular nucleic acids, originally identified as biological ‘waste’, moving to the forefront of cell and macroorganism regulation. The lack of relevant classification and differentiation of extracellular nucleic acids results in confusion as to how the same extracellular nucleic acid can play such diverse, and sometimes even contrasting, roles. We further propose that the collection of all extracellular nucleic acids within a study be known as the ‘extrabiome’. The recent discovery showing that different types of extracellular nucleic acids can simultaneously play multiple and previously unknown roles has triggered the long-standing need for the ‘extrabiome’ formulation and classification.For example, certain types of extracellular DNA and RNA have recently been shown to possess receptive and regulatory properties [4,5]. These DNA- and RNA-based receptors located on the outside of the membrane, called Teazeled receptors (TezRs), form the extracellular network that facilitates the interaction of the cell with any chemical, physical or biological factor. TezRs not only regulate the work of known protein-based receptors but also enable the reception and response of cells to factors whose reception and regulation were previously unknown, such as temperature, light and geomagnetic field. Moreover, TezRs are implicated in the formation and maintenance of cell memory, the cell's ability to ‘forget’ preceding events.Recent studies have shown that extracellular DNA possesses the capacity to trigger trans-kingdom misfolding of various proteins and change their heat-resistant properties [6–9]. The specificity of this effect is individual, depending on the type of organism from which this extracellular DNA originates. For example, the DNA of a particular bacterial strain, although sharing common features in terms of size with extracellular DNA of other related bacteria, was able to trigger Tau and β-amyloid misfolding. This highlights the dependence of the functionality of this DNA on more than just length or the presence of a CpG-rich DNA sequence [6,7].In cancer patients, different components of the extrabiome such as extracellular DNA and RNA released as free-floating nucleic acids or within extracellular vesicles, from tumor or normal cells (including a subset originating from neutrophils in the form of neutrophil extracellular traps, or from gut microbiota, can contribute to disease initiation and progression in multiple ways [10–13]. Tumor cell-derived extracellular nucleic acids can promote oncogenic transformation of normal epithelial cells via horizontal gene transfer [14]. Additionally, neutrophil extracellular traps promote primary tumor and metastatic growth, triggering the activation of prometastatic genes, cancer cell proliferation and awakening in the metastatic niche through ILK-β-parvin, cGAS-STING and PI3K signaling pathways [12].A certain type of bacterial extracellular DNA and RNA also contributes to oncogenic progression through other mechanisms – for example, by triggering an altered immune response through the TLR9-MYD88 signaling pathway, forming cancer-related heat-resistant proteins [15,16]. Moreover, an uncharacterized part of the extrabiome might contribute to the disease in other unknown ways. When studying the role of the extrabiome in a particular biological system, multiple effects of different components of the extrabiome present should be considered. For instance, extracellular nucleic acids that participate in horizontal gene transfer might possess multiple biological roles within either the same recipient or nonrecipient cells through mechanisms not related to gene transfer, such as through interaction with proteins.A further example is the role of extracellular DNA in microbial biofilms, which until recently has been solely seen as a structural component of the extracellular polymeric matrix that protects microbial communities, discounting the regulatory potential of the same nucleic acid [17,18].Although the components of the extrabiome seem to be polyfunctional, we believe they can still be classified based on their primary functions. Such an extrabiome classification is critical for exploring the individual roles and interplay between different components of the extrabiome and other elements of biological systems and will allow for a better understanding of their implications in health and disease. Here, we present the first functional classification of extracellular nucleic acids.Functional classification of extrabiome based on their biological effects1.Horizontal gene transfer 1.1.Extracellular nucleic acids for gene transfer 1.2.Extracellular nucleic acids regulating gene expression within horizontal gene transfer2.Reception and regulation 2.1.Primary and secondary TezRs 2.2.CpG-enriched DNA 2.3.DNA of neutrophil extracellular traps3.Alteration of protein isoform 3.1.Extracellular nucleic acid ‘pliers’ triggering formation of heat-resistant Tetz-proteins 3.2.Extracellular nucleic acid ‘pliers’ triggering cross β-sheet protein misfolding4.Structural integrity 4.1.Extracellular nucleic acids for the structural integrity in microbial biofilms 4.2.Extracellular nucleic acids for the structural integrity in eukaryotic multicellular organismsThe proposed concept of the extrabiome and its classification pave the way for a better understanding of the translational potential of extracellular nucleic acids in biology and medicine. The biggest challenge in studying the extrabiome is the lack of conventional and precise research tools and algorithms for differentiating the structural classes of extracellular nucleic acids, as well as their functions within multicellular macroorganisms and biological systems.Numerous studies have described the therapeutic potential of nonspecific DNases that prevent oncogenic transformation by destroying extracellular nucleic acids circulating in the blood and regulate the response of cancer cells to chemo- and immunotherapies [19]. The same has also been investigated in other conditions, such as autoimmune, neurological and neurodegenerative disorders, in which multiple extrabiome components play multiple disease-associated roles but whose multiple functionalities are not considered by researchers [20]. However, in most cases, authors analyze the results of such investigations through the lens of the destruction of only one part of the extrabiome. By looking at the role of the loss of neutrophil extracellular traps only, or by only studying the consequences of the destruction of bacterial-derived extracellular DNA, the importance of the impact of DNases on other extrabiome components is downplayed. Such an approach results in a lack of relevant controls, making it impossible to distinguish the effects of the loss of the ‘primary’ target compared with other parts of the extrabiome altered by the same therapy.Because the components of the extrabiome could play multiple biological roles that vary depending on the type and physiological state of the cell, the following aspects should be considered in extrabiome studies. In multicellular systems with multiple extrabiome components, the potential biological effects following the destruction or inactivation of various functional types of extracellular nucleic acids should be considered; the lack of relative controls for the effect of nucleases against each extrabiome component should therefore be considered a limitation of the study. In summary, the proposed introduction of the extrabiome and its classification could stimulate more precise analysis of the roles of extracellular nucleic acids as both regulatory elements and potential therapeutic targets.Financial & competing interests disclosureThe authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending or royalties.No writing assistance was utilized in the production of this manuscript.Open accessThis work is licensed under the Attribution-NonCommercial-NoDerivatives 4.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/4.0/