Wait, What? extracurricular DNA (eDNA)

by Christoph
 

Among biologists, DNA is a household term, the acronym for deoxyribonucleic acid, which hardly anyone pronounces in full. But can you find your way around the zoo of prefixes that are in use and in most cases are not separated from 'DNA' by a hyphen, as for example in Z-DNA? cccDNA, rcDNA (ocDNA), mtDNA, ecDNA, cDNA, bDNA, gDNA (chrDNA), kDNA, xDNA, rDNA, tDNA, ssDNA,… and eDNA.
 

Mechas had explained in eDNA everywhere for (almost) everything that the 'e' in eDNA stands for 'environmental' and that the term eDNA is largely synonymous with "metagenomic DNA," which refers to the genetic material from a mixed community in a sample. She pointed out that eDNA analysis is a relatively simple but powerful tool for monitoring bio­diversity at a site over time. And I gave an example in which eDNA analyses led to Finding the actual needle in a virtual haystack, so to speak, by reversing the process.
 

The 'e' in eDNA can also stand for "extracellular," and that's the way it is used in the context of research on bacterial multicellularity. Extracellular DNA (eDNA) is considered an integral matrix component of bacterial biofilms and has several functions that are not mutually exclusive (see Fig­ure). I will briefly walk you through a slide that Cynthia Whitchurch, director of the Biofilm Biology cluster at SCELSE, Singapore, showed during her talk at the recent MultiBac workshop in Berlin, Germany. (Thanks, Cynthia, for sharing the slide!) Note that eDNA – unsurprisingly – also plays a role in biofilms of Archaea not mentioned in Cynthia's slide. If you want to dig deeper, please look up the recent review of Archaeal biofilm for­mation by van Wolferen et al. (2018) for similarities and differences of bacterial and archaeal biofilms (Open Access).
 

Surface attachment Although bacterial cells usually have a (moderately) positive surface charge, small bacterial aggregates that are already embedded in a developing biofilm of exopolysaccharide (EPS), proteins – often amylogenic proteins – and extracellular DNA, can adhere to positively charged surfaces due to the polyanion character of the latter (sugar-phosphate backbone).

(click to enlarge) Figure by Laura Nolan and Cynthia Whitchurch

Biofilm development As comparatively large, predominantly long polymers, both exopoly­saccharides (EPS) and extracellular DNA (eDNA) have an important function in the three-dimensional structure of a biofilm over time. This highly dynamic 3D structure ultimately determines the distance between the cells enclosed in the biofilm and thus the diffusibility of macromolecules within/into/out of the biofilm. In addition, the chromosomal DNA (chrDNA) of newly lysed cells can be used by swarming cells/cell clusters ("rafts") as a kind of rail track or trail for forward movement by twitching motility, as has been shown by Gloag et al. (2013) for Pseudomonas aeruginosa.

Cation chelation to promote AMR Anti Microbial Resistance (AMR) of a number of (human) pathogens is increased through the polyanion char­acter of extracellular DNA (sugar-phosphate backbone), which efficiently chelates Mg⁺⁺ ions and small cationic peptides with antibiotic ac­tivity.

Niche defense  Like a relatively wide-meshed net, the gel-like matrix hinders, but does not prevent, the invasion of other bacteria and bacterio­phages into the biofilm by diffusion. For Caulobacter crescentus, it is known but not yet fully understood that eDNA in the biofilm prevents in­vasion by newborn swarmer cells. Berne et al. (2023) found that eDNA of lysed cells in the biofilm is bound by the swarmers, preventing them from entering and promoting their dispersal.

Horizontal gene transfer  Trans­for­ma­tion, that is, eDNA uptake by naturally competent cells is one of the main routes to HGT (see here in STC). The contact-dependent killing of neighbor cells and uptake of their re­leased chromosomal DNA, now eDNA, is described for Vibrio cholerae in Dial "V" for Murder. The Vibrio ComEA membrane complex then processes the "caught" double-stranded DNA molecule (dsDNA) such that one strand becomes single-stranded upon entry into the cytoplasm and serves for RecA‑dependent homologous recombination (see Rachel Diner's piece Shining a light on Vibrio DNA uptake). Be sure to watch this 3-sec video clip of a Vibrio wielding its T4P pilus (green), latching onto eDNA (red), and retracting into the cell (green) towards the ComEA complex from the work of Ellison et al. (2019).

Nutrient source The other strand of eDNA that enters the cell cytoplasm during DNA uptake (see above) is broken down to nucleotides that eventually serve as nutrient source, primarily by replenishing the cell's nucleotide pool.

Protection against heat, dehydration and UV Much like a sunscreen, the gel-like biofilm matrix (containing eDNA) provides a physicochemical environment for the embedded cells in which they can more easily respond to various physical stressors than planktonic cells.

Phenazine-mediated electron transfer To the amazement of the audience at the 2022 ISME18 meeting, Dianne Newman introduced the term "agathokakological" in her keynote lecture, and, to no less amazement, pointed out the role of extracellular phenazines and DNA for electron shuffling outside the cells (watch here a video based on Dianne's keynote).
 

Disclosure: I didn't come up with the catchphrase "extracurricular DNA." It was a typo – or an autocorrect blooper – of our esteemed colleague Kristen DeAngelis who tweeted live from her cell phone while completely captivated by Dianne Newman's keynote at the ISME18 meeting 2022 in Lausanne, Switzerland. She was terribly embarrassed about her blooper and immediately apologized, correcting that she of course meant "extra­cellular." No, Kristen, I replied, "extra­curricular" has long been the most fitting description for the various functions of DNA apart from its function as genetic material, which is what everyone immediately thinks of when they hear "DNA." You won't find the term "extracurricular DNA" (eDNA) in any textbook, except here in this blog post. But feel free to use it as a mnemonic, to help you remember the context.
 

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