by Sophia Swartz
figures by Abagail Burrus

It was only three weeks into the fall semester, and I was starting to sniffle. When I had woken up that morning with a tell-tale tickle in the back of my throat, I had tried to deny the obvious. However, by the end of the day, sneezing and sore, I surrendered to my cold and trudged to my local CVS.

But after the cold cleared up, I couldn’t credit my swift recovery entirely to that late-night CVS haul. Instead, it was mostly my circulatory and immune systems that did the trick.

When we are faced with an infection such as a cold virus, we rely on the cooperation between our blood and immune systems to get better. However, in plants, there’s no blood or specialized immune cells to retaliate against pathogens. So, how do plants ensure a speedy return to health?

Plants vs. Pathogens: Underground Warfare

One of the defense strategies plants have developed can be found underground. Rather than having their own circulating police force of immune cells, plants create a series of spider web-like traps at the root tip to catch harmful bacteria and fungi before infection (Figure 1). This alternative method of defense hinges on one key player: Extracellular DNA (exDNA).

DNA is a molecule that stores genetic information. It is generally found inside cells in a central compartment called the nucleus, but under certain circumstances, it can also be exported to the exterior of the cell. Once outside of the cell, this DNA, termed exDNA, tends to be very gooey and stringy. As such, when it is secreted by cells of a plant’s root, the exDNA can surround to the plant root tip with a sticky covering.

These coverings that exDNA creates are termed root extracellular traps (RETs) (Figure 1). By combining exDNA with other molecules and cells shed from the plant’s root, RETs ensnare bacteria and fungi coming from the soil. Wrapped up in strands of sticky exDNA, pathogens can’t infect the growing plant and make it sick.

Figure 1: Close-up of the growing plant root tip. This image shows various components of the root tip. In particular, the sinewy projections emanating from the root cap (red and pink) represent the RETs capturing bacterial pathogens (blue) and preventing their infection of the root tip. Additional components of the root tip are as follows: meristem initials (yellow-white), protoxylem (purple), endodermis (light blue), cortex (green), and epidermal cells (yellow-orange).

Until recently, scientists were unaware of the key role of exDNA in plant health. Today, research is still underway to better understand how plants produce exDNA and how RETs recognize and trap pathogens on a molecular level. To recap what researchers have learned so far about where exDNA comes from and how it protects the plant, it’s essential that we start somewhere very near and dear to plant development and growth: root border cells.

 Revenge of the Root Border Cells

Root border cells, produced by the root cap, form an upturned, thimble-like shield around the root tip (Figure 2). Corn, for example, is tiled with anywhere from 4,000 to 21,000 root border cells coating about the first millimeter of the plant root tip. Just like a thimble protects your finger when you are sewing, root border cells protect the root tip as the plant grows.

Surprisingly, however, the earliest descriptions of how root border cells might work weren’t very flattering. Some scientists even described its function as that of a “bullet-shaped…slimy battering ram.” Although it is true that root border cells’ primary function is to shed from the root tip and lubricate its passage through hard soil, recent research suggests root border cells also play much more complex, sensitive, and important roles in plant defense (Figure 2).

When root border cells shed, they accumulate into a thick covering over the root tip. Into this covering, they export exDNA, along with sugars and proteins, to create a sticky mucus. This coats the sensitive root tip in a slimy, protective sleeve reinforced with exDNA. Just like when you have a cold and your nose generates extra mucus to get rid of the harmful virus, the plant root tip exploits the exDNA of root border cells to create a sticky trap for pathogenic invaders.

Figure 2: Root border cells at the root tip. Root border cells, shed from the root cap (red and pink), help the root tip move downward through the soil (left image). These shed root border cells (shown in the right image) also create a sticky trap to immobilize harmful bacteria and fungi. Plant root tip anatomy is shown as follows: Root cap (red and pink), meristem initials (yellow-white), protoxylem (purple), endodermis (light blue), cortex (green), and epidermal cells (yellow-orange).

When exDNA Isn’t Enough

Sadly for plants, however, some bacteria cleverly developed ways to slip out of exDNA’s tight hold. In 2016, researchers at the University of Wisconsin explored how a bacterium found in the soil called Ralstonia solanacearum was able to infect tomato plants. The bacteria cause problems by sneaking into plant root tips and blocking plants’ water uptake. Although these researchers knew that tomato plants had many sticky exDNA traps along the root tip, they found that these traps did little to prevent infection. On average, three quarters of invading R. solanacearum bacteria successfully escaped.

To understand why, they selectively turned off certain genes in the bacteria. One of the genes they removed coded for an enzyme called nuclease. A nuclease acts like a pair of molecular scissors to cut up DNA. Bacteria evolved them long ago because DNA is made up of elements like nitrogen and carbon. With these scissors, they can break apart DNA molecules to get at the nutritious elements within. By knocking out the nuclease, the researchers wanted to see if R. solanacearum had repurposed these molecular scissors to slice up exDNA and escape RETs. If the tomato plants remained healthy after adding mutant bacteria with a disabled nuclease gene, then the researchers could conclude that the bacteria need nuclease to invade the root tip.

After treating tomato plants with mutant bacteria, researchers found that the plants remained healthy. However, when they treated tomato plants with bacteria with a functional nuclease gene, the plants became sick. They observed that when the unmodified bacteria got stuck in the exDNA, they would unleash their molecular scissors. These nucleases then sliced up the exDNA so the bacteria could wriggle free and infect the plant root tip (Figure 3). From these results, they were able to conclude that R. solanacearum needed nuclease to escape RETs.

Additionally, when other research teams looked for similar nucleases in other soil bacteria, they found that all documented harmful soil bacteria had developed this defense mechanism. Taken together, these findings suggest that bacteria and exDNA evolved alongside each other.

Figure 3: The impact of nuclease on the root tip. After treatment with a nuclease, the RET completely dissolves away and leaves the growing root tip bare and vulnerable. Shown here are also the physiological and spatial differences between shed root border cells (red, 3), the root cap (red, 1), and the root tip (red, 4). Plant root tip anatomy is shown as follows: Root cap (red and pink), meristem initials (yellow-white), protoxylem (purple), endodermis (light blue), cortex (green), epidermal cells (yellow-orange, 2), and bacteria (dark blue).

exDNA, A True Renaissance Molecule

Although the existence of the plant root cap and its shed root border cells has long been known, it was only recently that we started visualizing and appreciating the role of exDNA in creating and maintaining RETs. Today, more focused research needs to be devoted to understanding the molecular mechanisms behind their formation and development over time, and how we can apply these findings to crop improvement.

Currently, the United Nations reports that we must double food production by 2050 to fulfill growing food demands. However, anywhere from 20 to 40 percent of the food we produce is lost to pathogens, animals, and weeds. Malnutrition and famine exert lingering effects on countries’ social and economic future. But with a stronger understanding of exDNA and its role in immune defense at the plant root tip, we can better address these challenges and avert disaster. For example, a research team at the University of Wisconsin discovered that the bacterial wilt-resistant tomato line, Hawaii 7996, produced over three times as many root border cells as the bacterial wilt-susceptible tomato line, Bonny Best. These findings suggest that an easily quantifiable trait – root border cell number – can help plant breeders create new varieties that defend themselves better against soil-borne disease. Research to develop plants with higher root border cell counts, and thus higher exDNA amounts in the RET, could potentially offset some of the effects of famine by bolstering domestic food production.

Through continued research, the role of exDNA in the plant immune defense may be elucidated while also providing hints for the future development of new sustainable agriculture models. Ideally, these models will minimize the use of pesticides by providing natural solutions to soil-borne plant diseases. Many questions remain: What mediates root border cell shedding? How does the RET distinguish between harmful and friendly bacteria? Can root border cells produce more exDNA to replace strands cut up by nucleases? Whether plant or human, one thing is clear: The role of exDNA in health and hardship remains far understudied, yet of incredible topical relevance.

Sophia Swartz is a first-year undergraduate student planning to concentrate in Molecular and Cellular Biology with a secondary in French at Harvard University. You can find her on Medium as @sophia.swartz020.

Abagail Burrus is a third-year Organismic and Evolutionary Biology PhD student who studies elaiophore development.

For more information:

  • If you are interested in the role of exDNA in human health, check out this recent research profiling how higher levels of free exDNA circulating in the bloodstream can be used as a biomarker for active systemic lupus erythematosus (SLE).
  • To see exactly how nucleases affect RET structure and function, take a look at this paper examining how nuclease treatment cut up exDNA and effectively dissolved away the root traps.

4 thoughts on “Extracellular DNA, in Plant Health and Hardship

  1. Hi! My name is David Huskey and I’m a PhD candidate researching border cells at the University of Arizona. Your blog post is great and includes some of my work. I’m commenting here to let you know (in case you’re still interested in border cells) that we have some new publications highlighting really neat discoveries. Here are the links:

    “Use of rhodizonic acid for rapid detection of root border cell trapping of lead and reversal of trapping with DNase”

    “Trapping of lead (Pb) by corn and pea root border cells”

    Please feel free to contact me with any questions…I’m always happy to spread the word about border cells!

    1. Hi, David!

      Wonderful, thanks for sharing! Just happened by your comment tonight. Your work is definitely still an interest of mine and I love hearing updates, please keep them coming 🙂 I was wondering if you have done any sequencing work on the exDNA forming the traps?


  2. very impressive about the way that plants combat with pathogens, also it is like the masterpiece of God when created the plants.

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