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A self-regulated microbial system as an anti-pollutant for mercury contaminations

A programmed bacterial biofilm that autonomously switches between “growth” and “binding” states to detect and sequester toxic mercury from its environment opens the possibility for a green biological remediation strategy

By Benjamin Boettner

Mercury disseminated by humans, accumulating in environmental niches and spreading through food chains, in what is known as the ‘mercury cycle’, can lead to serious health problems, including damage to the brain, kidney and liver as well as developmental disorders in unborn children. Alarmingly, recent studies showed that mercury is an even more wide-spread soil and water pollutant than previously expected. The presently poor abilities to effectively sequester mercury in different soil and water environments calls for more innovative approaches capable of neutralizing the volatile and poisonous heavy metal also known as quicksilver.

In the mercury cycle, man-made and natural geochemical processes release mercury into the environment where it is absorbed by plants and animals in water and soil to become enriched in food chains. Credit: Wyss Institute at Harvard University

A team at Harvard’s Wyss Institute for Biologically Inspired Engineering lead by Core Faculty member Neel Joshi, has developed a green biological strategy that leverages bacterial biofilms as an effective tool to bind and sequester mercury from the environment. They designed and successfully tested a new method that is based on a self-regulating microbial system, which only in the presence of mercury triggers the production of self-assembling extra-cellular amyloid nanofibers to form an extensive biofilm matrix in the bacterial microenvironment. These dense nanofibers specifically bind to mercury ions from the environment, in essence acting as a biologically-generated sponge. This study is the team’s latest effort in designing ‘engineered living materials’ that are self-replicating, dynamic and autonomous.

In contrast to other biotechnological methods, that have attempted to use bacteria to either soak up mercury into their cell bodies or capture it with surface-exposed mercury-binding proteins, the Wyss team’s technology incorporates a synthetic biological circuit that dynamically responds to environmental mercury directly. Deploying engineered microbes in the field can be challenging, since they have a tendency to subvert their programming when it is an unnecessary burden to them. The synthetic circuit engineered by the team solves this problem by coupling the sensing of critical mercury levels to the production of a mercury-absorbing matrix. This is important because it provides a “pressure release” for the cells to balance their programming and their own proliferation, and it will also help mitigate issues related to the toxicity of rising mercury levels to the bacterial cells themselves, which limits their potential to regenerate.

The synthetic biological circuit at the core of the technology uses a regulatory DNA sequence that tightly controls the synthesis of the principle fiber-assembling protein. In the absence of mercury, a regulator protein called MerR tightly binds the sequence and blocks matrix production in the common laboratory bacterium E.coli. However, MerR also functions as a sensor that binds mercury ions as they seep into the bacterial cell. As a consequence, it changes its shape, causing it to fall off the DNA sequence to allow the fibrous matrix components to be produced. Joshi’s team finds that, once extruding amyloid fibers on their surface, the bacteria can absorb 4.5-fold more mercury than control bacterial cells at environmentally relevant concentrations of the heavy metal.

A self-regulated microbial system, in which environmental mercury ions (circles filled light blue) induce a synthetic biology circuit (purple) to produce a mercury-absorbing extra-cellular matrix (green) and the absence of mercury in the environment prevents matrix production, could become the basis of a new and effective bioremediation strategy. Credit: Wyss Institute at Harvard University

The synthetic biological circuit at the core of the technology uses a regulatory DNA sequence that tightly controls the synthesis of the principle fiber-assembling protein. In the absence of mercury, a regulator protein called MerR tightly binds the sequence and blocks matrix production in the common laboratory bacterium E.coli. However, MerR also functions as a sensor that binds mercury ions as they seep into the bacterial cell. As a consequence, it changes its shape, causing it to fall off the DNA sequence to allow the fibrous matrix components to be produced. Joshi’s team finds that, after assembling amyloid fibers on their surface, the bacteria can absorb 4.5-fold more mercury than control bacterial cells at environmentally relevant concentrations of the heavy metal.

“We have shown that nanofiber production and assembly can be repeatedly induced by a range of mercury concentrations, encompassing those commonly detected at mercury-contaminated sites, both in liquid and solid growth media, and that, in between, the bacterial population recovers and resumes growth. These engineered cells act as nanomaterial factories only when they sense mercury in the environment. Moreover, the assembled amyloid fibers work in mixed-metal environments, which is relevant to real-world applications, and retain bound mercury for more than 10 days, even with intermittent washes, meaning that they act as a strong and stable mercury sink,” said Wyss Technology Fellow Peter Nguyen, who with Graduate Student and co-first-author Pei Kun Tay performed the experiments.

The Wyss’ researchers think that the system can be further engineered towards even higher mercury-sensing and mercury-absorbing abilities and that it could be transferred to bacterial species typically thriving in the specific environments that frequently suffer from mercury contaminations. “Our long-term goal is to have an autonomously functioning engineered microbe that could be applied to a contaminated site or sample, and prevent mercury from spreading to plants or animals in the local environment,” said Joshi.

The article is published in ACS Synthetic Biology.

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