Serendipity and Biomechanics
by Thamarasee Maheshika Jeewandara
An early career researcher’s path is not always well-defined. Sometimes at this juncture, observing the accidental career trajectories of researchers who serendipitously made discoveries in science against all odds can be inspiring. Also at such passages, we become acutely aware of the environment surrounding us and our ability to make a difference. This narrative aims to combine such two seemingly disparate themes. In science, seemingly serendipitous inventions are based on collaborative efforts that stand on the shoulders of many great minds. From the discovery of penicillin, to radioactivity and even the serendipity of an apple falling at Newton’s feet, groundbreaking discoveries are made when creative-minded scientists follow-up on interesting observations with meticulous experiments. During the process of discovery, researchers converge from seemingly disparate disciplines to address a fundamental problem through careful study. This was particularly observed in the 1930’s when physicists were racing to discover new ideas and insights to enable our current understanding of the physical world. At other times the natural world can offer unexpected insights, to resolve fundamental questions in science. Key developments through years of research across disciplines have led to the currently exciting stage of scientific advancement. The role of serendipity and biomechanics is combined to highlight a recent discovery that was accidentally made while observing a natural phenomenon in a species of bacteria, leading to an environmental breakthrough.
Increasing Global Awareness
A team of scientists recently collaborated to understand the naturally evolved mechanism of the bacterium Ideonella sakaiensis to degrade synthetic polymers i.e., plastics, when they serendipitously engineered a better version of the enzyme. Plastic pollution is an escalating crisis on the planet, affecting numerous biological ecosystems. Efforts to increase global awareness have therefore become crucial, with notable recent attempts including this year’s theme for Earth Day and David Attenborough’s Blue Planet II series. In less than a century since its manufacture, plastic is ubiquitous due to its versatility and cheap cost, although its alarming resistance to biodegradability by lasting centuries or more in the environment, is best described as an ‘insidious nightmare.’ Approximately 6.3 billion tons of plastic waste is estimated to cover landfills and float in oceans, risking biological ecosystems and sustainability of marine life. With about 1 million plastic bottles sold per minute, and no sign of a remedy to the increasing wastelands of plastic, the search for an adequate mechanism of plastic recycling/degradation is imperative.
Scientists have previously investigated multiple pathways, including plastic-plucking robots and attempts to gauge the plastic pollution coverage from space. Thus the discovery of a mutant bacteria with ability to degrade the abundant synthetic plastic poly(ethylene) terephthalate (PET) and simply answer a long-quest was ‘a bit of a shock.’ The bacterium Ideonella sakaiensis was found in the waste from an industrial PET recycling facility. It is likely that the catabolic enzyme system PETase only developed recently given that PET was patented merely 80 years ago. While this highlights the remarkable speed of adaptation and evolution among microbes in nature. The discovery was even more important due to its potential to address the persistent challenge of polymer degradation in the natural environment. Scientists then immediately set-forth to solve the 3D crystal structure of the polymer-degrading PETase enzyme using X-ray crystallography.
Bioengineering a serendipitous outcome
A team of researchers from the University of Portsmouth and the Diamond Light Source in the United Kingdom, collaborated to gather information on the structure of the catabolic enzyme first. The diamond light source contains a synchrotron that uses intense beams of X-rays to act as a microscope and visualize individual atoms. In this instance, the I23 beamline was used to obtain an ultrahigh resolution of the 3D PETase enzyme structure in exquisite detail (Video 1). The ability to see the inner workings of the biological catalyst provided the blueprint to engineer a faster and more efficient version of the enzyme. The observation provided valuable information – in that the new catalyst had a similar structure to cutinase; an enzyme that breaks down cutin, a natural polymer in plants. PETase had a comparatively more open active-site to specifically accommodate man-made polymers. To test the hypothesis that adaptive evolution in a PET containing environment enabled bacteria to breakdown the synthetic polymer, researchers decided to mutate the active site of PETase to create a more cutinase-like conformation.
This is when the unexpected happened. Researchers engineered a double mutant PETase enzyme that was better than the natural PETase counterpart in degrading PET. The new enzyme can also degrade another variant of synthetic plastic, back to their original building blocks allowing a sustainable solution to recycling plastics. The implication of this innovative process can offer global solutions to eradicating plastic waste, while reversing synthetic polymers to their original components such as crude oil, with wide-ranging applications. The results of the study were published online in April 2018, with ongoing investigations to engineer an optimized version of the PETase enzyme.
Creating a scientifically advanced sustainable future
This experimental investigation and process of discovery is a classic example of the role of serendipity in fundamental scientific research. The process of discovery follows a familiar pattern by collaboratively designing a series of experiments to follow up on an interesting observation with global implications. An environmental breakthrough, standing on the shoulders of many scientific minds. Innovative solutions of this nature are merely the beginning. Further optimizations of the engineering process can create enzymes that accelerate the process of degradation to eliminate aggregates of plastic waste from landfills across ecosystems. The discovery provides substantial hope, moving forward from a bleaker environment. However, the development of efficient, plastic degradable-enzymes alone need not be an end to a means, as more conscientious efforts can be globally followed to reduce the rates of plastic use. In this way, reflecting on the undercurrents of the scientific process and the scientist’s ability to contribute towards fundamental change, may also shine a light to continue navigating into the unknown.
This post is based on the research carried out in the following publication: http://www.pnas.org/content/early/2018/04/16/1718804115
Video 1: in this article is Royalty-free hosted via Vimeo: https://vimeo.com/264972394
Featured image: Rey Perezoso shared under the CC-BY-SA 2.0 license.
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