Biochemical engineers want to transform the abundant and renewable wood into bioplastics, medically relevant chemicals, food additives, or fuel. However, the wood’s complex structure has been a major hurdle for this.
A researcher from Kobe University and his team have developed a test feed for a fungal molecular machine. This breakthrough lets them observe its natural actions, paving the way for improvements and potential industrial applications.
The Kobe University bioengineer KOH Sangho explains, “Wood is composed of different, chemically linked materials such as lignin and hemicellulose that first need to be separated to become available as source materials.”
In simple terms, wood needs to be broken down. Fungi produce enzymes that can do this, but making them requires a detailed understanding of their work. Previously, they lacked a suitable “substrate” material to study the enzymes effectively.
Koh said, “As a graduate student at Shinshu University, I failed to produce the typical enzymatic reaction dynamics graph we know from the textbooks using the commonly used test substrate. I even reached out to the researcher who first found the enzyme to ask what I was doing wrong, but he replied that I wasn’t doing anything wrong and that my results were typical of attempts to characterize this enzyme.”
Inspired by this need, the bioengineer and his team developed a new material that keeps essential features of the enzyme’s natural substrate. This new material is also simple enough for chemical modifications and computer simulations.
Koh said, “The key to our ability to create a suitable substrate was that we had previously found another enzyme that allowed us to create very specific hemicellulose fragments that could not be produced in any other way. Only with these fragments could we chemically synthesize a suitable test substrate.”
As the first team to observe the isolated enzyme in a near-natural environment, they determined its reaction speed and affinity. These parameters are essential for bioengineers studying enzymes.
Koh said, “When, as a result of using the substrate I designed, textbook-like reaction dynamics emerged, I was really happy. With this, we can finally characterize the enzyme’s ‘true’ nature and improve and apply it industrially, too.”
Their simulations revealed a crucial difference in their approach. Previous researchers focused only on the specific site in the substrate where the enzyme should cleave, using a test substrate that lacked essential features. In contrast, Koh’s new substrate includes a short hemicellulose tail attached to the reaction site. This tail is crucial, as it’s what the enzyme binds to while working.
Now that the researchers understand the enzyme’s performance and reaction mechanism, they plan to look for better alternatives in other fungi. They also want to modify the molecule to see how it affects performance chemically. Additionally, they believe their test substrate will help study how this enzyme interacts with others to break down different wood components.
Koh concludes, “We think this was a significant step towards the process’s industrial application to the generation of useful chemicals from the abundant natural resource.”
Journal Reference:
- S. Koh et al.: Synthesis of a natural core substrate with lignin-xylan cross-linkage for unveiling the productive kinetic parameters of glucuronoyl esterase. Biochemical and Biophysical Research Communications. DOI: 10.1016/j.bbrc.2024.150642
