Exploring the Potential of Biocatalysis: From Microbial Biochemistry to Advancing Ligninolytic Enzymes through Structural Characterization, Enzyme Engineering, and AI Innovations
Lígia Martins is a microbial and enzyme technology professor at ITQB, NOVA University Lisbon in Portugal. She started her career in microbial biochemistry, exploring the biosynthetic pathways of industrial exopolysaccharides like gellan in bacteria. During her post-doctoral research, she studied the archaeon Pyrococcus furiosus, which thrives at extreme temperatures of 80-100°C. They observed organic solutes accumulate in response to both osmotic stress and elevated temperatures, challenging existing notions of microbial physiology and highlighting their potential as thermal stabilizers in various applications. “Later, as a senior researcher, I investigated enzymes in the Bacillus subtilis spore coat, known for their role in the extreme resistance of dormant spores,” Prof. Martins explained. Her work with a laccase enzyme gained significant recognition, with two seminal papers cited over 450 times, laying the foundation for her independent career. This led her to focus on ligninolytic enzymes, particularly in bacterial systems, due to their untapped potential and the ease of gene cloning and enzyme engineering in bacteria. “I decided to focus my research on understanding the enzymes and mechanisms involved in the decomposition/conversion of lignocellulose, with a particular emphasis on lignin. Despite being considered a bio-waste, lignin, Earth's most abundant aromatic polymer, boasts endless applications”.
Prof. Martins has a particular affinity for metalloenzymes because of their fascinating organic-inorganic interplay. She finds the evolution of protein functions in conjunction with transition metals, influenced by their abundance in the universe and availability on Earth, captivating. “I also favour enzymes that use oxygen as an electron acceptor due to its critical role in most living organisms' metabolism,” she added. While Lígia is well-versed in working with bluish laccases (multicopper oxidases), her "favourite" enzymes are those that can be produced quickly and in decent yields, facilitating structural and functional studies.
Prof. Martins’ research focuses on identifying and characterizing new enzymes. Her team has pioneered the structural and functional characterization of not only laccases but also bacterial pyranose oxidases, which are pivotal for lignocellulose degradation, as H2O2 donors for lignin-degrading peroxidases and facilitating Fenton attack on cellulose, and DyP-type peroxidases, notable for their unique structural and mechanical features. “Additionally, we aim to advance the molecular understanding of these enzymes, revealing critical fingerprints and mechanisms, such as solvent accessibility of catalytic centres, electrostatic interactions modulating redox potential, and the molecular dynamics behind their stability and oxygen reduction to water”, she explained.
Prof. Martins emphasizes that they also engineer enzymes to enhance their performance and robustness through computational and directed evolution methodologies. This has led to the discovery of enzyme variants featuring 100-fold enhanced catalytic efficiency for lignin-related phenolics. Furthermore, they are designing sustainable bioprocesses using their fundamental findings, like the detailed mechanism of lignin-related phenolic oxidation by bacterial laccases and enzymatically producing numerous versatile aromatic scaffolds with biological activity.
Prof. Martins believes enzymes are pivotal in addressing global challenges by transforming renewable feedstocks into various bioproducts, materials, biofuels, and energy sources. She emphasized that this transformative capability is not just a scientific endeavor, but a crucial step towards a sustainable future, essential for tackling climate change and reducing our dependence on fossil fuels, aligning with initiatives like the European Green Deal. "By focusing on these processes, we can simultaneously address three mutually reinforcing goals: high employment levels, enhanced productivity, and social cohesion," she said.
She also highlighted recent advancements in computational tools, particularly deep learning and neural networks, which have accelerated structural and evolutionary studies, expediting enzyme discovery and engineering. Unlike traditional model-driven rational design, machine learning offers a data-driven approach that can generate novel biocatalysts based on patterns in existing data. Professor Martins noted, "AI systems hold the potential to create artificial enzymes from scratch, heralding a new era in biocatalysis within the next decade."
However, she cautioned that this brave new world comes with significant challenges and limitations that must be navigated as the field progresses. Lígia remains optimistic but aware of the hurdles ahead.
Link to Prof. Lígia O. Martins’ research group https://www.itqb.unl.pt/research/biological-chemistry/microbial-enzyme-technology
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