Developments in lignin degradation: new microorganisms and enzymes at play

Like all known life forms, plants have a body made of organic matter, including cell walls made of various components including lignin, a heterogenous polymer. Lignin is the second-most abundant organic substance on earth with great potential in the production of industrial chemicals, such as aromatic compounds.

Chemically, lignin is made up of multiple subunits linked by ‘ether’ and ‘carbon-carbon’ bonds, all of which need to be broken down for lignin decay. It is well known that microorganisms cleave ether bonds effectively through the production of extracellular enzymes, which aid in lignin degradation. Two microbes that perform this degradation were identified: white-rot fungi through the production of peroxidases and laccases and Sphingomonad bacteria with the help of intracellular enzymes.

These discoveries sparked curiosity among a team of researchers including Dr. Toshiki Furuya and Ms. Saki Oya from Tokyo University of Science, and Dr. Hiroshi Habe from National Institute of Advanced Industrial Science and Technology in Tokyo, on whether there are additional, unknown microorganisms that degrade lignin through different enzymes. Identifying these microorganisms and finding out how they degrade lignin could enhance the overall understanding of the carbon cycle and facilitate the biotechnological applications of these microorganisms for lignin commercialization. The team also realized that none of the previous studies have focused on how microorganisms transform or degrade 2-PAP.

To find an answer to these questions, Dr. Furuya and his team conducted a study, published in Scientific Reports  to screen microorganisms that utilize new ether-bond cleaving enzymes, to transform 2-PAP. The team initially used a direct screening method to isolate microorganisms from soil based on their ether-bond cleaving activity, by growing them on a medium containing humic acid, a soil-derived organic compound, as a carbon source. Next, they incubated the isolated microorganisms with 2-PAP to check specifically for 2-PAP ether bond-cleaving activity. The bond cleaving activity was confirmed depending on the presence of phenol, which is generally produced as a result of ether-bond cleavage.

This led to the isolation of not one, but eight 2-PAP–transforming microorganisms! These included 7 bacteria from the genus Acinetobacter, Cupriavidus, Nocardioides, and Streptomyces, and 1 fungus from the genus Penicillium. “To our knowledge, these are the first microorganisms demonstrated to cleave the ether bond of 2-PAP”, Dr. Furuya emphasized, when asked about these discoveries.

Among the isolated microorganisms, the team examined a gram-negative bacterium, Acinetobacter sp. TUS-SO1 in detail and discovered that it selectively and oxidatively cleaves ether bonds in 2-PAP, to produce phenol and benzoate. This was especially surprising, because β-etherase, a well-studied enzyme known to perform this cleaving, gives phenol and acetophenone. This implies that this bacterial strain cleaves the ether-bond of 2-PAP using an unidentified enzyme!

When asked about the implications of these findings, Dr. Furuya says, “These newly identified microorganisms might play important roles in the degradation of lignin-based compounds in nature. By clarifying the properties of these microorganisms, we can apply them to lignin-based compounds for the generation of aromatic compounds, as an alternative to petroleum. Moreover, they can be utilized for lignin valorization, especially for the conversion of low-molecular-weight compounds that have chemical structures similar to 2-PAP”.

How is the technique for the identification of lignin-degrading microorganisms useful in the long-run? Well, according to the authors, this established search technology can be widely applied to search for microorganisms that exhibit cleavage activity against other ether compounds, such as environmental pollutants.

These discoveries are indeed exciting and can lead to the developments not just in industries that use lignin, but also in mitigating the effects of environmental pollutants!

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Reference
DOI: 10.1038/s41598-022-06816-1

About The Tokyo University of Science
Tokyo University of Science (TUS) is a well-known and respected university, and the largest science-specialized private research university in Japan, with four campuses in central Tokyo and its suburbs and in Hokkaido. Established in 1881, the university has continually contributed to Japan's development in science through inculcating the love for science in researchers, technicians, and educators.

With a mission of “Creating science and technology for the harmonious development of nature, human beings, and society", TUS has undertaken a wide range of research from basic to applied science. TUS has embraced a multidisciplinary approach to research and undertaken intensive study in some of today's most vital fields. TUS is a meritocracy where the best in science is recognized and nurtured. It is the only private university in Japan that has produced a Nobel Prize winner and the only private university in Asia to produce Nobel Prize winners within the natural sciences field.
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About Associate Professor Toshiki Furuya from Tokyo University of Science
Dr. Toshiki Furuya is an Associate Professor at the Department of Applied Biological Science in Tokyo University of Science. He graduated from the Division of Science and Engineering at Waseda University Graduate School with a PhD in the field of applied chemistry. As part of his research, he focuses on the biotechnological applications of microorganisms and enzymes. In particular, he studies microbial metabolism, enzyme catalysis, bioproduction, and bioremediation. Dr. Furuya has over authored over forty publications and received multiple awards including the 24^th Excellent Paper Award, from the Society of Biotechnology in Japan.