Scientists Discover New Enzyme Families That Break Down Rare Bacterial Carbohydrates

Discovery of the new glycoside hydrolase families that break down β-1,2-glucans opens the door to synthetic carbohydrate production

Phylogenetic tree of SGL-clan enzymes, highlighting known (black), newly identified (red), and uncharacterized (blue) families. Known GH families are also marked in green, new ones in blue, and unknown groups in gray. Proteins used in this study are marked as red closed circles.

Enzymes in each group are superimposed with a GH144 enzyme. The GH144 enzyme and its substrate are shown in green and white, respectively. Group 1, Group 2, Group 3, TfSGL (GH162) and TiCGSTg(GH189) are shown in cyan, purple, light blue, orange, and pink, respectively.

Enzymes in each group are superimposed with a GH144 enzyme. The GH144 enzyme and its substrate are shown in green and white, respectively. Group 1, Group 2, Group 3, TfSGL (GH162) and TiCGSTg(GH189) are shown in cyan, purple, light blue, orange, and pink, respectively. Residue numbers are of enzymes in each group (top) and the GH144 enzyme (bottom). Residues highlighted in red represent those that are indicators of SGL clan enzymes. Catalytic residues and candidates for catalytic residues are highlighted in bold letters. Asterisks represent diversity in the positions of (candidate) base catalysts or a nucleophile, which is also represented schematically in the next figure.

Overview of three distinct reaction mechanisms used by SGL-clan enzymes to act on β-1,2-glucans. Catalytic residues (including candidates) and a nucleophile are highlighted in red letters to show mechanistic diversity across enzyme families.

β-1,2-glucans are rare bacterial carbohydrates involved in key biological processes, but their structural complexity has limited research progress. Now, a study led by researchers from Japan reports the discovery of new enzyme families that break down these molecules and proposes a new enzyme group called the “SGL clan.” These findings shed light on the molecular evolution of carbohydrate-degrading enzymes and open doors to engineering synthetic enzymes for producing novel carbohydrates.

The molecules that form the foundation of life on Earth are as diverse as they are complex. Among these, carbohydrates play a vital role as energy sources and in structural functions, such as forming cell walls. One class of carbohydrates, β-1,2-glucans, consists of glucose chains and is found in bacteria. These molecules are involved in various important biological processes, such as bacterial infection and environmental adaptation. Despite their biological significance, β-1,2-glucans are rare, compared to cellulose and laminarin, and structurally complex, making them particularly difficult to study.

In a recent study published in Volume 34, Issue 6 of the journal Protein Science on May 24, 2025, researchers from Tokyo University of Science (TUS) have made significant progress by identifying and characterizing new enzymes that break down glycan molecules. The team investigated a group of unclassified glycoside hydrolases (GH) related to known β-1,2-glucan-degrading enzymes in families GH144 and GH162. Through a combination of sequence, biochemical, structural, and phylogenetic analyzes, the team identified new phylogenetic groups that showed enzymatic activity toward β-1,2-glucans. β-1,2-glucanase (SGL) breaks down β-1,2-glucan into β-1,2-glucooligosaccharides.

The study was conducted by a team at TUS, led by Associate Professor Masahiro Nakajima and supported by former doctoral student Dr. Sei Motouchi, with additional collaboration from Associate Professor Hiroyuki Nakai of Niigata University and Dr. Kaito Kobayashi of National Institute of Advanced Industrial Science and Technology.

“Glycans serve numerous physiological functions, but due to their complexity and difficulty in synthesis, studying them is challenging in many cases. However, practical synthesis of glycans aids in exploring newer degrading enzymes, and these enzymes can potentially be used to synthesize glycans. This duo of synthesis and degradation helps in enriching the knowledge in the domain of carbohydrate-associated enzymes,” explains Dr. Nakajima, as the motivation behind the study. The team believes that by discovering new degrading enzymes, the exploration of additional enzymes based on that could be possible. This could revolutionize the development and study of different carbohydrate molecules.

The team began their investigation by analyzing sequences related to known SGLs (β-1,2-glucanases), enzymes that break down β-1,2-glucans. This led to the identification of four previously uncharacterized potential glycoside hydrolase (GH) families. Of these, three were found to degrade β-1,2-glucans as SGLs, marking a significant breakthrough. These enzymes showed only 16–20% amino acid sequence similarity to each other but shared structural features, such as the (α/α)6-barrel, which is also found in GH144 and GH162 enzymes. Additionally, they all shared a common anomer-inverting reaction mechanism to cleave β-1,2-glucan molecules.

Based on these findings, the researchers proposed a new enzyme group, termed the “SGL clan,” which includes GH144, GH162, and the three new GH families they have named GH192, GH193, and GH194. Though the GH189 family possesses an anomer-retaining mechanism rather than the other families, it has been included as a member of the SGL clan.

Remarkably, the study found that the irregular distribution of several patterns of reaction mechanisms was determined by the positions of catalytic residues across the SGL clan phylogenetically. Another significant finding is that even though the enzymes perform similar functions, they share only three conserved residues (E239, Y367, and F286), suggesting that these three residues are the SGL-clan defining residues. These two factors also suggest a unique path of molecular evolution.

By uncovering new enzyme families and revealing their unique molecular evolution within the SGL clan, this study significantly advances our understanding of carbohydrate metabolism and could lead to applications in medicine, agriculture, or biofuels.

“The identification of this clan showcases the extensive diversity of carbohydrate-active enzymes. If the reaction mechanism can be elucidated, it will be possible to use it to modify enzyme function, converting degradative enzymes into synthetic enzymes to synthesize new oligosaccharides,” concludes Dr. Nakajima.

This research thus demonstrates the potential for discovering enzymes that are involved in carbohydrate degradation, with special emphasis on their structure, molecular evolution, and distribution.

Reference
Title of original paper: New glycoside hydrolase families of β-1,2-glucanases
Journal: Protein Science
DOI: 10.1002/PRO.70147
Authors: Masahiro Nakajima1*, Nobukiyo Tanaka1, Sei Motouchi1, Kaito Kobayashi1,2, Hisaka Shimizu1, Koichi Abe1,3, Naoya Hosoyamada1, Naoya Abara1, Naoko Morimoto1, Narumi Hiramoto1, Ryosuke Nakata1, Akira Takashima1, Marie Hosoki1, Soichiro Suzuki1, Kako Shikano1, Takahiro Fujimaru1, Shiho Imagawa1, Yukiya Kawadai1, Ziyu Wang1, Yoshinao Kitano1, Takanori Nihira4,5, Hiroyuki Nakai4, and Hayao Taguchi1
Affiliations:
1 Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Japan
2 Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Japan
3 Department of Biotechnology, The University of Tokyo, Japan
4 Faculty of Agriculture, Niigata University, Japan
5 Faculty of Engineering, Niigata Institute of Technology, Japan

Further Information
Associate Professor Masahiro Nakajima
Department of Life and Biological Sciences,
Tokyo University of Science
Email: m-nakajima@rs.tus.ac.jp

Dr. Sei Motouchi
Department of Life and Biological Sciences,
Tokyo University of Science
Email: seimotouchi@rs.tus.ac.jp

Dr. Kaito Kobayashi
Artificial Intelligence Research Center
National Institute of Advanced Industrial Science and Technology (AIST)
Email: k-kobayashi@aist.go.jp

Associate Professor Hiroyuki Nakai
Department of Agriculture,
Niigata University
Email: nakai@agr.niigata-u.ac.jp

Funding information
This work was supported in part by JSPS KAKENHI (Grant number 23K05041) and JST SPRING (Grant number JPMJSP2151).

Media contact
Yoshimasa Iwasaki
Public Relations Division,
Tokyo University of Science
Email: mediaoffice@admin.tus.ac.jp
Website: https://www.tus.ac.jp/en/mediarelations/

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Branding and Public Relations Department
National Institute of Advanced Industrial Science and Technology (AIST)
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Public Relations Office Niigata University
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