Scientists discover new enzyme families that break down rare bacterial 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. 

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Reference 
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 
DOI: 10.1002/PRO.70147 
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 

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