Illustration of the enzyme DmCE1B
Illustration of the enzyme DmCE1B. The carbohydrate-binding domain is shown in green, and one of the catalytic domains in yellow, and these together constitute the solved protein structure. The linker between the two domains is shown in red, and the site where the catalysis happens (the active site) in magenta. The other catalytic domain that is also part of the complete enzyme is shown schematically as a blue pacman symbol.
Illustration: Scott Mazurkewich


Unique enzymes help gut bacteria compete for food

The bacterial composition of the human gut can affect health. To investigate this, researchers need increased knowledge of this diverse bacterial ecosystem. In a recently published study in the Journal of Biological Chemistry, researchers at Chalmers investigated the strategy used by one bacterial species in the gut to compete for nutrients in dietary fibre. The study was selected as one of the journal’s top ranked publications, the so-called Editors’ Picks.

The systems and strategies used by gut bacteria to digest dietary fibre in our food varies between different species. Research has shown connections between bacterial composition to both health and different diseases. Thus, basic understanding of how the “good” gut bacteria work is important, for example how well they compete with other bacteria for nutrients in the gut.

Protective groups complicates degradation of dietary fibre

​In the gut, bacteria use enzymes, proteins that catalyse chemical reactions, to break down the complex polysaccharides, i.e. long carbohydrate chains, in dietary fibre into simple sugars. However, some of these polysaccharides are protected by chemical groups, that hinder enzymatic degradation. 

“How gut bacteria handle these protective groups has not been studied in detail. In our study, we have explored how the gut bacterium Dysgonomona's mossii degrades the complex plant polysaccharide xylan. This is an important component in dietary fibre, but the carbohydrate chains are protected by several chemical groups that make them difficult to degrade,” says Johan Larsbrink, Associate Professor of Industrial Biotechnology at the Department of Biology and Biotechnological Engineering.

Found three enzymes used to remove protective groups 

Dysgonomonas mossii belongs to in the phylum Bacteroidetes, which is a dominant group in the gut microbiota of humans, and they are considered "good" bacteria. Previous research has shown that in these species, the genes encoding enzymes for degrading carbohydrate chains are often found in large gene clusters in the DNA, so-called polysaccharide utilisation loci (PULs).

“We found three interesting enzymes, carbohydrate esterases, with different properties in a PUL in the bacterium, and we have shown how they are used to remove protective groups from xylan,” says Cathleen Kmezik, doctoral student at the Department of Biology and Biotechnological Engineering.

The PUL with the esterase genes also contains several other enzymes which degrade complex xylan chains. The clustering of the studied esterases with these other enzymes indicates that the ability to remove protective groups from carbohydrate chains is important for the bacteria to obtain nutrients.

Solved one enzyme's 3D structure

One of the esterases consists of two fused, catalytic, domains, which is rare. If you compare an enzyme to a pair of scissors that cuts specific chemical bonds, this esterase consists of two pairs of scissors physically connected to each other.

“This enables the esterase to cut different chemical bonds that are situated very close to each other. However, one part of this enzyme was not very active on the molecules we tested in our lab experiments, but Scott Mazurkewich, a post-doctoral researcher managed to solve its 3D structure by X-ray crystallography. This means that we can see exactly what the enzyme looks like down to a tenth of a nanometre scale and provides us with a better understanding of what the enzyme is actually doing in the gut,” says Cathleen Kmezik.

Removal of protective groups may be important for survival

The ability to remove protective groups from polysaccharides may be important for survival in the gut, according to the researchers. More research is needed, though, to determine which niches different bacteria have in terms of what they can eat in the gut − and whether it leads to increased survival and persistence under certain conditions.

Future studies could allow different species of bacteria to grow simultaneously on different carbohydrates with many or few protective groups and compare who "wins" the battle for nutrition. There is also potential for the enzymes to be used industrially to accelerate the enzymatic degradation of plant biomass in the production of biofuels.

Read the article in the Journal of Biological ChemistryA polysaccharide utilization locus from the gut bacterium Dysgonomonas mossii encodes functionally distinct carbohydrate esterases

Scott Mazurkewich, Cathleen Kmezik and Johan Larsbrink at IndBio

From Chalmers the researchers Scott Mazurkewich, Cathleen Kmezik and Johan Larsbrink (above)from the Division of Industrial Biotechnology, Alexander Idström from Applied Chemistry, and Marina Armeni and Otto Savolainen from CMSI, participated in the study.

More about the esterases:

  • DmCE1A: enzyme from carbohydrate esterase family 1 (CE1), active on acetyl esters and cleaving coumaryl-like molecules of unknown structure from plant biomass.

  • DmCE1B: enzyme consisting of two fused CE1 domains – DmCE1B_nt and DmCE1_ct, connected through a carbohydrate-binding module. Out of the three enzymes, DmCE1B_nt is the only one with clear activity on feruloyl esters, which can crosslink xylan polysaccharides, and it was also active on acetyl esters. DmCE1B_ct was only weakly active on acetyl esters. Its 3D structure was solved together with the carbohydrate-binding module. The structure indicates that the enzyme targets larger molecules than those tested in the lab (see figure).

  • DmCE6A: enzyme from carbohydrate esterase family 6 (CE6), with significant activity on acetyl esters, both in model substrates and in complex biomass. The enzyme was shown to strongly contribute to a faster xylan degradation by enzymes targeting the polysaccharide itself (xylanases).

Text: Susanne Nilsson Lindh
Illustration: Scott Mazurkewich
Photo: Martina Butorac

Page manager Published: Fri 21 May 2021.