How did bacterial glycogen branching enzymes evolve?

Hello and welcome to Research Pod! Thank you for listening and joining us today.

 

In this episode we will be looking at the research of Dr Liang Wang, associate professor at the Institut Pasteur of Shanghai, Chinese Academy of Sciences. Dr Wang  and his team aim to better understand the structure and evolution of one of the essential genes for bacterial glycogen metabolism.

 

Glycogen is a sugar which plays important roles in carbon and energy storage in bacteria. Glycogen with a highly branched, compact structure offers a more durable energy source. This characteristic is associated with bacterial environmental durability –  such as the ability to survive in deep sea vents.

 

Dr Liang Wang at the Institut Pasteur of Shanghai, Chinese Academy of Sciences and Ms Qing-Hua Liu at Macau University of Science and Technology aim to better understand the structure and evolution of glycogen branching enzyme in bacteria. Previous research indicates there were two main types of the key branching enzymes – but new research indicates there is in fact a third.

 

Glycogen is a type of multi-branched sugar (or polysaccharide) used for energy storage in animals, fungi, and bacteria. It’s extremely useful as a quick and easily accessible source of glucose and therefore energy. In bacteria, it plays an important role in storing carbon as well as energy.

 

Bacteria are incredibly hardy organisms, capable of living in some of the most extreme environments on Earth, such as deep-sea vents. Bacteria are able to break down and use glycogen as an energy source during unfavourable times, helping to boost their chances of long-term survival.

 

There are a large number of enzymes related to the function of glycogen within bacteria. Among all of them, the glgB-encoded branching enzyme, otherwise known as GBE, is unquestionably one of the most important, and determines glycogen structure.

 

The GBE gene plays an essential role in forming alpha-1,6-glycosidic branching points, and determines the unique branching patterns in the glycogen sugar. It’s these branches that make them easily available for energy within organisms.

 

Dr Liang Wang at Institut Pasteur of Shanghai and Qing-Hua Liu at Macau University of Science and Technology sought to understand the GBE gene better by undertaking a study into its structure and evolution. Glycogen structure has been linked with blood glucose control in human type 2 diabetes, so a clearer understanding of the regulation of glycogen structure in bacteria might also shed some light on the structural abnormalities of glycogen in higher organisms.

 

Previous evolutionary analysis of a small set of GBEs had revealed that two types of GBEs might exist. This was based on their N-terminal domain organisation. The N-terminus is the amine group  located at the start of the polypeptide chain that forms a protein. The first type of GBE (Type 1) had both N1 and N2 domains, whereas the second GBE type (Type 2) only had an N2 domain.

 

The researchers initially analysed the N-terminal domains of 169 manually reviewed bacterial GBEs, using hidden Markov models. In probability theory, Markov models are used to model randomly changing systems. A hidden Markov model is used when a state is partially observable.

 

Phylogenetic analysis found clustered patterns of GBE types in certain bacterial phyla (the level of biological classification below kingdom and above class). This analysis revealed that the shorter Type 2 GBEs were predominantly found in Gram-positive species, while the longer Type 1 GBEs were mainly found in Gram-negative species.

 

Gram-positive and Gram-negative describe the difference in outer layers between bacteria. Gram-positive bacteria have thick peptidoglycan layers that can absorb surrounding materials, whereas Gram-negative bacteria have multiple thin membrane layers that can excrete toxins.

 

Interestingly, the research also turned up a previously unreported third group of GBE (Type 3). These Type 3 GBEs had around 100 amino acids ahead of their N1 domains.

 

Several previous in vitro studies have linked N1 domains with the transfer of short oligosaccharide chains during glycogen formation.  Oligosaccharide chains are sugar polymers, containing typically three to ten monosaccharides. This could in turn lead to small and compact glycogen structures.

 

These compact glycogen structures are degraded more slowly. As a result, they may serve as a particularly durable energy reserve, which could contribute to the enhanced environmental persistence shown by bacteria.

 

The researchers suggested that this could form the basis of a new class of GBEs based on their N-terminal domain. The team ran large-scale sequence analysis to find out whether any patterns could be found. Their goal was to understand the evolutionary pattern of the different types of GBEs through phylogenetic analysis (the study of the evolutionary development of a species or a group of organisms or a particular characteristic of an organism). They carried out phylogenetic analysis at both the species and the sequence levels. The researchers also performed three-dimensional modelling of the GBE N-termini, to provide structural comparisons.

 

The researchers systematically investigated GBEs in thousands of bacterial species from the perspective of sequence evolution and domain structures. They analysed 9,387 GBE sequences, and identified 147 GBEs that could potentially belong to a new group of Type 3 GBE. Most of these bacteria fall into the phylum of Actinobacteria – a group of Gram-positive bacteria that can live on land or in water. They have a high guanine and cytosine content in their DNA and do not have a distinct cell wall.

 

The researchers also looked at whether there was any correlation between the average length of glycogen chains within the different GBE types.  Despite some differences being observed, correlation analysis in their study did not show statistical significance between GBE types and glycogen primary structure. One possible explanation for non-correlation is the analysis had an insufficient amount of data from a variety of sources.

 

Dr Wang’s work suggests that future studies applying standardised glycogen extraction and structure characterisation techniques in more bacterial species would be beneficial.  The research team believes that given how important the GBE N-terminus is for glycogen structure, it would be worth looking into the functions of the extended N-terminus in Type 3 GBE, and compare the results with those from Type 1 and Type 2 GBEs. The team also suggests that setting up the in situ expression of three types of GBEs in a model microorganism and comparing glycogen fine molecular structures could give a hint as to how the different types of N-terminus correlate with glycogen primary structure.

 

Notably, the N-terminal domain in bacterial GBEs has a high variability and comparative uniqueness. This could potentially serve as a future drug for the development of antibiotic treatment or as a biotechnological tool for enzymatically manipulating the glycogen structure. Future treatments could help to weaken bacterial persistence through the potential linkage between glycogen structure and bacteria’s energy supply.

 

That’s all for this episode – thanks for listening, and stay subscribed to Research Pod for more of the latest science. See you again soon.