A new enzyme cocktail can digest plastic waste six times faster

Research undertaken at Diamond has allowed scientists to create a super-enzyme that degrades plastic bottles six times faster than before.

The super-enzyme, derived from bacteria that lives on a diet of plastic, enables the full recycling of plastic bottles. 

Plastic pollution is a global threat as plastics are rarely biodegradable and they can remain in the environment for centuries. One of the most abundant plastics that contributes hugely to this dire situation is poly(ethylene terephthalate) (PET). 
 
PET is used largely in textiles, where it is commonly referred to as polyester, but it is also used as packaging for liquids and foodstuffs. PET’s excellent water-repellent properties led to it being the plastic of choice for soft drink bottles. However, the water resistance of PET means that they are highly resistant to natural biodegradation and can take hundreds of years to break down in the environment. 

In 2018, researchers discovered that a unique bacterium (Ideonella sakaiensis 201-F6) was found feeding on waste from an industrial PET recycling facility. The bacterium had the amazing ability to degrade PET and use it to provide carbon for energy. Central to this ability was the production of a PET-digesting enzyme, known as PETase. 

Read more on the Diamond website

How cellular proteins control cancer spread

New finding may help focus the search for anti-cancer drugs

A new insight into cell signals that control cancer growth and migration could help in the search for effective anti-cancer drugs. A team of researchers has revealed key biochemical processes that advance our understanding of colorectal cancer, the third most common cancer among Canadians.

Using the CMCF beamline at the Canadian Light Source (CLS) at the University of Saskatchewan, scientists from McGill University and Osaka University in Japan were able to unlock the behavior of an enzyme involved in the spread of cancer cells. The team found that there is a delicate interaction between the enzyme, PRL3, and another protein that moves magnesium in and out of cells. This interaction is crucial to colorectal cancer growth.

A new insight into cell signals that control cancer growth and migration could help in the search for effective anti-cancer drugs. A team of researchers has revealed key biochemical processes that advance our understanding of colorectal cancer, the third most common cancer among Canadians.

Using the CMCF beamline at the Canadian Light Source (CLS) at the University of Saskatchewan, scientists from McGill University and Osaka University in Japan were able to unlock the behavior of an enzyme involved in the spread of cancer cells. The team found that there is a delicate interaction between the enzyme, PRL3, and another protein that moves magnesium in and out of cells. This interaction is crucial to colorectal cancer growth.

Read more on the Canadian Light Source website

Image: Members of the Gehring research laboratory discussing the results of a protein purification.

Research could lead to better herbicides and infection treatments

Researchers from the University of Queensland (UQ) have used the Australian Synchrotron and cryo-electron microscopy in China to determine the three-dimensional structure of a complex enzyme found in plants microbes that could be used to develop advanced herbicides and treatments for infection.

A large international team led by Prof Luke Guddat of UQ published the structure of the enzyme acetohydroxyacid synthase (AHAS) in the journal Nature and also explained the first step in how the enzyme regulates the biosynthesis of three essential amino acids, leucine, valine and isoleucine.

“The way that the complex regulates this pathway had been unknown until now. We were finally able to explain it by understanding how the entire structure was assembled,” said Prof Guddat, who has been researching this enzyme for twenty years.

Read more on the Australian Synchrotron website

Image: The 3D structure resembles a ‘Maltese Cross’.

New substance library to accelerate the search for active compounds

In order to accelerate the systematic development of drugs, the MX team at the Helmholtz-Zentrum Berlin (HZB) and the Drug Design Group at the University of Marburg have established a new substance library. It consists of 1103 organic molecules that could be used as building blocks for new drugs. The MX team has now validated this library in collaboration with the FragMAX group at MAX IV. The substance library of the HZB is available for research worldwide and also plays a role in the search for substances active against SARS-CoV-2.

For drugs to be effective, they usually have to dock to proteins in the organism. Like a key in a lock, part of the drug molecule must fit into recesses or cavities of the target protein. For several years now, the team of the Macromolecular Crystallography Department (MX) at HZB headed by Dr. Manfred Weiss together with the Drug Design Group headed by Prof. Gerhard Klebe (University of Marburg) has therefore been working on building up what are known as fragment libraries. These consist of small organic molecules (fragments) with which the functionally important cavities on the surface of proteins can be probed and mapped. Protein crystals are saturated with the fragments and then analysed using powerful X-ray light. This allows three-dimensional structural information to be obtained at levels of atomic resolution. Among other things, it is possible to find out how well a specific molecule fragment docks to the target protein. The development of these substance libraries took place as part of the joint Frag4Lead research project and was funded by the German Federal Ministry of Education and Research (BMBF).

Read more on the BESSY II website

Image : For the study, the enzyme endothiapepsin (grey) was combined with molecules from the fragment library. The analysis shows that numerous substances are able to dock to the enzyme (blue and orange molecules). Every substance found is a potential starting point for the development of larger molecules. 

Credit: Wollenhaupt/HZB

Helping our immune systems bypass antibiotic resistance

Over 700,000 people die each year due to drug-resistant diseases and this figure could increase to 10 million per year by 2050, according to a 2019 report.

As the search continues for new antibiotics to treat drug-resistant infections, a group of researchers used the Canadian Light Source (CLS) at the University of Saskatchewan to address the problem from a different direction, by trying to weaken the ability of bacteria to develop resistance in the first place.

“The goal is to knock the bacterial cells down in terms of their resistance,” said Dr. Anthony Clarke, Professor and Dean of Science at Wilfrid Laurier University and adjunct professor at the University of Guelph. “We haven’t been successful over the last 30 years in finding new classes of antibiotics so, in the short term, we’re trying to weaken the cells so our own immune system can take over to fight infection.”

The target for his team’s work is peptidoglycan, which gives bacterial cell walls their rigidity. “Think of it as building a brick wall around the bacteria’s cells,” said Clarke. Since peptidoglycan can be broken down by lysozyme, an enzyme that exists in human immune systems, bacteria have developed strategies that block these enzymes by modifying their peptidoglycan, thereby “cementing the bricks in place,” and resisting our defences.

Read more on the Canadian Light Source website

Image: Dr. Clarke inspecting flasks of bacterial cultures in a student laboratory.

Preventing hospital-acquired pneumonia

Researchers used the Canadian Light Source (CLS) at the University of Saskatchewan to identify a previously unrecognized family of enzymes that put us at risk for deadly diseases.

Klebsiella pneumoniae is responsible for a variety of hospital-acquired infections such as pneumonia and sepsis. The bacterium has become increasingly resistant to antibiotics, making it a focus of interest for health care professionals and researchers.

>Read more on the Canadian Light Source website

Image: Chris Whitfield has been working on polysaccharides like LPS throughout his career.

The future of fighting infections

Scientists analyze 3D model of proteins from disease-causing bacteria at the CLS.

Millions of people are affected by the Streptococcus pneumoniae bacterium, which can cause sinus infections, middle ear infections and more serious life-threatening diseases, like pneumonia, bacteremia, and meningitis. Up to forty percent of the population are carriers of this bacterium.
Researchers from the University of Victoria (UVic) used the Canadian Light Source (CLS) at the University of Saskatchewan to study proteins that the pathogen uses to break down sugar chains (glycans) present in human tissue during infections. These proteins are key tools the bacterium uses to cause disease.

They used the Canadian Macromolecular Crystallography Facility (CMCF) at the CLS to determine the three-dimensional structure of a specific protein, an enzyme, that the bacterium produces to figure out how it interacts with and breaks down glycans.

>Read more on the Canadian Light Source website

Image: The 3D structure of an enzyme from the disease-causing bacterium Streptococcus pneumoniae.

Scienstists make breakthrough in creating universal blood type

Enzymes in the human gut can convert A blood type into O.

Half of all Canadians will either need blood or know someone who needs it in their lifetime. Researchers from the University of British Columbia have made a breakthrough in their technique for converting A and B type blood into universal O, the type that is most needed by blood services and hospitals because anyone can receive it.
In a paper published in Nature Microbiology, Stephen Withers and a multidisciplinary team of researchers from the University of British Columbia show how they successfully converted a whole unit of A type blood to O type using their system.  They were able to remove the sugars from the surface of the red blood cells with help from a pair of enzymes that were isolated from the gut microbiome of an AB+ donor.
The Canadian Light Source (CLS) at the University of Saskatchewan (UofS) played a critical role in understanding the structure of a previously unknown enzyme that was part of this pair. The researchers were unable to identify what this unique enzyme looked like from the gene sequence they had.  Crystallography, done at the CLS, was crucial for the researchers to understand how this enzyme works and why it had a particular affinity for the A type blood.

>Read more on the Canadian Light Source website

“Molecular scissors” for plastic waste

A research team from the University of Greifswald and Helmholtz-Zentrum-Berlin (HZB) has solved the molecular structure of the important enzyme MHETase at BESSY II.

MHETase was discovered in bacteria and together with a second enzyme – PETase – is able to break down the widely used plastic PET into its basic building blocks. This 3D structure already allowed the researchers to produce a MHETase variant with optimized activity in order to use it, together with PETase, for a sustainable recycling of PET. The results have been published in the research journal Nature Communications.

Plastics are excellent materials: extremely versatile and almost eternally durable. But this is also exactly the problem, because after only about 100 years of producing plastics, plastic particles are now found everywhere – in groundwater, in the oceans, in the air, and in the food chain. Around 50 million tonnes of the industrially important polymer PET are produced every year. Just a tiny fraction of plastics is currently recycled at all by expensive and energy-consuming processes which yield either downgraded products or depend in turn on adding ‘fresh’ crude oil.

>Read more on the BESSY II at HZB website

Image: At the MX-Beamlines at BESSY II, Gottfried Palm, Gert Weber and Manfred Weiss could solve the 3D structure of MHETase.
Credit: F. K./HZB

Enzyme structure of bacteria that causes tuberculosis

Results on its interaction with antibiotics may lead to the development of new forms of treatment for this disease.

Tuberculosis is a chronic infection usually caused by a bacterium called Mycobacterium tuberculosis. This bacterium infects cells of the immune system called alveolar macrophages, which are responsible for removing pollutants and microorganisms from the surface of the alveoli, where the exchange of gases occurs during respiration.
It is estimated that approximately two billion people worldwide are infected with M. tuberculosis without symptoms. However, the clinical manifestations of the disease may appear at any time in life, especially when the immune system is weakened, such as due to malnutrition or diseases such as cancer and AIDS.
Tuberculosis is considered a curable disease when the patient is diagnosed and treated promptly with antibiotics. Nevertheless, the chronicity of this infection makes it difficult to eradicate bacteria altogether. Generally, patients must take the medication for several months, making it harder for them to persist in the treatment and favoring the emergence of antibiotic-resistant bacteria. In recent years, the emergence of new bacteria, resistant to routine treatments, has been a worldwide concern and it is imperative to seek new therapeutic strategies against this disease.

>Read more on the Brazilian Synchrotron Light Laboratory (LNLS) 

Image: (extract, full image here) Elements of the secondary structure of L,D-transpeptidase-3 from Mycobacterium tuberculosis acylated by an acetyl fragment derived from faropenem. Beta sheets in red, α-helices in yellow and the loops are shown in green. The figure shows, at the amino terminus (N-ter), the bacterial domain similar to immunoglobulin (BIg) and in the carboxy terminus the catalytic domain (CD). B-loop is a unique structure of this enzyme when compared to the other M. tuberculosis L,D-transpeptidases. In blue is shown an acetyl fragment covalently attached to cysteine 246 at the active site of the enzyme. Figure taken with Pymol.

Inorganic nanoparticles activity as artificial pro-enzymes

Research opens perspective for treatment of several diseases tailored to the needs of each patient

From the biochemical point of view, we are a complex set of interconnected chemical reactions. The molecules that make up our bodies are in constant transformation, and this is what makes it possible for us to get energy from food, to regenerate damage to our tissues, and to synthesize the compounds necessary for life.
These modifications usually occur with the aid of other molecules called enzymes, which promote and accelerate chemical reactions without being consumed during the process.

For the proper functioning of this complex system, the enzymes must act only at the necessary place and time. Hence, nature has developed an ingenious strategy for this to happen: inactive forms of enzymes, known as proenzymes, are continuously produced, but are activated only by specific stimuli.
The occurrence of a problem in the production of these enzymes can result in highly debilitating diseases. However, the treatment of patients by means of enzymatic replacement from natural sources is not always an adequate solution.
Therefore, researchers have been investigating synthetic systems to mimic the action of natural enzymes for biomedical applications and one of the most promising alternatives is the use of nanoparticles.

>Read more on the Brazilian Synchrotron Light Laboratory website

Image: Schematic figure of the action of the ultrafine cerium(III) hydroxide and cerium oxide CeO (2-x) nanoparticles . Back cover image from the Journal of Materials Chemistry B [1].

Canadian researchers unlock how seaweed is digested

Cattle on the Prairies are hundreds of kilometres from the coast and yet it’s possible that seaweed could make its way into their diet as an additive.

“Seaweed is an incredible opportunity. It is a sustainable feedstock. It grows rapidly, it doesn’t require arable land or fresh water to grow,” said Wade Abbott, research scientist at Agriculture and Agi-Food Canada’s Lethbridge Research and Development Centre.

It may seem like a leap to go from the human gut to that of cattle, but Abbott explained that by understanding the human gut microbiome, or microorganisms, and the microbiome’s ability to use the sugars found in seaweed in its symbiotic relationship with the host, he sees potential to expand what is now a limited use of algae products.

>Read more on the Canadian Light Source website

Image: Culturing gut bacteria in the lab (shown in these test tubes) allows researchers ‎to determine which genes in the genomes of bacteria are activated and discover new enzymes that digest rare substrates like agarose.
Credit: Wade Abbott

The proteins that bind

Researchers reveal the structure of a protein that helps bacteria aggregate

Serine-rich repeat proteins (SRRPs), which help bacteria attach to surfaces, have been structurally characterised in pathogenic bacteria but not in beneficial bacteria such as those present in the gut. Dr Nathalie Juge’s team at the Quadram Institute Bioscience has previously identified SRRP as a main adhesin in Lactobacillus reuteri strains from pigs and mice. Now, together with colleagues at the University of East Anglia, they have described the structure and activity of the binding region of L. reuteri SRRPs in a paper published in PNAS. Using the Macromolecular Crystallography beamlines (I03 and I04) at Diamond Light Source, they discovered that the structure of these proteins is unique among characterised SRRPs and is surprisingly similar to pectin degrading enzymes. Molecular simulations and binding experiments revealed a pH-dependent binding to pectin and to proteins from the epithelium known as mucins. Altogether, these findings shed light on the activity of a key protein in these bacteria and may help guide the development of more targeted probiotic interventions.

>Read more on the Diamond Light Source website

Figure: (Left) Cartoon representation of crystal structures of the binding region of SRRP53608. (Right) Cartoon representation of crystal structures of the binding region of SRRP100-23. The N-terminus is shown with blue balls and the C-terminus is shown with red balls.

Solution to plastic pollution on the horizon

Engineering a unique plastic-degrading enzyme

The inner workings of a recently discovered bacterium with a fascinating ability to use plastic as an energy source have been recently revealed in PNAS. The world’s unique Long-Wavelength Macromolecular Crystallography (MX) beamline here at Diamond Light Source was used to successfully solve the structure of the bacterial enzyme responsible for chopping up the plastic. This newly evolved enzyme could be the key to tackling the worldwide problem of plastic waste.

Plastic pollution is a global threat that desperately needs addressing. Plastics are rarely biodegradable and they can remain in the environment for centuries. One of the most abundant plastics that contributes hugely to this dire situation is poly(ethylene terephthalate) (PET).

PET is used largely in textiles, where it is commonly referred to as polyester, but it is also used as packaging for liquids and foodstuffs. In fact, PET’s excellent water-repellent properties led to it being the plastic of choice for soft drink bottles. However, once plastic bottles are discarded in the environment the water resistance of PET means that they are highly resistant to natural biodegradation. PET bottles can linger for hundreds of years and plastic waste like this will accumulate over time unless a solution is found to degrade them.

A recent breakthrough came in the discovery of a unique bacterium, Ideonella sakaiensis 201-F6, which was found feeding on waste from an industrial PET recycling facility. PET has only been widely used since the 1970s, so the bacterium had evolved at breakneck speed to be able to take advantage of the new food source.

The bacterium had the amazing ability to degrade PET and use it to provide carbon for energy. Central to this ability was the production of a PET-digesting enzyme, known as PETase.

>Read more on the Diamond Light Source website