HADDOCK shows how bacteria steal iron from the plants they infect


Researchers using the HADDOCK modelling software, a key part of the BioExcel community, have discovered how bacteria steal iron from plants, helping the bacteria cause infection.

Iron is an essential element for life. Mammals, for example, use it to carry oxygen in red blood cells, plants need it to transport electrons. Bacteria are not an exception, and they also need iron to infect other organisms and survive.

The problem for bacteria is that iron is not readily available in their environment. Animal and plant cells tend to ‘hide’ their iron inside proteins to prevent bacteria from getting it and stop infections before they start. So bacteria had to escalate the evolutionary war and come up with mechanisms to get the iron they need.

Rhys Grinter, a microbiologist based at Monash University in Australia, investigated how Pectobacterium (the bacteria responsible for blackleg disease in potatoes or for slime flux in many species of trees) sources iron from the plants it infects.

He and his colleagues found that Pectobacterium cells have a receptor – dubbed FusA – specially adapted to grab the iron from ferrodoxin proteins.

“Ferredoxin is a small iron-containing protein which plants use in a similar way to hemoglobin, but for transporting electrons rather than oxygen,” explains Grinter. “The fact that plants must produce this protein for their cells to function makes it a good target for Pectobacterium during infection.”

They first determined the molecular structure of FusA from Nuclear Magnetic Resonance (NMR) and X-ray crystallography data. Then the team used the HADDOCK docking tool to simulate how FusA binds to plant ferredoxins. HADDOCK is one of the key codes used within BioExcel.

“HADDOCK consistently ranks at the top of protein prediction experiments and is one of the best programs available for molecular docking,” says Grinter. “This allowed us to place a high degree of confidence in its predictions and to present a credible representation of the FusA/ferredoxin complex for our paper.” HADDOCK relies on High-Throughput Compute resources provided by the data centres of the EGI Federation.

Molecular simulation codes like HADDOCK allow researchers to investigate their targets in great detail, providing a level of detail that traditional lab techniques may not be able to reach. BioExcel is working to enable researchers in all life sciences to use codes like HADDOCK to improve their research capabilities.

In this case, using the HADDOCK software, the team learned that FusA is a glove-like structure, which is able to grab plant ferredoxins and squeeze them across the outer membrane of the bacteria.

“It’s very important for the bacteria that this opening of the hole in FusA is specific and temporary, because the bacterial membrane protects the cell from toxins and antibiotics which may be present in the environment,” says Grinter. “I kind of like to think of FusA as a drawbridge on a medieval castle, it can be specifically be opened and closed to allow ferredoxin to enter the cell.”

Now that the researchers know how Pectobacterium gets its iron, they can move on to further study plant-bacteria interactions, which are key in understanding how the bacterium infects plants and causes disease. This could form part of a treatment plan for plants suffering from a Pectobacterium infection. The use of HADDOCK has therefore had a significant impact on our understanding of how this particular bacterium operates.

The structure of the bacterial plant ferredoxin receptor FusA has been published in Nature Communications, DOI: 10.1038/ncomms13308.

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