Grid computing reveals secrets about anthrax bacterium
Researchers at the UK's North East Regional e-Science Centre have used grid computing to reveal why anthrax, despite being related to many bacteria that live and grow in soil, can only grow when it is living in an animal host. It is a fact that has been puzzling scientists for some time.
Tracy Craddock, Dr Anil Wipat, Professor Colin Harwood, and colleagues at the North East Regional e-Science Centre in Newcastle, northern England, revealed the new insights after developing a method for deducing and characterising the proteins a bacterium secretes, using information deriving solely from its genome sequence. These proteins can indicate a lot about the way the bacterium survives, because they are often very highly adapted to the bacterium’s natural environment.
As genes carry the code for proteins, researchers are able to use knowledge of a bacterium’s genes to deduce all the proteins it produces. However, it is very time consuming to separate the secreted proteins from the others present in the bacterium, particularly as some secrete more than 4,000 proteins. To solve this, the Newcastle researchers have developed an automatic method to identify, analyse, and compare the proteins.
Their method is based on the Taverna workflow technology, and was developed under myGrid, an e-Science project funded by the UK's Engineering and Physical Sciences Research Council. The genetic codes of all the Bacillus family, of which Anthrax is a member, were analysed to find the secreted proteins, which were then grouped according to their predicted functions.
The team found that the predicted secreted proteins from Bacillus anthracis help to explain its inability to grow in soil. ‘When we looked at the secreted proteins, we found that they’re not adapted to utilise molecules in the soil,’ says Professor Harwood.
Most of them enable the bacteria to grow in an animal host by breaking down muscle fibres. However there is still a whole group of proteins with unknown functions. ‘We don’t know what these latter proteins do, but we think they help the organism to evade the immune response,’ says Professor Harwood. ‘We’re beginning to understand why Bacillus anthracis behaves in the way that it does – and how it has adapted to grow only in the host and not in the soil.’
The team is setting up a website to guide users through the process for any bacterium whose genome is known. By identifying the secreted proteins it will be possible to determine some of the previously unsuspected properties of a bacterium, including whether it is likely to be pathogenic or not. The method is also showing promise of commercial application as many enzymes sold commercially, such as plant-derived enzymes used for biofuel production, are proteins harvested from bacteria which secrete them naturally.