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Professor Julian Parkhill talks about pathogenicity islands with Dr. Anna Protasio

Professor Julian Parkhill, from the Wellcome Sanger Institute, answers our questions on pathogenicity islands and genomics' research.
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Hello, and welcome to this interview with Professor Julian Parkhill, who is talking to us about pathogenicity islands. Hi, Julian. Hi. Anna. Can you tell us what a pathogenicity island is? So, a pathogenicity island is a part of the bacterial chromosome that will encode factors involved in the pathogenicity of the organism, and the reason they’re called ‘islands’ is because they look separate from the rest of the genome. They appear to have come in more recently. They’re clearly distinguishable from the rest of the genome. They look like islands in the genome. If these islands are different, in terms of their GC [(Guanine-Cytosine) content] and other factors, how come the bacteria does not defend against them?
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So, bacteria do defend against foreign DNA, and that’s at two levels. Firstly, they’ll defend against the acquisition of foreign DNA, and that can be through restriction-modification systems, for example. If the island does get integrated into the chromosome, then the bacteria often has mechanisms for shutting down transcription and translation of foreign DNA. So, it will suppress AT-rich DNA. So it will control how that DNA gets into the cell and how it gets expressed. But if that DNA is a benefit, then it can overcome those barriers because the DNA is a benefit, and it will use that benefit. How is it possible that these parasites of the bacteria can be beneficial for it?
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Pathogenicity islands will often carry genes that are beneficial to the bacteria. So, for example, you know, Salmonella typhi carries a pathogenicity island that encodes a surface polysaccharide that’s used by Salmonella typhi in its interactions with a human host, and you often find multiple different host-interaction factors encoded on these pathogenicity islands. And they’re kind of accessory to the core functions of the organism. So, they will encode functions that expand the repertoire of the bacterium, if you like, and that can be pathogenicity. But these islands can also carry additional metabolic pathways that allow them to expand the role and the range of nutrients they can use.
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So, it’s any function that isn’t part of the core that can expand the repertoire of the organism. Do these pathogenicity islands have a role in establishing disease? Yes, often. So, many different organisms, many different pathogens will carry genes on pathogenicity islands that will enable them, for example, to interact with different hosts. So, they have a different set of islands. They will interact with a different set of hosts. And that means often causing - you know- different diseases, or sometimes causing different diseases within a single host. So, it’s about using these accessory genes– this presence and absence of variable genes, to alter their range of niches that they can survive.
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Are there any particular features that we can look, within the bacterial genome, that will tell us where these pathogenicity islands are? So, often, these islands will have different nucleotide compositions. So, at a simple level, they’ll have a different GC,content for example, and the boundaries of that GC content are often very clearly defined and it allows you to identify the boundaries of the element. Why they have different GC content is not really understood. It used to be thought that it was because they were acquired from different organisms that had a lower GC content.
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But that doesn’t hold because all of them seem to have a low GC content, and that can’t always be the case; and often, these islands are exchanged amongst members of the same species, who are often coming from a completely different species. So, there may be something functional in having a lower GC content that enables the islands to move more easily, or integrate more easily, or be expressed more easily in different backgrounds. There are often other more-subtle features. So, we look at GC bias, which is the way in which the GC base pairs are oriented and leaving a lagging strand, and that often changes dramatically around the pathogenicity island.
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Because again, it has come into the chromosome more recently and isn’t subject to the biases of the background. So, there’s a number of different features you can look at that allow you to determine whether these islands are there and what the precise boundaries of them are. Excellent. Thank you, Julian, so much for your time and for talking to us about pathogenicity islands. You’re welcome. I hope you enjoyed this interview. You can leave your thoughts and your ideas in the comments area.

In this interview, Professor Julian Parkhill, from the Wellcome Sanger Institute, talks with Dr. Anna Protasio. He answers our questions on pathogenicity islands, describing what they are and explaining their important role in bacterial pathogenicity.

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