Behavioral Ecology Blog

Oh man, bacteria are so cool.. I’m Motivated in large by this story: (Genome Sequence Shows What Makes Bacteria Dangerous For Troops In Iraq). There, they find that the pathogenicity in a specific bacteria is mediated by a pathogenicity island (they call them alien islands). Most people outside of genomics, microbiology, and epidemiology are probably thinking- what the hell are pathogenicity islands…. A snippett from the story..

The DNA sequence analysis of A. baumannii revealed several important features including some that may allow researchers to design better drugs to treat infection. A surprising 17 percent of the DNA that codes for protein in this microorganism is present in “alien islands,” or sequences that originated in other microorganisms.

“It is like an old pair of jeans–no pun intended–which have been patched so many times that the patches represent a significant portion of the structure,” said Snyder. “Although not originally part of the organism, these ‘alien island’ sequences have become integrated into the A. baumannii DNA and now represent a significant portion of that genome.”

Bacteria typically acquire alien DNA from other microorganisms through a process known as “horizontal gene transfer,” and alien DNA is more likely to be retained and passed down to next generations of bacteria when it provides a survival benefit. This study reported that 16 of the presumed 28 alien islands in A. baumannii, contain genes implicated in virulence.

Something else cool about this story- they used 454 sequencing to sequence the whole genome in just a couple of weeks.. a task that would take months when using traditional methods.. 454 technology is expected to be the next large advancement in DNA sequencing technology. You may have heard of it as the guys working on Neanderthal genomics (but largely sequencing modern human DNA) are mostly using 454 technology.

Anyway, I thought that it might be really nice to write about pathogenicity islands, which have the following characteristics:

1. They usually encode virulence factors like genes for adhesion, invasion, antibiotic resistance, iron metabolism, toxins, and secretion systems (specifically type III).
2. They usually arise via horizontal gene transfer. This basically means that these genes have their origins in other bacterial species (whatever that might mean). Sometimes this is detectable as a result of different codon usage or different G+C content between putative island areas and host genome.
3. They are tens of Kb’s in length
4. They are usually associated with tRNA’s
5. They are usually flanked by direct repeats or insertion sequences. This is, obviously, for insertion into novel genomes.

Basically, these guys hop into novel genomes, and make otherwise commensal/mutualistic bacteria pathogenic.. Just imagine if while sequencing the human genome we found functional genes from rabbits, fugu, a newt, and eagle.. This, essentially is what people working with bacterial genomes find..

Here is the paper, in Emerging Infectious Diseases.