A UCC researcher who defined an important genetic blueprint has found himself on the front page of a leading US scientific journal, writes Dick Ahlstrom
Two suitcases are sometimes better than one when you go travelling - and a species of food bacteria seems to have figured this out in relation to its genetic blueprint. It holds most of its DNA in the nucleus but also carries other important genes in a separate parcel.
Having this extra suitcase, properly called a plasmid, may be what allows the versatile Lactobacillus salivarius colonise a variety of niches, explains University College Cork genetics lecturer, Dr Paul O'Toole.
L salivarius is a lactic acid bacteria typically found in milk. It is an interesting bacteria in its own right but it may also become an important one from the perspective of human health.
It produces a protein that can kill off other bacteria, a bacteriocin, and has recognised probiotic characteristics, says O'Toole who lectures in UCC's microbiology department and is a Science Foundation Ireland-funded principal investigator in UCC's alimentary pharmabiotic centre.
O'Toole and colleagues from UCC, the Sanger Centre in Cambridge, the Conway Institute at UCD and the Cork Cancer Research Centre at Mercy University Hospital Cork mapped out the genome architecture of a L salivarius strain and recently published their findings in the prestigious US journal, Proceedings of the National Academy of Sciences. Pictures of the bug also featured on the front page of the journal.
"There has been a long history of experiments in the EU and worldwide on the bacterium," states O'Toole. Researchers are always interested in organisms that produce bacteriocins. This makes them targets as possible probiotic food bacteria. In the case of the L salivarius strain, it may also have "very promising benefits in inflammation", he adds.
"If you find these things you try to isolate the part that gives the probiotic benefit," he explains. "The research is to figure out how they do what they do by looking at their genetic blueprint."
With this in mind they decided to catalogue the genomes of three L salivarius strains and their PNAS publication details their findings on the first strain, UCC118. They found that instead of holding its entire 2.13 million element genome in the nucleus, it shared it, storing 1.83 million elements in a chromosome and another 242,000 elements in a large "megaplasmid" and two smaller plasmids.
"Megaplasmids previously have not been characterised in lactic acid bacteria or intestinal lactobacilli," O'Toole and colleagues write in the PNAS report.
They sequenced the megaplasmid DNA and found it contained no essential "single-copy" genes, yet it did contain very important genes related to metabolism and carbohydrate utilisation.
"The megaplasmid contained a number of genes that complete biological pathways," says O'Toole. When they looked, they found other salivarius strains also contained megaplasmids but of widely varying sizes, from 100,000 up to 380,000 elements.
The research team's assumption is that salivarius as it adapts to novel environments uses its megaplasmid to store the extra genes it needs to colonise new territory. "The discovery of megaplasmids of widely varying size in L salivarius suggests a possible mechanism for genome expansion or contraction to adapt to different environments," as the authors put it in their paper.
The genes selected for the megaplasmid give selective advantages to the organism, says O'Toole. "Megaplasmids are in all the salivarius we have looked at. The megaplasmid confers extra properties. They can adapt to different niches in the GI tract or to different diets or different animals."
The bacteriocin-producing gene in L salivarius was also found in the megaplasmid and this serves to focus attention on this structure. "We are trying to figure out what does it mean to have different sized megaplasmids," says O'Toole. "Are they carrying extra genes and ifso what genes. We also want to exploit the megaplasmids for biotechnology."