For a more recent updated post on this topic go here.
Kat Holt, the super-geek pathological-genome breaker at U. Melbourne (who works upstairs from the Pundit, in a room full of expensive computers and a lovely view of sheep) is at it again. She’s found gene rearrangements in the German EAEC outbreak germ. She reports her work in her blog post ” Tn21 resistance transposon in the chromosome?”
These gene rearrangement are clearly the result of genetic engineering. The traces of this genetic engineering are right there in the bacteria’s DNA that has just been decoded by the scientists.
Super-computer whiz Kat has found a set of mobile set genes that once lived in another germ of a different species called Salmonella Paratyphi A. They are now neatly and precisely engineered into the main E. coli EHEC chromosome, Kat has discovered.
This discovery is explained by red color-code in the diagram below. The name pAKU1 refers to a mini-chromosome on which they lived when they were found in the dangerous Paratyphi germ — which is quite unconnected with the German outbreak. It’s not even an E. coli.
But its genes are in the German E. coli (shown in nice super-female purple). Blue shows genes almost identical to the quite distant African-grandparent of the German germ
Legend to Figure. Kat Holt’s latest discovery about the German EHEC germ. Purple color on the diagram is the BGI Institute data for the German outbreak strain. Blue show DNA code of an African parental strain Ec 55989 from French scientists. Red indicates detection of Paratyphoid like trans-genes in the E. coli genome.
These trans-genes confer resistance to antibiotics streptomycin, trimethoprim, sulfamethoxazole, and the antibacterial metal mercury.
Interestingly, German germ DNA also has a device made of DNA called an integron mentioned by Kat.
Integrons capture genes.
They are used to do genetic engineering.
But integrons are completely natural genetic tools. The genetic engineering with integrons is done by the germ itself.
(See for instance, the supporting quote from Dr Guillaume Cambray and colleagues fascinating and authoritative 2010 review provided below.)
Integrons are natural tools used by bacteria to systematically capture new genes. They are associated with certain mobile sets of genes that disseminate traits such as antibiotic resistance to new host chromosome locations.
They do exactly what human genetic engineers do. They clone DNA. In the current example the GMO was engineered by the German germ to produce a natural GMO which has new genes systematically inserted in its chromosome — they were cloned, as you can plainly see from the diagram.
That is what has made the German beast so dangerous – completely natural gene cloning.
There are even superintegrons that have been found. I am not kidding. These are exceptionally nasty natural weapons of germs encouraged to by circumstances of natural selection to do genetic engineering all by themselves.
Both integrons and superintegrons are famous among microbiologists for their amazing ability to capture numerous and diverse new genes at the DNA location of the integron DNA. Many examples of integrons have been found where they have provided bacteria with immunity to a wide range of antibiotics. People who don’t know about them- as for example a writer at a website putting forward conspiracy theories to explain the emergence of this dangerous EHEC germ, “it seems virtually impossible to imagine how this could happen all by itself in the natural world.” Bacteria do the “virtually impossible” with the help of integrons.
It seems a pity to disappoint the conspiracy theorists among the readership who are keen to blame heartless corporations for all this, but if they knew their modern genetics as well as they can fantasise about about evil plots by drug companies to increase sales, they would be expecting these superpunchlines.
In a later post, the Pundit will explain how integrons do their amazing cloning task, or provide links to where someone else has done a good clear job of explaining this fantastic genetic capability of supposedly simple germs.
In the meantime, the summaries of current science below will perhaps convince the uninitiated that the Pundit’s deadly serious about integrons doing genetic engineering. And perhaps readers should also ask themselves why the anti-GM activists never honestly discuss the extent of this perfectly natural genetic engineering, and why they seem exempt it from their risk calculations, as they have so tragically done in Germany in recent years. It’s not carefully regulated and thoroughly tested GM food that’s done harm, but dangerous natural germs that are well established as the main cause of food-borne illness.
Science of Integrons:
Although the first bacteria resistant toward mutiple antibiotics were isolated in the mid-1950s in Japan, it was not until the 1970s that it was determined that these phenotypes are frequently associated with transmissible plasmids [optional germ mini-chromosomes] and more specifically with transposable elements [mobile genes] located in these plasmids . Integrons were characterized even later, in the late 1980s. It was at this time that they were found to be the genetic system responsible for the gathering of resistance determinants in these mobile elements and termed integrons. It is now well established that these mobile integrons (termed as such because of their intimate association to transposons) constitute the major vectors of antibiotic multiresistance in Gram-negative [such as E. coli] and to a lesser extent in Gram-positive bacteria. Their importance in clinical and agricultural settings is reflected by the impressive amount of epidemiological studies monitoring their prevalence and evolution. The presence in the bacterial genomes [i.e. the main bacterial chromosome] of sedentary chromosomal integrons,which are not involved in resistance phenotype, was only established in the late 1990s with the discovery of the Vibrio cholerae superintegron. Similar loci were further identified in a significant fraction of environmental bacteria. The evolutionary history of such chromosomal integrons suggests that this adaptive genetic system has been maintained in the genome of Gram-negative bacteria [relatives of E. coli] for a long while to help facing a changing world and that these chromosomal elements are the source of the mobile integrons’ backbones and of their antibiotic resistance gene cassettes .
This quotation strongly supports the judgement expressed above that emergence of the German EAEC germ is entirely expected from the known natural genetic engineering abilities of E. coli and related gut bacteria.
Review: Integrons: agents of bacterial evolution
Integrons are assembly platforms — DNA elements that acquire open reading frames embedded in exogenous gene cassettes and convert them to functional genes by ensuring their correct expression. They were first identified by virtue of their important role in the spread of antibiotic-resistance genes. More recently, our understanding of their importance in bacterial genome evolution has broadened with the discovery of larger integron structures, termed superintegrons. These DNA elements contain hundreds of accessory genes and constitute a significant fraction of the genomes of many bacterial species. Here, the basic biology of integrons and superintegrons, their evolutionary history and the evidence for the existence of a novel recombination pathway is reviewed. Nature Reviews Microbiology 4, 608-620 (August 2006) | doi:10.1038/nrmicro1462
For additional analysis of the genome of the E. coli causing the German outbreak, see Comparisons of E. coli TY2482 against previously sequenced E. coli genomes by David Studholme and TY2482, LB226692 vs Genbank Ecoli by Konrad Paszkiewicz.