The food-borne pathogen E. coliO157:H7 has been sequenced. Its closest relative is the laboratory strain E. coli K. Has genetic engineering contributed towards its emergence?
E. coli 0157:H7 is a food-borne pathogenic strain of bacteria that emerged in the United States in the 1980s, and is now responsible for some 75 000 cases of infection annually in that country. It has also been responsible for major outbreaks in Scotland, Japan and elsewhere since.
The first outbreak was associated with infected hamburgers in 1982. The strain responsible, EDL933, isolated from ground beef in Michigan, has been studied as a reference strain. The complete sequence of its genome has recently been determined [1,2], and its closest relative turns out to be the laboratory strain K-12 MG1655. E. coli O157 has acquired shiga toxin genes (from the bacteria Shigella) and plasmids containing virulence factors by horizontal gene transfer.
The two strains, O157 and K12 share a common backbone with almost identical gene order. The 4.1 million base pairs in the genomes can be lined up side by side along their lengths except at one point where the O157 genome is reversed. Inversions around the starting point of replication are common in bacterial genome evolution.
Scattered roughly evenly within each genome are hundreds of sections of DNA that are unique to one or the other: 1.34 megabases coding for 1,387 genes in the O strain, the 'O islands'; and 0.53 megabases coding for 528 genes in the K strain, the 'K islands'. Most of the DNA in O and K islands has been acquired by horizontal gene transfer.
There are 106 O and K islands present at the same locations in the backbone. Only a subset of islands is associated with elements likely to be autonomously mobile. Most islands are horizontal transfers of relatively recent origin from a donor species with a different intrinsic base composition.
Of the 1 387 acquired genes in O157, 40% (561) can be assigned a function, another 338 genes of unknown function lie within clusters that are probably remnants of phage (bacterial virus) genomes. About 33% (59/177) of the O islands contain only genes of unknown function. Many classified proteins are related to proteins from other E. coli strains or related enterobacteria known to be associated with virulence, and include alternative metabolic capacities, prophages (integrated genomes of bacterial viruses) and other new functions.
There are 3574 protein-coding regions in the backbone, and the average nucleotide identity between O157 and K12 is high: 98.5%. Of these regions, 89% are of equal length and 25% encode identical proteins. Some chromosomal regions are more different (hypervariable) than the average, but they encode a comparable set of proteins at the same relative chromosomal positions. In the most extreme case (YadC), the proteins from the two strains exhibit only 34% identity. Four such genes encode known or putative biosynthesis operons of fimbrial proteins used in attachment to host cells. Another gene codes for a restriction/ modification system that breaks down foreign DNA.
From the extent of genetic differences between the strains, the authors estimate that E.coli O157:H7 and K12 shared a common ancestor about 4.5 million years ago. This estimate is highly questionable, however, as are all similar estimates.
Such estimates are based on the so-called molecular clock hypothesis, which assumes a steady, neutral (nonadaptive) random accumulation of genetic difference per unit time. One assumption is one percent per million years. But this is notoriously unreliable, as we now know that mutational changes vary directly in proportion to the number of DNA replication cycles. So, organisms with short life-cycles accumulate changes faster than those with long life-cycles. There are also many fluid genome processes that can rapidly change genomes. These include hypermutation, or mutations rates that are up to a million times faster than usual, recombination, and horizontal gene transfer. Horizontal gene transfer is well documented in all bacteria including E. coli, as is clear from the genome sequence data. Recombination too, appears to be an important mechanism in the evolution of the enterobacteria to which E. coli belongs. And hypermutation has been identified in several regions in the E. coli chromosome.
Another factor that would give an overestimate of divergence time is artificial genetic engineering. Artificial genetic engineering involves rampant recombination and transfer of genes across divergent species barriers. Now that sequence data are becoming widely available, one ought to be asking the serious question as to whether genetic engineering might have contributed towards the emergence of E. coliO157 some twenty years ago .
Researchers discovered new corn viruses belonging to a family which infect tomatoes. Has GM tomato containing CaMV promoter contributed to their emergence?
Two new corn viruses have been discovered, one in Arizona and the other one in Georgia. The one in Georgia has yet to be identified. Dr. Redinbaugh, a United States Department of Agriculture scientist who is characterising the viruses, said the virus has similar symptoms to several corn diseases including maize mosaic virus, maize chlorotic dwarf mosaic virus and maize rayado fino,
The Arizona virus has now been identified from corn leaf samples, thought to be infected with maize chlorotic dwarf virus (MCDV) . Instead, it yielded two other viruses: maize dwarf mosaic virus and a second virus which is completely new. The new virus produced severe symptoms on corn leaves that included pale green, yellow, or cream-coloured spots and streaks. As disease progressed, the spots and streaks became spindle-shaped, then coalesced into long, chlorotic bands that became translucent and necrotic around the edges. The stalks also die similarly. These distinctive symptoms were the basis for the naming the pathogen maize necrotic streak virus (MneSV). MNeSV had a small isometric particle, high titre in infected leaves, and a genomic structure similar to viruses in the family Tombusviridae which infect tomatoes.
This new virus is unusual in its mode of transmission, Redinbough (firstname.lastname@example.org) states, "Using three different techniques we've only been able to transmit the virus through the soil. And we don't know what's in the soil that transmits the virus." Most plant diseases are transmitted via an insect. The researchers used several common crop insects, such as the corn root aphid, green peach aphid, potato aphid, oat bird cherry aphid, corn leafhopper, black-faced leafhopper, corn planthopper and western rootworm to spread the disease from one plant sample to another. But none of the insects proved to be a vector of transmission. The researchers also attempted to transmit the virus by rubbing healthy leaves with the disease, without success.
Could these viruses have arisen by recombination with transgenic DNA in the soil, more specifically with the cauliflower mosaic virus (CaMV) promoter that is in all GM crops released so far?
I put the following questions to Dr. Redinbaugh
"Are the maize plants transgenic? If not, were the fields previously planted with transgenic plants? One prime suspect might be the cauliflower mosaic virus 35S promoter which is in practically all transgenic crops currently grown."
Here is her reply, which only answered some of my questions, and then not directly,
"The corn leaf samples infected with MNeSV and the virus from Georgia were sent to us by colleagues, because of our expertise in virus characterization, our ability to transmit and culture maize viruses and our facilities for working safely with emerging viruses. We developed cultures of the two viruses, then began to characterize their physical and biochemical properties. One part of our characterization is to determine the nature and sequence of the viral genome. Both MNeSV and the Georgia virus showed sufficient physical, biochemical and genomic sequence similarity with other plant-infecting viruses to be placed in a virus family. Although we did not specifically test these viruses to see if they arose through recombination, our methods for sequence analysis would have identified any viral sequences with substantial homology to known maize genes, including CaMV promoter-driven transgenes.
" [viruses] in the family Tombusviridae are transmitted in soil and not by insects. However, in contrast to most viruses in the Tombusviridae, MNeSV cannot be transmitted by leaf rub-inoculation. . Also, the sequence analysis showed that there were no sequences present in the virus derived from crop transgenes. Thus, there is no evidence that the virus arose from recombination with transgenic DNA. Finally, although we frequently use the word "new" when describing these viruses, the viruses themselves are actually not likely to be new. In most cases, the new virus just hasn't been previously characterized and is new to the scientific community. It would probably be more accurate to identify the viruses as 'recently discovered'."