By David N. Leff
A bacterium with a difference has just had its genome sequenced. What sets this microorganism apart from the dozens of other pathogens that had their genetic structures totally mapped in recent years is this one¿s dedication to infecting plants, not other forms of life.
¿Agrobacterium tumefaciens,¿ observed bacterial geneticist Steven Slater, ¿can naturally transfer its DNA to plant cells, where it forms crown gall tumors. Its DNA encodes genes that produce plant hormones that don¿t function in mammals, for example.¿ (See BioWorld Today, Oct. 31, 2000, p. 1.)
Slater is senior scientist at Cereon Genomics LLC in Cambridge, Mass. ¿ a subsidiary of Monsanto Co. He is senior author of a paper in Science dated Dec. 14, 2001 (but released Dec. 13). Its title: ¿Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens [strain] C58.¿
Back to back with this seminal announcement is a curiously similar article ¿ the cover story in Science of the same date ¿ titled, ¿The genome of the natural genetic engineer Agrobacterium tumefaciens [strain] C58.¿ Its principal author is microbiologist Eugene Nester, at the University of Seattle in Washington. The article¿s co-authors number 51, at 13 academic and commercial laboratories, including two in Brazil. The Cereon/Monsanto report has 31 co-authors, all from the U.S.
When these two parallel articles are viewed side by side, the box scores of their sequencing data are strikingly similar: Cereon posted 5,674,300 base pairs; Seattle, 5,674,062 base pairs.
¿The genomic differences between the two papers,¿ Slater told BioWorld Today, ¿are very small. There¿s a criterion in genome sequencing called the Bermuda Standard ¿ a measure of accuracy, so called because it was adopted at a meeting in Bermuda. That accuracy standard is one error in 10,000 base pairs. So when we compared our two sequences, first of all there were no significant differences in genome assembly. We both agreed that the order of the genes is the way that we¿d laid them out, and the genes are on each of the four different molecules in the way that we¿d laid them out. There are no major differences from that point of view. It¿s clear that the accuracy of the sequences from both groups is well above that required by the Bermuda Standard. Far fewer than one in 10,000 errors.¿
The Plasmid That Begat A Chromosome
Each research group discerned the same four molecular structures in the Agrobacterium cell: two hefty chromosomes ¿ one linear, one circular ¿ and two smaller plasmids. ¿Those are the DNA molecules inside the cell,¿ Slater pointed out. ¿The circular chromosome is pretty typical of bacterial chromosomes that carry all the genes for bacteria. The linear chromosome appears to have evolved from a plasmid at one point. Then there are these other two plasmids.
¿They are extra-chromosomal DNA,¿ he explained, ¿so they can replicate by themselves ¿ not a part of the chromosome per se. The linear chromosome has a great many essential genes that are required for the bacterium to do its everyday housekeeping and metabolic processes. And that linear molecule looks like a plasmid that became a chromosome by acquiring lots of essential genes, which at one point were probably all located on one large circular chromosome. Then over periods of time they got transferred to the linear chromosome. Exactly how that happened, and why, is still a sort of a mystery at this point. But it¿s clear that it did happen.
¿A. tumefaciens is a ubiquitous soil bacterium,¿ Slater noted. ¿If you went out to your backyard and picked up a handful of dirt, you could certainly isolate some Agrobacterium from it. It¿s a pretty typical Gram-negative rod-shaped microorganism, motile, with flagella so it can move around. Same size category as E. coli.
¿To appreciate its role in nature,¿ he said, ¿you have to think about it from Agrobacterium¿s point of view. That is: How can I set myself up to get myself an evolutionary advantage?¿ So it has figured out how to create a very happy little niche for itself ¿ a home inside a crown gall ¿ and get the plant to feed it. But besides causing these crown gall plant tumors, most of their time is actually spent in the soil. So they also have to be able to compete and grow in underground situations. But Agro¿s main useful application is creating transgenic plants.
¿We founded Cereon about four and a half years ago,¿ Slater recalled, as a collaboration between Monsanto and Millennium Pharmaceuticals Inc., as a way to get genomics jump-started in the agricultural field. One of our major goals has been not only to get this type of work up and rolling in a large way within Monsanto ¿ and an application for agricultural purposes ¿ but also starting to apply these techniques widely within the company. That¿s happening, so we¿re a little bit less unique than when we started. And that¿s good.¿
What Else Is Agrobacterium Good For?
¿A couple of putative applications arise from this genome-mapping of Agrobacterium,¿ Slater enumerated. ¿One is that our scientists who are involved in plant transformation now have a new tool that they can use to try to understand how they might be better able to either control or provide high-quality plant transformants. The more we¿re understanding that microorganism, the better able we may be to increase both quality and quantity of the transgenic plants that we produce.¿
He went on: ¿There may be genes that we find in there if we can demonstrate they¿re going to be of utility, and we can make an improvement in those genes ¿ or we find another gene that might be useful for some other purpose ¿ then certainly we¿ll file a patent on that use, as you would any other biotech-type application.
¿Any time we look into a new genome,¿ he added, ¿there are always new genes. And here¿s an organism that¿s in close proximity with plant cells, and may have many genes that are involved using plant metabolites. We may find some interesting genes in there that we might be able to use to modify plant metabolism in a way that¿s beneficial. In fact, we¿ve already found some of them ¿ but I can¿t give you details at the moment.¿