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Genomics

Proof of kinship

Lineage of that attacks grapes shares 98% of its genes with the strain that infects oranges

California University Biological control: the wasps used to combat the sharpshooters that transmit Xylella to the grapevinesCalifornia University

Comparing the set of genes of two organisms is a resource much used today in the search for the individualities of each being. In a work published in the February issue of the scientific magazine Journal of Bacteriology, a team of researchers from São Paulo compared the genomes of two varieties of the Xylella fastidiosa bacterium – one that causes Citrus Variegated Chlorosis in oranges, and another that causes Pierce’s disease in grapevines – and saw that the two strains are extremely similar: 98% of the genes of the grape pathogen are shared with the agent that infects the citrus, and the proteins produced by the two are almost identical (a similarity of 95.7%, on average). The grapevine Xylella has 2,066 genes, of which only 51 are not present in the orange bacterium, which, with its 2,249 genes, is slightly larger.

Such a degree of similarity led the scientists to the conclusion that both the pathogens probably resort to the same set of genes to infect and cause diseases in their respective victims. “The metabolic functions of the two strains are identical and make it possible to outline a converging strategy, in terms of the functional genome”, explains Marie-Anne Van Sluys, from the Biosciences Institute at the University of São Paulo, and the coordinator of the team that wrote the article. This means that, in the majority of cases, it is enough to understand the role of the genes in one of the bacteria to deduce its function in the other strain of Xylella. In practical terms, if, for example, a way is discovered for controlling the infection that leads to CVC, the yellowing disease, this knowledge will probably be useful for developing a similar strategy against Pierce’s disease – and vice-versa.

Besides being identical, to a great extent, the genes of the two bacteria occupy, in the majority of cases, the same place in the DNA. There are, though, internal rearrangements that make one genome different from the other. The phage (genomic segments coming from a virus) regions of the orange Xylella genome are, for example, different in number and content from those existing in the lineage that attacks grapes. A word of clarification: all the comparisons refer to the analysis of the genomes of the 9a5c lineage of Xylella, which attacks oranges in the interior of São Paulo, and of the strain of Xylella present in grapevines from the Temecula region of California. The situation is so serious in Temecula that the University of California, Riverside has imported a species of wasp from Mexico – Gonatocerus triguttatus, a natural enemy of the sharpshooter that transmits the bacterium to the grapes – to try to contain the dissemination of Pierce’s disease.

The two Xylellas were sequenced by researchers from Onsa, the virtual network of genomic laboratories created in São Paulo by FAPESP. The deciphering of the genome of the bacterium that causes the yellowing disease, which accounts for annual losses in the order of US$ 100 million to São Paulo orange growers alone, was made public in the pages of the July 13 2000 issue of Nature, one of the most important international scientific magazines. For having been the first work that did a complete sequencing of a pathogen that attacks plants, the article merited the cover of the periodical.

Still in that same year, the success of this pioneer venture earned the participants from Onsa an invitation from the United States Department of Agriculture (USDA), equivalent to a Ministry of Agriculture, to sequence the lineage of Xylella fastidiosa that causes Pierce’s disease in the grapevines of California, the main wine producing state in the USA, which has already suffered losses in the order of US$ 30 million because of this scourge. It was the result of this work, budgeted at US$ 500,000 and funded half and half by the Americans and FAPESP, that the scientists from São Paulo have now published in the Journal of Bacteriology.

More than simply providing the sequence of nucleotides (the chemical units) that make up the genome of the grapevine bacterium, the article by the team from the Agronomic and Environmental Genomes (AEG) network, a subnetwork of Onsa, tries to call attention to the possible genetic clues that may be useful for those who are seeking treatments for the diseases caused by the Xylella strains. The cure for Pierce’s disease (or the yellowing disease) is still far off, but a comparison of the genetic material of their pathogens is now supplying important clues for those who wish to pursue this objective.

“Several genes that are probably involved in the interaction between the Xylella and the grapevines have been identified”, says Edwin Civerolo, from the USDA’s Agricultural Research Service, who took part in the work with the researchers from São Paulo. “We can now see in experiments if the function of these genes is related to the bacterium’s pathogenicity or virulence.” According to Civerolo, the genes that have proved important in the occurrence of the infection or the development of Pierce’s disease may be the target of some kind of manipulation, in an attempt to combat this ailment.

Target gene
One of these genes that are candidates for future functional studies is the polygalacturonase enzyme. The presence of this protein facilitates the task of degrading the cell walls of the plant that is attacked by a pathogen. Pierce’s disease seems to be more aggressive than the yellowing disease – and the explanation for this difference in terms of virulence may, in part, be linked to with the condition of this gene in the strains of the bacterium that attacks grapes and oranges. “In the citrus Xylella, the gene appears truncated, perhaps non-functional”, explains Mariana Cabral de Oliveira, from the IB/USP, who took part in the work of sequencing both varieties.

“In the grapevine one, it is intact, entire.” The result of the comparison was so encouraging that the researchers from the AEG decided to check whether the polygalacturonase gene was intact in other strains of Xylella. They examined strains of the Xylellas that attack coffee and found that the gene was truncated, as happens with the orange bacterium. It makes sense to think, then, that a greater production of ploygalacturonase can be a determinant factor in the capacity for aggression of certain strains of Xylella.

After deciphering the gnome of the pathogen of Pierce’s disease, the researchers from the AEG are now dedicating themselves to close off and to analyze the genome of two more Xylella strains, one that attacks the ornamental plant called the common oleander, and another that affects almond trees. These two bacterial strains have been partly sequenced in the United States, but the most decisive part of the work will be carried out here. Budgeted at US$ 100,000, the project is an extension of the agreement signed with the USDA. At the end of this new stage, there will be four strains of Xylella totally sequenced, all with a prominent participation of Brazilian scientists.

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