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Agronomy

Of genes and dwarf plants

Genome of the bacterium provides clues on ratoon stunting disease in sugarcane

LUIS EDUARDO ARANHA CAMARGOEffects of the ratoon stunting disease: infected sugarcane (left) has a smaller distance between the knots of the stalk and may weigh half a healthy plant (right)LUIS EDUARDO ARANHA CAMARGO

In times of drought, when there is little water available, sugarcane, like most plants, resorts to an expedient for guaranteeing its survival: it stops growing. To minimize the effects of water stress, it remains almost dormant and unleashes a series of mechanisms of self-defense. For example, the stomata of its leaves are closed; they act like pores, responsible for the gases and water coming in and going out of the plant. One of the main hormones involved in this process of adaptation to drought is abscisic acid (ABA), produced naturally by sugarcane. Recent studies indicate that ABA also inhibits the expression of the plant’s defense genes, making it more susceptible to pathogens.

All this is known, it is in the books and scientific articles about plant physiology. The novelty is discovering that a bacterium that is harmful to sugarcane, the xyli subspecies of Leifsonia xyli, also appears to be capable of producing this hormone, and perhaps of using it to bring about a disease known as the ratoon stunting disease, for which there is no cure. A suspicion arose after São Paulo researchers finished sequencing the complete genome of the bacterium – which generated a scientific article published in August, with a call on the cover page, in the American magazine Molecular Plant-Microbe Interactions – and began to analyze the function of some of its 2,351 genes.

There are indications that the action of a gene called desA leads Leifsonia to produce abscisic acid inside the sugarcane. If this hypothesis is correct, ratoon stunting disease, which results in plants of a small size and with a weight of up to 50% lower, may be unleashed by the high concentrations of the hormone produced by the bacterium inside the sugarcane. It is as if the abscisic acid synthesized by the plant pathogen permanently sent a signal to the plant that there is little water available in the environment, and that the best thing to do is to stop growing. For good measure, the ABA also deactivates the sugarcane’s defense genes, creating ideal conditions for the bacterium to multiply.

“Up until now, there is no record of a bacterium of a plant that produces this hormone”, explains researcher Luis Eduardo Aranha Camargo, from the Luiz de Queiroz College of Agriculture of the University of São Paulo (Esalq/USP), one of the coordinators of the project that sequenced the bacterium’s genome. “But tests in vitro indicate that Leifsonia produces abscisic acid, and this fact may be important for us to understand its pathogenicity.” The following step is to confirm whether, inside the sugarcane, the bacterium really does produce the hormone and to establish a link between the acid and the disease in the plant.

Carried out under the auspices of the Agronomic and Environmental Genomes network, maintained by FAPESP, the venture that mapped the plant pathogen’s genome cost US$ 700,000. FAPESP went in with US$ 650,000 and Copersucar with US$ 50,000. Besides raising the question of the abscisic acid, the sequencing of the genome of Leifsonia – made up of a circular chromosome with 2.6 million base pairs, the chemical units that form the DNA – produced other important information for understanding the plant pathogen’s behavior.

The researchers found that 13% of the bacterium’s genes are actually pseudogenes: 307 of the 2,351 genes are truncated, incomplete. “These alterations may make the genes lose their function”, says researcher Claudia Barros Monteiro Vitorello, from Esalq-USP, another coordinator of the project. No other plant pathogen shows such a high quantity of apparently non-functional genes. Similar in size to that of Leifsonia, the genome of Xylella fastidiosa – a bacterium that causes citrus variegated chlorosis (CVC), a disease that caused yellowing in orange groves – shows only 2% of pseudogenes.

It may even be that the 307 incomplete genes of the Leifsonia are of no use for anything else and be just genetic debris, but the scientists believe that they have a meaning. They are an indication that the bacterium is passing through a process known as genomic decay. Genes that were once useful – and are now no longer so – progressively lose their integrity and functionality. Why does this happen? Possibly because the bacterium, in the cause of its biological evolution, has changed its way of life and does not need to maintain intact today as many genes as in the past.

Subspecies xyli of Leifsonia xyli is a microorganism that has specialized in living in a single place: in the vessels of the sugarcane xylem, the part of the plant charged with transporting water and mineral salts from the roots to the crown. Outside this habitat, the pathogen is not found. Accordingly, genes that are fundamental for the preservation of bacteria that live in the open air are not an item of the first necessity for the bacterium of the sugarcane. “It does not need many of its genes any more”, Aranha comments. This hypothesis is also being tested by means of a comparison between the xyli subspecies of Leifsonia xyli and open air species close to it.

To defend itself from the attack of other microorganisms that inhabit the xylem of the sugarcane, Leifsonia seems to boast a mechanism capable of ejecting from its organism toxins produced by other organisms that colonize sugarcane, such as the pathogenic bacterium Xanthomonas albilineans. Indeed, Xanthomonas itself has a “pump” that expels venoms emitted by other beings. This common trait may explain the two bacteria living together in the inside of the plant. In the long term, the researchers? goal is two understand how the protection system present Leifsonia and in Xanthomonas works – and which genes are involved in this mechanism. “In future, perhaps we may be able to alter sugarcane genetically and equip it with a bacterial pump that expels toxins produced by microorganisms that attack it”, says engineer agronomist Reinaldo Montrazi Barata, from Esalq. Accordingly, a variety of the plant could emerge that is more resistant to diseases.

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