There are many Alternaria pathogens that produce host-specific toxins. Alternaria host-specific toxins are classified in three groups in terms of the primary site action. First group of toxins have in common an epoxy-decatrienoic acid structure and exert their primary effect on the plasma membrane of susceptible cells. The second group is represented by ACR(L)-toxin, which induces changes in mitochondria, including swelling, vesiculation of cristae, decrease in the electron density of the matrix, increase in the rate of NADH oxidation, and inhibition of malate oxidation. The third group consists of AM-toxin, which appears to exert an early effect on both chloroplasts and plasma membranes.  

Ames and bacterial assays has demonstrated that Altertoxins I, II,  III, toxins AOH and AME  were mutagenic. A.N. Samokhvalov ( «A method for producing mutant strains of plant pathogen X. campesrtis». Invention certificate  No 1473360 of 15.12.1988 (USSR) has found that Alternaria brassicola caused similar mutation in different strains of X. campestris affected xanthomonadin synthesis and virulence of  the bacteria.

Is there any information about specific interaction between Alternaria toxins and bacterial/chloroplast or mitochondrial DNA?

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