Omics Methods for Probing the Mode of Action of Natural and Synthetic Phytotoxins

Abstract

For a little over a decade, omics methods (transcriptomics, proteomics, metabolomics, and physionomics) have been used to discover and probe the mode of action of both synthetic and natural phytotoxins. For mode of action discovery, the strategy for each of these approaches is to generate an omics profile for phytotoxins with known molecular targets and to compare this library of responses to the responses of compounds with unknown modes of action. Using more than one omics approach enhances the probability of success. Generally, compounds with the same mode of action generate similar responses with a particular omics method. Stress and detoxification responses to phytotoxins can be much clearer than effects directly related to the target site. Clues to new modes of action must be validated with in vitro enzyme effects or genetic approaches. Thus far, the only new phytotoxin target site discovered with omics approaches (metabolomics and physionomics) is that of cinmethylin and structurally related 5-benzyloxymethyl-1,2-isoxazolines. These omics approaches pointed to tyrosine amino-transferase as the target, which was verified by enzyme assays and genetic methods. In addition to being a useful tool of mode of action discovery, omics methods provide detailed information on genetic and biochemical impacts of phytotoxins. Such information can be useful in understanding the full impact of natural phytotoxins in both agricultural and natural ecosystems.

Expression Profiles of <i>psbA, ALS, EPSPS</i>, and Other Chloroplastic Genes in Response to PSII-, ALS-, and EPSPS-Inhibitor Treatments in <i>Kochia scoparia</i>

“…For example, chorismate, one of the major intermediates of the shikimate pathway involving EPSPS, serves as a branch point for synthesis of various branched chain aromatic amino acids [28]. The study of the effect of herbicides on their target-sites and other related gene networks helps in deciphering the cross-talk between various biochemical pathways and the events leading to plant death [29] [30].…”

On glyphosate

“…However, under such conditions, it is clear that further, thorough and rather elaborate investigations are necessary to unequivocally determine the environmental and human health risks of use of glyphosate, its by-products and formulations. In this respect "omics" studies, such as those of Martyniuk and Simmons (2016) and Duke et al (2013), could be the most promising. Additional research is also needed on the biological functions and the regulation of the individual steps in the biosynthesis of secondary plant metabolites in order to elucidate the antagonistic (and possibly synergistic) interactions of different metabolites derived from the shikimic acid pathway.…”

Isolation and Identification of Allelochemicals from Ascocarp of Tuber Species

“…Angelini et al ( 2015 ) reported that the allelochemicals such as linoleic, oleic and palmitic acids may offer a plausible explanation for the aggressive characteristics of the T. melanosporum and T. aestivum along with the strong cytotoxic effects observed in their brûlé (Streiblova et al 2012 ). Phytotoxic properties found within fatty acids have become part of the general knowledge in their respective fi elds of study (Duke et al 2013 ). It is believed that the mode of action in long-chain fatty acids is observable in the disruption of the cell wall building function as these can be utilised by the proteins that construct the cell walls as a sort of building block (Kim and Kim 2000 ).…”