Examination of the whole genome response in Arabidopsis thaliana to auxinic herbicide 2,4-dichlorophenoxyacetic acid coupled with adjuvant NUL1026

Foliage-applied herbicide formulations often consist of compounds known as surfactants that promote the uptake of herbicide molecules through leaf surfaces. Several lines of research have demonstrated that the efficacy of most herbicides relies on the amount of herbicide molecules successfully entering the plant tissues and reaching the target sites, rather than on increasing the dosage of the herbicides. Therefore, combining the right surfactant to a compatible herbicide formulation may lead to a decrease in the amount to active ingredients being used in weed control. Agrochemical companies are now investing into the development of surfactant products which perform very specific functions that complement herbicide chemistries, with the aim of developing novel herbicide formulations which are effective at lower active ingredients. This study took a genomic approach using microarray technology to elucidate the mode of action of an etheramine surfactant, called NUL1026. Knowledge gained from this study will aid in the identification of metabolic and physiological processes that may contribute to herbicide toxicity. The same gene expression profiling approach was also undertaken to investigate the synergistic effect of combining surfactant NUL1026 to the auxinic herbicide 2,4-dichlorophenoxyacetic acid. Arabidopsis thaliana plants (14 days) grown in vitro were separately sprayed using the Potter spray tower with either of the following solutions: water, 0.2% (v/v) surfactant NUL1026, 1.0 mM 2,4-D and 1.0 mM 2,4-D + 0.2% (v/v) surfactant NUL1026. The total RNA in response to each of the sprayed solutions was extracted and quantified at 1 h and 24 h post-application. The whole genome oligonucleotide microarray (ATH1-121501) manufactured by Affymetrix ® was used to measure gene expression levels of approximately 24,000 genes. Expression profiling results in response to surfactant NUL1026 treatment revealed that at both 1 h and 24 h, a number of gene transcripts involved in transcription factor activity, signal transduction pathways, cell wall organisation and biogenesis, disease response, detoxification, senescence and hormone signalling showed altered expression. Of note was the significant regulation of genes involved in jasmonic acid biosynthesis found to be exclusively regulated upon exposure to the surfactant Foliar-application of 1.0 mM 2,4-D resulted in the differential expression of 45 genes, 1 h post-treatment. Functional annotation of these genes showed that they were known auxin-response genes such as IAA1, SAUR and GH3 . In contrast, in response to 1.0 mM 2,4-D + 0.2% (v/v) surfactant NUL1026, there was approximately 10 times more genes being regulated for the same time point. This suggests that the surfactant may have promoted the uptake of the herbicide 2,4-D. Moreover, 248 and 354 genes were also exclusive differentially expressed after spraying with 1.0 mM 2,4-D + 0.2% (v/v) surfactant NUL1026, 1 h and 24 h respectively. More in-depth analysis of these exclusively regulated genes showed the increased expression of additional auxin-inducible genes at both time points. Also showing significant up-regulation was genes involved in detoxification and senescence while those transcripts associated with cell wall expansion and photosynthesis was down-regulated. The microarray results of this study highlighted the synergistic influence of surfactant NUL1026 in enhancing 2,4-D toxicity

A composite transcriptional signature differentiates responses towards closely related herbicides in Arabidopsis thaliana and Brassica napus

In this study, genome-wide expression profiling based on Affymetrix ATH1 arrays was used to identify discriminating responses of Arabidopsis thaliana to five herbicides, which contain active ingredients targeting two different branches of amino acid biosynthesis. One herbicide contained glyphosate, which targets 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), while the other four herbicides contain different acetolactate synthase (ALS) inhibiting compounds. In contrast to the herbicide containing glyphosate, which affected only a few transcripts, many effects of the ALS inhibiting herbicides were revealed based on transcriptional changes related to ribosome biogenesis and translation, secondary metabolism, cell wall modification and growth. The expression pattern of a set of 101 genes provided a specific, composite signature that was distinct from other major stress responses and differentiated among herbicides targeting the same enzyme (ALS) or containing the same chemical class of active ingredient (sulfonylurea). A set of homologous genes could be identified in Brassica napus that exhibited a similar expression pattern and correctly distinguished exposure to the five herbicides. Our results show the ability of a limited number of genes to classify and differentiate responses to closely related herbicides in A. thaliana and B. napus and the transferability of a complex transcriptional signature across species

The effect of carbohydrate carbon sources on the production of cellulase by Phlebia gigantea

Phlebia gigantea is an aggressive white rot fungus that colonizes conifer wood. The influence of different carbohydrates: glucose, xylose, carboxymethyl cellulose (CMC), microcrystalline cellulose (avicel) and cellobiose were evaluated as carbon sources for the production of cellulase by this saprophytic fungus. Carboxymethyl cellulose gave the highest yield, followed by cellobiose and avicel. Glucose and xylose did not produce any detectable cellulases which suggest the repression of cellulase in presence of these simple carbohydrates by P. gigantea. These results showed that the production of cellulase not only depends on the pH but also on the consumption of carbon sources in medium. The higher yield of cellulase in presence of CMC, the amorphous cellulose, and less in presence of cellobiose the soluble intermediate product of cellulose hydrolysis, indicates the requirement of crystallinity and complexity for the higher yield of cellulase by P. gigantea

Genome-wide microarray analysis of the effect of a surfactant application in Arabidopsis

Herbicides provide growers with the means to chemically manage weeds; surfactants are often an effective way of improving the performance of these herbicides. However, the mode of action of surfactants at the molecular level is not well understood. As a preliminary step towards understanding the molecular mechanism of action of an etheramine surfactant, plant gene expression in response to foliar application of surfactant NUL1026 was analysed in Arabidopsis thaliana, using the commercially available Affymetrix ATH1-121501 chip. One hundred and ninety-six genes were found to be significantly altered 1 h after plants were treated with 0.2% (V/V) of surfactant NUL1026. Functional category analysis of these genes revealed that the largest categories included metabolism, physiological processes, transport, protein metabolism, response to stimulus and transcription. A number of genes encoding detoxification proteins, such as cytochrome P450, glutathione S-transferase and members of the multidrug-resistance associated proteins, were upregulated. Interestingly, microarray results showed a number of genes encoding enzymes involved in the jasmonic acid biosynthesis pathway and also the 1-aminocyclopropane-1-carboxylate synthase gene for ethylene production were upregulated, indicating that treatment with surfactant NUL1026 affects the expression of a number of genes involved in the detoxification and signalling pathways

Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis

Transcriptional reprogramming forms a major part of a plant’s response to pathogen infection. Many individual components and pathways operating during plant defense have been identified, but our knowledge of how these different components interact is still rudimentary. We generated a high-resolution time series of gene expression profiles from a single Arabidopsis thaliana leaf during infection by the necrotrophic fungal pathogen Botrytis cinerea. Approximately one-third of the Arabidopsis genome is differentially expressed during the first 48 h after infection, with the majority of changes in gene expression occurring before significant lesion development. We used computational tools to obtain a detailed chronology of the defense response against B. cinerea, highlighting the times at which signaling and metabolic processes change, and identify transcription factor families operating at different times after infection. Motif enrichment and network inference predicted regulatory interactions, and testing of one such prediction identified a role for TGA3 in defense against necrotrophic pathogens. These data provide an unprecedented level of detail about transcriptional changes during a defense response and are suited to systems biology analyses to generate predictive models of the gene regulatory networks mediating the Arabidopsis response to B. cinerea