Selection of plants for roles in phytoremediation: the importance of glucosylation

Over-expression and transposon mutagenesis in root cultures of Arabidopsis thaliana demonstrated the importance of the family 1 glycosyltransferase UGT72B1 in catalysing the N-glucosylation of the persistent pollutant 3,4-dichloroaniline (DCA). In phytotoxicity studies with DCA in seedlings, over-expression of UGT72B1 enhanced sensitivity, whereas the knockouts were more resistant than the controls. In contrast, manipulating the expression of UGT72B1 had no effect on the O-glucosylation, or toxicity, of chlorophenols. When N-glucosylation was disrupted in plants, radioactivity derived from [14C]-DCA became covalently bound into high molecular weight insoluble material, principally associated with the lignin fraction. This suggested that insolubilization into stable cell wall components represented a more effective mechanism of DCA detoxification than the formation of N-glycosidic conjugates. A screen of plants used in remediation, identified low levels of N-glucosyltransferase activity in switchgrass and high activities in reed canary grass. When incubated with [14C]-DCA, reed canary grass plants accumulated soluble N-glycosides of DCA, whereas switchgrass formed insoluble residues. Consistent with the results obtained in studies with Arabidopsis, phytotoxicity trials with DCA demonstrated that switchgrass was more tolerant than reed canary grass. Our studies provide a new biochemical basis for selecting plants for useful remediating traits towards specific classes of pollutants

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

Functional and informatics analysis enables glycosyltransferase activity prediction

The elucidation and prediction of how changes in a protein result in altered activities and selectivities remain a major challenge in chemistry. Two hurdles have prevented accurate family-wide models: obtaining (i) diverse datasets and (ii) suitable parameter frameworks that encapsulate activities in large sets. Here, we show that a relatively small but broad activity dataset is sufficient to train algorithms for functional prediction over the entire glycosyltransferase superfamily 1 (GT1) of the plant Arabidopsis thaliana. Whereas sequence analysis alone failed for GT1 substrate utilization patterns, our chemical–bioinformatic model, GT-Predict, succeeded by coupling physicochemical features with isozyme-recognition patterns over the family. GT-Predict identified GT1 biocatalysts for novel substrates and enabled functional annotation of uncharacterized GT1s. Finally, analyses of GT-Predict decision pathways revealed structural modulators of substrate recognition, thus providing information on mechanisms. This multifaceted approach to enzyme prediction may guide the streamlined utilization (and design) of biocatalysts and the discovery of other family-wide protein functions

In re: ‘Experimental Music’

John Cage is universally associated with the phrase experimental music. But what did that phrase mean, for Cage and for Cage’s predecessors? I begin with Cage and Lejaren Hiller, both writing important texts on ‘experimental music’ in 1959. From there, I trace the phrase backwards, eventually reaching Emile Zola, Gertrude Stein, and William James. A final section traces the phrase forward to Cage and Hiller’s collaboration on HPSCHD (1969)

Functional importance of the family 1 glucosyltransferase UGT72B1 in the metabolism of xenobiotics in Arabidopsis thaliana

The Arabidopsis type 1 UDP-glucose-dependent glucosyltransferase UGT72B1 is highly active in conjugating the persistent pollutants 3,4-dichloroaniline (DCA) and 2,4,5-trichlorophenol (TCP). To determine its importance in detoxifying xenobiotics in planta, mutant plants where the respective gene has been disrupted by T-DNA insertion have been characterized. Extracts from the knockout ugt72B1 plants showed radically reduced conjugating activity towards DCA and TCP and the absence of immunodetectable UGT72B1 protein. In contrast, activities towards phenolic natural products were unaffected. When aseptic root cultures were fed [14C]-DCA, compared with wild types, the ugt72B1 plants showed a reduced rate of uptake of the xenobiotic and very little metabolism to soluble DCA-glucose or associated polar conjugates. Instead, the knockouts accumulated non-extractable radioactive residues, most probably associated with lignification. When the feeding studies were carried out with [14C]-TCP, rates and routes of metabolism were identical in the wild type and knockouts, with TCP-glucoside a major product in both cases. Similar differential effects on the metabolism of DCA and TCP were obtained in whole plant studies with wild type and ugt72B1 mutants, demonstrating that while UGT72B1 had a central role in metabolizing chloroanilines in Arabidopsis, additional UGTs could compensate for the conjugation of TCP in the knockout. TCP was equally toxic to wild type and ugt72B1 plants, while surprisingly, the knockouts were less sensitive to DCA. From this it was concluded that the glucosylation of DCA may not be as effective in xenobiotic detoxification as bound-residue formation

A kinetic model for the metabolism of the herbicide safener fenclorim in Arabidopsis thaliana.

Glutathione transferases (GSTs) catalyse the detoxification of a range of xenobiotics, including crop protection agents in plants. Recent studies in cultures of the model plant Arabidopsis thaliana have shown that the herbicide safener fenclorim (4,6-dichloro-2-phenylpyrimidine) is conjugated by GSTs acting in the cytosol which are induced in response to this chemical treatment. The primary glutathione conjugates are then hydrolyzed to S-(4-chloro-2-phenylpyrimidin-6-yl)-cysteine, which after accumulating transiently in the cells and medium is then metabolized by a series of competing lyases and transferases, including GSTs, to a series of polar derivatives. This system therefore represents an example of an inducible metabolic pathway, where GSTs are involved in multiple steps and where detailed information on the content of intermediates is available. Using this data, a kinetic model describing the biotransformations of differing concentrations of fenclorim in Arabidopsis has been established, which was able to quantitatively analyse fluxes and changes in metabolite levels over time as a function of the induction of GSTs by the safener. The model confirmed a regulatory role for GSTs and the hydrolytic enzymes acting on the resulting glutathione conjugates. In addition, model analysis indicated that fenclorim metabolism is capable of generating oscillations if kinetic parameters are allowed to vary. The model offers new insights into the metabolic regulation of inducible xenobiotic metabolism in plants which is important in both determining herbicide selectivity in cereal crops and the remediation of organic pollutants by plants