Herbicide-binding sites revealed in the structure of plant acetohydroxyacid synthase

Differential expression of acetohydroxyacid synthase genes in sunflower plantlets and its response to imazapyr herbicide

Acetohydroxyacid synthase (AHAS) catalyzes the first reaction in branch chain amino acids biosynthesis. This enzyme is the target of several herbicides, including all members of the imidazolinone family. Little is known about the expression of the three acetohydroxyacid synthase genes (ahas1, ahas2 and ahas3) in sunflower. The aim of this work was to evaluate ahas gene expression and AHAS activity in different tissues of sunflower plantlets. Three genotypes differing in imidazolinone resistance were evaluated, two of which carry an herbicide resistant-endowing mutation known as Ahasl1-1 allele. In vivo and in vitro AHAS activity and transcript levels were higher in leaves than in roots. The ahas3 transcript was the less abundant in both tissues. No significant difference was observed between ahas1 and ahas2 transcript levels of the susceptible genotype but a higher ahas1 transcript level was observed in leaves of genotypes carrying Ahasl1-1 allele. Similar transcript levels were found for ahas1 and ahas2 in roots of genotypes carrying Ahasl1-1 allele whereas higher ahas2 abundance was found in the susceptible genotype. Herbicide treatment triggered tissue-specific, gene and genotype-dependent changes in ahas gene expression. AHAS activity was highly inhibited in the susceptible genotype. Differential responses were observed between in vitro and in vivo AHAS inhibition assays. These findings enhance our understanding of AHAS expression in sunflower genotypes differing for herbicide resistance and its response to herbicide treatment.

Role of a highly conserved proline-126 in ThDP binding of Mycobacterium tuberculosis acetohydroxyacid synthase

Acetohydroxyacid synthase (AHAS) of Mycobacterium tuberculosis is a promising target for the development of anti-tuberculosis agents. With the absence of an available bacterial AHAS crystal structure, that of M. tuberculosis, site-directed mutagenesis has been a useful tool for determining its structural and functional features. In this study, a highly conserved proline residue (P126 of M. tuberculosis AHAS) was selected, and the possible role was evaluated by site-directed mutagenesis. P126 was replaced by valine, threonine, alanine, and glutamate to yield P126V, P126T, P126A, and P126E, respectively. All variants were expressed in their soluble forms in Escherichia coli and purified to near homogeneity. The molecular mass (SDS-PAGE) of the purified variants was ∼68 kDa, which is similar to that of wild-type AHAS. The P126V, P126T, and P126A variants exhibited significantly lower activity than wild-type AHAS, whereas P126E was inactive under the tested assay conditions. Furthermore, the P126V and P126T variants showed a significantly decreased preference toward pyruvate and ThDP as substrate and cofactor respectively, whereas the P126A showed similar kinetics to that of wild-type AHAS. Like in AHAS from yeast Saccharomyces cerevisiae (PDB ID: 1N0H), residue P126 is located in the ThDP binding pocket of M. tuberculosis AHAS homology model. Collectively, these results suggest that the conserved P126 plays a significant role in the ThDP binding of M. tuberculosis AHAS.

Synthesis and biological evaluation of nonsymmetrical aromatic disulfides as novel inhibitors of acetohydroxyacid synthase

46 Novel nonsymmetrical aromatic disulfides containing [1,3,4]thiadiazole or [1,3,4]oxadiazole groups were synthesized and their biological activities were evaluated as inhibitors of acetohydroxyacid synthase (AHAS, EC 2.2.1.6). Besides their strong in vitro inhibition against plant AHAS, compounds 3e and 3f also display 80-100% post-emergence herbicidal activities in greenhouse bioassay at 1500g /ha dosage. The assay of exogenous branched-chain amino acids supplementation on rape root growth of 3e suggests that the herbicidal activity has relationship with AHAS inhibition.

selection of transgenic sugarcane callus utilizing a plant gene encoding a mutant form of acetolactate synthase

Selection genes are routinely used in plant genetic transformation protocols to ensure the survival of transformed cells by limiting the regeneration of non-transgenic cells. In order to find alternatives to the use of antibiotics as selection agents, we followed a targeted approach utilizing a plant gene, encoding a mutant form of the enzyme acetolactate synthase, to convey resistance to herbicides. The sensitivity of sugarcane callus (Saccharum spp. hybrids, cv. NCo310) to a number of herbicides from the sulfonylurea and imidazolinone classes was tested. Callus growth was most affected by sulfonylurea herbicides, particularly 3.6 μg/l chlorsulfuron. Herbicide-resistant transgenic sugarcane plants containing mutant forms of a tobacco acetolactate synthase (als) gene were obtained following biolistic transformation. Post-bombardment, putative transgenic callus was selectively proliferated on MS medium containing 3 mg/l 2,4-dichlorophenoxyacetic acid (2,4-D), 20 g/l sucrose, 0.5 g/l casein, and 3.6 μg/l chlorsulfuron. Plant regeneration and rooting was done on MS medium lacking 2,4-D under similar selection conditions. Thirty vigorously growing putative transgenic plants were successfully ex vitro-acclimatized and established under glasshouse conditions. Glasshouse spraying of putative transgenic plants with 100 mg/l chlorsulfuron dramatically decreased the amount of non-transgenic plants that had escaped the in vitro selection regime. PCR analysis showed that six surviving plants were als-positive and that five of these expressed the mutant als gene. This report is the first to describe a selection system for sugarcane transformation that uses a selectable marker gene of plant origin targeted by a sulfonylurea herbicide.

Growth inhibition of pathogenic bacteria by sulfonylurea herbicides

Emerging resistance to current antibiotics raises the need for new microbial drug targets. We show that targeting branched-chain amino acid (BCAA) biosynthesis using sulfonylurea herbicides, which inhibit the BCAA biosynthetic enzyme acetohydroxyacid synthase (AHAS), can exert bacteriostatic effects on several pathogenic bacteria, including Burkholderia pseudomallei, Pseudomonas aeruginosa, and Acinetobacter baumannii. Our results suggest that targeting biosynthetic enzymes like AHAS, which are lacking in humans, could represent a promising antimicrobial drug strategy.

Acetohydroxyacid synthase (AHAS) in vivo assay for screening imidazolinone-resistance in sunflower (Helianthus annuus L.)

The objective of this work was to evaluate the in vivo acetohydroxyacid synthase (AHAS) activity response to imidazolinones and its possible use as a selection method for evaluating AHAS inhibitor resistance. In vivo AHAS assay and the comparison of parameters from dose-response curves have been used as a valid tool for comparing sunflower lines and hybrids differing in imidazolinone resistance. The sunflower resistant genotypes evaluated here were 100-fold and 20-fold more resistant compared with the susceptible line for imazethapyr and imazapyr, respectively. This assay also allowed discrimination of homozygous from heterozygous genotypes for I(mr1) locus that codify for the catalytic subunit of AHAS. The in vivo AHAS assay described in this study was useful for the selection of sunflower genotypes differing in herbicide resistance and could be a useful tool when breeding for imidazolinone resistance in sunflower.

Response of imidazolinone-tolerant and -susceptible volunteer oilseed rape (Brassica napus L.) to ALS inhibitors and alternative herbicides

BACKGROUND

Imidazolinone-tolerant oilseed rape (Brassica napus L.) varieties are currently grown in Canada, North America, Chile and Australia with high acreage. A Europe-wide introduction has started and will be pushed further for both spring and winter varieties. The primary aim of this study was to evaluate the impact of imidazolinone tolerance for future volunteer oilseed rape control in subsequent crops, particularly winter wheat.

RESULTS

A greenhouse bioassay showed cross-tolerance of imidazolinone-tolerant oilseed rape towards sulfonylureas, triazolopyrimidines and sulfonylaminocarbonyltriazolinones (resistance factors between 5 and 775), with a homozygous variety expressing a much higher tolerance level compared with a heterozygous variety. Calculated ED90 values suitable for controlling tolerant plants were always much higher than the recommended herbicide dose. Generally, results were confirmed under field conditions, but with higher efficacies than expected in some cases (e.g. florasulam). Herbicides with an alternative mode of action were found to be effective in controlling imidazolinone-tolerant volunteers in subsequent winter wheat crops.

CONCLUSION

Herbicide strategies have to be adjusted for volunteer control in subsequent crops if imidazolinone-tolerant oilseed rape varieties are to be grown. However, agronomic tools (harvest date, harvest technique, tillage) should be used conscientiously in the first place to keep volunteer oilseed rape densities at the lowest possible level.

Benzaldehyde is a precursor of phenylpropylamino alkaloids as revealed by targeted metabolic profiling and comparative biochemical analyses in Ephedra spp

Ephedrine and pseudoephedrine are phenylpropylamino alkaloids widely used in modern medicine. Some Ephedra species such as E. sinica Stapf (Ephedraceae), a widely used Chinese medicinal plant (Chinese name: Ma Huang), accumulate ephedrine alkaloids as active constituents. Other Ephedra species, such as E. foeminea Forssk. (syn. E. campylopoda C.A. Mey) lack ephedrine alkaloids and their postulated metabolic precursors 1-phenylpropane-1,2-dione and (S)-cathinone. Solid-phase microextraction analysis of freshly picked young E. sinica and E. foeminea stems revealed the presence of increased benzaldehyde levels in E. foeminea, whereas 1-phenylpropane-1,2-dione was detected only in E. sinica. Soluble protein preparations from E. sinica and E. foeminea stems catalyzed the conversion of benzaldehyde and pyruvate to (R)-phenylacetylcarbinol, (S)-phenylacetylcarbinol, (R)-2-hydroxypropiophenone (S)-2-hydroxypropiophenone and 1-phenylpropane-1,2-dione. The activity, termed benzaldehyde carboxyligase (BCL) required the presence of magnesium and thiamine pyrophosphate and was 40 times higher in E. sinica as compared to E. foeminea. The distribution patterns of BCL activity in E. sinica tissues correlates well with the distribution pattern of the ephedrine alkaloids. (S)-Cathinone reductase enzymatic activities generating (1R,2S)-norephedrine and (1S,1R)-norephedrine were significantly higher in E. sinica relative to the levels displayed by E. foeminea. Surprisingly, (1R,2S)-norephedrine N-methyltransferase activity which is a downstream enzyme in ephedrine biosynthesis was significantly higher in E. foeminea than in E. sinica. Our studies further support that benzaldehyde is the metabolic precursor to phenylpropylamino alkaloids in E. sinica.

Synthesis, crystal structure, in vitro acetohydroxyacid synthase inhibition, in vivo herbicidal activity, and 3D-QSAR of new asymmetric aryl disulfides

Acetohydroxyacid synthase (AHAS; EC 2.2.1.6) is an important bioactive target for the design of environmentally benign herbicides. On the basis of previous virtual screening, 50 asymmetric aryl disulfides containing [1,2,4]triazole groups were synthesized and characterized by (1)H NMR, HRMS, and crystal structure. Compounds I-a, I-b, and I-p show Ki values of 1.70, 4.69, and 5.57 μM, respectively, for wild type Arabidopsis thaliana AHAS (AtAHAS) and low resistance against mutant type AtAHAS W574L. At 100 mg L(-1) concentration, compounds I-a, II-a, and II-b exhibit 86.6, 81.7, and 87.5% in vivo rape root growth inhibition. CoMFA steric and electrostatic contour maps were established, and a possible binding mode was suggested from molecular docking, which provide valuable information to understand the key structural features of these disulfide compounds. To the authors' knowledge, this is the first comprehensive case suggesting that asymmetric aryl disulfides are novel AHAS inhibitors.

A novel amino acid substitution Ala-122-Tyr in ALS confers high-level and broad resistance across ALS-inhibiting herbicides

BACKGROUND

Wild radish, a problem weed worldwide, is a severe dicotyledonous weed in crops. In Australia, sustained reliance on ALS-inhibiting herbicides to control this species has led to the evolution of many resistant populations endowed by any of several ALS mutations. The molecular basis of ALS-inhibiting herbicide resistance in a novel resistant population was studied.

RESULTS

ALS gene sequencing revealed a previously unreported substitution of Tyr for Ala at amino acid position 122 in resistant individuals of a wild radish population (WARR30). A purified subpopulation individually homozygous for the Ala-122-Tyr mutation was generated and characterised in terms of its response to the different chemical classes of ALS-inhibiting herbicides. Whole-plant dose-response studies showed that the purified subpopulation was highly resistant to chlorsulfuron, metosulam and imazamox, with LD₅₀ or GR₅₀ R/S ratio of > 1024, > 512 and > 137 respectively. The resistance to imazypyr was found to be relatively moderate (but still substantial), with LD₅₀ and GR₅₀ R/S ratios of > 16 and > 7.8 respectively. In vitro ALS activity assays showed that Ala-122-Tyr ALS was highly resistant to all tested ALS-inhibiting herbicides.

CONCLUSION

The molecular basis of ALS-inhibiting herbicide resistance in wild radish population WARR30 was identified to be due to an Ala-122-Tyr mutation in the ALS gene. This is the first report of an amino acid substitution at Ala-122 in the plant ALS that confers high-level and broad-spectrum resistance to ALS-inhibiting herbicides, a remarkable contrast to the known mutation Ala-122-Thr endowing resistance to imidazolinone herbicide.

Isolation and expression of genes for acetolactate synthase and acetyl-CoA carboxylase in Echinochloa phyllopogon, a polyploid weed species

BACKGROUND

Target-site resistance is the major cause of herbicide resistance to acetolactate synthase (ALS)- and acetyl-CoA carboxylase (ACCase)-inhibiting herbicides in arable weeds, whereas non-target-site resistance is rarely reported. In the Echinochloa phyllopogon biotypes resistant to these herbicides, target-site resistance has not been reported, and non-target-site resistance is assumed to be the basis for resistance. To explore why target-site resistance had not occurred, the target-site genes for these herbicides were isolated from E. phyllopogon, and their expression levels in a resistant biotype were determined.

RESULTS

Two complete ALS genes and the carboxyltransferase domain of four ACCase genes were isolated. The expression levels of ALS and ACCase genes were higher in organs containing metabolically active meristems, except for ACC4, which was not expressed in any organ. The differential expression among examined organs was more prominent for ALS2 and ACC2 and less evident for ALS1, ACC1 and ACC3.

CONCLUSION

E. phyllopogon has multiple copies of the ALS and ACCase genes, and different expression patterns were observed among the copies. The existence of three active ACCase genes and the difference in their relative expression levels could influence the occurrence of target-site resistance to ACCase inhibitors in E. phyllopogon.

The structure-activity relationship in herbicidal monosubstituted sulfonylureas

BACKGROUND

The herbicide sulfonylurea (SU) belongs to one of the most important class of herbicides worldwide. It is well known for its ecofriendly, extreme low toxicity towards mammals and ultralow dosage application. The original inventor, G Levitt, set out structure-activity relationship (SAR) guidelines for SU structural design to attain superhigh bioactivity. A new approach to SU molecular design has been developed.

RESULTS

After the analysis of scores of SU products by X-ray diffraction methodology and after greenhouse herbicidal screening of 900 novel SU structures synthesised in the authors' laboratory, it was found that several SU structures containing a monosubstituted pyrimidine moiety retain excellent herbicidal characteristics, which has led to partial revision of the Levitt guidelines.

CONCLUSIONS

Among the novel SU molecules, monosulfuron and monosulfuron-ester have been developed into two new herbicides that have been officially approved for field application and applied in millet and wheat fields in China. A systematic structural study of the new substrate-target complex and the relative mode of action in comparison with conventional SU has been carried out. A new mode of action has been postulated.

Comparability of imazapyr-resistant Arabidopsis created by transgenesis and mutagenesis

The Arabidopsis CSR1 gene codes for the enzyme acetohydroxyacid synthase (AHAS, EC 2.2.1.6), also known as acetolactate synthase, which catalyzes the first step in branched-chain amino acid biosynthesis. It is inhibited by several classes of herbicides, including the imidazolinone herbicides, such as imazapyr; however, a substitution mutation in csr1-2 (Ser-653-Asn) confers selective resistance to the imidazolinones. The transcriptome of csr1-2 seedlings grown in the presence of imazapyr has been shown in a previous study (Manabe in Plant Cell Physiol 48:1340-1358, 2007) to be identical to that of wild-type seedlings indicating that AHAS is the sole target of imazapyr and that the mutation is not associated with pleiotropic effects detectable by transcriptome analysis. In this study, a lethal null mutant, csr1-7, created by a T-DNA insertion into the CSR1 gene was complemented with a randomly-inserted 35S/CSR1-2/NOS transgene in a subsequent genetic transformation event. A comparison of the csr1-2 substitution mutant with the transgenic lines revealed that all were resistant to imazapyr; however, the transgenic lines yielded significantly higher levels of resistance and greater biomass accumulation in the presence of imazapyr. Microarray analysis revealed few differences in their transcriptomes. The most notable was a sevenfold to tenfold elevation in the CSR1-2 transcript level. The data indicate that transgenesis did not create significant unintended pleiotropic effects on gene expression and that the mutant and transgenic lines were highly similar, except for the level of herbicide resistance.

Inheritance and molecular characterization of broad range tolerance to herbicides targeting acetohydroxyacid synthase in sunflower

Ahasl1 is a multilallelic locus where all the induced and natural mutations for herbicide tolerance were described thus far in sunflower (Helianthus annuus L.). The allele Ahasl1-1 confers moderate tolerance to imidazolinone (IMI), Ahasl1-2, and Ahasl1-3 provides high levels of tolerance solely to sulfonylurea (SU) and IMI, respectively. An Argentinean wild sunflower population showing plants with high level of tolerance to either an IMI and a SU herbicide was discovered and used to develop an inbred line designated RW-B. The objectives of this work were to determine the relative level and pattern of cross-tolerance to different AHAS-inhibiting herbicides, the mode of inheritance, and the molecular basis of herbicide tolerance in this line. Slight or no symptoms observed after application of different herbicides indicated that RW-B possesses a completely new pattern of tolerance to AHAS-inhibiting herbicides in sunflower. Biomass response to increasing doses of metsulfuron or imazapyr demonstrated a higher level of tolerance in RW-B with respect to Ahasl1-1/Ahasl1-1 and Ahasl1-2/Ahasl1-2 lines. On the basis of genetic analyses and cosegregation test, it was concluded that tolerance to imazapyr in the original population is inherited as a single, partially dominant nuclear gene and that this gene is controlling the tolerance to four different AHAS-inhibiting herbicides. Pseudo-allelism test permitted us to conclude that the tolerant allele present in RW-B is an allelic variant of Ahasl1-1 and was designated as Ahasl1-4. Nucleotide and deduced amino acid sequence indicated that the Ahasl1-4 allele sequence of RW-B has a leucine codon (TTG) at position 574 (relative to the Arabidopsis thaliana AHAS sequence), whereas the enzyme from susceptible lines has a tryptophan residue (TGG) at this position. The utilization of this new allele in the framework of weed control and crop rotation is discussed.

Response to imazapyr and dominance relationships of two imidazolinone-tolerant alleles at the Ahasl1 locus of sunflower

Imisun and CLPlus are two imidazolinone (IMI) tolerance traits in sunflower (Helianthus annuus L.) determined by the expression of different alleles at the same locus, Ahasl1-1 and Ahasl1-3, respectively. This paper reports the level of tolerance expressed by plants containing both alleles in a homozygous, heterozygous and in a heterozygous stacked state to increasing doses of IMI at the enzyme and whole plant levels. Six genotypes of the Ahasl1 gene were compared with each other in three different genetic backgrounds. These materials were treated at the V2-V4 stage with increasing doses of imazapyr (from 0 to 480 g a.i. ha(-1)) followed by an assessment of the aboveground biomass and herbicide phytotoxicity. The estimated dose of imazapyr required to reduce biomass accumulation by 50% (GR(50)) differed statistically for the six genotypes of the Ahasl1 gene. Homozygous CLPlus (Ahasl1-3/Ahasl1-3) genotypes and materials containing a combination of both tolerant alleles (Imisun/CLPlus heterozygous stack, Ahasl1-1/Ahasl1-3) showed the highest values of GR(50), 300 times higher than the susceptible genotypes and more than 2.5 times higher than homozygous Imisun materials (Ahasl1-1/Ahasl1-1). In vitro AHAS enzyme activity assays using increasing doses of herbicide (from 0 to 100 μM) showed similar trends, where homozygous CLPlus materials and those containing heterozygous stacks of Imisun/CLPlus were statistically similar and showed the least level of inhibition of enzyme activity to increasing doses of herbicide. The degree of dominance for the accumulation of biomass after herbicide application calculated for the Ahasl1-1 allele indicated that it is co-dominant to recessive depending on the imazapyr dose used. By the contrary, the Ahasl1-3 allele showed dominance to semi dominance according to the applied dose. This last allele is dominant over Ahasl1-1 over the entire range of herbicide rates tested. At the level of enzymatic activity, however, both alleles showed recessivity to semi-recessivity with respect to the wild-type allele, even though the Ahasl1-3 allele is dominant over Ahasl1-1 at all the herbicides rates used.

A structural biology perspective on bioactive small molecules and their plant targets

Structural biology efforts in recent years have generated numerous co-crystal structures of bioactive small molecules interacting with their plant targets. These studies include the targets of various phytohormones, pathogen-derived effectors, herbicides and other bioactive compounds. Here we discuss that this collection of structures contains excellent examples of nine collective observations: molecular glues, allostery, inhibitors, molecular mimicry, promiscuous binding sites, unexpected electron densities, natural selection at atomic resolution, and applications in structure-guided mutagenesis and small molecule design.

Isolation and Characterization of Rhodopseudomonas sp. S9-1 Capable of Degrading Pyrazosulfuron-Ethyl

A bacterial strain S9-1capable of degrading sulfonylurea herbicide pyrazosulfuron-ethyl (PSE) was isolated from contaminated soil through the enrichment incubation method. Based on morphology, colony and cultural properties, physiological and biochemical characteristics, living-cell absorption spectra, internal photosynthetic membrane, and phylogenetics of its 16S rRNA gene sequence, S9-1was preliminarily identified as belonging to the genus Rhodopseudomonas, a group of photosynthetic bacteria (PSB). The effects of PSE concentration, pH, and temperature on biodegradation were examined. The degradation rate was found to decrease with increasing PSE concentration. Optimal growth pH and temperature were found to be 7.0 and 30°C, respectively. The strain was able to degrade 47.51% of PSE at a concentration of 100 mg ml-1after 7 days of incubation at 30°C and could tolerate 800 mg ml-1PSE. S9-1was also able to completely co-metabolically transform 100 mg ml-1PSE at 30°C, pH 7.0, and 7500 lux in 15 days. As the concentration of PSE increased, the degradation process took longer to complete. The fragment encoding acetolactate synthase (ALS) gene from S9-1was cloned and sequenced. Comparison of deduced amino acid sequences was implemented, and the conserved sites were analyzed. To our knowledge, this is the first report of PSB in PSE biodegradation. These results highlight the potential of this bacterium as a detoxifying agent for use with PSE-contaminated soil and wastewater.

Chemical synthesis, in vitro acetohydroxyacid synthase (AHAS) inhibition, herbicidal activity, and computational studies of isatin derivatives

Acetohydroxyacid synthase (AHAS) catalyzes the first common step in the biosynthesis of the branched-chain amino acids. As a result of its metabolic importance in plants, it is a target for many commercial herbicides. Virtual screening analysis inspired the evaluation of 19 commercially available isatin analogues and 13 newly synthesized isatin derivatives as novel AHAS inhibitors and for their herbicidal activity. The best compound demonstrated 95% inhibition of the activity of Arabidopsis thaliana AHAS at a concentration of 100 mg L(-1), whereas the herbicidal activities of three compounds reached 50% inhibition at a concentration of 10 mg L(-1) using the rape root growth test. CoMFA contour models were established to understand the structure-activity relationships for this class of AHAS inhibitor. The compounds were docked to the active site cavity of A. thaliana AHAS using FlexX, and the dominant binding mode was consistent with frontier molecular orbital from DFT calculations. This is the first comprehensive study of isatin derivatives as AHAS inhibitors and provides a valuable starting point for the design of new herbicides.

Direct activation of Epac by sulfonylurea is isoform selective

Commonly used as a treatment for Type II diabetes, sulfonylureas (SUs) stimulate insulin secretion from pancreatic β cells by binding to sulfonylurea receptors. Recently, SUs have been shown to also activate exchange protein directly activated by cAMP 2 (Epac2), however, little is known about this molecular action. Using biosensor imaging and biochemical analysis, we show that SUs activate Epac2 and the downstream signaling via direct binding to Epac2. We further identify R447 of Epac2 to be critically involved in SU binding. This distinct binding site from cAMP points to a new mode of allosteric activation of Epac2. We also show that SUs selectively activate Epac2 isoform, but not the closely related Epac1, further establishing SUs as a new class of isoform-selective enzyme activators.

Preliminary X-ray crystallographic studies of the catalytic subunit of Escherichia coli AHAS II with its cofactors

Acetohydroxyacid synthase (AHAS) is the first common enzyme in the branched-chain amino-acid biosynthesis pathway and is the target of several classes of commercial herbicides. In this study, the Escherichia coli ilvG gene that encodes the catalytic subunit of AHAS II was cloned into the pET28a vector and expressed in soluble form at high levels in E. coli strain BL21 (DE3) cells. The protein was purified using Ni(2+)-chelating chromatography followed by size-exclusion chromatography. The catalytic subunit of E. coli AHAS II was cocrystallized with its cofactors Mg(2+), FAD and ThDP using the sitting-drop vapour-diffusion method and the crystals diffracted to 2.80 Å resolution.

Enantioselective phytotoxicity of the herbicide imazethapyr on the response of the antioxidant system and starch metabolism in Arabidopsis thaliana

BACKGROUND

The enantiomers of a chiral compound possess different biological activities, and one of the enantiomers usually shows a higher level of toxicity. Therefore, the exploration of the causative mechanism of enantioselective toxicity is regarded as one of primary goals of biological chemistry. Imazethapyr (IM) is an acetolactate synthase (ALS)-inhibiting chiral herbicide that has been widely used in recent years with racemate. We investigated the enantioselectivity between R- and S-IM to form reactive oxygen species (ROS) and to regulate antioxidant gene transcription and enzyme activity.

RESULTS

Dramatic differences between the enantiomers were observed: the enantiomer of R-IM powerfully induced ROS formation, yet drastically reduced antioxidant gene transcription and enzyme activity, which led to an oxidative stress. The mechanism by which IM affects carbohydrate metabolism in chloroplasts has long remained a mystery. Here we report evidence that enantioselectivity also exists in starch metabolism. The enantiomer of R-IM resulted in the accumulation of glucose, maltose and sucrose in the cytoplasm or the chloroplast and disturbed carbohydrates utilization.

CONCLUSION

The study suggests that R-IM more strongly retarded plant growth than S-IM not only by acting on ALS, but also by causing an imbalance in the antioxidant system and the disturbance of carbohydrate metabolism with enantioselective manner.

Single nucleotide mutation in the barley acetohydroxy acid synthase (AHAS) gene confers resistance to imidazolinone herbicides

Induced mutagenesis can be an effective way to increase variability in self-pollinated crops for a wide variety of agronomically important traits. Crop resistance to a given herbicide can be of practical value to control weeds with efficient chemical use. In some crops (for example, wheat, maize, and canola), resistance to imidazolinone herbicides (IMIs) has been introduced through mutation breeding and is extensively used commercially. However, this production system imposes plant-back restrictions on rotational crops because of herbicide residuals in the soil. In the case of barley, a preferred rotational crop after wheat, a period of 9-18 mo is required. Thus, introduction of barley varieties showing resistance to IMIs will provide greater flexibility as a rotational crop. The objective of the research reported was to identify resistance in barley for IMIs through induced mutagenesis. To achieve this objective, a sodium azide-treated M(2)/M(3) population of barley cultivar Bob was screened for resistance against acetohydroxy acid synthase (AHAS)-inhibiting herbicides. The phenotypic screening allowed identification of a mutant line showing resistance against IMIs. Molecular analysis identified a single-point mutation leading to a serine 653 to asparagine amino acid substitution in the herbicide-binding site of the barley AHAS gene. The transcription pattern of the AHAS gene in the mutant (Ser653Asn) and WT has been analyzed, and greater than fourfold difference in transcript abundance was observed. Phenotypic characteristics of the mutant line are promising and provide the base for the release of IMI-resistant barley cultivar(s).

Thiamin (vitamin B1) biosynthesis and regulation: a rich source of antimicrobial drug targets?

Drug resistance of pathogens has necessitated the identification of novel targets for antibiotics. Thiamin (vitamin B1) is an essential cofactor for all organisms in its active form thiamin diphosphate (ThDP). Therefore, its metabolic pathways might be one largely untapped source of antibiotics targets. This review describes bacterial thiamin biosynthetic, salvage, and transport pathways. Essential thiamin synthetic enzymes such as Dxs and ThiE are proposed as promising drug targets. The regulation mechanism of thiamin biosynthesis by ThDP riboswitch is also discussed. As drug targets of existing antimicrobial compound pyrithiamin, the ThDP riboswitch might serves as alternative targets for more antibiotics.

AHAS herbicide resistance endowing mutations: effect on AHAS functionality and plant growth

Twenty-two amino acid substitutions at seven conserved amino acid residues in the acetohydroxyacid synthase (AHAS) gene have been identified to date that confer target-site resistance to AHAS-inhibiting herbicides in biotypes of field-evolved resistant weed species. However, the effect of resistance mutations on AHAS functionality and plant growth has been investigated for only a very few mutations. This research investigates the effect of various AHAS resistance mutations in Lolium rigidum on AHAS functionality and plant growth. The enzyme kinetics of AHAS from five purified L. rigidum populations, each homozygous for the resistance mutations Pro-197-Ala, Pro-197-Arg, Pro-197-Gln, Pro-197-Ser or Trp-574-Leu, were characterized and the pleiotropic effect of three mutations on plant growth was assessed via relative growth rate analysis. All these resistance mutations endowed a herbicide-resistant AHAS and most resulted in higher extractable AHAS activity, with no-to-minor changes in AHAS kinetics. The Pro-197-Arg mutation slightly (but significantly) increased the K(m) for pyruvate and remarkably increased sensitivity to feedback inhibition by branched chain amino acids. Whereas the Pro-197-Ser and Trp-574-Leu mutations exhibited no significant effects on plant growth, the Pro-197-Arg mutation resulted in lower growth rates. It is clear that, at least in L. rigidum, these five AHAS resistance mutations have no major impact on AHAS functionality and hence probably no plant resistance costs. These results, in part, explain why so many Pro-197 AHAS resistance mutations in AHAS have evolved and why the Pro-197-Ser and the Trp-574-Leu AHAS resistance mutations are frequently found in many weed species.

Comparative analysis of phytohormone-responsive phosphoproteins in Arabidopsis thaliana using TiO2-phosphopeptide enrichment and mass accuracy precursor alignment

Protein phosphorylation/dephosphorylation is a central post-translational modification in plant hormone signaling, but little is known about its extent and function. Although pertinent protein kinases and phosphatases have been predicted and identified for a variety of hormone responses, classical biochemical approaches have so far revealed only a few candidate proteins and even fewer phosphorylation sites. Here we performed a global quantitative analysis of the Arabidopsis phosphoproteome in response to a time course of treatments with various plant hormones using phosphopeptide enrichment and subsequent mass accuracy precursor alignment (MAPA). The use of three time points, 1, 3 and 6 h, in combination with five phytohormone treatments, abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellic acid (GA), jasmonic acid (JA) and kinetin, resulted in 324,000 precursor ions from 54 LC-Orbitrap-MS analyses quantified and aligned in a data matrix with the dimension of 6000 x 54 using the ProtMax algorithm. To dissect the phytohormone responses, multivariate principal/independent components analysis was performed. In total, 152 phosphopeptides were identified as differentially regulated; these phosphopeptides are involved in a wide variety of signaling pathways. New phosphorylation sites were identified for ABA response element binding factors that showed a specific increase in response to ABA. New phosphorylation sites were also found for RLKs and auxin transporters. We found that different hormones regulate distinct amino acid residues of members of the same protein families. In contrast, tyrosine phosphorylation of the G alpha subunit appeared to be a common response for multiple hormones, demonstrating global cross-talk among hormone signaling pathways.

Molecular mechanism of enantioselective inhibition of acetolactate synthase by imazethapyr enantiomers

Chiral compounds usually behave enantioselectively in phyto-biochemical processes. Imidazolinones are a class of chiral herbicides that are widely used. They inhibit branched-chain amino acid biosynthesis in plants by targeting acetolactate synthase (ALS). It has been reported that the imidazolinone enantiomers show different inhibiting activities to maize (Zea mays L.) seedlings and ALS. However, to date, the mechanism of enantioselective inhibition of imazethapyr (IM) on ALS activity has not been well studied. In this study, pure enantiomers of IM were used for characterizing their differences in activity to ALS. Computational molecular docking was performed to discover the molecular interaction between IM enantiomers and ALS at the first time. Results showed that the IM enantiomers enantioselectively suppressed the in vitro and in vivo ALS activity of maize leaves. R-(-)-IM was more active than S-(+)-IM. The in vivo ALS activity study showed only a 2-fold difference between R-(-)-IM and S-(+)-IM. Quite different from the in vivo study, the in vitro study showed that the difference in inhibition between the enantiomers fell sharply as concentration increased. At the lowest concentration of 40 microg L(-1), R-(-)-IM appeared 25 times more active than S-(+)-IM, but only 7 times at 200 microg L(-1). At the highest concentration of 25 mg L(-1), in vitro ALS activity was almost completely inhibited by S-(+)-, R-(-)-IM and (+/-)-IM, there was only 1.1 times differences between S-(+)- and R-(-)-IM. Molecular modeling results provide the rational structural basis to understand the mechanism of enantioselective inhibition of IM on ALS activity.

Evolution in action: plants resistant to herbicides

Modern herbicides make major contributions to global food production by easily removing weeds and substituting for destructive soil cultivation. However, persistent herbicide selection of huge weed numbers across vast areas can result in the rapid evolution of herbicide resistance. Herbicides target specific enzymes, and mutations are selected that confer resistance-endowing amino acid substitutions, decreasing herbicide binding. Where herbicides bind within an enzyme catalytic site very few mutations give resistance while conserving enzyme functionality. Where herbicides bind away from a catalytic site many resistance-endowing mutations may evolve. Increasingly, resistance evolves due to mechanisms limiting herbicide reaching target sites. Especially threatening are herbicide-degrading cytochrome P450 enzymes able to detoxify existing, new, and even herbicides yet to be discovered. Global weed species are accumulating resistance mechanisms, displaying multiple resistance across many herbicides and posing a great challenge to herbicide sustainability in world agriculture. Fascinating genetic issues associated with resistance evolution remain to be investigated, especially the possibility of herbicide stress unleashing epigenetic gene expression. Understanding resistance and building sustainable solutions to herbicide resistance evolution are necessary and worthy challenges.

Branched-Chain Amino Acid Metabolism in Arabidopsis thaliana

Valine, leucine and isoleucine form the small group of branched-chain amino acids (BCAAs) classified by their small branched hydrocarbon residues. Unlike animals, plants are able to de novo synthesize these amino acids from pyruvate, 2-oxobutanoate and acetyl-CoA. In plants, biosynthesis follows the typical reaction pathways established for the formation of these amino acids in microorganisms. Val and Ile are synthesized in two parallel pathways using a single set of enzymes. The pathway to Leu branches of from the final intermediate of Val biosynthesis. The formation of this amino acid requires a three-step pathway generating a 2-oxoacid elongated by a methylene group. In Arabidopsis thaliana and other Brassicaceae, a homologous three-step pathway is also involved in Met chain elongation required for the biosynthesis of aliphatic glucosinolates, an important class of specialized metabolites in Brassicaceae. This is a prime example for the evolutionary relationship of pathways from primary and specialized metabolism. Similar to animals, plants also have the ability to degrade BCAAs. The importance of BCAA turnover has long been unclear, but now it seems apparent that the breakdown process might by relevant under certain environmental conditions. In this review, I summarize the current knowledge about BCAA metabolism, its regulation and its particular features in Arabidopsis thaliana.

Recent progress in deciphering the biosynthesis of aspartate-derived amino acids in plants

Plants are either directly or indirectly the source of most of the essential amino acids in animal diets. Four of these essential amino acids-methionine, threonine, isoleucine, and lysine-are all produced from aspartate via a well studied biosynthesis pathway. Given the nutritional interest in essential amino acids, the aspartate-derived amino acid pathway has been the subject of extensive research. Additionally, several pathway enzymes serve as targets for economically important herbicides, and some of the downstream products are biosynthetic precursors for other essential plant metabolites such as ethylene and S-adenosylmethionine. Recent and ongoing research on the aspartate-derived family of amino acids has identified new enzyme activities, regulatory mechanisms, and in vivo metabolic functions. Together, these discoveries will open up new possibilities for plant metabolic engineering.

Docking and 3D-QSAR studies of acetohydroxy acid synthase inhibitor sulfonylurea derivatives

Docking and three dimensional quantitative-structure activity relationship (3D-QSAR) studies were performed on acetohydroxy acid synthase (AHAS) inhibitor sulfonylurea analogues with potential herbicidal activity. The 3D-QSAR studies were carried out using shape, spatial and electronic descriptors along with a few structural parameters. Genetic function approximation (GFA) was used as the chemometric tool for this analysis. The whole data set (n = 45) was divided into a training set (75% of the data set) and a test set (remaining 25%) on the basis of the K-means clustering technique on a standardised topological, physicochemical and structural descriptor matrix. Models developed from the training set were used to predict the activity of the test set compounds. All models were validated internally, externally and using the Y-randomisation technique. Docking studies suggested that the molecules bind within a pocket of the enzyme formed by some important amino acid residues (Met351, Asp375, Arg377, Gly509, Met570 and Val571). In QSAR studies, molecular shape analysis showed that bulky substitution at the R(1) position may enhance AHAS inhibitory activity. Charged surface area descriptors suggested that negative charge distributed over a large surface area may enhance this activity. The hydrogen bond acceptor parameter supported the charged surface area descriptors and suggested that, for better activity, the number of electronegative atoms present in the molecule should be high. The spatial descriptors show that, for better activity, the molecules should possess a bulky substituent and a small substitution at the R(2) and R(3) positions, respectively.

Multiple allelic forms of acetohydroxyacid synthase are responsible for herbicide resistance in Setaria viridis

In weed species, resistance to herbicides inhibiting acetohydroxyacid synthase (AHAS) is often conferred by genetic mutations at one of six codons in the AHAS gene. These mutations provide plants with various levels of resistance to different chemical classes of AHAS inhibitors. Five green foxtail [Setaria viridis (L.) Beauv.] populations were reported in Ontario with potential resistance to the AHAS-inhibiting herbicide imazethapyr. The objectives of this study were to confirm resistance, establish the resistance spectrum for each of the five populations, and determine its genetic basis. Dose response curves were generated for whole plant growth and enzyme activity, and the AHAS gene was sequenced. Resistance was confirmed by determining the resistance factor to imazethapyr in the five resistant green foxtail populations for whole plant dose response experiments (21- to 182-fold) and enzyme assays (15- to 260-fold). All five imazethapyr-resistant populations showed cross-resistance to nicosulfuron and flucarbazone while only three populations had cross-resistance to pyrithiobac. Sequence analyses revealed single base-pair mutations in the resistant populations of green foxtail. These mutations were coded for Thr, Asn, or Ile substitution at Ser(653). In addition, a new mutation was found in one population that coded for an Asp substitution at Gly(654). There is an agreement between the spectra of resistance observed and the type of resistance known to be conferred by these substitutions. Moreover, it indicates that, under similar selection pressure (imazethapyr), a variety of mutations can be selected for different populations, making the resistance pattern difficult to predict from herbicide exposure history.

Thiamin diphosphate in biological chemistry: analogues of thiamin diphosphate in studies of enzymes and riboswitches

The role of thiamin diphosphate (ThDP) as a cofactor for enzymes has been known for many decades. This minireview covers the progress made in understanding the catalytic mechanism of ThDP-dependent enzymes through the use of ThDP analogues. Many such analogues have been synthesized and have provided information on the functional groups necessary for the binding and catalytic activity of the cofactor. Through these studies, the important role of hydrophobic interactions in stabilizing reaction intermediates in the catalytic cycle has been recognized. Stable analogues of intermediates in the ThDP-catalysed reaction mechanism have also been synthesized and crystallographic studies using these analogues have allowed enzyme structures to be solved that represent snapshots of the reaction in progress. As well as providing mechanistic information about ThDP-dependent enzymes, many analogues are potent inhibitors of these enzymes. The potential of these compounds as therapeutic targets and as important herbicidal agents is discussed. More recently, the way that ThDP regulates the genes for its own biosynthesis through the action of riboswitches has been discovered. This opens a new branch of thiamin research with the potential to provide new therapeutic targets in the fight against infection.

Conformational changes in a plant ketol-acid reductoisomerase upon Mg(2+) and NADPH binding as revealed by two crystal structures

Ketol-acid reductoisomerase (KARI; EC 1.1.1.86) is an enzyme in the branched-chain amino acid biosynthesis pathway where it catalyzes the conversion of 2-acetolactate into (2R)-2,3-dihydroxy-3-isovalerate or the conversion of 2-aceto-2-hydroxybutyrate into (2R,3R)-2,3-dihydroxy-3-methylvalerate. KARI catalyzes two reactions-alkyl migration and reduction-and requires Mg(2+) and NADPH for activity. To date, the only reported structures for a plant KARI are those of the spinach enzyme-Mn(2+)-(phospho)ADP ribose-(2R,3R)-2,3-dihydroxy-3-methylvalerate complex and the spinach KARI-Mg(2)(+)-NADPH-N-hydroxy-N-isopropyloxamate complex, where N-hydroxy-N-isopropyloxamate is a predicted transition-state analog. These studies demonstrated that the enzyme consists of two domains, N-domain and C-domain, with the active site at the interface of these domains. Here, we have determined the structures of the rice KARI-Mg(2+) and rice KARI-Mg(2)(+)-NADPH complexes to 1.55 A and 2.80 A resolutions, respectively. In comparing the structures of all the complexes, several differences are observed. Firstly, the N-domain is rotated up to 15 degrees relative to the C-domain, expanding the active site by up to 4 A. Secondly, an alpha-helix in the C-domain that includes residues V510-T519 and forms part of the active site moves by approximately 3.9 A upon binding of NADPH. Thirdly, the 15 C-terminal amino acid residues in the rice KARI-Mg(2+) complex are disordered. In the rice KARI-Mg(2)(+)-NADPH complex and the spinach KARI structures, many of the 15 residues bind to NADPH and the N-domain and cover the active site. Fourthly, the location of the metal ions within the active site can vary by up to 2.7 A. The new structures allow us to propose that an induced-fit mechanism operates to (i) allow substrate to enter the active site, (ii) close over the active site during catalysis, and (iii) open the active site to facilitate product release.