Proteolytic Pathways Induced by Herbicides That Inhibit Amino Acid Biosynthesis

The herbicides glyphosate (Gly) and imazamox (Imx) inhibit the biosynthesis of aromatic and branched-chain amino acids, respectively. Although these herbicides inhibit different pathways, they have been reported to show several common physiological effects in their modes of action, such as increasing free amino acid contents and decreasing soluble protein contents. To investigate proteolytic activities upon treatment with Gly and Imx, pea plants grown in hydroponic culture were treated with Imx or Gly, and the proteolytic profile of the roots was evaluated through fluorogenic kinetic assays and activity-based protein profiling.  Several common changes in proteolytic activity were detected following Gly and Imx treatment. Both herbicides induced the ubiquitin-26 S proteasome system and papain-like cysteine proteases. In contrast, the activities of vacuolar processing enzymes, cysteine proteases and metacaspase 9 were reduced following treatment with both herbicides. Moreover, the activities of several putative serine protease were similarly increased or decreased following treatment with both herbicides. In contrast, an increase in YVADase activity was observed under Imx treatment versus a decrease under Gly treatment.  These results suggest that several proteolytic pathways are responsible for protein degradation upon herbicide treatment, although the specific role of each proteolytic activity remains to be determined.

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title: Action mechanisms of acetolactate synthase-inhibiting herbicides ☆
abstract: Herbicides that target the acetolactate synthase (ALS) are among the most widely used weed control chemicals since their introduction into the marketplace in the early 1980s, including five classes (sulfonylureas, imidazolinones, triazolopyrimidines, pyrimidinylthio (or oxy)-benzoates and sulfonylamino-carbonyltriazolinones). The mechanism researches have progressed unprecedentedly in the last two decades. Primary mode of action of the ALS-inhibiting herbicides that interfere with the activity of ALS enzyme seems no longer in doubt. Three lines of investigation from physiology, genetics, molecular and chemical structure aspects came together to prove that ALS is the site of action. Researches on the effects of branched chain amino acids (BCAAs) synthesis or protein metabolism caused by ALS-inhibiting herbicide elicit lots of disputations. Besides these two main works, other secondary effects of ALS inhibition, such as buildup of 2-ketobutyrate (α-ketobutyrate or 2-KB) or 2-aminobutyrate (2-AB, the transamination product of 2-KB), depletion of intermediates of the pathway for some critical processes, disruption of photosynthesis transport and respiration system etc., have also been implicated in the mechanism of plant death. However, there are still some disputations and doubts on the precise mechanisms that need further probing into. Further more, as many ALS-inhibiting herbicides and their derivatives are chiral with one or even more enantiomers, which may behave quite differently in biochemical processes, the effects and the environmental fate of chiral herbicides need to be investigated stereospecifically. By this, we can have a better understanding about the herbicides and avoid unnecessary pollution load.

title: The herbicide glyphosate is a potent inhibitor of 5-enolpyruvyl-shikimic acid-3-phosphate synthase.
abstract: The broadspectrum herbicide glyphosate (N-[phosphonomethyl]-glycine), which causes the accumulation of shikimic acid in plant tissues, inhibits the enzymatic conversion of shikimic acid to anthranilic acid in a cell-free extract of Aerobacter , aerogenes 50% at 5 to 7 μM concentrations. Of the four enzymes involved in the transformation, only 5-enolpyruvylshikimic acid-3-phosphate synthase is inhibited by the herbicide.

title: Evolved glyphosate-resistant weeds around the world: lessons to be learnt.
abstract: Glyphosate is the world's most important herbicide, with many uses that deliver effective and sustained control of a wide spectrum of unwanted (weedy) plant species. Until recently there were relatively few reports of weedy plant species evolving resistance to glyphosate. Since 1996, the advent and subsequent high adoption of transgenic glyphosate-resistant crops in the Americas has meant unprecedented and often exclusive use of glyphosate for weed control over very large areas. Consequently, in regions of the USA where transgenic glyphosate-resistant crops dominate, there are now evolved glyphosate-resistant populations of the economically damaging weed species Ambrosia artemissifolia L., Ambrosia trifida L., Amaranthus palmeri S Watson, Amaranthus rudis JD Sauer, Amaranthus tuberculatus (Moq) JD Sauer and various Conyza and Lolium spp. Likewise, in areas of transgenic glyphosate-resistant crops in Argentina and Brazil, there are now evolved glyphosate-resistant populations of Sorghum halepense (L.) Pers and Euphorbia heterophylla L. respectively. As transgenic glyphosate-resistant crops will remain very popular with producers, it is anticipated that glyphosate-resistant biotypes of other prominent weed species will evolve over the next few years. Therefore, evolved glyphosate-resistant weeds are a major risk for the continued success of glyphosate and transgenic glyphosate-resistant crops. However, glyphosate-resistant weeds are not yet a problem in many parts of the world, and lessons can be learnt and actions taken to achieve glyphosate sustainability. A major lesson is that maintenance of diversity in weed management systems is crucial for glyphosate to be sustainable. Glyphosate is essential for present and future world food production, and action to secure its sustainability for future generations is a global imperative.

title: Fermentative metabolism is induced by inhibiting different enzymes of the branched-chain amino acid biosynthesis pathway in pea plants.
abstract: The inhibition of branched-chain amino acid (BCAA) biosynthesis was evaluated in pea plants in relation to the ability for induction of fermentative metabolism under aerobic conditions. Chlorsulfuron and imazethapyr (inhibitors of acetolactate synthase, ALS, EC 4.1.3.18) produced a strong induction of pyruvate decarboxylase (PDC, EC 4.1.1.1) and alcohol dehydrogenase (ADH, EC 1.1.1.1) activities and a lesser induction of lactate dehydrogenase (LDH, EC 1.1.1.27) and alanine aminotransferase (AlaAT, EC 2.6.1.2) activities in roots. Inhibition of the second enzyme of the BCAA biosynthesis (ketol-acid reductoisomerase, KARI, EC 1.1.1.86) by Hoe 704 (2-dimethylphosphinoyl-2-hydroxyacetic acid) and CPCA (1,1-cyclopropanedicarboxylic acid) enhanced fermentative enzyme activities including PDC, ADH, and AlaAT. Fermentative metabolism induction occurring with ALS- and KARI-inhibitors was related to a higher expression of PDC. In the case of KARI inhibition, it is proposed that fermentation induction is due to an inhibition of ALS activity resulted from an increase in acetolactate concentration. Fermentative metabolism induction in roots, or at least ethanolic fermentation, appeared to be a general physiological response to the BCAA biosynthesis inhibition.

title: Impairment of carbon metabolism induced by the herbicide glyphosate.
abstract: The herbicide glyphosate reduces plant growth and causes plant death by inhibiting the biosynthesis of aromatic amino acids. The objective of this work was to determine whether glyphosate-treated plants show a carbon metabolism pattern comparable to that of plants treated with herbicides that inhibit branched-chain amino acid biosynthesis. Glyphosate-treated plants showed impaired carbon metabolism with an accumulation of carbohydrates in the leaves and roots. The growth inhibition detected after glyphosate treatment suggested impaired metabolism that impedes the utilization of available carbohydrates or energy at the expected rate. These effects were common to both types of amino acid biosynthesis inhibitors. Under aerobic conditions, ethanolic fermentative metabolism was enhanced in the roots of glyphosate-treated plants. This fermentative response was not related to changes in the respiratory rate or to a limitation of the energy charge. This response, which was similar for both types of herbicides, might be considered a general response to stress conditions.

title: Carbohydrate accumulation in leaves of plants treated with the herbicide chlorsulfuron or imazethapyr is due to a decrease in sink strength.
abstract: Herbicides that inhibit branched chain amino acid biosynthesis produce a rapid carbohydrate increase in leaves of treated plants. The relationship between these processes is not known nor is the importance of carbohydrate accumulation in the growth inhibition caused by these herbicides. This work analyzes carbohydrate concentration in sources and sinks after herbicide treatments in pea (Pisum sativum L.), as well as photosynthetic carbon assimilation, using two classes of chemicals, chlorsulfuron and imazethapyr, applied to roots or leaves. The most remarkable result was that, in addition to carbohydrate accumulation in leaves, accumulation of sucrose and/or starch in roots was detected. This pattern of carbohydrate accumulation was similar for both herbicides and independent of whether the herbicides were applied to leaves or roots. This indicates that root growth inhibition was not caused by sugar starvation in sinks. Nevertheless, the results are consistent with a decrease in sink strength, leading to the inhibition of photoassimilate translocation.

title: The possible role of quinate in the mode of action of glyphosate and acetolactate synthase inhibitors.
abstract: The herbicide glyphosate inhibits the biosynthesis of aromatic amino acids by blocking the shikimate pathway. Imazethapyr and chlorsulfuron are two herbicides that act by inhibiting branched-chain amino acid biosynthesis. These herbicides stimulate secondary metabolism derived from the aromatic amino acids. The aim of this study was to test if they cause any cross-effect in the amino acid content and if they have similar effects on the shikimate pathway.



The herbicides inhibiting two different amino acid biosynthesis pathways showed a common pattern in general content of free amino acids. There was a general increase in total free amino acid content, with a transient decrease in the proportion of amino acids whose pathways were specifically inhibited. Afterwards, an increase in these inhibited amino acids was detected; this was probably related to proteolysis. All herbicides caused quinate accumulation. Exogenous application of quinate arrested growth, decreased net photosynthesis and stomatal conductance and was ultimately lethal, similarly to glyphosate and imazethapyr.



Quinate accumulation was a common effect of the two different classes of herbicide. Moreover, exogenous quinate application had phytotoxic effects, showing that this plant metabolite can trigger the toxic effects of the herbicides. This ability to mimic the herbicide effects suggests a possible link between the mode of action of these herbicides and the potential role of quinate as a natural herbicide.

title: Nitrogen assimilation studies using 15N in soybean plants treated with imazethapyr, an inhibitor of branched-chain amino acid biosynthesis.
abstract: The pattern of nitrogen assimilation in soybean plants treated with a herbicide that inhibits branched-chain amino acid biosynthesis was evaluated by (15)N isotopic analysis. The herbicide imazethapyr caused a strong decrease in nitrate uptake by roots, partly due to a reduced stomatal conductance. The inhibition of (15)N uptake was accompanied by a decrease in the (15)N content in the plant and, concomitantly, an inhibition of translocation to the shoot. Imazethapyr inhibited nitrate reductase activity in leaves and roots. Among all parameters studied, "de novo" synthesis of proteins was the first parameter of the N assimilation metabolism affected by the herbicide. These results show that this class of herbicides totally damages N metabolism and indicates a regulatory effect on N uptake and translocation that would be mediated by the increase in free amino acid pool provoked by the inhibition of branched-chain amino acid biosynthesis.

title: Unraveling the role of fermentation in the mode of action of acetolactate synthase inhibitors by metabolic profiling.
abstract: Herbicides that inhibit branched chain amino acid biosynthesis induce aerobic fermentation. The role of fermentation in the mode of action of these herbicides is not known, nor is the importance of this physiological response in the growth inhibition and the lethality caused by them. Metabolic profiling was used to compare the effects of the herbicide imazethapyr (IM) on pea plants with two other treatments that also induce fermentation: hypoxia and the exogenous supply pyruvate for seven days. While hypoxic roots did not show internal anoxia, feeding pyruvate or applying IM to the roots led to internal anoxia, probably related to the respiratory burst detected. The three treatments induced ethanol fermentation, but fermentation induced following herbicide treatment was earlier than that following pyruvate supply and was not associated with a decrease in the energy status. No striking changes were detected in the metabolic profiling of hypoxic roots, indicating that metabolism was only slightly impaired. Feeding pyruvate resulted in marked succinate accumulation and a general amino acid accumulation. IM-treated roots showed a general accumulation of glycolytic metabolites upstream of pyruvate, a decrease in some TCA intermediates and an increase in the free amino acid pool sizes. All treatments caused GABA and putrescine accumulation. Our results indicate that IM supply impairs carbon/nitrogen metabolism and this impaired metabolism is likely to be related to the growth arrest detected. As growth is arrested, carbohydrates and glycolytic intermediates accumulate and energy becomes more available.

title: Branched-chain amino acid biosynthesis inhibitors: herbicide efficacy is associated with an induced carbon-nitrogen imbalance.
abstract: Acetolactate synthase (ALS; EC 4.1.3.18) and ketol-acid reductoisomerase (KARI; EC 1.1.1.86) are two consecutive enzymes in the biosynthesis of branched-chain amino acids. Several commercial herbicides inhibit ALS as their primary site of action. KARI has also attracted attention as a potential target for herbicides. Although potent and selective inhibitors of KARI have been discovered, these inhibitors display less herbicidal activity than ALS-inhibiting herbicides. To obtain a better understanding of these findings, we have compared the physiological effects induced in pea plants after KARI or ALS inhibition. Although, both types of inhibitors induce growth arrest and photosynthesis inhibition, plant death occurs more rapidly under ALS inhibition than KARI inhibition. Carbohydrates accumulated in the leaves and roots following treatments with both inhibitors. The carbohydrate accumulation in the leaves occurred as a consequence of a decrease in sink strength. In contrast, the free amino acid content was only affected through ALS inhibition. These results indicate that although KARI and ALS inhibition block the same biosynthetic pathway and exert common effects on carbon metabolism, nitrogen metabolism is more affected via ALS than KARI inhibition. Thus, metabolic alterations in nitrogen metabolism induced through ALS inhibitors might contribute to the increased efficacy of these chemicals as herbicides.

title: Imazethapyr, an inhibitor of the branched-chain amino acid biosynthesis, induces aerobic fermentation in pea plants.
abstract: Acetolactate synthase (ALS; EC 4.1.3.18) inhibition is the primary mechanism of action of imazethapyr (IM). However, the precise mechanisms that links ALS inhibition with plant death have not been elucidated. Supply of IM to pea (Pisum sativum L) plants produced an immediate cessation of growth, caused a 50% inhibition of the in vivo ALS activity within 1 day of treatment, and a remarkable accumulation (2.7-times) of free amino acids after 3 days. Carbohydrates (soluble and starch) were accumulated in both leaves and roots. Accumulation of soluble sugars in roots preceded that of starch in leaves, suggesting that the accumulation of carbohydrates in leaves is not the reason for the arrested root growth. A transient pyruvate accumulation was observed in roots, 1 day after the onset of IM supply. This was coincident with an increase in pyruvate decarboxylase (EC 4.1.1.1), and later increases in alcohol dehydrogenase (EC 1.1.1.1), lactate dehydrogenase (EC 1.1.1.27), and alanine amino transferase (EC 2.6.1.2) activities. This enhancement of fermentative activities was coincident with a slight decrease in aerobic respiration. The overall data suggest that the impairment of ALS activity may lead to a fermentative metabolism that may be involved in growth inhibition and plant death.

title: Amino Acid Metabolism of Lemna minor L. : II. Responses to Chlorsulfuron.
abstract: Chlorsulfuron, an inhibitor of acetolactate synthase (EC 4.1.3.18) (TB Ray 1984 Plant Physiol 75: 827-831), markedly inhibited the growth of Lemna minor at concentrations of 10(-8) molar and above, but had no inhibitory effects on growth at 10(-9) molar. At growth inhibitory concentrations, chlorsulfuron caused a pronounced increase in total free amino acid levels within 24 hours. Valine, leucine, and isoleucine, however, became smaller percentages of the total free amino acid pool as the concentration of chlorsulfuron was increased. At concentrations of chlorsulfuron of 10(-8) molar and above, a new amino acid was accumulated in the free pool. This amino acid was identified as alpha-amino-n-butyrate by chemical ionization and electron impact gas chromatography-mass spectrometry. The amount of alpha-amino-n-butyrate increased from undetectable levels in untreated plants, to as high as 840 nanomoles per gram fresh weight (2.44% of the total free pool) in plants treated with 10(-4) molar chlorsulfuron for 24 hours. The accumulation of this amino acid was completely inhibited by methionine sulfoximine. Chlorsulfuron did not inhibit the methionine sulfoximine induced accumulations of valine, leucine, and isoleucine, supporting the idea that the accumulation of the branched-chain amino acids in methionine sulfoximine treated plants is the result of protein turnover rather than enhanced synthesis. Protein turnover may be primarily responsible for the failure to achieve complete depletion of valine, leucine, and isoleucine even at concentrations of chlorsulfuron some 10(4) times greater than that required to inhibit growth. Tracer studies with (15)N demonstrate that chlorsulfuron inhibits the incorporation of (15)N into valine, leucine, and isoleucine. The alpha-amino-n-butyrate accumulated in the presence of chlorsulfuron and [(15)N]H(4) (+) was heavily labeled with (15)N at early time points and appeared to be derived by transamination from a rapidly labeled amino acid such as glutamate or alanine. We propose that chlorsulfuron inhibition of acetolactate synthase may lead to accumulation of 2-oxobutyrate in the isoleucine branch of the pathway, and transamination of 2-oxobutyrate to alpha-amino-n-butyrate by a constitutive transaminase utilizing either glutamate or alanine as alpha-amino-N donors.

title: Structure, function and regulation of plant proteasomes.
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title: Contribution of Proteasomal β-Subunits to the Cleavage of Peptide Substrates Analyzed with Yeast Mutants*
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title: Storage Protein Accumulation in the Absence of the Vacuolar Processing Enzyme Family of Cysteine Proteases Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.016378.
abstract: The role(s) of specific proteases in seed protein processing is only vaguely understood; indeed, the overall role of processing in stable protein deposition has been the subject of more speculation than direct investigation. Seed-type members of the vacuolar processing enzyme (VPE) family were hypothesized to perform a unique function in seed protein processing, but we demonstrated previously that Asn-specific protein processing in developing Arabidopsis seeds occurs independently of this VPE activity. Here, we describe the unexpected expression of vegetative-type VPEs in developing seeds and test the role(s) of all VPEs in seed storage protein accumulation by systematically stacking knockout mutant alleles of all four members (αVPE, βVPE, γVPE, and δVPE) of the VPE gene family in Arabidopsis. The complete removal of VPE function in the αvpe βvpe γvpe δvpe quadruple mutant resulted in a total shift of storage protein accumulation from wild-type processed polypeptides to a finite number of prominent alternatively processed polypeptides cleaved at sites other than the conserved Asn residues targeted by VPE. Although alternatively proteolyzed legumin-type globulin polypeptides largely accumulated as intrasubunit disulfide-linked polypeptides with apparent molecular masses similar to those of VPE-processed legumin polypeptides, they showed markedly altered solubility and protein assembly characteristics. Instead of forming 11S hexamers, alternatively processed legumin polypeptides were deposited primarily as 9S complexes. However, despite the impact on seed protein processing, plants devoid of all known functional VPE genes appeared unchanged with regard to protein content in mature seeds, relative mobilization rates of protein reserves during germination, and vegetative growth. These findings indicate that VPE-mediated Asn-specific proteolytic processing, and the physiochemical property changes attributed to this specific processing step, are not required for the successful deposition and mobilization of seed storage protein in the protein storage vacuoles of Arabidopsis seeds.

title: A Plant Vacuolar Protease, VPE, Mediates Virus-Induced Hypersensitive Cell Death
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title: Selective inhibition of plant serine hydrolases by agrochemicals revealed by competitive ABPP.
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title: Changes in the Expression and the Enzymic Properties of the 20S Proteasome in Sugar-Starved Maize Roots. Evidence for an in Vivo Oxidation of the Proteasome1
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title: Caspase-like activity in the seedlings of Pisum sativum eliminates weaker shoots during early vegetative development by induction of cell death.
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title: 20S proteasome and accumulation of oxidized and ubiquitinated proteins in maize leaves subjected to cadmium stress.
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title: Serpin1 of Arabidopsis thaliana is a suicide inhibitor for metacaspase 9.
abstract: Metacaspases are distant relatives of animal caspases found in plants, fungi and protozoa. We demonstrated previously that two type II metacaspases of Arabidopsis thaliana, AtMC4 and AtMC9 are Arg/Lys-specific cysteine-dependent proteases. We screened a combinatorial tetrapeptide library of 130,321 substrates with AtMC9. Here, we show that AtMC9 is a strict Arg/Lys-specific protease. Based on the position-specific scoring matrix derived from the substrate library results, the tetrapeptide Val-Arg-Pro-Arg was identified as an optimized substrate. AtMC9 had a kcat/KM of 4.6x10(5) M-1 s-1 for Ac-Val-Arg-Pro-Arg-amido-4-methyl-coumarin, representing a more than 10-fold improvement over existing fluorogenic substrates. A yeast two-hybrid screen with catalytically inactive AtMC9 as bait identified a serine protease inhibitor, designated AtSerpin1, which was found to be a potent inhibitor of AtMC9 activity in vitro through cleavage of its reactive center loop and covalent binding to AtMC9. On the basis of the substrate profiling of AtMC9 and confirmation through site-directed mutagenesis, the inhibitory P4-P1 cleavage site of AtSerpin1 was determined to be Ile-Lys-Leu-Arg351. Further mutagenesis of the AtSerpin1 inhibitory cleavage site modulated AtMC9 inhibition positively or negatively. Both AtMC9 and AtSerpin1 were localized in the extracellular space, suggesting an in vivo interaction as well. To our knowledge, this is the first report of plant protease inhibition by a plant serpin.

title: Proteasome activity profiling: a simple, robust and versatile method revealing subunit-selective inhibitors and cytoplasmic, defense-induced proteasome activities.
abstract: The proteasome plays essential roles in nearly all biological processes in plant defense and development, yet simple methods for displaying proteasome activities in extracts and living tissues are not available to plant science. Here, we introduce an easy and robust method to simultaneously display the activities of all three catalytic proteasome subunits in plant extracts or living plant tissues. The method is based on a membrane-permeable, small-molecule fluorescent probe that irreversibly reacts with the catalytic site of the proteasome catalytic subunits in an activity-dependent manner. Activities can be quantified from fluorescent protein gels and used to study proteasome activities in vitro and in vivo. We demonstrate that proteasome catalytic subunits can be selectively inhibited by aldehyde-based inhibitors, including the notorious caspase-3 inhibitor DEVD. Furthermore, we show that the proteasome activity, but not its abundance, is significantly increased in Arabidopsis upon treatment with benzothiadiazole (BTH). This upregulation of proteasome activity depends on NPR1, and occurs mostly in the cytoplasm. The simplicity, robustness and versatility of this method will make this method widely applicable in plant science.

title: Activity profiling of vacuolar processing enzymes reveals a role for VPE during oomycete infection.
abstract: Vacuolar processing enzymes (VPEs) are important cysteine proteases that are implicated in the maturation of seed storage proteins, and programmed cell death during plant-microbe interactions and development. Here, we introduce a specific, cell-permeable, activity-based probe for VPEs. This probe is highly specific for all four Arabidopsis VPEs, and labeling is activity-dependent, as illustrated by sensitivity for inhibitors, pH and reducing agents. We show that the probe can be used for in vivo imaging and displays multiple active isoforms of VPEs in various tissues and in both monocot and dicot plant species. Thus, VPE activity profiling is a robust, simple and powerful tool for plant research for a wide range of applications. Using VPE activity profiling, we discovered that VPE activity is increased during infection with the oomycete pathogen Hyaloperonospora arabidopsidis (Hpa). The enhanced VPE activity is host-derived and EDS1-independent. Sporulation of Hpa is reduced on vpe mutant plants, demonstrating a role for VPE during compatible interactions that is presumably independent of programmed cell death. Our data indicate that, as an obligate biotroph, Hpa takes advantage of increased VPE activity in the host, e.g. to mediate protein turnover and nutrient release.

title: Heterologous Expression and Molecular and Cellular Characterization of CaPUB1 Encoding a Hot Pepper U-Box E3 Ubiquitin Ligase Homolog1[C]
abstract: The U-box motif is a conserved domain found in the diverse isoforms of E3 ubiquitin ligase in eukaryotes. From water-stressed hot pepper (Capsicum annuum L. cv Pukang) plants, we isolated C. annuum putative U-box protein 1 (CaPUB1), which encodes a protein containing a single U-box motif in its N-terminal region. In vitro ubiquitination and site-directed mutagenesis assays revealed that CaPUB1 possessed E3 ubiquitin ligase activity and that the U-box motif was indeed essential for its enzyme activity. RNA gel-blot analysis showed that CaPUB1 mRNA was induced rapidly by a broad spectrum of abiotic stresses, including drought, high salinity, cold temperature, and mechanical wounding, but not in response to ethylene, abscisic acid, or a bacterial pathogen, suggesting its role in the early events in the abiotic-related defense response. Because transgenic work was extremely difficult in hot pepper, in this study we overexpressed CaPUB1 in Arabidopsis (Arabidopsis thaliana) to provide cellular information on the function of this gene in the development and plant responses to abiotic stresses. Transgenic Arabidopsis plants that constitutively expressed the CaPUB1 gene under the control of the cauliflower mosaic virus 35S promoter had markedly longer hypocotyls and roots and grew more rapidly than the wild type, leading to an early bolting phenotype. Microscopic analysis showed that 35S∷CaPUB1 roots had increased numbers of small-sized cells, resulting in disordered, highly populated cell layers in the cortex, endodermis, and stele. In addition, CaPUB1-overexpressing plants displayed increased sensitivity to water stress and mild salinity. These results indicate that CaPUB1 is functional in Arabidopsis cells, thereby effectively altering cell and tissue growth and also the response to abiotic stresses. Comparative proteomic analysis showed that the level of RPN6 protein, a non-ATPase subunit of the 26S proteasome complex, was significantly reduced in 35S∷CaPUB1 seedlings as compared to the wild type. Pull-down and ubiquitination assays demonstrated that RPN6 interacted physically with CaPUB1 and was ubiquitinated in a CaPUB1-dependent manner in vitro. Although the physiological function of CaPUB1 is not yet clear, there are several possibilities for its involvement in a subset of physiological responses to counteract dehydration and high-salinity stresses in transgenic Arabidopsis seedlings.

title: The ubiquitin/26S proteasome pathway, the complex last chapter in the life of many plant proteins.
abstract: Plants use a repertoire of methods to control the level and activity of their constituent proteins. One method, whose prominence is only now being appreciated, is selective protein breakdown by the ubiquitin/26S proteasome pathway. Remarkably, recent analyses of the near-complete Arabidopsis thaliana genome identified >1300 genes, or approximately 5% of the proteome, involved in the ubiquitin/26S proteasome pathway, making it one of the most elaborate regulatory mechanisms in plants. Molecular genetic analyses have also connected individual components to almost all aspects of plant biology, including the cell-cycle, embryogenesis, photomorphogenesis, circadian rhythms, hormone signaling, homeosis, disease resistance and senescence. Consequently, it appears that the ubiquitin/26S proteasome pathway rivals transcription complexes and protein kinase cascades as the main player in plant cell regulation.

title: Protein degradation in signaling.
abstract: Recent studies have linked proteolysis by the ubiquitin/proteasome pathway to a variety of signaling pathways in higher plants. These links were uncovered by characterization of mutants altered in signaling or by targeted disruption of components of the proteolytic pathway. Significant advances have recently revealed connections between proteolysis and hormone responses, light perception, environmental adaptation, and floral development.

title: Dynamics of ubiquitin conjugation during heat-shock response revealed by using a monoclonal antibody specific to multi-ubiquitin chains.
abstract: Levels of intracellular multi-ubiquitinated proteins in heat-shocked HeLa cells were investigated using a monoclonal antibody specific to multi-ubiquitin chains. After heat-shock treatment at 42-44 degrees C for 30 min, the level of multi-ubiquitinated proteins increased within the first 2 h at 37 degrees C and returned to the initial level within the following 2 h. The accumulation of multi-ubiquitin conjugates was elevated by increasing the temperature, while the opposite was the case for the level of ubiquitinated histone H2A. Immunocytochemical analysis revealed that the amount of ubiquitin conjugates rapidly increased in the cytosol and concomitantly decreased in the nucleus under heat-shock conditions. The heat-shock treatment elicited little apparent change in the activity of the 26S proteasome, but it did induce a gradual increase in activity of the ubiquitinating enzyme system. These results strongly suggest that the level of cytoplasmic multi-ubiquitinated proteins and that of nuclear ubiquitinated histone H2A increases and decreases, respectively, in response to heat shock and that the heat-shock-induced accumulation of multi-ubiquitinated proteins is caused by activation of the ubiquitinating enzyme system rather than inactivation of the 26S proteasome.

title: Ubiquitin- and proteasome-dependent proteolysis in plants.
abstract: In recent years it has become obvious that protein degradation is an important catabolic process during development in plants and animals. One very conserved degradative system is the ubiquitin- and proteasome-dependent proteolytic pathway, which is found in all eukaryotes from yeast to mammals and plants. The pathway consists of two parts, one in which chains of ubiquitin are conjugated to substrate proteins, and one in which these substrate proteins are either degraded by the 26S proteasome or are de-ubiquitinated. The ubiquitin- and proteasome-dependent pathway degrades a wide range of proteins in the nucleus and cytoplasm. It is highly specific, but controls a large number of cellular events due to the diversity in the conjugating enzymes. This pathway is important for removal of abnormal/damaged proteins that have had their recognition sites exposed as well as for control of specific transcription factors and cell cycle regulators. In plants, ubiquitin- and proteasome-dependent proteolysis is known to be involved in regulation of the cell cycle and transcription factors as well as endoplasmic reticulum-associated protein degradation, stress response and developmental processes, such as xylogenesis and senescence.

title: Proteolytic system in sunflower (Helianthus annuus L.) leaves under cadmium stress.
abstract: The effect of oxidative stress induced by cadmium on growth parameters and on the balance between protein synthesis and degradation was studied in sunflower (Helianthus annuus L.) leaves. Plants were germinated for 10 days and then transferred to hydroponic medium devoid (control) or containing 100, 200 and 300μM CdCl2. Analyses were performed between days 0 and 4 of Cd-treatment. All Cd(2+) concentrations significantly reduced leaf area and, fresh and dry weight, but leaf relative water content only decreased with 200 and 300μM Cd(2+). Control and treated plants had similar soluble protein content and showed the same rate of soluble protein labeling under the assay conditions. Although protease activity increased with cadmium treatment, proteasome activity was significantly inhibited. Expression of 20S proteasome remained similar to controls in cadmium treated plants. Cadmium caused an increase in ubiquitin-conjugated proteins and carbonyl groups content of treated plants, compared to control values. Cadmium induced an increase in protease specific activity; nevertheless, this increase was not relevant enough to avoid accumulation of oxidized proteins. Oxidation of proteins is one of the most important effects of cadmium treatment. The results presented here provide evidence for the role of the proteolytic system in sunflower plants subjected to cadmium stress.

title: Heavy metals effects on proteolytic system in sunflower leaves.
abstract: Plant proteolytic system includes proteases, mainly localized inside the organelles, and the ubiquitin-proteasome pathway in both, the cytoplasm and the nucleus. It was recently demonstrated that under severe Cd stress sunflower (Helianthus annuus L.) proteasome activity is reduced and this results in accumulation of oxidized proteins. In order to test if under other heavy metal stresses sunflower proteolytic system undergoes similar changes, an hydroponic experiment was carried out. Ten days old sunflower plants were transferred to hydroponic culture solutions devoid (control) or containing 100 microM of AlCl(3), CoCl(2), CuCl(2), CrCl(3), HgCl(2), NiCl(2), PbCl(2) or ZnCl(2) and analyzed for protein oxidative damage and proteolytic activities. After 4 days of metal treatment, only Co(2+), Cu(2+), Hg(2+), and Ni(2+) were found to increase carbonyl groups content. Except for Al(3+) and Zn(2+), all metals tested significantly reduced all proteasome activities (chymotrypsin-like, trypsin-like and PGPH) and acid and neutral proteases activities. The effect on basic proteases was more variable. Abundance of 20S protein after metal treatments was similar to that obtained for control samples.  Hg(2+), Ni(2+), Cr(3+), and Pb(2+) induced accumulation of ubiquitin conjugated proteins. It is concluded that heavy metal effects on proteolytic system cannot be generalized; however, impairment of proteasome functionality and decreased proteases activities seem to be a common feature involved in metal toxicity to plants.

title: Minitags for small molecules: detecting targets of reactive small molecules in living plant tissues using 'click chemistry'.
abstract: Small molecules offer unprecedented opportunities for plant research since plants respond to, metabolize, and react with a diverse range of endogenous and exogenous small molecules. Many of these small molecules become covalently attached to proteins. To display these small molecule targets in plants, we introduce a two-step labelling method for minitagged small molecules. Minitags are small chemical moieties (azide or alkyne) that are inert under biological conditions and have little influence on the membrane permeability and specificity of the small molecule. After labelling, proteomes are extracted under denaturing conditions and minitagged proteins are coupled to reporter tags through a 'click chemistry' reaction. We introduce this two-step labelling procedure in plants by studying the well-characterized targets of E-64, a small molecule cysteine protease inhibitor. In contrast to biotinylated E-64, minitagged E-64 efficiently labels vacuolar proteases in vivo. We displayed, purified and identified targets of a minitagged inhibitor that targets the proteasome and cysteine proteases in living plant cells. Chemical interference assays with inhibitors showed that MG132, a frequently used proteasome inhibitor, preferentially inhibits cysteine proteases in vivo. The two-step labelling procedure can be applied on detached leaves, cell cultures, seedlings and other living plant tissues and, when combined with photoreactive groups, can be used to identify targets of herbicides, phytohormones and reactive small molecules selected from chemical genetic screens.

title: Mining the active proteome in plant science and biotechnology.
abstract: Protein activity is essential functional information, yet difficult to predict from transcript or protein data. Activity-based protein profiling (ABPP) displays active proteins in proteomes using small molecule probes that irreversibly label proteins in their active state. Here, we review proof-of-concept ABPP studies in plant science. These studies displayed activities of dozens of plant cysteine proteases, lipases, methylesterases and the proteasome. ABPP in plants revealed differential protein activities in development and immunity and uncovered striking selectivity of pathogen-derived inhibitors and unexpected targets of commercial inhibitors. The unique, high-content information of ABPP and the robustness and simplicity of the assays will make ABPP a powerful tool in future plant science and biotechnology.

title: L-trans-Epoxysuccinyl-leucylamido(4-guanidino)butane (E-64) and its analogues as inhibitors of cysteine proteinases including cathepsins B, H and L.
abstract: 1. L-trans-Epoxysuccinyl-leucylamido(4-guanidino)butane (E-64) at a concentration of 0.5 mM had no effect on the serine proteinases plasma kallikrein and leucocyte elastase or the metalloproteinases thermolysin and clostridial collagenase. In contrast, 10 muM-E-64 rapidly inactivated the cysteine proteinases cathepsins B, H and L and papain (t0.5 = 0.1-17.3s). The streptococcal cysteine proteinase reacted much more slowly, and there was no irreversible inactivation of clostripain. The cysteine-dependent exopeptidase dipeptidyl peptidase I was very slowly inactivated by E-64. 2. the active-site-directed nature of the interaction of cathepsin B and papain with E-64 was established by protection of the enzyme in the presence of the reversible competitive inhibitor leupeptin and by the stereospecificity for inhibition by the L as opposed to the D compound. 3. It was shown that the rapid stoichiometric reaction of the cysteine proteinases related to papain can be used to determine the operational molarity of solutions of the enzymes and thus to calibrate rate assays. 4. The apparent second-order rate constants for the inactivation of human cathepsins B and H and rat cathepsin L by a series of structural analogues of E-64 are reported, and compared with those for some other active-site-directed inhibitors of cysteine proteinases. 5. L-trans-Epoxysuccinyl-leucylamido(3-methyl)butane (Ep-475) was found to inhibit cathepsins B and L more rapidly than E-64. 6. Fumaryl-leucylamido(3-methyl)butane (Dc-11) was 100-fold less reactive than the corresponding epoxide, but was nevertheless about as effective as iodoacetate.

title: Arabidopsis sensitivity to protein synthesis inhibitors depends on 26S proteasome activity
abstract: The 26S proteasome (26SP), the central protease of the ubiquitin-dependent proteolysis pathway, controls the regulated proteolysis of functional proteins and the removal of misfolded and damaged proteins. In Arabidopsis, cellular and stress response phenotypes of a number of mutants with partially impaired 26SP function have been reported. Here, we describe the responses of proteasome mutants to protein synthesis inhibitors. We show that the rpt2a-3, rpn10-1 and rpn12a-1 mutants are hypersensitive to the antibiotic hygromycin B, and tolerant to the translation inhibitor cycloheximide (CHX) and herbicide l-phosphinothricin (PPT). In addition to the novel mechanism for herbicide tolerance, our data suggests that the combination of hygromycin B, CHX and PPT growth-response assays could be used as a facile diagnostic tool to detect altered 26SP function in plant mutants and transgenic lines.

title: VPEγ Exhibits a Caspase-like Activity that Contributes to Defense against Pathogens
abstract: Caspases are a family of aspartate-specific cysteine proteases that play an essential role in initiating and executing programmed cell death (PCD) in metazoans. Caspase-like activities have been shown to be required for the initiation of PCD in plants, but the genes encoding those activities have not been identified. VPEgamma, a cysteine protease, is induced during senescence, a form of PCD in plants, and is localized in precursor protease vesicles and vacuoles, compartments associated with PCD processes in plants.



We show that VPEgamma binds in vivo to a general caspase inhibitor and to caspase-1-specific inhibitors, which block the activity of VPEgamma. A cysteine protease inhibitor, cystatin, accumulates to 20-fold higher levels in vpegamma mutants. Homologs of cystatin are known to suppress hypersensitive cell death in plant and animal systems. We also report that infection with an avirulent strain of Pseudomonas syringae results in an increase of caspase-1 activity, and this increase is partially suppressed in vpegamma mutants. Plants overexpressing VPEgamma exhibit a greater amount of ion leakage during infection with P. syringae, suggesting that VPEgamma may regulate cell death progression during plant-pathogen interaction. VPEgamma expression is induced after infection with P. syringae, Botrytis cinerea, and turnip mosaic virus, and knockout of VPEgamma results in increased susceptibility to these pathogens.



We conclude that VPEgamma is a caspase-like enzyme that has been recruited in plants to regulate vacuole-mediated cell dismantling during cell death, a process that has significant influence in the outcome of a diverse set of plant-pathogen interactions.

title: Vacuolar processing enzyme is self‐catalytically activated by sequential removal of the C‐terminal and N‐terminal propeptides
abstract: A vacuolar processing enzyme (VPE) responsible for maturation of various vacuolar proteins is synthesized as an inactive precursor. To clarify how to convert the VPE precursor into the active enzyme, we expressed point mutated VPE precursors of castor bean in the pep4 strain of Saccharomyces cerevisiae. A VPE with a substitution of the active site Cys with Gly showed no ability to convert itself into the mature form, although a wild VPE had the ability. The mutated VPE was converted by the action of the VPE that had been purified from castor bean. Substitution of the conserved Asp‐Asp at the putative cleavage site of the C‐terminal propeptide with Gly‐Gly abolished both the conversion into the mature form and the activation of the mutated VPE. In vitro assay with synthetic peptides demonstrated that a VPE exhibited activity towards Asp residues and that a VPE cleaved an Asp‐Gln bond to remove the N‐terminal propeptide. Taken together, the results indicate that the VPE is self‐catalytically maturated to be converted into the active enzyme by removal of the C‐terminal propeptide and subsequent removal of the N‐terminal one.

title: Identification of early intermediates of caspase activation using selective inhibitors and activity-based probes.
abstract: Caspases are cysteine proteases that are key effectors in apoptotic cell death. Currently, there is a lack of tools that can be used to monitor the regulation of specific caspases in the context of distinct apoptotic programs. We describe the development of highly selective inhibitors and active site probes and their applications to directly monitor executioner (caspase-3 and -7) and initiator (caspase-8 and -9) caspase activity. Specifically, these reagents were used to dissect the kinetics of caspase activation upon stimulation of apoptosis in cell-free extracts and intact cells. These studies identified a full-length caspase-7 intermediate that becomes catalytically activated early in the pathway and whose further processing is mediated by mature executioner caspases rather than initiator caspases. This form also shows distinct inhibitor sensitivity compared to processed caspase-7. Our data suggest that caspase-7 activation proceeds through a previously uncharacterized intermediate that is formed without cleavage of the intact zymogen.

title: The Involvement of Cysteine Proteases and Protease Inhibitor Genes in the Regulation of Programmed Cell Death in Plants
abstract: Programmed cell death (PCD) is a process by which cells in many organisms die. The basic morphological and biochemical features of PCD are conserved between the animal and plant kingdoms. Cysteine proteases have emerged as key enzymes in the regulation of animal PCD. Here, we show that in soybean cells, PCD-activating oxidative stress induced a set of cysteine proteases. The activation of one or more of the cysteine proteases was instrumental in the PCD of soybean cells. Inhibition of the cysteine proteases by ectopic expression of cystatin, an endogenous cysteine protease inhibitor gene, inhibited induced cysteine protease activity and blocked PCD triggered either by an avirulent strain of Pseudomonas syringae pv glycinea or directly by oxidative stress. Similar expression of serine protease inhibitors was ineffective. A glutathione S-transferase–cystatin fusion protein was used to purify and characterize the induced proteases. Taken together, our results suggest that plant PCD can be regulated by activity poised between the cysteine proteases and the cysteine protease inhibitors. We also propose a new role for proteinase inhibitor genes as modulators of PCD in plants.

title: Arabidopsis Type I Metacaspases Control Cell Death
abstract: The Yin and Yang of Plant Caspases The function of plant metacaspases, identified by limited sequence homology to the animal caspases that control cell death, has remained elusive. Coll et al. (p. 1393) have now elucidated the actions of two metacaspases in the small plant Arabidopsis. One metacaspase, AtMC1, promoted cell death, and the other, AtMC2, acted antagonistically to stall cell death. The results help to elucidate the mechanisms by which plants control cell survival during development and defend against pathogen attack. An ancient link between cell death control and innate immune receptor function has been discovered in plants. Metacaspases are distant relatives of animal caspases found in protozoa, fungi, and plants. Limited experimental data exist defining their function(s), despite their discovery by homology modeling a decade ago. We demonstrated that two type I metacaspases, AtMC1 and AtMC2, antagonistically control programmed cell death in Arabidopsis. AtMC1 is a positive regulator of cell death and requires conserved caspase-like putative catalytic residues for its function. AtMC2 negatively regulates cell death. This function is independent of the putative catalytic residues. Manipulation of the Arabidopsis type I metacaspase regulatory module can nearly eliminate the hypersensitive cell death response (HR) activated by plant intracellular immune receptors. This does not lead to enhanced pathogen proliferation, decoupling HR from restriction of pathogen growth.

title: Diversity of Serine Hydrolase Activities of Unchallenged and Botrytis-infected Arabidopsis thaliana*S
abstract: Activity-based protein profiling is a powerful method to display enzyme activities in proteomes and provides crucial information on enzyme activity rather than protein or transcript abundance. We applied activity-based protein profiling using fluorophosphonate-based probes to display the activities of Ser hydrolases in the model plant Arabidopsis thaliana. Multidimensional protein identification technology and in-gel analysis of fluorophosphonate-labeled leaf extracts revealed over 50 Ser hydrolases, including dozens of proteases, esterases, and lipases, representing over 10 different enzyme families. Except for some well characterized Ser hydrolases like subtilases TPP2 and ARA12, prolyl oligopeptidase acylamino acid-releasing enzyme, serine carboxypeptidase-like SNG1 and BRS1, carboxylesterase-like CXE12, methylesterases MES2 and MES3, and S-formylglutathione hydrolase, the majority of these serine hydrolases have not been described before. We studied transiently expressed SNG1 and investigated plants infected with the fungal pathogen Botrytis cinerea. Besides the down-regulation of several Arabidopsis Ser hydrolase activities during Botrytis infection, we detected the activities of Botrytis-derived cutinases and lipases, which are thought to contribute to pathogenicity.

title: Natural products in crop protection.
abstract: The tremendous increase in crop yields associated with the 'green' revolution has been possible in part by the discovery and utilization of chemicals for pest control. However, concerns over the potential impact of pesticides on human health and the environment has led to the introduction of new pesticide registration procedures, such as the Food Quality Protection Act in the United States. These new regulations have reduced the number of synthetic pesticides available in agriculture. Therefore, the current paradigm of relying almost exclusively on chemicals for pest control may need to be reconsidered. New pesticides, including natural product-based pesticides are being discovered and developed to replace the compounds lost due to the new registration requirements. This review covers the historical use of natural products in agricultural practices, the impact of natural products on the development of new pesticides, and the future prospects for natural products-based pest management.

title: Why have no new herbicide modes of action appeared in recent years?
abstract: Herbicides with new modes of action are badly needed to manage the evolution of resistance of weeds to existing herbicides. Yet no major new mode of action has been introduced to the market place for about 20 years. There are probably several reasons for this. New potential products may have remained dormant owing to concerns that glyphosate-resistant (GR) crops have reduced the market for a new herbicide. The capture of a large fraction of the herbicide market by glyphosate with GR crops led to significantly diminished herbicide discovery efforts. Some of the reduced herbicide discovery research was also due to company consolidations and the availability of more generic herbicides. Another problem might be that the best herbicide molecular target sites may have already been discovered. However, target sites that are not utilized, for which there are inhibitors that are highly effective at killing plants, suggests that this is not true. Results of modern methods of target site discovery (e.g. gene knockout methods) are mostly not public, but there is no evidence of good herbicides with new target sites coming from these approaches. In summary, there are several reasons for a long dry period for new herbicide target sites; however, the relative magnitude of each is unclear. The economic stimulus to the herbicide industry caused by the evolution of herbicide-resistant weeds, especially GR weeds, may result in one or more new modes of action becoming available in the not too distant future.