Degradation of fibrin-ß amyloid co-aggregate: A novel function attributed to ubiquitin.

Human placental extract contains numerous bioactive components that are effective wound healing, antimicrobial and anti-inflammatory agents. During our investigation on the therapeutic potency of human placental extract, we have purified ubiquitin-like molecules that showed strong fibrino(geno)lytic activity. Further investigation confirmed similar potency of ubiquitin purified from adult human erythrocyte. Additionally, ubiquitin efficiently degraded disordered amyloid ß 42 peptide (Aß42) aggregate and fibrin-Aß42 co-aggregate in vitro and reduced co-aggregate induced cytotoxicity in SH-SY5Y human neuroblastoma cells as compared to plasmin. Ubiquitin also degraded abnormal co-aggregates of fibrin with other plasma proteins such as fibronectin, albumin, lysozyme, tranthyretin and α-synuclein. To elucidate the mechanism of degradation, synthetic peptides (ADG, GKT, DQQ, QRL, LIF, AGK, HLVL) derived from ubiquitin template as well as synthetic ubiquitin (8565.32 Da) were employed. Synthetic ubiquitin completely degraded preformed Aß 42 aggregate and fibrin-Aß42 co-aggregate, whereas, the smaller synthetic peptides showed varying degrees of degradation. These observations attribute a novel function of ubiquitin that may be used for degrading abnormal fibrin clots in human body. Thorough investigation might unfold a novel molecular mechanism of ubiquitin in protein homeostasis.

Mass Spectrometric Analysis of Lewy Body-Enriched α-Synuclein in Parkinson's Disease.

Parkinson's disease (PD) is characterized by intraneuronal inclusions of aggregated α-synuclein protein (so-called Lewy bodies) in distinct brain regions. Multiple posttranslational modifications may affect the structure and function of α-synuclein. Mass spectrometry-based analysis may be useful for the characterization and quantitation of α-synuclein forms, but has proven challenging, mainly due to the insolubility of Lewy bodies in aqueous buffer. In the present study, we developed a novel method by combining differential solubilization with immunoprecipitation and targeted proteomics using liquid chromatography and tandem mass spectrometry. Brain tissue homogenization and sample preparation were modified to facilitate analysis of soluble, detergent-soluble, and detergent-insoluble protein fractions (Lewy body-enriched). The method was used to compare α-synuclein forms from cingulate cortex (affected) and occipital cortex (unaffected) in two study sets of PD patients and controls. We identified ∼20 modified α-synuclein variants, including species with N-terminal acetylation and C-terminal truncations at amino acids 103 and 119. The levels of α-synuclein forms Ac-α-syn1-6, α-syn13-21, α-syn35-43, α-syn46-58, α-syn61-80, and α-syn81-96 except α-syn103-119 were significantly increased in PD cingulate region compared to controls in the Lewy body-enriched α-synuclein fraction. In the soluble fraction, only Ac-α-syn1-6 was significantly increased in PD compared to controls. None of the detected α-synuclein variants were Lewy body-specific, but acetylated forms should be examined further as potential biomarkers for abnormal α-synuclein accumulation.

Distinct transcriptional and processing regulations control miR167a level in tomato during stress.

Besides their definite role in plant developmental processes miR167 also serve as mediator of stress response. Although differential expression of miR167 occurs during stresses, the regulatory-mechanism of biogenesis remained elusive. Therefore, using tomato as the model plant we have explored the mechanism of regulation of miR167a expression during stresses. Fungus or virus infections and exposure to cold stress raised the level of miR167a expression. Whereas, salt, drought and heat treatments resulted in the downregulation, indicating different stresses activated alternative mechanisms for miR167a regulation. Interestingly, the relative expression level of precursors in control versus temperature stressed plants differed from the pattern observed in the mature miR167a expression, suggesting that both transcriptional and processing regulation were important for biogenesis. The promoter-regulatory sequence of the major isoform MIR167a harbours several development and stress-related regulatory sites. Accordingly, promoter assays using transient transformation and transgenic tobacco plants proved stress-dependent regulation of the promoter. Further analyses corroborated the role of tomato DREB2A protein in the transcriptional regulation during temperature stress. Finally, in vitro assays established the importance of processing factors in cold-stress dependent efficient processing of MIR167a precursors. These data confirm distinct role of transcriptional and processing machinery in stress-influenced regulation of tomato miR167a biogenesis.

Functional characterization of tomato membrane-bound NAC transcription factors.

KEY MESSAGE: Genome-wide analysis was carried out to identify and analyze differential expression pattern of tomato membrane bound NAC transcription factors (SlNACMTFs) during stresses. Two biotic-stress-related SlNACMTFs have been characterized to elucidate their regulatory function. NAC transcription factors are known regulators of stress-related gene expression. As Stresses are perceived and transmitted by membrane-bound proteins, functional characterization of membrane-associated NAC transcription factors in tomato can reveal valuable insight about membrane-mediated stress-signalling. Tomato genome encodes 13 NAC genes which have predicted transmembrane domain(s) (SlNACMTFs). mRNA of 12 SlNACMTFs were readily detected in multiple tissues, and also in polysome isolated from leaf, confirming active transcription and translation from these genes occur under normal physiological condition. Additionally, most of the SlNACMTFs were differentially regulated during stresses and stress-related transcription factor binding sites are prevalent in their promoters. SlNACMTF3 and 8 were majorly regulated in biotic and abiotic stresses. Like other MTFs, SlNACMTF3 was translocated to the plasma membrane, whereas the C-terminus truncated (ΔC) form localized in the cytoplasm and the nucleus. Accordingly, the ΔC forms significantly influenced the activity of promoters harbouring NAC binding sites (NACbs). Furthermore, the NAC domain of these transcription factors could directly interact with an NACbs, and the proteins failed to regulate a promoter lacking a crucial NACbs. Interestingly, the type of influence to an NACbs containing promoter was dependent on the context of the NACbs, as the same SlNACMTF showed an alternative mode of regulation on different promoters, as well as the same promoter activity was oppositely regulated by two different SlNACMTF. Finally, both SlNACMTFs demonstrated the differential regulatory effect on the expression of several stress-related genes by interacting with the putative NACbs in their promoter region, suggesting their direct role in plant stress response.

Factor V activator from Daboia russelli russelli venom destabilizes ß-amyloid aggregate, the hallmark of Alzheimer disease.

Formation of plaque by fibrils of ß-amyloid (Aß) peptide in the brain is the characteristic feature of Alzheimer disease (AD). Inhibition of the process of aggregate formation from Aß-monomer and destabilization of the aggregate could be useful for prevention and propagation of the disease respectively. Russell's viper venom (RVV) contains protein(s) that destabilize Aß aggregates as revealed from the thioflavin T assay. The active component was identified as factor V activator (RVV-V). Among the possible mechanisms of destabilization, RVV-V-mediated proteolysis was ruled out from mass spectrometric data and the thioflavin T assay. The alternate hypothesis that small peptides derived from RVV-V destabilize the aggregate is better supported by experimental results. Six small peptides were synthesized using RVV-V as the template, and three unrelated peptides were synthesized to serve as controls. Destabilization of Aß aggregate by these peptides was studied using spectrofluorometric assays, atomic force microscopy, transmission electron microscopy, and confocal microscopy. Among the peptides, CTNIF and the mixture of the six peptides were most potent in converting the aggregates to the monomeric state and thus, preventing cytotoxicity in SH-SY5Y human neuroblastoma cells. The control peptides failed to show similar effects. Moreover, some of these peptides are stable in blood for 24 h. Therefore, these venom-derived peptides offer an encouraging opportunity to prevent amyloidosis and may provide information to combat AD.

Destabilization of ß-amyloid aggregates by thrombin derived peptide: plausible role of thrombin in neuroprotection.

ß-amyloid (Aß) aggregates involved in Alzheimer's disease (AD) are resistant to proteases but could be destabilized by small peptides designed to target specific hydrophobic regions of Aß that take part in aggregate assembly. Since thrombin and AD are intricately connected, and elastase modulates thrombin activity, elastase-digested thrombin peptides were verified for intervention in the Aß-aggregation pathway. Intact or elastase-digested thrombin destabilized Aß fibril, as demonstrated by thioflavin T assay. Peptides were synthesized employing thrombin as a template, of which, a hexapeptide (T3) showed maximum destabilization at 1 µm. ExPASy peptide cutter software coupled with mass spectrometric analysis confirmed the generation of T3 peptide from elastase-digested thrombin. TEM micrographs revealed that 30-day incubation of preformed Aß fibrils or monomers with T3 resulted in destabilization or inhibition, respectively, leading mostly to particles of 1.74 ± 0.17 nm, which roughly corresponded to Aß monomer. Surface plasmon resonance employing CM5 chip coupled with Aß40 mouse monoclonal antibody showed a drop in response when T3 was incubated with Aß fibrils between 2 and 8 h. 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide and confocal microscopy demonstrated the ability of T3 to rescue neuroblastoma cells from Aß oligomer-induced cytotoxic damage. Although no [Aß-T3] adduct could be detected by mass spectrometry, an initial interaction appeared to facilitate the process of destabilization/inhibition of aggregation. T3 was comparable to standard ß-sheet breaker peptides, LPFFD and KLVFF in terms of Aß aggregate destabilization. High hydrophobicity values coupled with recognition and breaking elements make T3 a potential candidate for future therapeutic applications.

Method to Study Dynamics of Membrane-Bound Plant Transcription Factors During Biotic Interactions in Tomato.

Sequestration of a transcription factor in a cellular membrane and releasing it on demand is an additional layer of gene regulation that is considered a rapid mode to reprogram a gene expression cascade when a plasma membrane stress signal is perceived. Better understanding of the dynamic exchange of membrane-bound transcription factors (MTFs) during biotic stress requires the development of a simple, efficient, and quick assay system. Here we report an Agrobacterium-based transient transformation method to assay the localization of fluorescent protein-tagged MTFs in tomato leaf epidermal peels that are subsequently infected with a pathogenic fungus. Essentially, our method mimics natural infection and facilitates the realistic monitoring of MTF movement during activation of a signaling event.

Detection of α-Synuclein in Biological Samples Using Mass Spectrometry.

Here we describe a method using mass spectrometry to characterize and quantify immuno-enriched α-synuclein forms from biochemically fractionated brain tissue.

Aristolochic acid and its derivatives as inhibitors of snake venom L-amino acid oxidase.

Snake venom L-amino acid oxidase (LAAO) exerts toxicity by inducing hemorrhage, pneumorrhagia, pulmonary edema, cardiac edema, liver cell necrosis etc. Being well conserved, inhibitors of the enzyme may be synthesized using the template of the substrate, substrate binding site and features of the catalytic site of the enzyme. Previous findings showed that aristolochic acid (AA), a major constituent of Aristolochia indica, inhibits Russell's viper venom LAAO enzyme activity since, AA interacts with DNA and causes genotoxicity, derivatives of this compound were synthesized by replacing the nitro group to reduce toxicity while retaining the inhibitory potency. The interactions of AA and its derivatives with LAAO were followed by inhibition kinetics and surface plasmon resonance. Similar interactions with DNA were followed by absorption spectroscopy and atomic force microscopy. LAAO-induced cytotoxicity was evaluated by generation of reactive oxygen species (ROS), cell viability assays, confocal and epifluorescence microscopy. The hydroxyl (AA-OH) and chloro (AA-Cl) derivatives acted as inhibitors of LAAO but did not interact with DNA. The derivatives significantly reduced LAAO-induced ROS generation and cytotoxicity in human embryonic kidney (HEK 293) and hepatoma (HepG2) cell lines. Confocal images indicated that AA, AA-OH and AA-Cl interfered with the binding of LAAO to the cell membrane. AA-OH and AA-Cl significantly inhibited LAAO activity and reduced LAAO-induced cytotoxicity.

Chelerythrine down regulates expression of VEGFA, BCL2 and KRAS by arresting G-Quadruplex structures at their promoter regions.

A putative anticancer plant alkaloid, Chelerythrine binds to G-quadruplexes at promoters of VEGFA, BCL2 and KRAS genes and down regulates their expression. The association of Chelerythrine to G-quadruplex at the promoters of these oncogenes were monitored using UV absorption spectroscopy, fluorescence anisotropy, circular dichroism spectroscopy, CD melting, isothermal titration calorimetry, molecular dynamics simulation and quantitative RT-PCR technique. The pronounced hypochromism accompanied by red shifts in UV absorption spectroscopy in conjunction with ethidium bromide displacement assay indicates end stacking mode of interaction of Chelerythrine with the corresponding G-quadruplex structures. An increase in fluorescence anisotropy and CD melting temperature of Chelerythrine-quadruplex complex revealed the formation of stable Chelerythrine-quadruplex complex. Isothermal titration calorimetry data confirmed that Chelerythrine-quadruplex complex formation is thermodynamically favourable. Results of quantative RT-PCR experiment in combination with luciferase assay showed that Chelerythrine treatment to MCF7 breast cancer cells effectively down regulated transcript level of all three genes, suggesting that Chelerythrine efficiently binds to in cellulo quadruplex motifs. MD simulation provides the molecular picture showing interaction between Chelerythrine and G-quadruplex. Binding of Chelerythrine with BCL2, VEGFA and KRAS genes involved in evasion, angiogenesis and self sufficiency of cancer cells provides a new insight for the development of future therapeutics against cancer.

An Enzyme from Aristolochia indica Destabilizes Fibrin-ß Amyloid Co-Aggregate: Implication in Cerebrovascular Diseases.

Fibrinogen and ß-amyloid (Aß) peptide independently form ordered aggregates but in combination, they form disordered structures which are resistant to fibrinolytic enzymes like plasmin and cause severity in cerebral amyloid angiopathy (CAA). A novel enzyme of 31.3 kDa has been isolated from the root of the medicinal plant Aristolochia indica that showed fibrinolytic as well as fibrin-Aß co-aggregate destabilizing properties. This enzyme is functionally distinct from plasmin. Thrombolytic action of the enzyme was demonstrated in rat model. The potency of the plant enzyme in degrading fibrin and fibrin-plasma protein (Aß, human serum albumin, lysozyme, transthyretin and fibronectin) co-aggregates was demonstrated by atomic force microscopy, scanning electron microscopy and confocal microscopy that showed better potency of the plant enzyme as compared to plasmin. Moreover, the plant enzyme inhibited localization of the co-aggregate inside SH-SY5Y human neuroblastoma cells and also co-aggregate induced cytotoxicity. Plasmin was inefficient in this respect. In the background of limited options for fragmentation of these co-aggregates, the plant enzyme may appear as a potential proteolytic enzyme.

Characterization of the aqueous extract of the root of Aristolochia indica: evaluation of its traditional use as an antidote for snake bites.

ETHNOPHARMACOLOGICAL RELEVANCE: The aqueous extract of the roots of Aristolochia indica is used as a decoction for the ailment of a number of diseases including snake bite treatment. Though the alcoholic extract of the different parts of the plant are well studied, information on the aqueous extract is limited. We have estimated aristolochic acid, different enzymes, enzyme inhibitors and anti-snake venom potency of its root extract. MATERIALS AND METHODS: Reverse phase-HPLC was used to quantify aristolochic acid. Zymography, DQ-gelatin assay and atomic force microscopy were done to demonstrate gelatinase and collagenase activities of the extract. SDS-PAGE followed by MS/MS analysis revealed the identity of major protein components. Toxicity of the extract was estimated on animal model. Interaction of the extract with Russell's viper venom components was followed by Rayleigh scattering and enzyme assay. RESULTS: The aristolochic acid content of the root extract is 3.08 ± 1.88 × 10(-3)mg/ml. The extract possesses strong gelatinolytic, collagenase, peroxidase and nuclease activities together with l-amino acid oxidase and protease inhibitory potencies. Partial proteomic studies indicated presence of starch branching enzymes as major protein constituent of the extract. The extract did not show any acute and sub-chronic toxicity in animals at lower doses, but high dose causes liver and kidney damage. The extract elongated duration of survival of animals after application of Russell's viper venom. CONCLUSIONS: Considering the low aristolochic acid content of the extract, its consumption for a short time at moderate dose does not appear to cause serious toxicity. Strong inhibition of l-amino acid oxidase may give partial relief from snake bite after topical application of the extract.

Thermal detoxification of the venom from Daboia russelli russelli of Eastern India with restoration of fibrinolytic activity.

The fibrinolytic components of venom have been evaluated for long in the enzymatic treatment of thrombosis. Russell's viper venom has fibrinolytic activity that is associated with hemorrhagic activity. Here it has been investigated whether the crude venom could be detoxified by thermal denaturation retaining fibrinolytic activity. The venom at 0.05 mg/ml in 20 mM K-phosphate, pH 7.5 when exposed to 100 °C for 5 min followed by cooling at 25 °C for 1 h led to its detoxification, while 80-85% of the fibrinolytic activity was recovered. Assessment of toxicity of the renatured venom in mice after injection at 5 fold excess of the lethal dose showed no lethality including hemorrhage, myotoxicity, cytotoxicity and liver toxicity. This simple method for preparation of fibrinolytic component for therapeutic use may be developed.