Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mutational analysis of the carbohydrate-binding activity of the NeuAc(alpha-2,6)Gal/GalNAc-specific type 2 ribosome-inactivating protein from elderberry (Sambucus nigra) fruits.

ABSTRACT: Sambucus nigra agglutinin I (SNA-I) is a type 2 ribosome-inactivating protein. Site-directed mutagenesis was used to mimic the conversion of the highly active B-chain of fruit-specific SNA (SNA-If) into the completely inactive B-chain of the closely related and naturally occurring loss-of-activity mutant called S. nigra agglutinin lectin-related protein. In the first mutant SNA-If-M1 the high-affinity site 2 of SNA-If was disrupted by replacing the presumed critical residue Asp231 with Glu231. In the double mutant SNA-If-M2, site 1 of SNA-If-M1 was also disrupted by substituting the presumed critical residue Asn48 with Ser48. The parent type 2 ribosome-inactivating protein and both mutants were expressed in Nicotiana tabacum Samsun NN and the recombinant proteins were purified and analysed. Recombinant SNA-If agglutinated rabbit erythrocytes equally well as SNA-If, but both mutants were completely inactive in this test. Binding assays to immobilized galactose and fetuin revealed that the mutation Asp231-->Glu231 reduces the affinity of the B-chain for galactose and fetuin by more than 50%. Furthermore, the introduction of the second mutation Asn48-->Ser48 reduces the binding activity to less than 20% of the original activity.

SUBMITTER: Chen Y

PROVIDER: S-EPMC1222605 | biostudies-other | 2002 Jun

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Sambucus nigra

Project description:Sambucus nigra overview

| PRJNA882168 | ENA

Molecular cloning and in-depth bioinformatics analysis of type II ribosome-inactivating protein isolated from <i>Sambucus ebulus</i>.

Project description:Plant ribosome-inactivating proteins (RIPs) are N-glycosidases which inhibit protein synthesis through depurination of the ribosomal RNA sequence. Type II RIPs are heterodimer proteins which can bind to cell surfaces. The cytotoxicity of these RIPs is different. Sambucus spp. are a rich source of RIP proteins with different properties. In the present study, a type II RIP was isolated from S. ebulus plant that grows widely in the north of Iran, and different bioinformatics tools were used for the evaluation of physicochemical, functional and 3D protein characteristics. The results showed significant differences among isolated RIP and other Sambucus RIP proteins. The study of these differences can not only expand our insight into the functioning mechanisms of plant RIPs but also provide information about a novel RIP protein with potential biological applications.

| S-EPMC7253926 | biostudies-literature

A lectin from elder (Sambucus nigra L.) bark.

Project description:A lectin was isolated from elder (Sambucus nigra) bark by affinity chromatography on fetuin-agarose. It is a tetrameric molecule (Mr 140000) composed of two different subunits of Mr 34500 and 37500 respectively, held together by intramolecular disulphide bridges. The lectin is a glycoprotein and is especially rich in asparagine/aspartic acid, glutamine/glutamic acid, valine and leucine. It is also the first lectin isolated from a species belonging to the plant family Caprifoliaceae.

| S-EPMC1144016 | biostudies-other

Serum transferrin carrying the xeno-tetrasaccharide NeuAc-Gal-GlcNAc2 is a biomarker of ALG1-CDG.

Project description:ALG1-CDG (formerly CDG-Ik) is a subtype of congenital disorders of glycosylation (CDG) where the genetic defect disrupts the synthesis of the lipid-linked oligosaccharide precursor required for N-glycosylation. The initial step in the investigation for these disorders involves the demonstration of hypoglycosylated serum transferrin (TF). There are no specific biomarkers of this CDG subtype known to date. An LC/MS approach was used to analyze sera from patients with ALG1-CDG, PMM2-CDG, suspected CDG, and individuals with alcohol abuse. We show mass spectrometric data combined with data from enzymatic digestions that suggest the presence of a tetrasaccharide consisting of two N-acetylglucosamines, one galactose, and one sialic acid, appearing on serum TF, is a biomarker of this particular CDG subtype. This is the first time analysis of serum TF can suggest a specific CDG type I subtype and we suggest this tetrasaccharide be used in the clinic to guide the ALG1-CDG diagnostic process.

| S-EPMC4822552 | biostudies-literature

Molecular characterization of a novel Aureusvirus infecting elderberry (Sambucus nigra L.).

Project description:A novel virus infecting elderberry was identified by high-throughput Illumina sequencing of double strand RNAs isolated form elderberry leaves. The complete genome sequence obtained (4512 nucleotides in length) shows an organization typical for aureusviruses, with five open reading frames (ORFs) and the typical ORF1-RT expression by the readthrough of an amber stop codon. The analysis of the RNA-dependent RNA polymerase (RdRp) and coat protein (CP) sequences showed the highest identity (respectively 75.7% and 55%) with the corresponding amino acid sequences of Pothos latent virus. These two values, below the species demarcation criteria for the genus, indicate that the detected virus is a new member of genus Aureusvirus, family Tombusviridae, with the proposed name Elderberry aureusvirus 1 (ElAV1). A survey confirmed the wide distribution of ElAV1 in elderberry in the Czech Republic. Phylogenetic analyses of RdRp and CP sequences showed distinct microevolution of geographically separated isolates, with a tendency for isolates coming from close localities or from the same region to cluster together but heterogeneity of viral populations down to a local scale was also observed. The symptomatology of the new virus is not fully clear, but many infected trees were either asymptomatic or showed mild chlorotic mosaics. More severe symptoms, potentially impacting yields of flowers or berries, were observed in plants with mixed infections of ElAV1 and other elderberry viruses. Further efforts are now needed to determine ElAV1 prevalence outside the Czech Republic and to unravel its epidemiology.

| S-EPMC6095521 | biostudies-literature

The Phenolic Contents and Antioxidant Activities of Infusions of Sambucus nigra L.

Project description:The aim of this work was to evaluate the antioxidant potential of teas prepared from twenty-four commercially available berries and flowers of Sambucus nigra L. in relation to their phenolic profile, as reflected by the most representative phenolic acids (caffeic, chlorogenic, p-coumaric, ferulic, gallic and syringic acids); flavonols (quercetin, kaempferol, myricetin and rutin); and total phenolic (TPC), phenolic acid (TAC) and flavonoid (TFC) contents. The infusions prepared from elderflowers contained more abundant phenolic compounds than the elderberry infusions. The TPC of these infusions ranged from 19.81 to 23.90 mg of gallic acid equivalents/g dry weight of sample (GAE/g DW) for elderberries and from 15.23 to 35.57 mg GAE/g DW for elderflowers, whereas the TFC ranged from 2.60 to 4.49 mg of rutin equivalents/g dry weight of sample (RUTE/g DW) in elderberry infusions and from 5.27 to 13.19 mg RUTE/g DW in elderflower infusions. Among the phenolic compounds quantified in this study, quercetin (2.07-9.48 mg/g DW) and myricetin (1.17-9.62 mg/g DW) had the highest concentrations in the teas prepared from berries and flowers, respectively. Moreover, the antioxidant potential of elder infusions assessed by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical and ferric reducing antioxidant power (FRAP) assays revealed that the teas prepared from flowers had higher mean DPPH and FRAP activities than the teas prepared from berries. Therefore, elder beverages could be important dietary sources of natural antioxidants that contribute to the prevention of diseases caused by oxidative stress.

| S-EPMC5325840 | biostudies-literature

Ribosome Inactivating Proteins from Rosaceae.

Project description:Ribosome-inactivating proteins (RIPs) are widespread among higher plants of different taxonomic orders. In this study, we report on the RIP sequences found in the genome/transcriptome of several important Rosaceae species, including many economically important edible fruits such as apple, pear, peach, apricot, and strawberry. All RIP domains from Rosaceae share high sequence similarity with conserved residues in the catalytic site and the carbohydrate binding sites. The genomes of Malus domestica and Pyrus communis contain both type 1 and type 2 RIP sequences, whereas for Prunus mume, Prunus persica, Pyrus bretschneideri, and Pyrus communis a complex set of type 1 RIP sequences was retrieved. Heterologous expression and purification of the type 1 as well as the type 2 RIP from apple allowed to characterize the biological activity of the proteins. Both RIPs from Malus domestica can inhibit protein synthesis. Furthermore, molecular modelling suggests that RIPs from Rosaceae possess three-dimensional structures that are highly similar to the model proteins and can bind to RIP substrates. Screening of the recombinant type 2 RIP from apple on a glycan array revealed that this type 2 RIP interacts with terminal sialic acid residues. Our data suggest that the RIPs from Rosaceae are biologically active proteins.

| S-EPMC6274481 | biostudies-literature

Chemical Characterization of Sambucus nigra L. Flowers Aqueous Extract and Its Biological Implications.

Project description:The main goal of this study was to chemically characterize an aqueous S. nigra flower extract and validate it as a bioactive agent. The elderflower aqueous extraction was performed at different temperatures (50, 70 and 90 °C). The extract obtained at 90 °C exhibited the highest phenolic content and antiradical activity. Therefore, this extract was analyzed by GC-MS and HPLC-MS, which allowed the identification of 46 compounds, being quercetin and chlorogenic acid derivatives representative of 86% of the total of phenolic compounds identified in hydrophilic fraction of the aqueous extract. Naringenin (27.2%) was the major compound present in the lipophilic fraction. The antiproliferative effects of the S. nigra extract were evaluated using the colon cancer cell lines RKO, HCT-116, Caco-2 and the extract's antigenotoxic potential was evaluated by the Comet assay in RKO cells. The RKO cells were the most susceptible to S. nigra flower extract (IC50 = 1250 µg mL-1). Moreover, the extract showed antimicrobial activity against Gram-positive bacteria, particularly Staphylococcus aureus and S. epidermidis. These results show that S. nigra-based extracts can be an important dietary source of bioactive phenolic compounds that contribute to health-span improving life quality, demonstrating their potential as nutraceutical, functional foods and/or cosmetic components for therapeutic purposes.

| S-EPMC8391949 | biostudies-literature

Elderberry (<i>Sambucus nigra</i> L.) extracts promote anti-inflammatory and cellular antioxidant activity.

Project description:Despite the high value of Portuguese elderberries, recognized for decades by European markets, only a few studies address their beneficial effects at cellular level. Aiming to explore the anti-inflammatory and the cellular antioxidant potential characterized extracts from the three main Portuguese elderberry cultivars (Sabugueiro, Sabugueira, Bastardeira) were used. Lipopolysaccharide-stimulated RAW 264.7 cells pre-exposed to elderberry extracts exhibited dose-dependent inhibition of nitric oxide release, evidencing anti-inflammatory activity. Concerning cellular antioxidant protection, HepG2 and Caco-2 cells pre-exposure to elderberry extracts (50 µg/mL) prevented up-to 90 % of tert-butyl hydroperoxide (t-BOOH)-induced toxicity. In Caco-2 cells, elderberry extracts prevented glutathione depletion, reactive oxygen species production, abnormal morphological changes and DNA fragmentation, in response to t-BOOH oxidative insult. Results demonstrated that elderberries have high potential in reducing cellular oxidative stress as well as in preventing inflammatory processes. Thus, elderberries have high potential as health promoters, acting as functional foods or as sources of nutraceuticals.

| S-EPMC9532789 | biostudies-literature

A Newfangled Collagenase Inhibitor Topical Formulation Based on Ethosomes with Sambucus nigra L. Extract.

Project description:Sambucus nigra L. (S. nigra) is a shrub widespread in Europe and western Asia, traditionally used in medicine, that has become popular in recent years as a potential source of a wide range of interesting bioactive compounds. The aim of the present work was to develop a topical S. nigra extract formulation based on ethosomes and thus to support its health claims with scientific evidence. S. nigra extract was prepared by an ultrasound-assisted method and then included in ethosomes. The ethosomes were analyzed in terms of their size, stability over time, morphology, entrapment capacity (EC), extract release profile, stability over time and several biological activities. The prepared ethosomes were indicated to be well defined, presenting sizes around 600 nm. The extract entrapment capacity in ethosomes was 73.9 ± 24.8%, with an interesting slow extract release profile over 24 h. The extract-loaded ethosomes presented collagenase inhibition activity and a very good skin compatibility after human application. This study demonstrates the potential use of S. nigra extract incorporated in ethosomes as a potential cosmeceutical ingredient and on further studies should be performed to better understand the impact of S. nigra compounds on skin care over the time.

| S-EPMC8155848 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data