An Improved Kinetic Assay for the Characterization of Metal-Dependent Pectate Lyases

Author(s):  
Darryl R. Jones ◽  
Richard McLean ◽  
D. Wade Abbott
Keyword(s):  
2021 ◽  
Author(s):  
Amrutha Bindu ◽  
Lakshmi Devi

Abstract The focus of present study was to characterize antimicrobial peptide produced by probiotic cultures, Enterococcus durans DB-1aa (MCC4243), Lactobacillus plantarum Cu2-PM7 (MCC4246) and Lactobacillus fermentum Cu3-PM8 (MCC4233) against Staphylococus aureus and E. coli. The growth kinetic assay revealed 24 h of incubation to be optimum for bacteriocin production. The partially purified compound after ion-exchange chromatography was found to be thermoresistant and stable under wide range of pH. The compound was sensitive to proteinase-K, but resistant to trypsin, a-amylase and lipase. The apparent molecular weight of bacteriocin from MCC4243 and MCC4246 was found to be 3.5 KDa. Translated partial amino acid sequence of plnA gene in MCC4246 displayed 48 amino acid sequences showing 100% similarity with plantaricin A of Lactobacillus plantarum (WP_0036419). The sequence revealed 7 β sheets, 6 α sheets, 6 predicted coils and 9 predicted turns. The functions on cytoplasm show 10.82 isoelectric point and 48.6% hydrophobicity. The molecular approach of using Geneious Prime software and protein prediction data base for characterization of bacteriocin is novel and predicts “KSSAYSLQMGATAIKQVKKLFKKWGW” as peptide responsible for antimicrobial activity. The study provides information about broad spectrum bacteriocin in native probiotic culture and paves a way towards its application in functional foods as biopreservative agents.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 687-687 ◽  
Author(s):  
Andreas M Hohlbaum ◽  
Stefan Trentman ◽  
Hendrik Gille ◽  
Andrea Allersdorfer ◽  
Rachida Siham Belaiba ◽  
...  

Abstract Abstract 687 Rationale: Anticalins® have been developed as a new class of therapeutic proteins based on human lipocalins. We reasoned that given the diversity of compounds that these molecules naturally bind, it should be possible to engineer and identify Anticalins with specificity for small, biologically active compounds, including constrained peptides. To test this hypothesis, we asked whether it would be possible to identify an engineered lipocalin that could specifically block hepcidin, a 25 amino acid hepatic hormone. The central role of hepcidin in regulating iron homeostasis through its interaction with the only known cellular iron exporter ferroportin is supported by human genetics and preclinical data and suggests that sub-population of patients with anemia, exhibiting elevated serum levels of hepcidin, may be responsive to therapies directed at blocking hepcidin. Hepcidin-specific antagonistic Anticalins with different pharmacokinetic properties were generated to develop Anticalin drug candidates with different PK/PD relationships as different clearance rates of the Anticalin-hepcidin complex may be desirable when used as a therapeutic approach in different patient populations. Methods: State of the art phage display technology and high throughput screening were used to isolate a human lipocalin-derived Anticalin to specifically bind and antagonize hepcidin. Randomization of Anticalin binding loops and affinity-based phage display selection were used for affinity maturation and optimization of drug-like properties. Anticalins (MW ∼21 kDa) were produced in E.coli and subjected to site-directed PEGylation with different size PEG molecules. Affinity constants for hepcidin from different species were determined using ELISA-based assays and surface plasmon resonance. We then examined the ability of these Anticalin drug candidates to neutralize human hepcidin activities in cellular and in vivo assays. In addition, PK properties were determined in different animal species to predict PK properties in humans by allometric scaling. Results and Discussion: By using 2 different assay formats the lead candidate displayed high affinity (sub-nM) against human hepcidin and the extension of its plasma half-life by site directed PEGylation did not impact target binding. For example, in an SPR kinetic assay where the PEGylated Anticalin was immobilized and human hepcidin used as analyte, a dissociation constant of Kd = 50±3 pM (n=3) was determined for an Anticalin conjugated with a 40 kDa branched PEG molecule. A stable cell line expressing ferroportin fused to green fluorescent protein was established to determine blockade of hepcidin in vitro by measuring hepcidin-induced ferroportin (FPN) internalization and degradation. Hepcidin bioactivity was completely inhibited by the PEGylated Anticalin at concentrations at or above ∼40 nM (n=6), thus demonstrating the ability of the Anticalin to neutralize hepcidin's principal biological activity on the iron exporter FPN. Furthermore, the ability of PRS-080 to neutralize short-term hypoferremic effects was evaluated in mice after stimulation via a single intraperitoneal injection of 1 mg/kg synthetic human hepcidin. The PEGylated version of PRS-080, administered intravenously several hours prior to hepcidin injection, completely prevented the hypoferremic response at a dose of 95 mg/kg and showed partial prevention at 30 mg/kg (59%) and 9.5 mg/kg (23%). Tunable PK properties were demonstrated with an additional set of PEGylated molecules, tested in rats at a dose of 10 mg/kg, and exhibited terminal half-lives of 9.2, 14.2, 20.4, and 40 hours for Anticalins conjugated with 12, 20, 30 kDa linear and 40 kDa branched PEG, respectively. Conclusions: Our data describe the discovery and characterization of a hepcidin-antagonistic Anticalin for the treatment of anemia. PRS-080 displays numerous differentiating features posited to be relevant for the proposed therapeutic concept of inhibiting hepcidin-mediated hypoferremic effects, including: binding of its relatively small target with high affinity and specificity (pocket binding), favourable safety and tolerability (human scaffold, lack of immune effector cell interactions), tunable half-life and low production costs (bacterial expression). Anticalins provide a powerful novel therapeutic approach to develop antagonists against hepcidin and bioactive peptides in general. Disclosures: Hohlbaum: Pieris AG: Employment, Patents & Royalties. Trentman:Pieris AG: Employment, Patents & Royalties. Gille:Pieris AG: Employment, Patents & Royalties. Allersdorfer:Pieris AG: Employment. Belaiba:Pieris AG: Employment. Huelsmeyer:Pieris AG: Employment, Patents & Royalties. Christian:Pieris AG: Employment, Patents & Royalties. Sandal:Pieris AG: Employment. Matschiner:Pieris AG: Employment, Patents & Royalties. Jensen:Pieris AG: Employment, Patents & Royalties. Skerra:Pieris AG: Consultancy, Patents & Royalties, Research Funding. Audoly:Pieris AG: Employment.


2009 ◽  
Vol 81 (19) ◽  
pp. 8244-8248 ◽  
Author(s):  
Sebastian Schätzle ◽  
Matthias Höhne ◽  
Erik Redestad ◽  
Karen Robins ◽  
Uwe T. Bornscheuer
Keyword(s):  

2010 ◽  
Vol 76 (15) ◽  
pp. 5214-5220 ◽  
Author(s):  
Honor� G. Ouattara ◽  
Sylvie Reverchon ◽  
S�bastien L. Niamke ◽  
William Nasser

ABSTRACT Pectinolytic enzymes play an important role in cocoa fermentation. In this study, we characterized three extracellular pectate lyases (Pels) produced by bacilli isolated from fermenting cocoa beans. These enzymes, named Pel-22, Pel-66, and Pel-90, were synthesized by Bacillus pumilus BS22, Bacillus subtilis BS66, and Bacillus fusiformis BS90, respectively. The three Pels were produced under their natural conditions and purified from the supernatants using a one-step chromatography method. The purified enzymes exhibited optimum activity at 60�C, and the half-time of thermoinactivation at this temperature was approximately 30 min. Pel-22 had a low specific activity compared with the other two enzymes. However, it displayed high affinity for the substrate, about 2.5-fold higher than those of Pel-66 and Pel-90. The optimum pHs were 7.5 for Pel-22 and 8.0 for Pel-66 and Pel-90. The three enzymes trans-eliminated polygalacturonate in a random manner to generate two long oligogalacturonides, as well as trimers and dimers. A synergistic effect was observed between Pel-22 and Pel-66 and between Pel-22 and Pel-90, but not between Pel-90 and Pel-66. The Pels were also strongly active on highly methylated pectins (up to 60% for Pel-66 and Pel-90 and up to 75% for Pel-22). Fe2+ was found to be a better cofactor than Ca2+ for Pel-22 activity, while Ca2+ was the best cofactor for Pel-66 and Pel-90. The amino acid sequences deduced from the cloned genes showed the characteristics of Pels belonging to Family 1. The pel-66 and pel-90 genes appear to be very similar, but they are different from the pel-22 gene. The characterized enzymes form two groups, Pel-66/Pel-90 and Pel-22; members of the different groups might cooperate to depolymerize pectin during the fermentation of cocoa beans.


2003 ◽  
Vol 69 (10) ◽  
pp. 6235-6242 ◽  
Author(s):  
S. Voget ◽  
C. Leggewie ◽  
A. Uesbeck ◽  
C. Raasch ◽  
K.-E. Jaeger ◽  
...  

ABSTRACT The metagenomes of complex microbial communities are rich sources of novel biocatalysts. We exploited the metagenome of a mixed microbial population for isolation of more than 15 different genes encoding novel biocatalysts by using a combined cultivation and direct cloning strategy. A 16S rRNA sequence analysis revealed the presence of hitherto uncultured microbes closely related to the genera Pseudomonas, Agrobacterium, Xanthomonas, Microbulbifer, and Janthinobacterium. Total genomic DNA from this bacterial community was used to construct cosmid DNA libraries, which were functionally searched for novel enzymes of biotechnological value. Our searches in combination with cosmid sequencing resulted in identification of four clones encoding 12 putative agarase genes, most of which were organized in clusters consisting of two or three genes. Interestingly, nine of these agarase genes probably originated from gene duplications. Furthermore, we identified by DNA sequencing several other biocatalyst-encoding genes, including genes encoding a putative stereoselective amidase (amiA), two cellulases (gnuB and uvs080), an α-amylase (amyA), a 1,4-α-glucan branching enzyme (amyB), and two pectate lyases (pelA and uvs119). Also, a conserved cluster of two lipase genes was identified, which was linked to genes encoding a type I secretion system. The novel gene aguB was overexpressed in Escherichia coli, and the enzyme activities were determined. Finally, we describe more than 162 kb of DNA sequence that provides a strong platform for further characterization of this microbial consortium.


2005 ◽  
Vol 40 (6) ◽  
pp. 453-459 ◽  
Author(s):  
R. Margesin ◽  
V. Fauster ◽  
P.-A. Fonteyne
Keyword(s):  

2010 ◽  
Vol 76 (17) ◽  
pp. 6006-6009 ◽  
Author(s):  
Whitney E. Boland ◽  
Emily DeCrescenzo Henriksen ◽  
Joy Doran-Peterson

ABSTRACT Two pectate lyases were identified from Paenibacillus amylolyticus 27C64; both enzymes demonstrated activity on methylated pectin in addition to polygalacturonic acid. PelA is in a subclass of the pectate lyase family III. PelB shows some features of pectate lyase family I but is highly divergent.


2009 ◽  
Vol 384 (1) ◽  
pp. 56-67 ◽  
Author(s):  
Min Li ◽  
Paolo Luraghi ◽  
Augustin Amour ◽  
Xiao-Dong Qian ◽  
Paul S. Carter ◽  
...  

JIMD Reports ◽  
2019 ◽  
Vol 48 (1) ◽  
pp. 75-82
Author(s):  
Nikolay Mayanskiy ◽  
Ekaterina Brzhozovskaya ◽  
Alexander Pushkov ◽  
Tatiana Strokova ◽  
Nikolay Vlasov ◽  
...  

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