Identification of the hydantoin alkaloids parazoanthines as novel CXCR4 antagonists by computational and in vitro functional characterization

Most Gram-positive bacteria contain a membrane-bound transpeptidase known as sortase which covalently incorporates the surface proteins on to the cell wall. The sortase-displayed protein structures are involved in cell attachment, nutrient uptake and aerial hyphae formation. Among the six classes of sortase (A–F), sortase A of S. aureus is the well-characterized housekeeping enzyme considered as an ideal drug target and a valuable biochemical reagent for protein engineering. Similar to SrtA, class E sortase in GC rich bacteria plays a housekeeping role which is not studied extensively. However, C. glutamicum ATCC 13032, an industrially important organism known for amino acid production, carries a single putative sortase (NCgl2838) gene but neither in vitro peptide cleavage activity nor biochemical characterizations have been investigated. Here, we identified that the gene is having a sortase activity and analyzed its structural similarity with Cd-SrtF. The purified enzyme showed a greater affinity toward LAXTG substrate with a calculated KM of 12 ± 1 µM, one of the highest affinities reported for this class of enzyme. Moreover, site-directed mutation studies were carried to ascertain the structure functional relationship of Cg-SrtE and all these are new findings which will enable us to perceive exciting protein engineering applications with this class of enzyme from a non-pathogenic microbe.

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Novel Toxin-antitoxin System Xn-mazEF from Xenorhabdus nematophi-la: Identification, Characterization and Functional Exploration

Current Computer - Aided Drug Design ◽

10.2174/1573409916666200625135850 ◽

2020 ◽

Vol 16 ◽

Author(s):

Jogendra Singh Nim ◽

Mohit Yadav ◽

Lalit Kumar Gautam ◽

Chaitali Ghosh ◽

Shakti Sahi ◽

...

Keyword(s):

Interaction Analysis ◽

Functional Characterization ◽

Host Cells ◽

System Control ◽

Xenorhabdus Nematophila ◽

Functional Features ◽

Dynamics Simulations ◽

Species Specific ◽

Rna Interaction

Background: Xenorhabdus nematophila maintains species-specific mutual interaction with nematodes of Steinernema genus. Type II Toxin Antitoxin (TA) systems, the mazEF TA system controls stress and programmed cell death in bacteria. Objective: This study elucidates the functional characterization of Xn-mazEF, a mazEF homolog in X. nematophila by computational and in vitro approaches. Methods: 3 D- structural models for Xn-MazE toxin and Xn-MazF antitoxin were generated, validated and characterized for protein - RNA interaction analysis. Further biological and cellular functions of Xn-MazF toxin were also predicted. Molecular dynamics simulations of 50ns for Xn-MazF toxin complexed with nucleic acid units (DU, RU, RC, and RU) were performed. The MazF toxin and complete MazEF operon were endogenously expressed and monitored for the killing of Escherichia coli host cells under arabinose induced tightly regulated system. Results: Upon induction, E. coli expressing toxin showed rapid killing within four hours and attained up to 65% growth inhibition, while the expression of the entire operon did not show significant killing. The observation suggests that the Xn-mazEF TA system control transcriptional regulation in X. nematophila and helps to manage stress or cause toxicity leading to programmed death of cells. Conclusion: The study provides insights into structural and functional features of novel toxin, XnMazF and provides an initial inference on control of X. nematophila growth regulated by TA systems.

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Functional identification of ygiP as a positive regulator of the ttdA-ttdB-ygjE operon

Microbiology ◽

10.1099/mic.0.28753-0 ◽

2006 ◽

Vol 152 (7) ◽

pp. 2129-2135 ◽

Cited By ~ 17

Author(s):

Taku Oshima ◽

Francis Biville

Keyword(s):

Functional Characterization ◽

Anaerobic Growth ◽

Functional Identification ◽

New Members ◽

E Coli ◽

Inner Membrane Protein ◽

Tartrate Dehydratase

Functional characterization of unknown genes is currently a major task in biology. The search for gene function involves a combination of various in silico, in vitro and in vivo approaches. Available knowledge from the study of more than 21 LysR-type regulators in Escherichia coli has facilitated the classification of new members of the family. From sequence similarities and its location on the E. coli chromosome, it is suggested that ygiP encodes a lysR regulator controlling the expression of a neighbouring operon; this operon encodes the two subunits of tartrate dehydratase (TtdA, TtdB) and YgiE, an integral inner-membrane protein possibly involved in tartrate uptake. Expression of tartrate dehydratase, which converts tartrate to oxaloacetate, is required for anaerobic growth on glycerol as carbon source in the presence of tartrate. Here, it has been demonstrated that disruption of ygiP, ttdA or ygjE abolishes tartrate-dependent anaerobic growth on glycerol. It has also been shown that tartrate-dependent induction of the ttdA-ttdB-ygjE operon requires a functional YgiP.

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Functional Characterization of the mazEF Toxin-Antitoxin System in the Pathogenic Bacterium Agrobacterium tumefaciens

Microorganisms ◽

10.3390/microorganisms9051107 ◽

2021 ◽

Vol 9 (5) ◽

pp. 1107

Author(s):

Wonho Choi ◽

Yoshihiro Yamaguchi ◽

Ji-Young Park ◽

Sang-Hyun Park ◽

Hyeok-Won Lee ◽

...

Keyword(s):

Agrobacterium Tumefaciens ◽

Physiological Function ◽

Functional Characterization ◽

Site Directed Mutagenesis ◽

In Vitro Assays ◽

Cell Growth Inhibition ◽

The Right

Agrobacterium tumefaciens is a pathogen of various plants which transfers its own DNA (T-DNA) to the host plants. It is used for producing genetically modified plants with this ability. To control T-DNA transfer to the right place, toxin-antitoxin (TA) systems of A. tumefaciens were used to control the target site of transfer without any unintentional targeting. Here, we describe a toxin-antitoxin system, Atu0939 (mazE-at) and Atu0940 (mazF-at), in the chromosome of Agrobacterium tumefaciens. The toxin in the TA system has 33.3% identity and 45.5% similarity with MazF in Escherichia coli. The expression of MazF-at caused cell growth inhibition, while cells with MazF-at co-expressed with MazE-at grew normally. In vivo and in vitro assays revealed that MazF-at inhibited protein synthesis by decreasing the cellular mRNA stability. Moreover, the catalytic residue of MazF-at was determined to be the 24th glutamic acid using site-directed mutagenesis. From the results, we concluded that MazF-at is a type II toxin-antitoxin system and a ribosome-independent endoribonuclease. Here, we characterized a TA system in A. tumefaciens whose understanding might help to find its physiological function and to develop further applications.

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Multifunctional Coatings for Robotic Implanted Device

International Journal of Molecular Sciences ◽

10.3390/ijms20205126 ◽

2019 ◽

Vol 20 (20) ◽

pp. 5126 ◽

Cited By ~ 2

Author(s):

Caterina Cristallini ◽

Serena Danti ◽

Bahareh Azimi ◽

Veronika Tempesti ◽

Claudio Ricci ◽

...

Keyword(s):

Acrylic Acid ◽

Vinyl Alcohol ◽

Soft Tissues ◽

Functional Characterization ◽

Titanium Substrate ◽

Repair Process ◽

Chemical Imaging ◽

In Vitro Cytotoxicity ◽

Poly Vinyl Alcohol

The objective of this study was the preparation and physico-chemical, mechanical, biological, and functional characterization of a multifunctional coating for an innovative, fully implantable device. The multifunctional coating was designed to have three fundamental properties: adhesion to device, close mechanical resemblance to human soft tissues, and control of the inflammatory response and tissue repair process. This aim was fulfilled by preparing a multilayered coating based on three components: a hydrophilic primer to allow device adhesion, a poly(vinyl alcohol) hydrogel layer to provide good mechanical compliance with the human tissue, and a layer of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) fibers. The use of biopolymer fibers offered the potential for a long-term interface able to modulate the release of an anti-inflammatory drug (dexamethasone), thus contrasting acute and chronic inflammation response following device implantation. Two copolymers, poly(vinyl acetate-acrylic acid) and poly(vinyl alcohol-acrylic acid), were synthetized and characterized using thermal analysis (DSC, TGA), Fourier transform infrared spectroscopy (FT-IR chemical imaging), in vitro cell viability, and an adhesion test. The resulting hydrogels were biocompatible, biostable, mechanically compatible with soft tissues, and able to incorporate and release the drug. Finally, the multifunctional coating showed a good adhesion to titanium substrate, no in vitro cytotoxicity, and a prolonged and controlled drug release.

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Identification of Positive Allosteric Modulators of Glycine Receptors from a High-Throughput Screen Using a Fluorescent Membrane Potential Assay

CrossRef Listing of Deleted DOIs ◽

10.1177/1087057116657779 ◽

2016 ◽

Vol 21 (10) ◽

pp. 1042-1053 ◽

Cited By ~ 11

Author(s):

Clara Stead ◽

Adam Brown ◽

Cathryn Adams ◽

Sarah J. Nickolls ◽

Gareth Young ◽

...

Keyword(s):

Membrane Potential ◽

High Throughput ◽

Glycine Receptor ◽

Functional Characterization ◽

In Vitro Assays ◽

Allosteric Modulators ◽

Inhibitory Neurotransmission ◽

Starting Point ◽

Positive Allosteric Modulators

Glycine receptor 3 (GlyRα3) is a ligand-gated ion channel of the cys-loop family that plays a key role in mediating inhibitory neurotransmission and regulation of pain signaling in the dorsal horn. Potentiation of GlyRα3 function is therefore of interest as a putative analgesic mechanism with which to target new therapeutics. However, to date, positive allosteric modulators (PAMs) of this receptor with sufficient selectivity to enable target validation studies have not been described. To address this lack of pharmacological tools, we developed a suite of in vitro assays comprising a high-throughput fluorescent membrane potential screen and a medium-throughput electrophysiology assay using IonFlux HT together with conventional manual patch clamp. Using these assays, we conducted a primary screening campaign and report the structures of hit compounds identified as GlyR PAMs. Our functional characterization data reveal a hit compound with high efficacy relative to current known potentiators and selectivity over GABAAR, another major class of inhibitory neurotransmission receptors of importance to pain. These small-molecule GlyR PAMs have high potential both as early tool compounds to enable pharmacological studies of GlyR inhibitory neurotransmission and as a starting point for the development of potent, selective GlyRα3 PAMs as novel analgesics.

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NFB-01. FUNCTIONAL CHARACTERIZATION OF ATRX LOSS IN NF1-ASSOCIATED GLIOMA AND MPNST

Neuro-Oncology ◽

10.1093/neuonc/noaa222.605 ◽

2020 ◽

Vol 22 (Supplement_3) ◽

pp. iii417-iii418

Author(s):

Ming Yuan ◽

Karlyne Reilly ◽

Christine Pratilas ◽

Christopher Heaphy ◽

Fausto Rodriguez

Keyword(s):

Cell Lines ◽

Functional Characterization ◽

Tert Promoter ◽

Aggressive Tumors ◽

Sirna Knockdown ◽

Nih 3T3 ◽

Vitro Effect ◽

Murine Glioma

Abstract To identify the biologic relevance of ATRX loss in NF1-associated gliomagenesis, we studied the effects of Atrx loss using four previously characterized Nf1+/-Trp53+/- murine glioma lines. Lines 130G#3 and 158D#8 (corresponding to grade IV and III gliomas, respectively) displayed preserved ATRX protein expression compared to NIH-3T3 cells. We studied the effects of Atrx knockdown in these two lines in the presence and absence of the TERT inhibitor, BIRBR1532. Using a telomere-specific FISH assay, we identified increased signal intensity after Atrx knockdown, only in the presence of the TERT inhibitor. These features are reminiscent of ALT, although there were no significant alterations in cell growth. Next, we studied the effect of ATRX loss in MPNST lines ST88-14, NF90-8, STS-26T. These cell lines all expressed ATRX and DAXX. However, STS-26T contained a TERT promoter mutation and ST88-14 had a known SNP in the TERT promoter, while NF90-8 had no alterations. ATRX siRNA knockdown showed no significant effects in cell proliferation or apoptosis. However, ATRX knockdown resulted in rare ultra-bright foci, indicative of ALT. Next, we studied the in vitro effect of the ATR inhibitor VE-821 in MPNST cell lines. Only NF90-8 (lacking TERT alterations) demonstrated a decrease in growth after ATRX knockdown and VE-821 treatment. However, ATRX knockdown alone did not affect sensitivity to carboplatin. Our findings further support a role for ATRX loss with subsequent ALT activation in a biologic subset of NF1-associated malignancies, thereby opening an opportunity for therapeutic targeting of these aggressive tumors using specific classes of drugs.

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Functional characterization of the NF-kappa B p65 transcriptional activator and an alternatively spliced derivative

Molecular and Cellular Biology ◽

10.1128/mcb.12.2.444-454.1992 ◽

1992 ◽

Vol 12 (2) ◽

pp. 444-454

Author(s):

S M Ruben ◽

R Narayanan ◽

J F Klement ◽

C H Chen ◽

C A Rosen

Keyword(s):

Dna Binding ◽

Complex Formation ◽

Functional Characterization ◽

Transcriptional Activator ◽

Single Amino Acid ◽

Nf Kappa B ◽

Mobility Shift ◽

Activation Domain ◽

Transcriptional Activator Protein

The NF-kappa B transcription factor complex is composed of two proteins, designated p50 and p65, both having considerable homology to the product of the rel oncogene. We present evidence that the p65 subunit is a potent transcriptional activator in the apparent absence of the p50 subunit, consistent with in vitro results demonstrating that p65 can interact with DNA on its own. To identify the minimal activation domain, chimeric fusion proteins between the DNA binding domain of the yeast transcriptional activator protein GAL4 and regions of the carboxy terminus of p65 were constructed, and their transcriptional activity was assessed by using a GAL4 upstream activation sequence-driven promoter-chloramphenicol acetyltransferase fusion. This analysis suggests that the boundaries of the activation domain lie between amino acids 415 and 550. Moreover, single amino acid changes within residues 435 to 459 greatly diminished activation. Similar to other activation domains, this region contains a leucine zipper-like motif as well as an overall net negative charge. To identify those residues essential for DNA binding, we made use of a naturally occurring derivative of p65, lacking residues 222 to 231 (hereafter referred to as p65 delta), and produced via an alternative splice site. Gel mobility shift analysis using bacterially expressed p65, p65 delta, and various mutants indicates that residues 222 to 231 are important for binding to kappa B DNA. Coimmunoprecipitation analysis suggests that these residues likely contribute to the multimerization function required for homomeric complex formation or heteromeric complex formation with p50 in that no association of p65 delta with itself or with p50 was evident. However, p65 delta was able to form weak heteromeric complexes with p65 that were greatly reduced in their ability to bind DNA. On the basis of these findings, we suggest that subtle changes within the proposed multimerization domain can elicit different effects with the individual Rel-related proteins and that a potential role of p65 delta may be to negatively regulate NF-kappa B function through formation of nonfunctional heteromeric complexes.

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Functional Characterization of GABAA Receptor Ligands In Vitro

Molecular Neuropharmacology ◽

10.1007/978-1-59259-672-0_4 ◽

2004 ◽

pp. 85-94

Author(s):

Bjarke Ebert ◽

Sally Anne Thompson ◽

Signe Í. Stórustovu ◽

Keith A. Wafford

Keyword(s):

Gabaa Receptor ◽

Functional Characterization ◽

Receptor Ligands

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Transcriptomic Insight into Terpenoid Biosynthesis and Functional Characterization of Three Diterpene Synthases in Scutellaria barbata

Molecules ◽

10.3390/molecules23112952 ◽

2018 ◽

Vol 23 (11) ◽

pp. 2952 ◽

Cited By ~ 4

Author(s):

Huabei Zhang ◽

Baolong Jin ◽

Junling Bu ◽

Juan Guo ◽

Tong Chen ◽

...

Keyword(s):

Average Length ◽

Functional Characterization ◽

Terpene Synthase ◽

Terpenoid Biosynthesis ◽

Vitro Assay ◽

Scutellaria Barbata ◽

Aerial Parts ◽

Diterpene Synthase ◽

Clerodane Diterpenoids

Scutellaria barbata (Lamiaceae) is an important medicinal herb widely used in China, Korea, India, and other Asian countries. Neo-clerodane diterpenoids are the largest known group of Scutellaria diterpenoids and show promising cytotoxic activity against several cancer cell lines. Here, Illumina-based deep transcriptome analysis of flowers, the aerial parts (leaf and stem), and roots of S. barbata was used to explore terpenoid-related genes. In total, 121,958,564 clean RNA-sequence reads were assembled into 88,980 transcripts, with an average length of 1370 nt and N50 length of 2144 nt, indicating high assembly quality. We identified nearly all known terpenoid-related genes (33 genes) involved in biosynthesis of the terpenoid backbone and 14 terpene synthase genes which generate skeletons for different terpenoids. Three full length diterpene synthase genes were functionally identified using an in vitro assay. SbTPS8 and SbTPS9 were identified as normal-CPP and ent-CPP synthase, respectively. SbTPS12 reacts with SbTPS8 to produce miltiradiene. Furthermore, SbTPS12 was proven to be a less promiscuous class I diterpene synthase. These results give a comprehensive understanding of the terpenoid biosynthesis in S. barbata and provide useful information for enhancing the production of bioactive neo-clerodane diterpenoids through genetic engineering.

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