scholarly journals Hydrophobic Forces Are Relevant to Bacteria-Nanoparticle Interactions: Pseudomonas putida Capture Efficiency by Using Arginine, Cysteine or Oxalate Wrapped Magnetic Nanoparticles

2018 ◽  
Vol 2 (3) ◽  
pp. 29 ◽  
Author(s):  
Federico Figueredo ◽  
Albert Saavedra ◽  
Eduardo Cortón ◽  
Virginia Diz
Keyword(s):  
Amino Acid ◽  
Pseudomonas Putida ◽  
Surface Characteristics ◽  
Magnetic Core ◽  
Capture Efficiency ◽  
Homogeneous Distribution ◽  
Infrared Spectrometry ◽  
Ideal Situation ◽  
High Level ◽  
Surface Modified

Size, shape and surface characteristics strongly affect interfacial interactions, as the presented among iron oxide nanoparticles (NPs) aqueous colloids and bacteria. In other to find the forces among this interaction, we compare three types of surface modified NPs (exposing oxalate, arginine or cysteine residues), based on a simple synthesis and derivation procedure, that allows us to obtain very similar NPs (size and shape of the magnetic core). In this way, we assure that the main difference in the synthesized NPs are the oxalate or amino acid residue exposed, an ideal situation to compare their bacterial capture performance, and so too the interactions among them. Field emission scanning electron microscopy showed homogeneous distribution of particle sizes for all systems synthesized, close to 10 nm. Magnetization, zeta potential, Fourier transformed infrared spectrometry and other studies allow us further characterization. Capture experiments of Pseudomonas putida bacterial strain showed a high level of efficiency, independently of the amino acid used to wrap the NP, when compared with oxalate. We show that bacterial capture efficiency cannot be related mostly to the bacterial and NP superficial charge relationship (as determined by z potential), but instead capture can be correlated with hydrophobic and hydrophilic forces among them.

scholarly journals The davDT Operon of Pseudomonas putida, Involved in Lysine Catabolism, Is Induced in Response to the Pathway Intermediate δ-Aminovaleric Acid

2004 ◽  
Vol 186 (11) ◽  
pp. 3439-3446 ◽  
Author(s):  
Olga Revelles ◽  
Manuel Espinosa-Urgel ◽  
Soeren Molin ◽  
Juan L. Ramos
Keyword(s):  
Amino Acid ◽  
Pseudomonas Putida ◽  
Culture Medium ◽  
Wild Type Strain ◽  
Gene Products ◽  
Wild Type ◽  
Basal Expression ◽  
Efficient Uptake ◽  
High Level ◽  
Lysine Catabolism

ABSTRACT Pseudomonas putida KT2440 is a soil microorganism that attaches to seeds and efficiently colonizes the plant's rhizosphere. Lysine is one of the major compounds in root exudates, and P. putida KT2440 uses this amino acid as a source of carbon, nitrogen, and energy. Lysine is channeled to δ-aminovaleric acid and then further degraded to glutaric acid via the action of the davDT gene products. We show that the davDT genes form an operon transcribed from a single σ70-dependent promoter. The relatively high level of basal expression from the davD promoter increased about fourfold in response to the addition of exogenous lysine to the culture medium. However, the true inducer of this operon seems to be δ-aminovaleric acid because in a mutant unable to metabolize lysine to δ-aminovaleric acid, this compound, but not lysine, acted as an effector. Effective induction of the P. putida P davD promoter by exogenously added lysine requires efficient uptake of this amino acid, which seems to proceed by at least two uptake systems for basic amino acids that belong to the superfamily of ABC transporters. Mutants in these ABC uptake systems retained basal expression from the davD promoter but exhibited lower induction levels in response to exogenous lysine than the wild-type strain.

Evaluation of Surface-modified Superparamagnetic Iron Oxide Nanoparticles to Optimize Bacterial Immobilization for Bio-separation with the Least Inhibitory Effect on Microorganism Activity

2020 ◽  
Vol 10 (2) ◽  
pp. 166-174
Author(s):  
Mehdi Khoshneviszadeh ◽  
Sarah Zargarnezhad ◽  
Younes Ghasemi ◽  
Ahmad Gholami
Keyword(s):  
Iron Oxide ◽  
Amino Acid ◽  
Magnetic Nanoparticles ◽  
Iron Oxide Nanoparticles ◽  
Surface Coating ◽  
Superparamagnetic Iron Oxide ◽  
Superparamagnetic Iron Oxide Nanoparticles ◽  
Oxide Nanoparticles ◽  
Surface Charges ◽  
Surface Modified

Background: Magnetic cell immobilization has been introduced as a novel, facile and highly efficient approach for cell separation. A stable attachment between bacterial cell wall with superparamagnetic iron oxide nanoparticles (SPIONs) would enable the microorganisms to be affected by an outer magnetic field. At high concentrations, SPIONs produce reactive oxygen species in cytoplasm, which induce apoptosis or necrosis in microorganisms. Choosing a proper surface coating could cover the defects and increase the efficiency. Methods: In this study, asparagine, APTES, lipo-amino acid and PEG surface modified SPIONs was synthesized by co-precipitation method and characterized by FTIR, TEM, VSM, XRD, DLS techniques. Then, their protective effects against four Gram-positive and Gram-negative bacterial strains including Enterococcus faecalis, Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa were examined through microdilution broth and compared to naked SPION. Results: The evaluation of characterization results showed that functionalization of magnetic nanoparticles could change their MS value, size and surface charges. Also, the microbial analysis revealed that lipo-amino acid coated magnetic nanoparticles has the least adverse effect on microbial strain among tested SPIONs. Conclusion: This study showed lipo-amino acid could be considered as the most protective and even promotive surface coating, which is explained by its optimizing effect on cell penetration and negligible reductive effects on magnetic properties of SPIONs. lipo-amino acid coated magnetic nanoparticles could be used in microbial biotechnology and industrial microbiology.

scholarly journals Prototypical Recombinant Multi-Protease-Inhibitor-Resistant Infectious Molecular Clones of Human Immunodeficiency Virus Type 1

2013 ◽  
Vol 57 (9) ◽  
pp. 4290-4299 ◽  
Author(s):  
Vici Varghese ◽  
Yumi Mitsuya ◽  
W. Jeffrey Fessel ◽  
Tommy F. Liu ◽  
George L. Melikian ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protease Inhibitor ◽  
Cross Resistance ◽  
Amino Acid Substitutions ◽  
Phenotypic Properties ◽  
The Public ◽  
Immunodeficiency Virus ◽  
The Many ◽  
High Level ◽  
Infectious Molecular Clones

ABSTRACTThe many genetic manifestations of HIV-1 protease inhibitor (PI) resistance present challenges to research into the mechanisms of PI resistance and the assessment of new PIs. To address these challenges, we created a panel of recombinant multi-PI-resistant infectious molecular clones designed to represent the spectrum of clinically relevant multi-PI-resistant viruses. To assess the representativeness of this panel, we examined the sequences of the panel's viruses in the context of a correlation network of PI resistance amino acid substitutions in sequences from more than 10,000 patients. The panel of recombinant infectious molecular clones comprised 29 of 41 study-defined PI resistance amino acid substitutions and 23 of the 27 tightest amino acid substitution clusters. Based on their phenotypic properties, the clones were classified into four groups with increasing cross-resistance to the PIs most commonly used for salvage therapy: lopinavir (LPV), tipranavir (TPV), and darunavir (DRV). The panel of recombinant infectious molecular clones has been made available without restriction through the NIH AIDS Research and Reference Reagent Program. The public availability of the panel makes it possible to compare the inhibitory activities of different PIs with one another. The diversity of the panel and the high-level PI resistance of its clones suggest that investigational PIs active against the clones in this panel will retain antiviral activity against most if not all clinically relevant PI-resistant viruses.

CAN SEMIEMPIRICAL QUANTUM MODELS CALCULATE THE BINDING ENERGY OF HYDROGEN BONDING FOR BIOLOGICAL SYSTEMS?

2009 ◽  
Vol 08 (04) ◽  
pp. 691-711 ◽  
Author(s):  
FENG FENG ◽  
HUAN WANG ◽  
WEI-HAI FANG ◽  
JIAN-GUO YU
Keyword(s):  
Hydrogen Bonding ◽  
Amino Acid ◽  
Amino Acid Residue ◽  
Density Functional ◽  
Biological Systems ◽  
Binding Energies ◽  
Semiempirical Model ◽  
Hydrogen Bonded Systems ◽  
High Level ◽  
Hydrogen Bonded

A modified semiempirical model named RM1BH, which is based on RM1 parameterizations, is proposed to simulate varied biological hydrogen-bonded systems. The RM1BH is formulated by adding Gaussian functions to the core–core repulsion items in original RM1 formula to reproduce the binding energies of hydrogen bonding of experimental and high-level computational results. In the parameterizations of our new model, 35 base-pair dimers, 18 amino acid residue dimers, 14 dimers between a base and an amino acid residue, and 20 other multimers were included. The results performed with RM1BH were compared with experimental values and the benchmark density-functional (B3LYP/6-31G**/BSSE) and Möller–Plesset perturbation (MP2/6-31G**/BSSE) calculations on various biological hydrogen-bonded systems. It was demonstrated that RM1BH model outperforms the PM3 and RM1 models in the calculations of the binding energies of biological hydrogen-bonded systems by very close agreement with the values of both high-level calculations and experiments. These results provide insight into the ideas, methods, and views of semiempirical modifications to investigate the weak interactions of biological systems.

scholarly journals ampG Gene of Pseudomonas aeruginosa and Its Role in β-Lactamase Expression

2010 ◽  
Vol 54 (11) ◽  
pp. 4772-4779 ◽  
Author(s):  
Ying Zhang ◽  
Qiyu Bao ◽  
Luc A. Gagnon ◽  
Ann Huletsky ◽  
Antonio Oliver ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Transmembrane Protein ◽  
Amino Acid Identity ◽  
Clinical Isolates ◽  
Signal Molecules ◽  
Carbonyl Cyanide ◽  
Increased Sensitivity ◽  
Potential Strategy ◽  
High Level

ABSTRACT In enterobacteria, the ampG gene encodes a transmembrane protein (permease) that transports 1,6-GlcNAc-anhydro-MurNAc and the 1,6-GlcNAc-anhydro-MurNAc peptide from the periplasm to the cytoplasm, which serve as signal molecules for the induction of ampC β-lactamase. The role of AmpG as a transporter is also essential for cell wall recycling. Pseudomonas aeruginosa carries two AmpG homologues, AmpG (PA4393) and AmpGh1 (PA4218), with 45 and 41% amino acid sequence identity, respectively, to Escherichia coli AmpG, while the two homologues share only 19% amino acid identity. In P. aeruginosa strains PAO1 and PAK, inactivation of ampG drastically repressed the intrinsic β-lactam resistance while ampGh1 deletion had little effect on the resistance. Further, deletion of ampG in an ampD-null mutant abolished the high-level β-lactam resistance that is associated with the loss of AmpD activity. The cloned ampG gene is able to complement both the P. aeruginosa and the E. coli ampG mutants, while that of ampGh1 failed to do so, suggesting that PA4393 encodes the only functional AmpG protein in P. aeruginosa. We also demonstrate that the function of AmpG in laboratory strains of P. aeruginosa can effectively be inhibited by carbonyl cyanide m-chlorophenylhydrazone (CCCP), causing an increased sensitivity to β-lactams among laboratory as well as clinical isolates of P. aeruginosa. Our results suggest that inhibition of the AmpG activity is a potential strategy for enhancing the efficacy of β-lactams against P. aeruginosa, which carries inducible chromosomal ampC, especially in AmpC-hyperproducing clinical isolates.

Characterization and High-level Production of D-Amino Acid Oxidase in Candida boidinii

2001 ◽  
Vol 65 (3) ◽  
pp. 627-633 ◽  
Author(s):  
Hiroya YURIMOTO ◽  
Tetsuya HASEGAWA ◽  
Yasuyoshi SAKAI ◽  
Nobuo KATO
Keyword(s):  
Amino Acid ◽  
Candida Boidinii ◽  
Acid Oxidase ◽  
Amino Acid Oxidase ◽  
High Level ◽  
Level Production

scholarly journals The Connection between Czc and Cad Systems Involved in Cadmium Resistance in Pseudomonas putida

2021 ◽  
Vol 22 (18) ◽  
pp. 9697
Author(s):  
Huizhong Liu ◽  
Yu Zhang ◽  
Yingsi Wang ◽  
Xiaobao Xie ◽  
Qingshan Shi
Keyword(s):  
Pseudomonas Putida ◽  
Efflux Pump ◽  
Response Regulator ◽  
Cadmium Stress ◽  
Cadmium Resistance ◽  
Cad Systems ◽  
Cad System ◽  
Considerable Resistance ◽  
High Level ◽  
The Relationship

Heavy metal pollution is widespread and persistent, and causes serious harm to the environment. Pseudomonas putida, a representative environmental microorganism, has strong resistance to heavy metals due to its multiple efflux systems. Although the functions of many efflux systems have been well-studied, the relationship between them remains unclear. Here, the relationship between the Czc and Cad systems that are predominantly responsible for cadmium efflux in P. putida KT2440 is identified. The results demonstrated that CzcR3, the response regulator of two-component system CzcRS3 in the Czc system, activates the expression of efflux pump genes czcCBA1 and czcCBA2 by directly binding to their promoters, thereby helping the strain resist cadmium stress. CzcR3 can also bind to its own promoter, but it has only a weak regulatory effect. The high-level expression of czcRS3 needs to be induced by Cd2+, and this relies on the regulation of CadR, a key regulator in the Cad system, which showed affinity to czcRS3 promoter. Our study indicates that the Cad system is involved in the regulation of the Czc system, and this relationship is important for maintaining the considerable resistance to cadmium in P. putida.

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