scholarly journals Exponential Amplification by Redox Cross-Catalysis and Unmasking of Doubly Protected Molecular Probes

2021 ◽  
Author(s):  
Justine Pallu ◽  
Charlie Rabin ◽  
Pan Hui ◽  
Thamires Moreira ◽  
Corentin Calvet ◽  
...  
Keyword(s):  
Bioanalytical Methods ◽  
Reaction Network ◽  
Redox Cycling ◽  
Molecular Probes ◽  
Enzyme Substrate ◽  
Redox Active ◽  
Powerful Means ◽  
Depth Study ◽  
Amplification System ◽  
Critical Reason

The strength of autocatalytic reactions lies in their ability to provide a powerful means of molecular amplification, which can be very useful for improving the analytical performances of a multitude of analytical and bioanalytical methods. However, one of the major difficulties in designing an efficient autocatalytic amplification system is the requirement for reactants that are both highly reactive and chemically stable in order to avoid limitations imposed by undesirable background amplifications. In the present work, we devised a reaction network based on a redox cross-catalysis principle, in which two catalytic loops activate each other. The first loop, catalyzed by H2O2, involves the oxi-dative deprotection of a naphthylboronate ester probe into a redox-active naphthohydroquinone, which in turn catalyzes the production of H2O2 by redox cycling in the presence of a reducing enzyme/substrate couple. We present here a set of new molecular probes with improved reactivity and stability, resulting in particularly steep sigmoidal kinetic traces and enhanced discrimination between specific and nonspecific responses. This translates into the sensitive de-tection of H2O2 down to a few nM in less than 10 minutes or a redox cycling compound such as the 2-amino-3-chloro-1,4-naphthoquinone H2O2 down to 50 pM in less than 30 minutes. The critical reason leading to these remarkably good performances is the extended stability stemming from the double masking of the naphthohydroquinone core by two boronate groups, a counterintuitive strategy if we consider the need for two equivalents of H2O2 for full deprotection. An in-depth study of the mechanism and dynamics of this complex reaction network is conducted in order to better understand, predict and optimize its functioning. From this investigation, the time response as well as detection limit are found highly dependent on pH, nature of buffer, and concentration of the reducing enzyme.

Redox-active antibiotics enhance phosphorus bioavailability

Science ◽  
2021 ◽  
Vol 371 (6533) ◽  
pp. 1033-1037 ◽  
Author(s):  
Darcy L. McRose ◽  
Dianne K. Newman
Keyword(s):  
Iron Oxides ◽  
Microbial Growth ◽  
Antibiotic Production ◽  
Phosphorus Limitation ◽  
Redox Cycling ◽  
Reductive Dissolution ◽  
Phosphorus Acquisition ◽  
Redox Active ◽  
Life On Earth

Microbial production of antibiotics is common, but our understanding of their roles in the environment is limited. In this study, we explore long-standing observations that microbes increase the production of redox-active antibiotics under phosphorus limitation. The availability of phosphorus, a nutrient required by all life on Earth and essential for agriculture, can be controlled by adsorption to and release from iron minerals by means of redox cycling. Using phenazine antibiotic production by pseudomonads as a case study, we show that phenazines are regulated by phosphorus, solubilize phosphorus through reductive dissolution of iron oxides in the lab and field, and increase phosphorus-limited microbial growth. Phenazines are just one of many examples of phosphorus-regulated antibiotics. Our work suggests a widespread but previously unappreciated role for redox-active antibiotics in phosphorus acquisition and cycling.

scholarly journals Naphthalene SOA: redox activity and naphthoquinone gas–particle partitioning

2013 ◽  
Vol 13 (19) ◽  
pp. 9731-9744 ◽  
Author(s):  
R. D. McWhinney ◽  
S. Zhou ◽  
J. P. D. Abbatt
Keyword(s):  
Average Rate ◽  
Organic Aerosol ◽  
Redox Cycling ◽  
Oxidation Products ◽  
Redox Activity ◽  
Particle Phase ◽  
Ambient Particles ◽  
Redox Active ◽  
Potential Impact ◽  
Measured Particle

Abstract. Chamber secondary organic aerosol (SOA) from low-NOx photooxidation of naphthalene by hydroxyl radical was examined with respect to its redox cycling behaviour using the dithiothreitol (DTT) assay. Naphthalene SOA was highly redox-active, consuming DTT at an average rate of 118 ± 14 pmol per minute per μg of SOA material. Measured particle-phase masses of the major previously identified redox active products, 1,2- and 1,4-naphthoquinone, accounted for only 21 ± 3% of the observed redox cycling activity. The redox-active 5-hydroxy-1,4-naphthoquinone was identified as a new minor product of naphthalene oxidation, and including this species in redox activity predictions increased the predicted DTT reactivity to 30 ± 5% of observations. These results suggest that there are substantial unidentified redox-active SOA constituents beyond the small quinones that may be important toxic components of these particles. A gas-to-SOA particle partitioning coefficient was calculated to be (7.0 ± 2.5) × 10−4 m3 μg−1 for 1,4-naphthoquinone at 25 °C. This value suggests that under typical warm conditions, 1,4-naphthoquinone is unlikely to contribute strongly to redox behaviour of ambient particles, although further work is needed to determine the potential impact under conditions such as low temperatures where partitioning to the particle is more favourable. Also, higher order oxidation products that likely account for a substantial fraction of the redox cycling capability of the naphthalene SOA are likely to partition much more strongly to the particle phase.

scholarly journals Nanocavity crossbar arrays for parallel electrochemical sensing on a chip

2014 ◽  
Vol 5 ◽  
pp. 1137-1143 ◽  
Author(s):  
Enno Kätelhön ◽  
Dirk Mayer ◽  
Marko Banzet ◽  
Andreas Offenhäusser ◽  
Bernhard Wolfrum
Keyword(s):  
High Spatial Resolution ◽  
Redox Cycling ◽  
Electrochemical Sensing ◽  
Wafer Surface ◽  
Novel Device ◽  
Redox Active ◽  
Parallel Data ◽  
Acquisition Mode ◽  
Parallel Band ◽  
Very High

We introduce a novel device for the mapping of redox-active compounds at high spatial resolution based on a crossbar electrode architecture. The sensor array is formed by two sets of 16 parallel band electrodes that are arranged perpendicular to each other on the wafer surface. At each intersection, the crossing bars are separated by a ca. 65 nm high nanocavity, which is stabilized by the surrounding passivation layer. During operation, perpendicular bar electrodes are biased to potentials above and below the redox potential of species under investigation, thus, enabling repeated subsequent reactions at the two electrodes. By this means, a redox cycling current is formed across the gap that can be measured externally. As the nanocavity devices feature a very high current amplification in redox cycling mode, individual sensing spots can be addressed in parallel, enabling high-throughput electrochemical imaging. This paper introduces the design of the device, discusses the fabrication process and demonstrates its capabilities in sequential and parallel data acquisition mode by using a hexacyanoferrate probe.

scholarly journals HOCl Responsive Lanthanide Complexes Using Hydroquinone Caging Units

Molecules ◽  
2020 ◽  
Vol 25 (8) ◽  
pp. 1959
Author(s):  
Elena Del Giorgio ◽  
Thomas Just Sørensen
Keyword(s):  
Lanthanide Complexes ◽  
Design Principle ◽  
Hypochlorous Acid ◽  
Molecular Probes ◽  
Lanthanide Ions ◽  
Redox Biology ◽  
Redox Active ◽  
Trivalent Lanthanide ◽  
Sustained Effort ◽  
Triton X

Redox biology is still looking for tools to monitor redox potential in cellular biology and, despite a large and sustained effort, reliable molecular probes have yet to emerge. In contrast, molecular probes for reactive oxygen and nitrogen have been widely explored. In this manuscript, three kinetically inert lanthanide complexes that selectively react with hypochlorous acid are prepared and characterized. The design is based on 1,4,7,10-tetraazacyclododecane-1,4,7-triacetic acid (DO3A) and 1,4,7,10-tetraazacyclododecane-1,7-diacetic acid (DO2A) ligands appended with one or two redox active hydroquinone derived arms, thereby forming octadentate ligands ideally suited to complex trivalent lanthanide ions. The three complexes are found to react selectively with hypochlorous acid to form highly symmetric lanthanide(III) 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacedic acid (DOTA) complexes. The conversion of the probe to [Ln.DOTA]− is followed by luminescence, absorption, and NMR spectroscopy in a model system comprised of a Triton-X modified HEPES buffer. It was concluded that the design principle works, and that simple caging units like hydroquinones can work well in conjugation with lanthanide(III) complexes.

Bridged oligonucleotides as molecular probes for investigation of enzyme-substrate interaction and allele-specific analysis of DNA

2009 ◽  
Vol 74 (9) ◽  
pp. 1009-1020 ◽  
Author(s):  
I. A. Pyshnaya ◽  
O. A. Vinogradova ◽  
M. R. Kabilov ◽  
E. M. Ivanova ◽  
D. V. Pyshnyi
Keyword(s):  
Molecular Probes ◽  
Substrate Interaction ◽  
Enzyme Substrate ◽  
Specific Analysis ◽  
Allele Specific

scholarly journals Urm1, not quite a ubiquitin-like modifier?

2021 ◽  
Vol 8 (11) ◽  
pp. 256-261
Author(s):  
Lars Kaduhr ◽  
Cindy Brachmann ◽  
Keerthiraju Ethiraju Ravichandran ◽  
James D. West ◽  
Sebastian Glatt ◽  
...  
Keyword(s):  
Organic Peroxide ◽  
Active Centers ◽  
Redox Biology ◽  
Dual Functional ◽  
Redox Active ◽  
Acceptor Activity ◽  
Depth Study ◽  
Potential Link ◽  
Molecular Nature

Ubiquitin related modifier 1 (Urm1) is a unique eukaryotic member of the ubiquitin-fold (UbF) protein family and conserved from yeast to humans. Urm1 is dual-functional, acting both as a sulfur carrier for thiolation of tRNA anticodons and as a protein modifier in a lysine-directed Ub-like conjugation also known as urmylation. Although Urm1 conjugation coincides with oxidative stress and targets proteins like 2-Cys peroxiredoxins from yeast (Ahp1) and fly (Prx5), it was unclear how urmylation proceeds molecularly and whether it is affected by the activity of these antioxidant enzymes. An in-depth study of Ahp1 urmylation in yeast from our laboratory (Brachmann et al., 2020) uncovered that promiscuous lysine target sites and specific redox requirements determine the Urm1 acceptor activity of the peroxiredoxin. The results clearly show that the dimer interface and the 2-Cys based redox-active centers of Ahp1 are affecting the Urm1 conjugation reaction. Together with in vivo assays demonstrating that high organic peroxide concentrations can prevent Ahp1 from being urmylated, Brachmann et al. provide insights into a potential link between Urm1 utilization and oxidant defense of cells. Here, we highlight these major findings and discuss wider implications with regards to an emerging link between Urm1 conjugation and redox biology. Moreover, from these studies we propose to redefine our perspective on Urm1 and the molecular nature of urmylation, a post-translational conjugation that may not be that ubiquitin-like after all.

scholarly journals Bidirectional redox cycling of phenazine-1-carboxylic acid by Citrobacter portucalensis MBL drives increased nitrate reduction

2020 ◽  
Author(s):  
Lev M. Tsypin ◽  
Dianne K. Newman
Keyword(s):  
Carboxylic Acid ◽  
Electron Acceptor ◽  
Nitrate Reduction ◽  
Redox Cycling ◽  
Redox Activity ◽  
Dependent Manner ◽  
Terminal Electron Acceptor ◽  
Anoxic Environments ◽  
Redox Active ◽  
Oxygen Starvation

ABSTRACTPhenazines are secreted metabolites that microbes use in diverse ways, from quorum sensing to antimicrobial warfare to energy conservation. Phenazines are able to contribute to these activities due to their redox activity. The physiological consequences of cellular phenazine reduction have been extensively studied, but the counterpart phenazine oxidation has been largely overlooked. Phenazine-1-carboxylic acid (PCA) is common in the environment and readily reduced by its producers. Here, we describe its anaerobic oxidation by Citrobacter portucalensis strain MBL, which was isolated from topsoil in Falmouth, MA, and which does not produce phenazines itself. This activity depends on the availability of a suitable terminal electron acceptor, specifically nitrate or fumarate. When C. portucalensis MBL is provided reduced PCA and either nitrate or fumarate, it continuously oxidizes the PCA. We compared this terminal electron acceptor-dependent PCA-oxidizing activity of C. portucalensis MBL to that of several other γ-proteobacteria with varying capacities to respire nitrate and/or fumarate. We found that PCA oxidation by these strains in a fumarate-or nitrate-dependent manner is decoupled from growth and correlated with their possession of the fumarate or periplasmic nitrate reductases, respectively. We infer that bacterial PCA oxidation is widespread and genetically determined. Notably, reduced PCA enhances the rate of nitrate reduction to nitrite by C. portucalensis MBL beyond the stoichiometric prediction, which we attribute to C. portucalensis MBL’s ability to also reduce oxidized PCA, thereby catalyzing a complete PCA redox cycle. This bidirectionality highlights the versatility of PCA as a biological redox agent.IMPORTANCEPhenazines are increasingly appreciated for their roles in structuring microbial communities. These tricyclic aromatic molecules have been found to regulate gene expression, be toxic, promote antibiotic tolerance, and promote survival under oxygen starvation. In all of these contexts, however, phenazines are studied as electron acceptors. Even if their utility arises primarily from being readily reduced, they would need to be oxidized in order to be recycled. While oxygen and ferric iron can oxidize phenazines abiotically, biotic oxidation of phenazines has not been studied previously. We observed bacteria that readily oxidize phenazine-1-carboxylic acid (PCA) in a nitrate-dependent fashion, concomitantly increasing the rate of nitrate reduction to nitrite. Because nitrate is a prevalent terminal electron acceptor in diverse anoxic environments, including soils, and phenazine-producers are widespread, this observation of linked phenazine and nitrogen redox cycling suggests an underappreciated role for redox-active secreted metabolites in the environment.

scholarly journals Long-term dynamics of multisite phosphorylation

2016 ◽  
Vol 27 (14) ◽  
pp. 2331-2340 ◽  
Author(s):  
Boris Y. Rubinstein ◽  
Henry H. Mattingly ◽  
Alexander M. Berezhkovskii ◽  
Stanislav Y. Shvartsman
Keyword(s):  
Reaction Network ◽  
Dynamic Interactions ◽  
Systematic Analysis ◽  
Enzyme Substrate ◽  
Multisite Phosphorylation ◽  
Extracellular Signal ◽  
Analysis Of Dynamics ◽  
Predictive Understanding ◽  
Multiple Network

Multisite phosphorylation cycles are ubiquitous in cell regulation systems and are studied at multiple levels of complexity, from molecules to organisms, with the ultimate goal of establishing predictive understanding of the effects of genetic and pharmacological perturbations of protein phosphorylation in vivo. Achieving this goal is essentially impossible without mathematical models, which provide a systematic framework for exploring dynamic interactions of multiple network components. Most of the models studied to date do not discriminate between the distinct partially phosphorylated forms and focus on two limiting reaction regimes, distributive and processive, which differ in the number of enzyme–substrate binding events needed for complete phosphorylation or dephosphorylation. Here we use a minimal model of extracellular signal-related kinase regulation to explore the dynamics of a reaction network that includes all essential phosphorylation forms and arbitrary levels of reaction processivity. In addition to bistability, which has been studied extensively in distributive mechanisms, this network can generate periodic oscillations. Both bistability and oscillations can be realized at high levels of reaction processivity. Our work provides a general framework for systematic analysis of dynamics in multisite phosphorylation systems.

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