scholarly journals Rapid evaluation of the substrate specificity of 3-nitrobenzoic acid dioxygenase MnbAB via colorimetric detection using Saltzman reagent

2021 ◽  
Author(s):  
Hiroya Tomita ◽  
Yohei Katsuyama ◽  
Yasuo Ohnishi
Keyword(s):  
Substrate Specificity ◽  
Colorimetric Detection ◽  
Environmental Pollutants ◽  
Nitroaromatic Compounds ◽  
Ortho Position ◽  
Sensitive Assay ◽  
Substrate Specificities ◽  
Nitrobenzoic Acid ◽  
Potential Applications ◽  
Methylene Group

Abstract Nitroaromatic compounds are essential materials for chemical industry, but they are also potentially toxic environmental pollutants. Therefore, their sensitive detection and degradation are important concerns. The microbial degradation pathways of nitroaromatic compounds have been studied in detail, but their usefulness needs to be evaluated to understand their potential applications in bioremediation. Here, we developed a rapid and relatively sensitive assay system to evaluate the activities and substrate specificities of nitroaromatic dioxygenases involved in the oxidative biodegradation of nitroaromatic compounds. In this system, nitrous acid, which was released from the nitroaromatic compounds by the dioxygenases, was detected and quantified using the Saltzman reagent. Escherichia coli producing the 3-nitrobenzoic acid dioxygenase complex MnbAB from Comamonas sp. JS46 clearly showed the apparent substrate specificity of MnbAB as follows. MnbAB accepted not only 3-nitrobenzoic acid but also several other p- and m-nitrobenzoic acid derivatives as substrates, although it much preferred 3-nitrobenzoic acid to others. Furthermore, the presence of a hydroxy or an amino group at the ortho position of the nitro group decreased the activity of MnbAB. In addition, MnbAB accepted 2-(4-nitrophenyl)acetic acid as a substrate, which has one additional methylene group between the aromatic ring and the carboxy group of 3-nitrobenzoic acid. This is the first report about the detailed substrate specificity of MnbAB. Our system can be used for other nitroaromatic dioxygenases and contribute to their characterization.

scholarly journals Isoelectric focusing of glutathione S-transferases from rat liver and kidney

1978 ◽  
Vol 175 (3) ◽  
pp. 937-943 ◽  
Author(s):  
Barbara F. Hales ◽  
Valerie Jaeger ◽  
Allen H. Neims
Keyword(s):  
Substrate Specificity ◽  
Isoelectric Focusing ◽  
Transferase Activity ◽  
Sprague Dawley ◽  
Substrate Specificities ◽  
Liver Cytosol ◽  
Sprague Dawley Rats ◽  
Isoelectric Points ◽  
Liver And Kidney ◽  
Glutathione S Transferases

The glutathione S-transferases that were purified to homogeneity from liver cytosol have overlapping but distinct substrate specificities and different isoelectric points. This report explores the possibility of using preparative electrofocusing to compare the composition of the transferases in liver and kidney cytosol. Hepatic cytosol from adult male Sprague–Dawley rats was resolved by isoelectric focusing on Sephadex columns into five peaks of transferase activity, each with characteristic substrate specificity. The first four peaks of transferase activity (in order of decreasing basicity) are identified as transferases AA, B, A and C respectively, on the basis of substrate specificity, but the fifth peak (pI6.6) does not correspond to a previously described transferase. Isoelectric focusing of renal cytosol resolves only three major peaks of transferase activity, each with narrow substrate specificity. In the kidney, peak 1 (pI9.0) has most of the activity toward 1-chloro-2,4-dinitrobenzene, peak 2 (pI8.5) toward p-nitrobenzyl chloride, and peak 3 (pI7.0) toward trans-4-phenylbut-3-en-2-one. Renal transferase peak 1 (pI9.0) appears to correspond to transferase B on the basis of pI, substrate specificity and antigenicity. Kidney transferase peaks 2 (pI8.5) and 3 (pI7.0) do not correspond to previously described glutathione S-transferases, although kidney transferase peak 3 is similar to the transferase peak 5 from focused hepatic cytosol. Transferases A and C were not found in kidney cytosol, and transferase AA was detected in only one out of six replicates. Thus it is important to recognize the contribution of individual transferases to total transferase activity in that each transferase may be regulated independently.

Recent Developments in Organically Doped Sol-Gel Sensors: A Microns-Scale Probe; Successful Trapping of Purified Polyclonal Antibodies; Solutions to the Dopant-Leaching Problem

1994 ◽  
Vol 346 ◽  
Author(s):  
N. Aharonson ◽  
M. Altstein ◽  
G. Avidan ◽  
D. Avnir ◽  
A. Bronshtein ◽  
...  
Keyword(s):  
Excited State ◽  
Polyclonal Antibodies ◽  
Near Field ◽  
Sol Gel ◽  
Environmental Pollutants ◽  
Covalent Bond ◽  
Ph Indicator ◽  
In Doping ◽  
Recent Developments ◽  
Potential Applications

ABSTRACTWe describe recent advances made in our laboratories in the general field of organically and bio-organically doped sol-gel sensors. The developments described are: (a) The first miniaturization of a sol-gel sensor down to the microns scale, with potential applications to near-field optical microscopy, using a fluorescent pH-indicator. (b) The first successful sol-gel encapsulation of purified polyclonal antibodies, and in particular an anti-nitroaromatics immunoglobulin, with which selective sensing of nitroaromatics, an important class of environmental pollutants, was demonstrated, (c) The leaching problem, occasionally encountered in doping procedures, is solved by two methodologies: First, TMOS polymerization at high acidity and low water content was found to result in non-leachable yet reactive matrices, as demonstrated with O2 sensing by excited state pyrene and with H+ sensing by excited state pyranine; and second, doping with molecules capable of forming a covalent bond within the encapsulating cage results in the permanent anchoring of the dopant. Thus, Methyl-Red, a pH indicator, was derivatized with a silylating residue, and a polymerizing TMOS was doped with it forming a pH-shifted indicator. With both methodologies, leachability was practically zero.

scholarly journals Origin and evolution of transporter substrate specificity within the NPF family

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Morten Egevang Jørgensen ◽  
Deyang Xu ◽  
Christoph Crocoll ◽  
Heidi Asschenfeldt Ernst ◽  
David Ramírez ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Biochemical Characterization ◽  
Biosynthetic Pathways ◽  
Cyanogenic Glucosides ◽  
Evolutionary Path ◽  
Substrate Specificities ◽  
Origin And Evolution ◽  
Glucosinolate Biosynthesis ◽  
Phylogenetic Lineage

Despite vast diversity in metabolites and the matching substrate specificity of their transporters, little is known about how evolution of transporter substrate specificities is linked to emergence of substrates via evolution of biosynthetic pathways. Transporter specificity towards the recently evolved glucosinolates characteristic of Brassicales is shown to evolve prior to emergence of glucosinolate biosynthesis. Furthermore, we show that glucosinolate transporters belonging to the ubiquitous NRT1/PTR FAMILY (NPF) likely evolved from transporters of the ancestral cyanogenic glucosides found across more than 2500 species outside of the Brassicales. Biochemical characterization of orthologs along the phylogenetic lineage from cassava to A. thaliana, suggests that alterations in the electrogenicity of the transporters accompanied changes in substrate specificity. Linking the evolutionary path of transporter substrate specificities to that of the biosynthetic pathways, exemplify how transporter substrate specificities originate and evolve as new biosynthesis pathways emerge.

scholarly journals Structural and evolutionary relationships of “AT-less” type I polyketide synthase ketosynthases

2015 ◽  
Vol 112 (41) ◽  
pp. 12693-12698 ◽  
Author(s):  
Jeremy R. Lohman ◽  
Ming Ma ◽  
Jerzy Osipiuk ◽  
Boguslaw Nocek ◽  
Youngchang Kim ◽  
...  
Keyword(s):  
Amino Acid ◽  
Substrate Specificity ◽  
Polyketide Synthase ◽  
Acyl Carrier Protein ◽  
Structural Diversity ◽  
Type I ◽  
Substrate Specificities ◽  
In Trans ◽  
Canonical Type ◽  
Insight Into

Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, acyl carrier protein (ACP), and ketosynthase (KS) domains. Structures of canonical type I PKS KS-AT didomains reveal structured linkers that connect the two domains. AT-less type I PKS KSs have remnants of these linkers, which have been hypothesized to be AT docking domains. Natural products produced by AT-less type I PKSs are very complex because of an increased representation of unique modifying domains. AT-less type I PKS KSs possess substrate specificity and fall into phylogenetic clades that correlate with their substrates, whereas canonical type I PKS KSs are monophyletic. We have solved crystal structures of seven AT-less type I PKS KS domains that represent various sequence clusters, revealing insight into the large structural and subtle amino acid residue differences that lead to unique active site topologies and substrate specificities. One set of structures represents a larger group of KS domains from both canonical and AT-less type I PKSs that accept amino acid-containing substrates. One structure has a partial AT-domain, revealing the structural consequences of a type I PKS KS evolving into an AT-less type I PKS KS. These structures highlight the structural diversity within the AT-less type I PKS KS family, and most important, provide a unique opportunity to study the molecular evolution of substrate specificity within the type I PKSs.

scholarly journals An improved spectrophotometric assay for leucine aminopeptidase

1987 ◽  
Vol 242 (1) ◽  
pp. 281-283 ◽  
Author(s):  
R E Beattie ◽  
D J S Guthrie ◽  
D T Elmore ◽  
C H Williams ◽  
B Walker
Keyword(s):  
Leucine Aminopeptidase ◽  
Spectrophotometric Assay ◽  
Sensitive Assay ◽  
Spectrophotometric Measurement ◽  
Thiol Ester ◽  
Nitrobenzoic Acid ◽  
Specificity Constant ◽  
Hydrolysis Of

A sensitive assay to determine the activity of leucine aminopeptidase (EC 3.4.11.1), using L-leucine thiobenzyl ester as substrate, was developed. Hydrolysis of the ester by leucine aminopeptidase can be monitored in the presence of 5,5-dithiobis-(2-nitrobenzoic acid) by continuous spectrophotometric measurement at 412 nm. Comparison with some amide substrates showed that the thiol ester provides a much more sensitive assay, its specificity constant (Vmax./Km) being some 3000-fold higher than that of leucine p-nitroanilide.

scholarly journals Substrate Specificities of Hybrid Naphthalene and 2,4-Dinitrotoluene Dioxygenase Enzyme Systems

1998 ◽  
Vol 180 (9) ◽  
pp. 2337-2344 ◽  
Author(s):  
Rebecca E. Parales ◽  
Matthew D. Emig ◽  
Nancy A. Lynch ◽  
David T. Gibson
Keyword(s):  
Escherichia Coli ◽  
Substrate Specificity ◽  
Product Formation ◽  
Small Subunit ◽  
Enantiomeric Purity ◽  
Oxidation Products ◽  
Substrate Specificities ◽  
Enzyme Systems ◽  
Α And Β Subunits ◽  
Dioxygenase Enzymes

ABSTRACT Bacterial three-component dioxygenase systems consist of reductase and ferredoxin components which transfer electrons from NAD(P)H to a terminal oxygenase. In most cases, the oxygenase consists of two different subunits (α and β). To assess the contributions of the α and β subunits of the oxygenase to substrate specificity, hybrid dioxygenase enzymes were formed by coexpressing genes from two compatible plasmids in Escherichia coli. The activities of hybrid naphthalene and 2,4-dinitrotoluene dioxygenases containing four different β subunits were tested with four substrates (indole, naphthalene, 2,4-dinitrotoluene, and 2-nitrotoluene). In the active hybrids, replacement of small subunits affected the rate of product formation but had no effect on the substrate range, regiospecificity, or enantiomeric purity of oxidation products with the substrates tested. These studies indicate that the small subunit of the oxygenase is essential for activity but does not play a major role in determining the specificity of these enzymes.

scholarly journals Reactions Involved in the Lower Pathway for Degradation of 4-Nitrotoluene by Mycobacterium Strain HL 4-NT-1

2000 ◽  
Vol 66 (7) ◽  
pp. 3010-3015 ◽  
Author(s):  
Zhongqi He ◽  
Jim C. Spain
Keyword(s):  
Aromatic Compounds ◽  
Nitroaromatic Compounds ◽  
Aerobic Biodegradation ◽  
Ring Cleavage ◽  
Pseudomonas Pseudoalcaligenes ◽  
Substrate Specificities ◽  
Number Of Microorganisms

ABSTRACT In spite of the variety of initial reactions, the aerobic biodegradation of aromatic compounds generally yields dihydroxy intermediates for ring cleavage. Recent investigation of the degradation of nitroaromatic compounds revealed that some nitroaromatic compounds are initially converted to 2-aminophenol rather than dihydroxy intermediates by a number of microorganisms. The complete pathway for the metabolism of 2-aminophenol during the degradation of nitrobenzene by Pseudomonas pseudoalcaligenes JS45 has been elucidated previously. The pathway is parallel to the catechol extradiol ring cleavage pathway, except that 2-aminophenol is the ring cleavage substrate. Here we report the elucidation of the pathway of 2-amino-4-methylphenol (6-amino-m-cresol) metabolism during the degradation of 4-nitrotoluene by Mycobacterium strain HL 4-NT-1 and the comparison of the substrate specificities of the relevant enzymes in strains JS45 and HL 4-NT-1. The results indicate that the 2-aminophenol ring cleavage pathway in strain JS45 is not unique but is representative of the pathways of metabolism of othero-aminophenolic compounds.

scholarly journals Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains

mBio ◽  
2015 ◽  
Vol 6 (5) ◽  
Author(s):  
Qingping Xu ◽  
Dominique Mengin-Lecreulx ◽  
Xueqian W. Liu ◽  
Delphine Patin ◽  
Carol L. Farr ◽  
...  
Keyword(s):  
Cell Wall ◽  
Amino Acid ◽  
Substrate Specificity ◽  
Catalytic Domain ◽  
Substrate Binding ◽  
Diaminopimelic Acid ◽  
Single Mutation ◽  
Molecular Architecture ◽  
Substrate Specificities ◽  
Cell Wall Hydrolases

ABSTRACTBacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. These enzymes all have γ-d-Glu-A2pm (A2pm is diaminopimelic acid) cysteine amidase (ordl-endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminall-Ala. Their crystal structures revealed a highly conserved structure consisting of two SH3b domains and a C-terminal NlpC/P60 catalytic domain, despite very low sequence identity. Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. Remarkably, the cell wall lysin can be converted into a recycling enzyme with a single mutation.IMPORTANCEPeptidoglycan is a meshlike polymer that envelops the bacterial plasma membrane and bestows structural integrity. Cell wall lysins and recycling enzymes are part of a set of lytic enzymes that target covalent bonds connecting the amino acid and amino sugar building blocks of the PG network. These hydrolases are involved in processes such as cell growth and division, autolysis, invasion, and PG turnover and recycling. To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and structural analysis of three modular NlpC/P60 hydrolases, one lysin, and two recycling enzymes, show that they may have evolved from a common molecular architecture, where the substrate preference is modulated by local changes. These results also suggest that new pathways for recycling PG turnover products, such as tracheal cytotoxin, may have evolved in bacteria in the human gut microbiome that involve NlpC/P60 cell wall hydrolases.

scholarly journals Bio-inspired Maillard-Like reactions enable a simple and sensitive assay for colorimetric detection of methylglyoxal

2015 ◽  
Vol 51 (55) ◽  
pp. 11026-11029 ◽  
Author(s):  
Shih-Ting Wang ◽  
Yiyang Lin ◽  
Christopher D. Spicer ◽  
Molly M. Stevens
Keyword(s):  
Gold Nanoparticles ◽  
Colorimetric Detection ◽  
Sensitive Assay

A simple and selective assay for methylglyoxal (MGO) detection was developed by combining a bio-inspired reaction with anti-aggregation of gold nanoparticles.

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