Microbial sensors for determination of aromatics and their chloroderivatives. Part II: Determination of chlorinated phenols using a Rhodococcus-containing biosensor

An amperometric biosensor for determination of phenol and chlorophenols using Rhodococcus has been developed. This sensor is more sensitive to phenol and chlorophenols, especially to mono- and dichlorinated phenol, than to benzoate and monochlorobenzoates. The incubation of the sensor with phenol and its chlorinated derivatives enhanced the activity of the microbial sensor for these compounds. A linear relationship between the current range and the concentration of phenol, 2-, 3- and 4-chlorophenol was observed up to 20 mol/l. The detection limit for all studied substrates was 4 mol/l. The current difference was reproducible within 5.5% when the test solution contained 40 mol phenol/l. Correspondence to: K. Riedel     

Quantitative imaging using genetically encoded sensors for small molecules in plants

Quantitative imaging in live cells is a powerful method for monitoring the dynamics of biomolecules at an excellent spatio-temporal resolution. Such an approach, initially limited to a small number of substrates for which specific dyes were available, has become possible for a large number of biomolecules due to the development of genetically encoded, protein-based sensors. These sensors, which can be introduced into live cells through a transgenic approach, offer the benefits of quantitative imaging, with an extra advantage of non-invasiveness. In the past decade there has been a drastic expansion in the number of biomolecules for which genetically encoded sensors are available, and the functional properties of existing sensors are being improved at a dramatic pace. A number of technical improvements have now made the application of genetically encoded sensors in plants rather straightforward, and some of the sensors such as calcium indicator proteins have become standard analytical tools in many plant laboratories. The use of a handful of probes has already revealed an amazing specificity of cellular biomolecule dynamics in plants, which leads us to believe that there are many more discoveries to be made using genetically encoded sensors. In this short review, we will summarize the progress made in the past 15?years in the development in genetically encoded sensors, and highlight significant discoveries made in plant biology.     

Microbial sensors for determination of aromatics and their chloroderivatives I. Determination of 3-chlorobenzoate using a Pseudomonas-containing biosensor

Summary An amperometric biosensor for the determination of benzoate and 3-chlorobenzoate using Pseudomonas has been developed. The influence of preincubation of the biosensor with desired substrates on sensitivity and specificity was investigated. The Pseudomonas sensor was more sensitive to benzoate and 3-chlorobenzoate than to 2- and 4-chloro-, 2,4-dichlorobenzoate and 2,4-dichlorophenol. Incubation of the sensor with benzoate and 3-chlorobenzoate enhanced the activity of the microbial sensor. Other chlorobenzoates tested caused a decrease of sensitivity. A linear relationship between the current range and the concentration of benzoate was observed up to 160 mol/l. In the case of 3-chlorobenzoate a linear relationship was observed for concentrations up to 200 mol/l. The signal is reproducible within 5.5% when the test solution contains 40 mol/l of 3-chlorobenzoate. Offprint requests to: K. Riedel     

Microbial production of small medicinal molecules and biologics: From nature to synthetic pathways

Natural products are promising chemicals due to their structural diversity and bioactivities. Over the decades, a vast variety of gene clusters encoding natural products have been identified and overexpressed in microbes. Recently, the development of metabolic engineering, synthetic biology and bioinformatics strategies have facilitated target discovery and design. Microbial cells have been therefore constantly engineered for product accumulation. This review summarizes approaches of domesticating microbial hosts in producing major classes of natural products, with an emphasis on recent advances.     

Microbial sensors for determination of aromatics and their chloro derivatives. Part III: Determination of chlorinated phenols using a biosensor containing Trichosporon beigelii (cutaneum)

An amperometric biosensor for the determination of phenol and chlorophenols using Trichosporon beigelii (cutaneum) has been developed. This sensor is more sensitive to chlorophenols, especially to mono- and dichlorinated phenols, than to phenol and is insensitive to benzoate. A linear relationship between the current range and the concentration of 4-chlorophenol is observed up to 40 mol/l. The detection limit for all substrates studies is 2 mol/l. the current difference is reproducible within 5.5% when the test solution contains 0.40 mol 4-chlorophenol.     

RNA as a target for small molecules

Proteins are folded to form a small binding site for catalysis or ligand recognition and this small binding site is traditionally the target for drug discovery. An alternative target for potential drug candidates is the translational process, which requires a precise reading of the entire mRNA sequence and, therefore, can be interrupted with small molecules that bind to mRNA sequence-specifically. RNA thus presents itself as a new upstream target for drug discovery because of the critical role it plays in the life of pathogens and in the progression of diseases. In this post-genomic era, RNA is becoming increasingly amenable to small-molecule therapy as greater structural and functional information accumulates with regard to important RNA functional domains. The study of aminoglycoside antibiotics and their binding to 16S ribosomal RNA has been a paradigm for our understanding of the ways in which small molecules can be developed to affect the function of RNA.     

Recent advances in the development of biosensor for phenol: a review

Phenol and its derivatives are widespread contaminants whose sources are both natural and industrial. Phenol is massively produced and used as a starting material for synthetic polymers and fibers. Although phenolic compounds play important biochemical and physiological roles in living systems, their accumulation in the environment as a result of intensive human activity may result in drastic ecological problem. Various analytical techniques are available for the detection of phenol in environmental samples. But they need complex sample pre-treatment so as are time consuming, costly and use heavy devices. On the other hand a biosensor is a device that gives rapid detection, cost effective and easy. A review study was carried out to accumulate the possible biosensors for the detection of phenolic compounds in environmental samples. A number of biological components including microorganisms, enzymes, antibodies, antigens, nucleic acids etc. can be used for the construction of biosensors that was found to detect phenolic compounds. Of all type of biological components microorganisms and enzymes are mostly used. The microorganisms are Pseudomonas, Moraxella, Arthrobacter, Rhodococcus, and Trichosporon. The most used enzymes are tyrosinase, peroxidase, laccase, glucose dehydrogenase, cellobiose dehydrogenase etc. Antibody sensors can detect a very trace level. The biorecognition of DNA biosensors occur by hybridization of DNA. Biosensors are found to work well when the biological sensing element is immobilized. A variety of immobilization techniques were found to use as adsorption, covalent binding, entrapment, cross-linking etc. For immobilization the matrices used was polyvinyl alcohol, Osmium complex, nafion/sol?Cgel silicate, chitosan, silica gel etc.     

Mesoderm-inducing factors: a small class of molecules

Mesoderm-inducing factors (MIF's) from chick embryos, XTC cells and WEHI-3 cells were studied using various procedures. The object was to find whether they are similar to heparin-binding growth factors (HBGFs-the only known pure mesoderm-inducing substances) and, if not, whether they are similar to each other. The major active components from all three MIF sources behave as somewhat hydrophobic, acid-stable molecules and do not bind to heparin. They all have relative molecular masses of about 13,000 measured by HPLC size exclusion chromatography. The isoelectric points measured by chromatofocusing were 6.7 (WEHI) and 7.7 (XTC). The chick MIF seemed somewhat heterogeneous by chromatofocusing and a portion of its activity bound to heparin sepharose. All three MIFs have similar effects on explants of Xenopus blastula ectoderm to the heparin-binding growth factors, causing an elongation at the time of gastrulation followed by the development of mesenchyme, mesothelium and muscle cells, the proportion of muscle increasing with dose. Unlike the HBGFs they all also induce notochord if sufficiently high concentrations are used. Our study shows that the MIFs examined here form a small group of potent agents distinct from the HBGFs and from other known growth and differentiations factors. Their occurrence in various tissues and cell lines suggests that they have functions in the adult organism as well as during early development.     

Phytohormones and microRNAs as sensors and regulators of leaf senescence: Assigning macro roles to small molecules

Ageing or senescence is an intricate and highly synchronized developmental phase in the life of plant parts including leaf. Senescence not only means death of a plant part, but during this process, different macromolecules undergo degradation and the resulting components are transported to other parts of the plant. During the period from when a leaf is young and green to the stage when it senesces, a multitude of factors such as hormones, environmental factors and senescence associated genes (SAGs) are involved. Plant hormones including salicylic acid, abscisic acid, jasmonic acid and ethylene advance leaf senescence, whereas others like cytokinins, gibberellins, and auxins delay this process. The environmental factors which generally affect plant development and growth, can hasten senescence, the examples being nutrient dearth, water stress, pathogen attack, radiations, high temperature and light intensity, waterlogging, and air, water or soil contamination. Other important influences include carbohydrate accumulation and high carbon/nitrogen level. To date, although several genes involved in this complex process have been identified, still not much information exists in the literature on the signalling mechanism of leaf senescence. Now, the Arabidopsis mutants have paved our way and opened new vistas to elucidate the signalling mechanism of leaf senescence for which various mutants are being utilized. Recent studies demonstrating the role of microRNAs in leaf senescence have reinforced our knowledge of this intricate process. This review provides a comprehensive and critical analysis of the information gained particularly on the roles of several plant growth regulators and microRNAs in regulation of leaf senescence.     

NMR fragment-based screening for development of the CD44-binding small molecules

The cell-surface protein CD44, a primary receptor for hyaluronic acid (HA), is one of the most promising targets for cancer therapies. It is prominently involved in the process of tumor growth and metastasis. The possibility of modulating the CD44-HA interaction with a pharmacological inhibitor is therefore of great importance, yet until now there are only few small molecules reported to bind to CD44. Here, we describe the results of the NMR fragment-based screening conducted against CD44 by which we found eight new hit compounds that bind to the receptor with the affinity in milimolar range. The NMR-based characterization revealed that there are two possible binding modes for these compounds, and for some of them the binding is no longer possible in the presence of hyaluronic acid. This could provide an interesting starting point for the development of new high-affinity ligands targeting the CD44-HA axis.     

Microbial enzymes for oxidation of organic molecules

Enzymatic systems employed by microorganisms for oxidative transformation of various organic molecules include laccases, ligninases, tyrosinases, monooxygenases, and dioxygenases. Reactions performed by these enzymes play a significant role in maintaining the global carbon cycle through either transformation or complete mineralization of organic molecules. Additionally, oxidative enzymes are instrumental in modification or degradation of the ever-increasing man-made chemicals constantly released into our environment. Due to their inherent stereo- and regioselectivity and high efficiency, oxidative enzymes have attracted attention as potential biocatalysts for various biotechnological processes. Successful commercial application of these enzymes will be possible through employing new methodologies, such as use of organic solvents in the reaction mixtures, immobilization of either the intact microorganisms or isolated enzyme preparations on various supports, and genetic engineering technology.     

Affinity ligand selection from a library of small molecules: assay development, screening, and application

A facile and cost-effective process for screening synthetic libraries for an affinity ligand is described. A high throughput 96-well plate filtration method was designed to screen both discrete compounds and mixtures of compounds attached to a solid support. Human serum albumin (HSA) was used as a target protein to demonstrate the proof of concept. Detection and quantitation by fluorescence was accomplished with the use of fluorescamine to conjugate the protein in the filtrate. It is found that mixtures demonstrating low average binding reflect an overall lower hit rate of the components, whereas deconvolution of mixtures with high protein binding consistently provides a high hit rate. This differs from many of the previous experiences screening solid-phase mixtures in which high false positive rates are noted to occur. A total of 100K compounds were tested: 25K as discrete samples and 75K as mixtures. An overall hit rate of 8% was observed. Secondary screening of compounds measured specificity, recovery, and dynamic binding capacity. The effectiveness of the method is illustrated using an affinity column made with a representative lead compound. A similar purity was achieved in a single-step purification of HSA from serum as compared to that obtained by two steps of ion-exchange chromatography. The process for primary screening of a large number of compounds is simple, inexpensive, and applicable to any soluble target protein of known or unknown function from crude mixtures and may have additional utility as a generic chemical affinity tool for the functional characterization of novel proteins emerging from proteomics work.     

Microbial fuel cell-based biosensor for fast analysis of biodegradable organic matter

The current study was made to develop a biosensor based on a single-chamber microbial fuel cell in which anaerobes were retained in the anode compartment separated from the cathode compartment by a proton exchange membrane. In the sensor a replaceable anaerobic consortium was used for analyzing biodegradable organic matter. The anaerobes acted as biocatalysts in oxidizing organic matter and transferring electrons to the anode. The biocatalysts were renewed for each sample analysis by replacing the old anaerobic consortium with an equal amount of fresh one. A glucose standard solution was used as the target substrate. To obtain the maximum sensor output, the MFC-based sensor system was optimized using an 800 Ω resistor as the load to the external electric circuit and 25 mM phosphate buffer with 50 mM NaCl as catholyte in the aerobic compartment. The temperature of anaerobic compartment was maintained at optimal 37 °C. The cell potential across the electrodes increased with increasing loading of glucose. The sensor response was linear against concentration of glucose up to 25 g l⁻¹. The detection limit was found as 0.025 g l⁻¹. The microbial fuel cell with replaceable anaerobic consortium could be used as a biosensor for on-line monitoring of organic matter.     

Minitags for small molecules: detecting targets of reactive small molecules in living plant tissues using 'click chemistry'

Small molecules offer unprecedented opportunities for plant research since plants respond to, metabolize, and react with a diverse range of endogenous and exogenous small molecules. Many of these small molecules become covalently attached to proteins. To display these small molecule targets in plants, we introduce a two-step labelling method for minitagged small molecules. Minitags are small chemical moieties (azide or alkyne) that are inert under biological conditions and have little influence on the membrane permeability and specificity of the small molecule. After labelling, proteomes are extracted under denaturing conditions and minitagged proteins are coupled to reporter tags through a 'click chemistry' reaction. We introduce this two-step labelling procedure in plants by studying the well-characterized targets of E-64, a small molecule cysteine protease inhibitor. In contrast to biotinylated E-64, minitagged E-64 efficiently labels vacuolar proteases in vivo . We displayed, purified and identified targets of a minitagged inhibitor that targets the proteasome and cysteine proteases in living plant cells. Chemical interference assays with inhibitors showed that MG132, a frequently used proteasome inhibitor, preferentially inhibits cysteine proteases in vivo . The two-step labelling procedure can be applied on detached leaves, cell cultures, seedlings and other living plant tissues and, when combined with photoreactive groups, can be used to identify targets of herbicides, phytohormones and reactive small molecules selected from chemical genetic screens.     

Glycosyltransferases: managers of small molecules

Studies of the glycosyltransferases (GTs) of small molecules have greatly increased in recent years as new approaches have been used to identify their genes and characterize their catalytic activities. These enzymes recognize diverse acceptors, including plant metabolites, phytotoxins and xenobiotics. Glycosylation alters the hydrophilicity of the acceptors, their stability and chemical properties, their subcellular localisation and often their bioactivity. Considerable progress has been made in understanding the role of GTs in the plant and the utility of GTs as biocatalysts, the latter arising from their regio- and enantioselectivity and their ability to recognize substrates that are not limited to plant metabolites.     

Microbial fuel cell biosensor for in situ assessment of microbial activity

Microbial fuel cell (MFC)-based sensing was explored to provide useful information for the development of an approach to in situ monitoring of substrate concentration and microbial respiration rate. The ability of a MFC to provide meaningful information about in situ microbial respiration and analyte concentration was examined in column systems, where Geobacter sulfurreducens used an external electron acceptor (an electrode) to metabolize acetate. Column systems inoculated with G. sulfurreducens were operated with influent media at varying concentrations of acetate and monitored for current generation. Current generation was mirrored by bulk phase acetate concentration, and a correlation (R(2)=0.92) was developed between current values (0-0.30 mA) and acetate concentrations (0-2.3 mM). The MFC-system was also exposed to shock loading (pulses of oxygen), after which electricity production resumed immediately after media flow recommenced, underlining the resilience of the system and allowing for additional sensing capacity. Thus, the electrical signal produced by the MFC-system provided real-time data for electron donor availability and biological activity. These results have practical implications for development of a biosensor for inexpensive real-time monitoring of in situ bioremediation processes, where MFC technology provides information on the rate and nature of biodegradation processes.