Esterases receive special attention because of their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases' substrate promiscuity level from sequence data and the molecular reasons why certain such enzymes are more promiscuous than others remain to be elucidated. This limits the surveillance of the sequence space for esterases potentially leading to new versatile biocatalysts and new insights into their role in cellular function. Here, we performed an extensive analysis of the substrate spectra of 145 phylogenetically and environmentally diverse microbial esterases, when tested with 96 diverse esters. We determined the primary factors shaping their substrate range by analyzing substrate range patterns in combination with structural analysis and protein-ligand simulations. We found a structural parameter that helps rank (classify) the promiscuity level of esterases from sequence data at 94% accuracy. This parameter, the active site effective volume, exemplifies the topology of the catalytic environment by measuring the active site cavity volume corrected by the relative solvent accessible surface area (SASA) of the catalytic triad. Sequences encoding esterases with active site effective volumes (cavity volume/SASA) above a threshold show greater substrate spectra, which can be further extended in combination with phylogenetic data. This measure provides also a valuable tool for interrogating substrates capable of being converted. This measure, found to be transferred to phosphatases of the haloalkanoic acid dehalogenase superfamily and possibly other enzymatic systems, represents a powerful tool for low-cost bioprospecting for esterases with broad substrate ranges, in large scale sequence data sets.

Six strongly fluorescent four-coordinate organoboron N,Cchelates, containing an arylisoquinoline skeleton, were prepared. Remarkably, the fluorescence quantum yields reach values of up to 0.74 in oxygen-free toluene. The strong B-N interaction was corroborated by the single-crystal X-ray analysis of two dyes. The intramolecular charge-transfer (ICT) character of the fluorophores was evidenced by solvatochromic studies and time-dependent density-functional-theory calculations at the PCM(toluene)/CAM-B3LYP/6-311++G(2d,p)//PCM(toluene)/B3LYP/6-311G(2d,p) level of theory. The compounds combine high chemical stability with high photostability (especially when equipped with electron-donating substituents). The strong fluorescence and the large Stokes shifts predestine these compounds for their use in confocal fluorescence microscopy. This was demonstrated for the imaging of the N13 mouse microgial cell line. As a surplus, significant two-photon absorption cross sections (up to 61 GM) allow the use of excitation wavelengths in the near-infrared region (> 800 nm).

Microbial metabolism in aromatic-contaminated environments has important ecological implications, and obtaining a complete understanding of this process remains a relevant goal. To understand the roles of biodiversity and aromatic-mediated genetic and metabolic rearrangements, we conducted ‘OMIC’ investigations in an anthropogenically influenced and polyaromatic hydrocarbon (PAH)-contaminated soil with (Nbs) or without (N) bio-stimulation with calcium ammonia nitrate, NH4NO3 and KH2PO4 and the commercial surfactant Iveysol, plus two naphthalene-enriched communities derived from both soils (CN2 and CN1, respectively). Using a metagenomic approach, a total of 52, 53, 14 and 12 distinct species (according to operational phylogenetic units (OPU) in our work equivalent to taxonomic species) were identified in the N, Nbs, CN1 and CN2 communities, respectively. Approximately 10 out of 95 distinct species and 238 out of 3293 clusters of orthologous groups (COGs) protein families identified were clearly stimulated under the assayed conditions, whereas only two species and 1465 COGs conformed to the common set in all of the mesocosms. Results indicated distinct biodegradation capabilities for the utilisation of potential growth-supporting aromatics, which results in bio-stimulated communities being extremely fit to naphthalene utilisation and non-stimulated communities exhibiting a greater metabolic window than previously predicted. On the basis of comparing protein expression profiles and metagenome data sets, inter-alia interactions among members were hypothesised. The utilisation of curated databases is discussed and used for first time to reconstruct ‘presumptive’ degradation networks for complex microbial communities.

The esterases and lipases from the ␣/␤ hydrolase superfamily exhibit an enormous sequence diversity, fold plasticity, and activities. Here, we present the comprehensive sequence and biochemical analyses of seven distinct esterases and lipases from the metagenome of Lake Arreo, an evaporite karstic lake in Spain (42°46=N, 2°59=W; altitude, 655 m). Together with oligonucleotide usage patterns and BLASTP analysis, our study of esterases/lipases mined from Lake Arreo suggests that its sediment contains moderately halophilic and cold-adapted proteobacteria containing DNA fragments of distantly related plasmids or chromosomal genomic islands of plasmid and phage origins. This metagenome encodes esterases/lipases with broad substrate profiles (tested over a set of 101 structurally diverse esters) and habitat-specific characteristics, as they exhibit maximal activity at alkaline pH (8.0 to 8.5) and temperature of 16 to 40°C, and they are stimulated (1.5 to 2.2 times) by chloride ions (0.1 to 1.2 M), reflecting an adaptation to environmental conditions. Our work provides further insights into the potential significance of the Lake Arreo esterases/lipases for biotechnology processes (i.e., production of enantiomers and sugar esters), because these enzymes are salt tolerant and are active at low temperatures and against a broad range of substrates. As an example, the ability of a single protein to hydrolyze triacylglycerols, (non)halogenated alkyl and aryl esters, cinnamoyl and carbohydrate esters, lactones, and chiral epoxides to a similar extent was demonstrated. E sterases and lipases from the ␣/␤ hydrolase family have received considerable attention, because they are widely distributed within the microbial communities operating in most of environments where they have important physiological functions (1) and because they are one of the most important groups of biocatalysts for biotechnological applications (2-4). Upon searching the list of genes using Pfam (the protein family database [5]) from the approximately 140 metagenomic projects in various stages of sequencing on the GOLD website (Genomes OnLine Database; http://www.genomesonline.org/) and the available sequences of esterases and lipases, more than 72,000 predicted esterases/lipases of the ␣/␤ hydrolase superfamily were retrieved, which revealed the richness of uncultured biodiversity (6), to provide wide collections of such biocatalysts. This is one of the largest protein families with available sequences. In relation to the cultivation-independent methods used to identify them, it should be highlighted that sequence-based metagenomics only provide the presumptive compositional and functional blueprint represented in the community genome (7,8), but at the same time, this method causes serious problems regarding both sequencing errors (9) and the erroneous assignment of substrate specificity (10). In contrast, the activity-directed techniques have been shown to provide a direct view of known or new protein families and functionalities (for examples, see referen...

A series of boronic acid derived salicylidenehydrazone (BASHY) complexes was prepared and photophysically characterized. The dye platform can be modified by (a) electronic tuning along the cyanine-type axis via modification of the donor-acceptor pair and (b) functional tuning via the boronic acid residue. On the one hand, approach (a) allows the control of photophysical parameters such as Stokes shift, emission color, and two-photon-absorption (2PA) cross section. The resulting dyes show emission light-up behavior in nonpolar media and are characterized by high fluorescence quantum yields (ca. 0.5-0.7) and brightness (ca. 35000-40000 M cm). Moreover, the 2PA cross sections reach values in the order of 200-300 GM. On the other hand, the variation of the dye structure through the boronic acid derived moiety (approach (b)) enables the functionalization of the BASHY platform for a broad spectrum of potential applications, ranging from biorelevant contexts to optoelectronic materials. Importantly, this functionalization is generally electronically orthogonal with respect to the dye's photophysical properties, which are only determined by the electronic structure of the cyanine-type backbone (approach (a)). Rare exceptions to this generalization are the presence of redox-active residues (such a triphenylamine or pyrene). Finally, the advantageous photophysics is complemented by a significant photostability.