High-throughput assays for lipases and esterases

In the past few years a considerable number of high-throughput screening (HTS) systems have been developed, especially for lipases and esterases. In this review, a range of HTS methods for the directed evolution of these hydrolases are covered. This includes spectrophotometric and fluorimetric formats as well as other approaches to allow for fast, efficient and reliable identification of desired enzyme variants within large mutant libraries. In addition, methods for library creation and application of lipases and esterases are briefly covered.     

Methods to increase enantioselectivity of lipases and esterases

Lipases and esterases are frequently used in the synthesis of optically pure compounds; however, natural enzymes do not always show sufficiently high enantioselectivity. Variation of the structure of the substrates, modification of the reaction system or protein engineering (e.g. the expression of pure enzymes, rational design or directed evolution) are strategies that can be employed to improve the distinction between two enantiomers or enantiotopic groups.     

GDSL family of serine esterases/lipases

GDSL esterases and lipases are hydrolytic enzymes with multifunctional properties such as broad substrate specificity and regiospecificity. They have potential for use in the hydrolysis and synthesis of important ester compounds of pharmaceutical, food, biochemical, and biological interests. This new subclass of lipolytic enzymes possesses a distinct GDSL sequence motif different from the GxSxG motif found in many lipases. Unlike the common lipases, GDSL enzymes do not have the so called nucleophile elbow. Studies show that GDSL hydrolases have a flexible active site that appears to change conformation with the presence and binding of the different substrates, much like the induced fit mechanism proposed by Koshland. Some of the GDSL enzymes have thioesterase, protease, arylesterase, and lysophospholipase activity, yet they appear to be the same protein with similar molecular weight (22–60 kDa for most esterases), although some have multiple glycosylation sites with higher apparent molecular weight. GDSL enzymes have five consensus sequence (I–V) and four invariant important catalytic residues Ser, Gly, Asn, and His in blocks I, II, III, and V, respectively. The oxyanion structure led to a new designation of these enzymes as SGNH-hydrolase superfamily or subfamily. Phylogenetic analysis revealed that block IIA which belonged to the SGNH-hydrolases was found only in clade I. Therefore, this family of hydrolases represents a new example of convergent evolution of lipolytic enzymes. These enzymes have little sequence homology to true lipases. Another important differentiating feature of GDSL subfamily of lipolytic enzymes is that the serine-containing motif is closer to the N-terminus unlike other lipases where the GxSxG motif is near the center. Since the first classification of these subclass or subfamily of lipases as GDSL(S) hydrolase, progress has been made in determining the consensus sequence, crystal structure, active site and oxyanion residues, secondary structure, mechanism of catalysis, and understanding the conformational changes. Nevertheless, much still needs to be done to gain better understanding of in vivo biological function, 3-D structure, how this group of enzymes evolved to utilize many different substrates, and the mechanism of reactions. Protein engineering is needed to improve the substrate specificity, enantioselectivity, specific activity, thermostability, and heterologous expression in other hosts (especially food grade microorganisms) leading to eventual large scale production and applications. We hope that this review will rekindle interest among researchers and the industry to study and find uses for these unique enzymes.     

Selectivity of lipases and esterases towards phenol esters

The selectivity of 28 lipases and esterases in the hydrolysis of butanoates of o-, m- or p-substituted phenols was investigated in a microtiterplate format. The phenols released during enzyme-catalyzed hydrolysis were converted in situ with Gibbs’ reagent to form a blue indophenol complex, which was quantified spectrophotometrically at 600 nm. Substantial differences in rates were found, which exhibits that the type and position of the substituent at the alkyl group has a strong influence on the selectivity of the enzymes. For various enzymes, the p-nitro derivative was the best substrate, whereas for other enzymes the m-Cl-derivative was preferentially hydrolyzed. Analysis of the data using the Hammett equation showed that sometimes the observed changes followed a predictable trend, but in several cases the result is very unexpected.     

Synthesis activity-based zymography for detection of lipases and esterases

A new zymography method for lipases and esterases was developed on the basis of the esterification reaction between fatty acids and alcohols. The enzymes were separated by SDS-PAGE and native PAGE. The gel was washed and then incubated in an aqueous solution containing fatty acids (oleic acid 18:1 or caprylic acid 8:0) and dodecanol. Synthesis was visualized by in situ precipitation of water-insoluble and non-diffusible fatty acid esters, such as dodecyl oleate and dodecyl octanoate. The synthesis activity-based zymography was confirmed with different enzyme samples, including commercial lipase preparations, purified recombinant lipase and cutinase, and crude culture supernatants of lipolytic enzyme-producing soil bacteria.     

MELDB: a database for microbial esterases and lipases

MELDB is a comprehensive protein database of microbial esterases and lipases which are hydrolytic enzymes important in the modern industry. Proteins in MELDB are clustered into groups according to their sequence similarities based on a local pairwise alignment algorithm and a graph clustering algorithm (TribeMCL). This differs from traditional approaches that use global pairwise alignment and joining methods. Our procedure was able to reduce the noise caused by dubious alignment in the distantly related or unrelated regions in the sequences. In the database, 883 esterase and lipase sequences derived from microbial sources are deposited and conserved parts of each protein are identified. HMM profiles of each cluster were generated to classify unknown sequences. Contents of the database can be keyword-searched and query sequences can be aligned to sequence profiles and sequences themselves.     

A simple activity staining protocol for lipases and esterases

A simple activity staining protocol for rapid detection and differentiation of lipases and esterases was developed based on pH drop due to fatty acids released following lipolysis. Though the detection of lipolysis as a function of drop in pH is not new, the present method has been made more sensitive by the judicious selection of the initial pH of the chromogenic substrate, which has been set near the end point of the dye so that even a slight drop in pH results in immediate color change. In the present case, the dye phenol red was taken, which has the end point at pH 7.3–7.4 where the color is pink. A slight drop due to fatty acid release results in yellow coloration. The assay has high reproducibility and can detect as low as 0.5 p-NPP enzyme units within 15 min. In addition, this method can be used for various lipidic substrates such as oils and tributyrin, making it suitable for both lipases and esterases.     

How do lipases and esterases work: the electrostatic contribution

This work explores the role of one of the factors explaining lipase/esterase activity: the contribution of electrostatic interactions to lipase/esterase activity. The electrostatic potential distribution on the molecular surface of an enzyme as a function of pH determines, to a large extent, the enzyme's pH activity profile. Other important factors include the presence and distribution of polar and hydrophobic residues in the active cleft. We have mapped the electrostatic potential distribution as a function of pH on the molecular surface of nine lipases/esterases for which the 3D structure is experimentally known. A comparison of these potential maps at different pH values with the corresponding pH-activity profile, pH optimum or pH range where the activity displayed by the enzyme is maximum, has revealed a considerable correlation. A negative potential in the active site appears correlated with maximum activity towards triglycerides, which has prompted us to propose a model for product release ('The electrostatic catapult model') after cleavage of an ester bond. At the same time as the bottom of the active site cleft becomes negatively charged, other nearby regions also titrate and become negatively charged when pH becomes more alkaline, for some of the studied lipases. If such lipases also show phospholipase activity (such as guinea pig lipase-related proteins 2 chimera) we raise the hypothesis that such other titratable regions after becoming negatively charged might stabilise the positive charge present in the polar head of phospholipids, such as phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine. The distribution of polar, weak polar and non-polar residues on the molecular surface of each studied lipase, in particular the active site region, was compared for all the lipases studied. The combination of graphical visualisation of the electrostatic potential maps and the polarity maps combined with knowledge about the location of key residues on the protein surface allows us to envision atomic models for lipolytic activity.     

Expansion and evolutionary patterns of GDSL-type esterases/lipases in Rosaceae genomes

GDSL-type esterase/lipase (GELP) is mainly characterized by a conserved GDSL domain at N terminus, and is widely found in all living species, both prokaryotes and eukaryotes. GELP gene family consists of a wide range of members playing important roles in plant physiological processes, such as development, stress responses, and functional divergences. In our study, 597 GELP genes were identified from six Rosaceae genomes (i.e., Fragaria vesca, Prunus persica, Prunus avium, Prunus mume, Pyrus bretschneideri, and Malus domestica) by a comprehensive analysis. All GELP genes were further divided into ten subfamilies based on phylogenetic tree analysis. Subfamily D and subfamily E are the two largest subfamilies. Microcollinearity analysis suggested that WGD/segmental events contribute to the expansion of the GELP gene family in M. domestica and P. bretschneideri compared to F. vesca, P. persica, P. avium, and P. mume. Some PbGELPs were expressed during the fruit development of P. bretschneideri and pollen tubes, indicating their activity in these tissues. The expression divergence of PbGELP duplication gene pairs suggests that many mutations were allowed during evolution, although the structure of GELP genes was highly conserved. The current study results provided the feasibility to understand the expansion and evolution patterns of GELP in Rosaceae genomes, and highlight the function during P. bretschneideri fruits and pollen tubes development.     

Gel filtration applied to the study of lipases and other esterases

1. Sephadex G-100 and G-200 gel-filtration columns were calibrated for molecular-weight estimation with proteins of known molecular weights, and used to study the composition of several lipase or esterase preparations. 2. Enzymes from cow's milk, rat adipose tissue and pig pancreas were detected in the column effluents by their ability to liberate free acid from emulsified tributyrin at pH 8·5. 3. Four tributyrinases were detected in preparations from individual cow's milks. Molecular weights 62000, 75000 and 112000 were estimated for three of them, but although the fourth may be of unusually low molecular weight an estimate was not possible. 4. Extracts of rat adipose tissue apparently contained six tributyrinases (molecular weights 39000, 47000, 55000, 68000, 75000 and 200000) but the relative amounts of these enzymes varied widely from rat to rat. 5. Tributyrinase activity in juice expressed from pig pancreatic tissue was due mainly to one enzyme (molecular weight 42000). On the other hand, activity in extracts of acetone-dried pancreas was confined to material of molecular weight > 10⁶, which may be an aggregated form of the lower-molecular-weight enzyme. 6. Activity in fractionated wheat-germ extracts was assayed with emulsified triacetin substrate, and was evidently due to one enzyme (molecular weight 51000). 7. Some problems arising in the application of gel filtration to the study of lipase–esterase systems were indicated.     

Gene identification and proteomic analysis of the esterases of the cotton bollworm,Helicoverpa armigera

Some of the resistance of Helicoverpa armigera to conventional insecticides such as organophosphates and synthetic pyrethroids appears to be due to metabolic detoxification by carboxylesterases. To investigate the H. armigera carboxyl/cholinesterases, we created a data set of 39 putative paralogous H. armigera carboxyl/cholinesterase sequences from cDNA libraries and other sources. Phylogenetic analysis revealed a close relationship between these sequences and 70 carboxyl/cholinesterases from the recently sequenced genome of the silkworm, Bombyx mori, including several conserved clades of non-catalytic proteins. A juvenile hormone esterase candidate from H. armigera was identified, and B. mori orthologues were proposed for 31% of the sequences examined, however low similarity was found between lepidopteran sequences and esterases previously associated with insecticide resistance from other insect orders. A proteomic analysis of larval esterases then enabled us to match seven of the H. armigera carboxyl/cholinesterase sequences to specific esterase isozymes. All identified sequences were predicted to encode catalytically active carboxylesterases, including six proteins with N-terminal signal peptides and N-glycans, with two also containing C-terminal signals for glycosylphosphatidylinositol anchor attachment. Five of these sequences were matched to zones of activity on native PAGE at relative mobility values previously associated with insecticide resistance in this species.     

IGF-I- and IGFBP-3-expression in cultured human preadipocytes and adipocytes.

The expression and secretion of IGF-I and IGFBP-3 were investigated in cultured human preadipocytes and in in vitro differentiated adipocytes derived from human subcutaneous adipose tissue under chemically defined culture conditions. Human preadipocytes expressed mRNAs for IGF-I and IGFBP-3 and secreted the corresponding proteins into the culture medium as measured by sensitive radioimmunoassays. In human adipocytes; specific mRNA-expression was comparable to that found in preadipocytes, but IGF-I secretion was increased 10-fold (3.87 +/- 0.69 vs. 0.41 +/- 0.11 ng/ml/10(6) cells/48 hrs, p < 0.05) and IGFBP-3 secretion 2.5-fold (7.34+/-1.15 vs. 3.27+/-0.38 ng/ml/10(6) cells/48 hrs, p<0.05) in the presence of adipogenic medium probably resulting in an increase of unbound IGF-I. Under serum-free, chemically defined conditions human growth hormone (hGH) and insulin were found to be positive regulators and cortisol was found to be a negative regulator of IGF-I and IGFBP-3 secretion in preadipocytes. In cultured human adipocytes, hGH showed no effect on IGF-I and IGFBP-3 secretion, whereas insulin stimulated and cortisol inhibited the secretion of both proteins. We conclude that IGF-I and IGFBP-3 may not only exert their actions in human adipose tissue via circulation, but also in an auto/paracrine way.     

Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking

Background  

Previously, ways to adapt docking programs that were developed for modelling inhibitor-receptor interaction have been explored. Two main issues were discussed. First, when trying to model catalysis a reaction intermediate of the substrate is expected to provide more valid information than the ground state of the substrate. Second, the incorporation of protein flexibility is essential for reliable predictions.     

Functional differentiation in bryozoan colonies: a proteomic analysis

Bryozoans are typical modular organisms. They consist of repetitive structural units, the zooids. Bryozoan colonies grow by zooidal budding, with the distribution pattern of the budding loci underlying the diversity of colony forms. Budding is usually restricted to the colony periphery, where a “growing edge” or local terminal growth zones are formed. Non-budding parts of the colony can be functionally subdivided, too. In many species colonies consist of regular, often repetitive zones of feeding and non-feeding modules, associated with a periodical degeneration and regeneration of the polypide retractile tentacle crown with a gut and the accompanying musculature. The mechanisms of functional differentiation in bryozoan colonies are unknown. Presumably, budding and/or polypide recycling are induced or inhibited by certain determinants of functional specialization in different colony parts. An effective tool of their identification is the comparison of proteomes in functionally different zones. Here we report the results of proteomic analysis of three bryozoan species from the White Sea with a different colony form: Flustrellidra hispida, Terminoflustra membranaceotruncata and Securiflustra securifrons. Using differential two-dimensional electrophoresis (2D-DIGE), we compared proteomes of the growing edge, the zone with polypides and the zone without polypides. We assessed the general level of differences between the zones and revealed proteins whose relative abundance changed gradually along the proximal-distal colony axis. These proteins might be involved in the determination of the functional differentiation of the colony.     

A proteomic analysis of human bile

We have carried out a comprehensive characterization of human bile to define the bile proteome. Our approach involved fractionation of bile by one-dimensional gel electrophoresis and lectin affinity chromatography followed by liquid chromatography tandem mass spectrometry. Overall, we identified 87 unique proteins, including several novel proteins as well as known proteins whose functions are unknown. A large majority of the identified proteins have not been previously described in bile. Using lectin affinity chromatography and enzymatically labeling of asparagine residues carrying glycan moieties by (18)O, we have identified a total of 33 glycosylation sites. The strategy described in this study should be generally applicable for a detailed proteomic analysis of most body fluids. In combination with "tagging" approaches for differential proteomics, our method could be used for identification of cancer biomarkers from any body fluid.     

Comprehensive proteomic analysis of human bile

Bile serves diverse functions from metabolism to transport. In addition to acids and salts, bile is composed of proteins secreted or shed by the hepatobiliary system. Although there have been previous efforts to catalog biliary proteins, an in-depth analysis of the bile proteome has not yet been reported. We carried out fractionation of non-cancerous bile samples using a multipronged approach (SDS-PAGE, SCX and OFFGEL) followed by MS analysis on an LTQ-Orbitrap Velos mass spectrometer using high resolution at both MS and MS/MS levels. We identified 2552 proteins - the largest number of proteins reported in human bile till date. To our knowledge, there are no previous studies employing high-resolution MS reporting a more detailed catalog of any body fluid proteome in a single study. We propose that extensive fractionation coupled to high-resolution MS can be used as a standard methodology for in-depth characterization of any body fluid. This catalog should serve as a baseline for the future studies aimed at discovering biomarkers from bile in gallbladder, hepatic, and biliary cancers.     

Polymer membrane ion-selective electrodes as a convenient tool for lipases and esterases assays

We have proposed a novel assay for lipases and esterases activity determination based on potentiometry with ion-selective electrodes (ISEs). Enzyme preparations, obtained from the living cells, are complex mixtures of various proteins, short peptides, lipids, carbohydrates, and other compounds. The most commonly used quantitative methods in enzyme studies are based on spectrophotometric or spectroflourimetric protocols which has significant limitations. They are not valid for samples that are turbid or strongly colored. To overcome those drawbacks we have proposed an assay based on potentiometry with ISEs for lipases and esterases activity determination. This electrochemical methodology represents an attractive tool for enzyme analysis, because of its low detection limit, independence from sample volume and from sample turbidity. The usefulness of this assay has been proven by the determination of the activity of various raw enzymes “acetone powders” isolated from animal tissues. Moreover, activities of fractions obtained during purification of one of those raw biocatalysts were also determined that way. The reliability of determination enzyme activity with ISE assay was proven by comparison with a classical spectrophotometric method.