By Overexpression in the YeastPichia pastoris to Enhanced Enantioselectivity: New Aspects in the Application of Pig Liver Esterase

Catalytic reductive desymmetrization of malonic esters

Desymmetrization of fully substituted carbons with a pair of enantiotopic functional groups is a practical strategy for the synthesis of quaternary stereocentres, as it divides the tasks of enantioselection and C-C bond formation. The use of disubstituted malonic esters as the substrate of desymmetrization is particularly attractive, given their easy and modular preparation, as well as the high synthetic values of the chiral monoester products. Here, we report that a dinuclear zinc complex with a tetradentate ligand can selectively hydrosilylate one of the carbonyls of malonic esters to give α-quaternary β-hydroxyesters, providing a promising alternative to the desymmetric hydrolysis using carboxylesterases. The asymmetric reduction features excellent enantiocontrol that can differentiate sterically similar substituents and high chemoselectivity towards the diester motif of substrates. Together with the versatile preparation of malonic ester substrates and post-reduction derivatization, the desymmetric reduction has enabled the synthesis of a diverse array of quaternary stereocentres with distinct structural features.

Third-Generation Sequencing and Analysis of Four Complete Pig Liver Esterase Gene Sequences in Clones Identified by Screening BAC Library

AIM

Pig liver carboxylesterase (PLE) gene sequences in GenBank are incomplete, which has led to difficulties in studying the genetic structure and regulation mechanisms of gene expression of PLE family genes. The aim of this study was to obtain and analysis of complete gene sequences of PLE family by screening from a Rongchang pig BAC library and third-generation PacBio gene sequencing.

METHODS

After a number of existing incomplete PLE isoform gene sequences were analysed, primers were designed based on conserved regions in PLE exons, and the whole pig genome used as a template for Polymerase chain reaction (PCR) amplification. Specific primers were then selected based on the PCR amplification results. A three-step PCR screening method was used to identify PLE-positive clones by screening a Rongchang pig BAC library and PacBio third-generation sequencing was performed. BLAST comparisons and other bioinformatics methods were applied for sequence analysis.

RESULTS

Five PLE-positive BAC clones, designated BAC-10, BAC-70, BAC-75, BAC-119 and BAC-206, were identified. Sequence analysis yielded the complete sequences of four PLE genes, PLE1, PLE-B9, PLE-C4, and PLE-G2. Complete PLE gene sequences were defined as those containing regulatory sequences, exons, and introns. It was found that, not only did the PLE exon sequences of the four genes show a high degree of homology, but also that the intron sequences were highly similar. Additionally, the regulatory region of the genes contained two 720bps reverse complement sequences that may have an important function in the regulation of PLE gene expression.

SIGNIFICANCE

This is the first report to confirm the complete sequences of four PLE genes. In addition, the study demonstrates that each PLE isoform is encoded by a single gene and that the various genes exhibit a high degree of sequence homology, suggesting that the PLE family evolved from a single ancestral gene. Obtaining the complete sequences of these PLE genes provides the necessary foundation for investigation of the genetic structure, function, and regulatory mechanisms of the PLE gene family.

The metagenome-derived enzymes LipS and LipT increase the diversity of known lipases

Triacylglycerol lipases (EC 3.1.1.3) catalyze both hydrolysis and synthesis reactions with a broad spectrum of substrates rendering them especially suitable for many biotechnological applications. Most lipases used today originate from mesophilic organisms and are susceptible to thermal denaturation whereas only few possess high thermotolerance. Here, we report on the identification and characterization of two novel thermostable bacterial lipases identified by functional metagenomic screenings. Metagenomic libraries were constructed from enrichment cultures maintained at 65 to 75 °C and screened resulting in the identification of initially 10 clones with lipolytic activities. Subsequently, two ORFs were identified encoding lipases, LipS and LipT. Comparative sequence analyses suggested that both enzymes are members of novel lipase families. LipS is a 30.2 kDa protein and revealed a half-life of 48 h at 70 °C. The lipT gene encoded for a multimeric enzyme with a half-life of 3 h at 70 °C. LipS had an optimum temperature at 70 °C and LipT at 75 °C. Both enzymes catalyzed hydrolysis of long-chain (C(12) and C(14)) fatty acid esters and additionally hydrolyzed a number of industry-relevant substrates. LipS was highly specific for (R)-ibuprofen-phenyl ester with an enantiomeric excess (ee) of 99%. Furthermore, LipS was able to synthesize 1-propyl laurate and 1-tetradecyl myristate at 70 °C with rates similar to those of the lipase CalB from Candida antarctica. LipS represents the first example of a thermostable metagenome-derived lipase with significant synthesis activities. Its X-ray structure was solved with a resolution of 1.99 Å revealing an unusually compact lid structure.

Purification and characterization of an extracellular lipase from Mucor hiemalis f. corticola isolated from soil

We have screened 39 microfungi isolates originated from soil in terms of lipolytic activity. Out of all screened, a novel strain of Mucor hiemalis f. corticola was determined to have the highest lipase activity. The extracellular lipase was produced in response to 2% glucose and 2.1% peptone. The lipase was purified 12.63-folds with a final yield of 27.7% through following purification steps; ammonium sulfate precipitation, dialysis, gel filtration column chromatography and ion exchange chromatography, respectively. MALDI-TOF MS analysis revealed 31% amino-acid identity to a known lipase from Rhizomucor miehei species. The molecular weight of the lipase was determined as 46 kDa using SDS-PAGE and analytical gel filtration. Optimal pH and temperature of the lipase were determined as 7.0 and 40°C, respectively. The enzyme activity was observed to be stable at the pH range of 7.0-9.0. Thermostability assays demonstrated that the lipase was stable up to 50°C for 60 min. The lipase was more stable in ethanol and methanol than other organic solvents tested. Furthermore, the activity of the lipase was slightly enhanced by SDS and PMSF. In the presence of p-NPP as substrate, K(m) and V(max) values of the lipase were calculated by Hanes-Woolf plot as 1.327 mM and 91.11 μmol/min, respectively.

Simulation on the structure of pig liver esterase

A homology model for pig liver esterase was generated on the basis of human carboxyl esterase (hCE) and subjected to extensive molecular dynamics simulations. By virtual mutations the isoenzymes PLE1-6 and APLE were obtained, and the PLE1 trimer was built from the respective model of hCE. Stable structures for all systems were attained after simulations in solution for 12-18 ns, and contact zones between the monomers in the trimer are described. By evaluation of RMSD values of the residues in the monomer a rigid backplane with a number of β-strands and a flexible front part containing several α helices are distinguished. All mutations are concentrated in the soft part, and significant differences in the folding states of the helices were distinguished between the isoenzymes. Substrate access to the active site passes through two helices whose structures are affected by mutations. Variations in substrate specificity between the isoenzymes are ascribed to the structure of the entrance channel rather than to the conformation of the active site itself. The assignment of the residue with a negative side chain stabilizing the histidine protonation in the catalytic triad was revised, being GLU 452 in some isoenzymes rather than GLU 336, which would be the correspondent to most hydrolases. Arguments for this new assignment are given on the basis of simulations and statistics from the 3DM database for hydrolases.

Protein engineering of microbial enzymes

Protein engineering has emerged as an important tool to overcome the limitations of natural enzymes as biocatalysts. Recent advances have mainly focused on applying directed evolution to enzymes, especially important for organic synthesis, such as monooxygenases, ketoreductases, lipases or aldolases in order to improve their activity, enantioselectivity, and stability. The combination of directed evolution and rational protein design using computational tools is becoming increasingly important in order to explore enzyme sequence-space and to create improved or novel enzymes. These developments should allow to further expand the application of microbial enzymes in industry.

Identification of pig liver esterase variants by tandem mass spectroscopy analysis and their characterization

Pig liver esterase (PLE) is probably the most important carboxyl esterase in organic synthesis and is commercially obtained by extraction of the animal tissue. However, problems occur in its application due to the presence of several isoenzymes (alpha-, beta- and gamma-PLE). The functional expression of the gamma-isoenzyme was already shown and differences in the enantioselectivity compared to the commercial preparations were confirmed. The amino acid and nucleotide sequences of the alpha- and beta-PLE are still unknown. In this work, putative sequences of the alpha-isoenzyme were identified from a commercial PLE preparation by 2D gel electrophoresis, digestion with proteases and analysis using Matrix-assisted laser desorption/ionization-time of flight (TOF) and electrospray ionisation quadrupole-TOF mass spectrometry. Based on these results, three amino acid exchanges were introduced into the gene encoding gamma-rPLE by site-directed mutagenesis, and the proteins were expressed in E. coli Origami (DE3). The produced PLE mutants were characterised with respect to their substrate specificity and enantioselectivity. No significant differences in the activity towards methyl butyrate were found, but several variants showed substantially enhanced enantioselectivity in the resolution of (R,S)-1-phenyl-2-butyl acetate with E = 100 for the best mutant V236P/A237G.

A versatile esterase fromBacillus subtilis: Cloning, expression, characterization, and its application in biocatalysis

An esterase from Bacillus subtilis DSM402 (BS2) was cloned and functionally expressed in E. coli. The enzyme is active up to 50 degrees C, and the V(max) (1449 mM/min) and K(M) values (119 mM) were determined using p-nitrophenyl acetate as substrate. BS2 belongs to the few hydrolases that can act on tertiary alcohols and was therefore used to resolve racemic acetates of selected tertiary alcohols, but also to selectively remove the tert-butyl ester protecting group from peptides. In addition, the enzyme shows promiscuous amidase activity.

Functional expression of the gamma-isoenzyme of pig liver carboxyl esterase in Escherichia coli

The previously reported functional expression of the gamma-isoenzyme of pig liver carboxylesterase (gamma-rPLE) in Pichia pastoris is hampered by the small amount of active enzyme formed. Earlier attempts for expression in Escherichia coli failed completely and not even inactive protein was detected. The lack of glycosylation ability of E. coli was ruled out as a possible reason, as it could be shown in this work that deglycosylated PLE also is active. Expression of gamma-rPLE was studied using a range of E. coli strains with careful design of the constructs used and control of the cultivation conditions. Indeed, expression in E. coli strains Rosetta, Origami and Rosetta-gami was successful, but the majority of enzymes was present as inclusion bodies and only little soluble but inactive protein was detected. Denaturation and refolding of inclusion bodies failed. However, with the E. coli strain Origami, coexpressing the molecular chaperones GroEL und GroES, a functional expression of gamma-rPLE was possible. The recombinant enzyme was released by cell disruption and subjected to His-tag purification. The purified esterase had a specific activity of 92 U mg(-1) protein and a V (max)/K (m) value of 10.8x10(-3) min(-1) towards p-nitrophenyl acetate. Activity staining of native polyacrylamide gels gave a single band at 175 kDa with esterolytic activity indicating a trimeric form of gamma-rPLE ( approximately 60 kDa per monomer). gamma-rPLE was biochemically characterized and its properties were compared to the enzyme previously expressed in P. pastoris. pH and temperature profiles were identical and highest activity was found at pH 8-8.5 and 60 degrees C, respectively. In the kinetic resolution of (R,S)-1-phenyl-2-butyl acetate with esterase from both expression hosts, similar enantioselectivities (E=50) were found.

Directed Assembly of Transition-Metal-Coordinated Molecular Loops and Squares from Salen-Type Components. Examples of Metalation-Controlled Structural Conversion

A series of transition-metal-containing molecular "loops" and "squares" has been prepared via a directed-assembly approach and characterized. The molecular loops were prepared from the reaction of cis-(PEt(3))(2)Pt(OTf)(2) with bis(4-pyridyl)-functionalized free-base salen-type ligands. Zn(II)-metalation of the salen-type ligands in the molecular loops converts the loops to molecular squares. Alternatively, the squares can be obtained by the directed assembly of cis-(PEt(3))(2)Pt(OTf)(2) and bis(4-pyridyl)-functionalized Zn(II)-salen-type ligands. A concentration-dependent dynamic equilibrium between cyclic species was observed when bis(3-pyridyl)-functionalized free-base salen-type ligand was employed in the reaction. Zn(II) or Cr(III) metalation of the free-base ligand shifted the equilibrium to the single dimeric species. The incorporation of multiple reactive metal sites into a single, cavity-containing supramolecular structure points toward catalytic applications for these new assemblies.

A molecular mechanism of enantiorecognition of tertiary alcohols by carboxylesterases

Carboxylesterases containing the sequence motif GGGX catalyze the hydrolysis of esters of chiral tertiary alcohols, albeit with only low to moderate enantioselectivity, for three model substrates (linalyl acetate, methyl-1-pentin-1-yl acetate, 2-phenyl-3-butin-2-yl acetate). In order to understand the molecular mechanism of enantiorecognition and to improve enantioselectivity for this interesting substrate class, the interaction of both enantiomers with the substrate binding sites of acetylcholinesterases and p-nitrobenzyl esterase from Bacillus subtilis was modeled and correlated to experimental enantioselectivity. For all substrate-enzyme pairs, enantiopreference and ranking by enantioselectivity could be predicted by the model. In p-nitrobenzyl esterase, one of the key residues in determining enantioselectivity was G105: exchange of this amino acid for an alanine residue led to a sixfold increase of enantioselectivity (E = 19) towards 2-phenyl-3-butin-2-yl acetate. However, the effect of this mutation is specific: the same mutant had the opposite enantiopreference towards the substrate linalyl acetate. Thus, depending on the substrate structure, the same mutant has either increased enantioselectivity or opposite enantiopreference compared to the wild-type enzyme.

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.

Cloning, functional expression, and characterization of recombinant pig liver esterase

The N-terminal amino acid sequence of pig liver esterase (PLE) from a commercial sample was determined and shown to match closely to a published sequence encoding a proline-beta-naphthylamidase from pig liver. Next, mRNA isolated from pig liver was transcribed into cDNA and primers deduced from the N-terminal sequence were used to clone the 1698 base pairs of PLE cDNA. Initial attempts to express the cDNA in Escherichia coli and Pichia pastoris with different expression vectors and secretion signal sequences failed. Only after deletion of the putative C-terminal sequence His-Ala-Glu-Leu, usually considered as an endoplasmic reticulum retention signal, could heterologous expression of PLE be readily achieved in the methylotrophic yeast P. pastoris. Recombinant PLE (rPLE) was secreted into the medium and exhibited a specific activity of approximately 600 Umg(-1) and a Vmax/Km value of 139 micromolmin(-1)mM(-1) with p-nitrophenyl acetate as a substrate. Activity staining of renatured sodium dodecylsulfate-polyacrylamide gels gave a single band with esterolytic activity for rPLE, whereas several bands are visible in crude commercial PLE preparations. This was confirmed by native gels, which also show that rPLE is active as a trimer. Biochemical characterization of the recombinant enzyme and comparison with properties of commercial PLE preparations as well as with published data confirmed that we expressed a single PLE isoenzyme which showed a high preference for proline-beta-naphthylamide. This is a substrate specificity for the so-called gamma subunit of PLE. The optimum pH value and temperature for the recombinant PLE were 8.0 and 60 degrees C, respectively. The determined molecular weight of the secreted enzyme was approximately 61-62 kDa, which closely matches the calculated value of 62.419 kDa. The active site residues are located at Ser203, His448, and Asp97, and the typical consensus sequence motif for hydrolases was found around the active site serine (Gly-Glu-Ser-Ala-Gly).