Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis

Protein thermostability is a crucial factor for biotechnological enzyme applications. Protein engineering studies aimed at improving thermostability have successfully applied both directed evolution and rational design. However, for rational approaches, the major challenge remains the prediction of mutation sites and optimal amino acid substitutions. Recently, we showed that such mutation sites can be identified as structural weak spots by rigidity theory-based thermal unfolding simulations of proteins. Here, we describe and validate a unique, ensemble-based, yet highly efficient strategy to predict optimal amino acid substitutions at structural weak spots for improving a protein’s thermostability. For this, we exploit the fact that in the majority of cases an increased structural rigidity of the folded state has been found as the cause for thermostability. When applied prospectively to lipase A from Bacillus subtilis, we achieved both a high success rate (25% over all experimentally tested mutations, which raises to 60% if small-to-large residue mutations and mutations in the active site are excluded) in predicting significantly thermostabilized lipase variants and a remarkably large increase in those variants’ thermostability (up to 6.6°C) based on single amino acid mutations. When considering negative controls in addition and evaluating the performance of our approach as a binary classifier, the accuracy is 63% and increases to 83% if small-to-large residue mutations and mutations in the active site are excluded. The gain in precision (predictive value for increased thermostability) over random classification is 1.6-fold (2.4-fold). Furthermore, an increase in thermostability predicted by our approach significantly points to increased experimental thermostability (p < 0.05). These results suggest that our strategy is a valuable complement to existing methods for rational protein design aimed at improving thermostability

Structural and Functional Characterisation of TesA - A Novel Lysophospholipase A from Pseudomonas aeruginosa

TesA from Pseudomonas aeruginosa belongs to the GDSL hydrolase family of serine esterases and lipases that possess a broad substrate- and regiospecificity. It shows high sequence homology to TAP, a multifunctional enzyme from Escherichia coli exhibiting thioesterase, lysophospholipase A, protease and arylesterase activities. Recently, we demonstrated high arylesterase activity for TesA, but only minor thioesterase and no protease activity. Here, we present a comparative analysis of TesA and TAP at the structural, biochemical and physiological levels. The crystal structure of TesA was determined at 1.9 Å and structural differences were identified, providing a possible explanation for the differences in substrate specificities. The comparison of TesA with other GDSL-hydrolase structures revealed that the flexibility of active-site loops significantly affects their substrate specificity. This assumption was tested using a rational approach: we have engineered the putative coenzyme A thioester binding site of E. coli TAP into TesA of P. aeruginosa by introducing mutations D17S and L162R. This TesA variant showed increased thioesterase activity comparable to that of TAP. TesA is the first lysophospholipase A described for the opportunistic human pathogen P. aeruginosa. The enzyme is localized in the periplasm and may exert important functions in the homeostasis of phospholipids or detoxification of lysophospholipids

Bacterial lipases

Many different bacterial species produce lipases which hydrolyze esters of glycerol with preferably long-chain fatty acids. They act at the interface generated by a hydrophobic lipid substrate in a hydrophilic aqueous medium. A characteristic property of lipases is called interfacial activation, meaning a sharp increase in lipase activity observed when the substrate starts to form an emulsion, thereby presenting to the enzyme an interfacial area. As a consequence, the kinetics of a lipase reaction do not follow the classical Michaelis-Menten model. With only a few exceptions, bacterial lipases are able to completely hydrolyze a triacylglycerol substrate although a certain preference for primary ester bonds has been observed. Numerous lipase assay methods are available using coloured or fluorescent substrates which allow spectroscopic and fluorimetric detection of lipase activity. Another important assay is based on titration of fatty acids released from the substrate. Newly developed methods allow to exactly determine lipase activity via controlled surface pressure or by means of a computer-controlled oil drop tensiometer. The synthesis and secretion of lipases by bacteria is influenced by a variety of environmental factors like ions, carbon sources, or presence of non-metabolizable polysaccharides. The secretion pathway is known for Pseudomonas lipases with P. aeruginosa lipase using a two-step mechanism and P. fluorescens lipase using a one-step mechanism. Additionally, some Pseudomonas lipases need specific chaperone-like proteins assisting their correct folding in the periplasm. These lipase-specific foldases (Lif-proteins) which show a high degree of amino acid sequence homology among different Pseudomonas species are coded for by genes located immediately downstream the lipase structural genes. A comparison of different bacterial lipases on the basis of primary structure revealed only very limited sequence homology. However, determination of the three-dimensional structure of the P. glumae lipase indicated that at least some of the bacterial lipases will presumably reveal a conserved folding pattern called the α/β-hydrolase fold, which has been described for other microbial and human lipases. The catalytic site of lipases is buried inside the protein and contains a serine-protease-like catalytic triad consisting of the amino acids serine, histidine, and aspartate (or glutamate). The Ser-residue is located in a strictly conserved β-εSer-α motif. The active site is covered by a lid-like α-helical structure which moves away upon contact of the lipase with its substrate, thereby exposing hydrophobic residues at the protein's surface mediating the contact between protein and substrate. This movable lid-like α-helix explains at a molecular level the lipase-specific phenomenon of interfacial activation. At least some of the pathogenic bacterial species produce a lipase which has been studied with respect to its role as a virulence factor. Lipases of Propionibacterium acnes and Staphylococcus epidermidis may be involved in colonization and persistence of these bacteria on the human skin. Lipases of S. aureus and P. aeruginosa are produced during the bacterial infection process and, at least in vitro, considerably impair the function of different cell types involved in the human immune response like macrophages or platelets. The present state of knowledge suggests to classify the lipases as important bacterial virulence factors which exert their harmful effects in combination with other bacterial enzymes, in particular the phospholipases C. Most of the steadily increasing interest in bacterial lipases is based on their biotechnological applications which are partly based on their potential to catalyze not only hydrolysis but also synthesis of a variety of industrially valuable products. Optically active compounds, various esters and lactones are among the substances synthesized using bacterial lipases. Recently, an important application emerged with the addition of bacterial lipases to household detergents in order to reduce or even replace synthetic detergent chemicals which pose considerable environmental problems. As a main conclusion, lipases represent an extremely versatile group of bacterial extracellular enzymes that are capable of performing a variety of important reactions, thereby presenting a fascinating field tot future research.

How to Engineer Organic Solvent Resistant Enzymes: Insights from Combined Molecular Dynamics and Directed Evolution Study

Expanding synthetic capabilities to routinely employ enzymes in organic solvents (OSs) is a dream for protein engineers and synthetic chemists. Despite significant advances in the field of protein engineering, general and transferable design principles to improve the OS resistance of enzymes are poorly understood. Herein, we report a combined computational and directed evolution study of Bacillus subtlis lipase A (BSLA) in three OSs (i. e., 1,4-dioxane, dimethyl sulfoxide, 2,2,2-trifluoroethanol) to devise a rational strategy to guide engineering OS resistant enzymes. Molecular dynamics simulations showed that OSs reduce BSLA activity and resistance in OSs by (i) stripping off essential water molecules from the BLSA surface mainly through H-bonds binding; and (ii) penetrating the substrate binding cleft leading to inhibition and conformational change. Interestingly, integration of computational results with “BSLA-SSM” variant library (3439 variants; all natural diversity with amino acid exchange) revealed two complementary rational design strategies: (i) surface charge engineering, and (ii) substrate binding cleft engineering. These strategies are most likely applicable to stabilize other lipases and enzymes and assist experimentalists to design organic solvent resistant enzymes with reduced time and screening effort in lab experiments. © 2020 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGa

Are Directed Evolution Approaches Efficient in Exploring Nature’s Potential to Stabilize a Lipase in Organic Cosolvents?

Despite the significant advances in the field of protein engineering, general design principles to improve organic cosolvent resistance of enzymes still remain undiscovered. Previous studies drew conclusions to engineer enzymes for their use in water-miscible organic solvents based on few amino acid substitutions. In this study, we conduct a comparison of a Bacillus subtilis lipase A (BSLA) library—covering the full natural diversity of single amino acid substitutions at all 181 positions of BSLA—with three state of the art random mutagenesis methods: error-prone PCR (epPCR) with low and high mutagenesis frequency (epPCR-low and high) as well as a transversion-enriched Sequence Saturation Mutagenesis (SeSaM-Tv P/P) method. Libraries were searched for amino acid substitutions that increase the enzyme’s resistance to the water-miscible organic cosolvents 1,4-dioxane (DOX), 2,2,2-trifluoroethanol (TFE), and dimethyl sulfoxide (DMSO). Our analysis revealed that 5%–11% of all possible single substitutions (BSLA site-saturation mutagenesis (SSM) library) contribute to improved cosolvent resistance. However, only a fraction of these substitutions (7%–12%) could be detected in the three random mutagenesis libraries. To our knowledge, this is the first study that quantifies the capability of these diversity generation methods generally employed in directed evolution campaigns and compares them to the entire natural diversity with a single substitution. Additionally, the investigation of the BSLA SSM library revealed only few common beneficial substitutions for all three cosolvents as well as the importance of introducing surface charges for organic cosolvent resistance—most likely due to a stronger attraction of water molecules. © 2017 by the authors

Metabolic Engineering of Pseudomonas putida KT2440 for enhanced rhamnolipid production

The production of chemicals and fuels is mainly based on fossil resources. The reduced availability of these resources and thus the increasing prices for crude oil as well as the resulting pollution of the environment require alternative strategies to be developed. One approach is the employment of microorganisms for the production of platform molecules using renewable resources as substrate. Biosurfactants, such as rhamnolipids, are an example for such products as they can be naturally produced by microorganisms and are biodegradable in contrast to chemical surfactants. The bio-based production of chemicals has to be efficient and sustainable to become competitive on the market. Several strategies can be applied to increase the efficiency of a microbial cell factory, e.g., streamlining the chassis. Here, we show the heterologous production of rhamnolipids with the non-pathogenic Pseudomonas putida KT2440 with the aim of increasing the yield. P. putida KT2440 is a well-characterized microorganism and its genome is sequenced and well annotated. Thus, the targeted removal of genes is possible and can lead to a reduction of the metabolic burden and by-product formation, which can result in a higher yield. Furthermore, the efficient supply of precursors is an important factor for optimized production processes. Rhamnolipids are amphiphilic molecules containing rhamnose and ß-hydroxy fatty acids. These precursors are synthesized by two pathways, the fatty acid de novo synthesis and the rhamnose pathway. We performed gene deletions to avoid the synthesis of by-products, like pyoverdine, exopolysaccharides, and large surface proteins and energy consuming devices as the flagellum. Most of the genome-reduced mutants reached a higher yield compared to the strain with wildtype background. With the best chassis, the yield could be increased by 35%. Furthermore, we conducted the overexpression of genes for precursor supply, either plasmid-based or genomically integrated. In this regard, the genes for the phosphoglucomutase, the complete rhamnose-synthesis pathway operon, and different enzymes in the pathway for acetyl-CoA synthesis were targeted. Various combinations were tested, and the highest yield reached was 51% higher compared to the initial rhamnolipid producer. Finally, a genome-reduced mutant was equipped with the overexpression modules and the rhamnolipid titer was increased from approximately 590 mg/L for the wildtype background to 960 mg/L, which represents a 63% increase. In conclusion, we were able to enhance the yield of rhamnolipids per glucose using metabolic engineering

Engineering a lipase for organic cosolvent resistance - How do current directed evolution approaches compete with the potential that nature offers?

Our desire to design enzymes resistant to organic cosolvents is still challenged by our level of molecular understanding of this important issue. This is why currently directed evolution is utilized as the method of choice to discover promising enzyme variants. As directed evolution-based studies typically report only few beneficial amino acid exchanges, the deduction of general principles for the design of enzymes with increased resistance to water/organic solvent mixtures is challenging. Here, we present the comparative analysis of a Bacillus subtilis lipase A (BSLA) library, covering the full diversity of single amino acid exchanges at all 181 positions of BSLA (BSLA SSM library), and three random mutagenesis libraries (error-prone PCR with low and high mutagenesis frequencies, as well as a transversion-enriched Sequence Saturation Mutagenesis (SeSaM-Tv P/P) library). Screening of the BSLA SSM library for resistance to the water-miscible organic cosolvents 1,4‑dioxane (DOX), 2,2,2 trifluoroethanol (TFE), and dimethyl sulfoxide (DMSO) revealed that 5 – 11% of all possible single substitutions promote organic cosolvent resistance. However, only 7 – 12% of these beneficial substitutions were identified in the three random mutagenesis libraries. To our knowledge, this is the first study quantifying the number of beneficial substitutions obtainable by random mutagenesis compared to the total number of beneficial single-substitutions (BSLA SSM library). Moreover, comprehensive analysis of the BSLA SSM library revealed that only few beneficial amino acid substitutions were common for all three organic cosolvents tested. These findings illustrate that – even when the total single-substitution diversity is available – our understanding of organic cosolvent resistance still remains incomplete. Hence, deducing general design principles based on relatively few amino acid exchanges, as it is common practice in directed evolution campaigns, seems counterintuitive. Furthermore, analysis of the BSLA SSM library conferred valuable insights into the role of surface-exposed charges for organic cosolvent resistance. Structural inspection of beneficial variants revealed that this is due to the attraction of water rather than to the formation of salt bridges. Please click Additional Files below to see the full abstract