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Tesis inédita de la Universidad Autónoma de Madrid, Facultad de Ciencias. Fecha de lectura: 03-10-2019. Esta tesis tiene embargado el acceso al texto completo hasta el 11-03-2020, [EN] The aryl-alcohol oxidase (AAO) is a fungal flavoenzyme that supplies H2O2 to the ligninolytic consortium during natural wood decay. Being active on a wide array of aromatic alcohols, this GMC oxidase presents a highly enantioselective mechanism of great interest in organic synthesis processes. The most powerful strategy for the AAO to meet industrial standards is the engineering of its properties by directed evolution. In the present Doctoral Thesis, an evolutionary platform for the AAO from Pleurotus eryngii was developed in order to: (i) obtain functional expression in yeasts, (ii) design a secondary benzyl-alcohol oxidase, and (iii) explore the enzymatic conversion of furfural derivatives. To achieve functional expression in Saccharomyces cerevisiae, the AAO gene was fused to different signal peptides including chimeric versions of the mating-α factor and the killer K1 toxin preprosequences. The platform for in vitro evolution was completed with a dual high-throughput screening assay to detect H2O2 that included a method based on the Fenton reaction. To enhance secretion, several libraries were created combining classical evolution (i.e. mutagenic PCR and DNA shuffling) with structure-guided evolution by MORPHING. The final secretion variant FX9, carried four mutations in the signal peptide and two substitutions in the mature protein including the consensus/ancestral H91N. The FX9 improved secretion up to 4.5 mg/L and presented high stability and kinetic values similar to the native enzyme. FX9 was cloned and expressed in Pichia pastoris maintaining expression levels and main biochemical properties. When the production was scaled-up in 5L fermenter, AAO production was increased to 25.5 mg/L. FX9 was further evolved to selectively oxidize secondary benzyl alcohols. The residual activity on chiral molecules was unlocked with the modulation for the catalytic pocket by combinatorial saturation mutagenesis. After four generations, that included a site-directed recombination step to polish mutations, LanDo variant harbored five new substitutions increasing the catalytic efficiency with 1-(p-methoxyphenyl)-ethanol in 3 orders of magnitude with a 99% ee. Exploring the transformation of 5-hydroxymethylfurfural (HMF) into furan-2,5-dicarboxylic acid (FDCA), FX9 acquired mutation F501W that improved catalytic efficiency on HMF 3-fold and showed for the first time the performance of three consecutive oxidations for the AAO., [ES] La aril-alcohol oxidasa (AAO) es una flavoenzima fúngica que suple H2O2 al consorcio ligninolítico durante la degradación natural de la madera. Siendo activa con una amplia variedad de alcoholes aromáticos, esta oxidasa GMC presenta un mecanismo altamente enantioselectivo de gran interés en procesos de síntesis orgánica. La estrategia más potente para adaptar a la AAO a estándares industriales es la ingeniería de sus propiedades mediante técnicas de evolución dirigida. En la presente Tesis Doctoral, una plataforma evolutiva para la AAO de Pleurotus eryngii fue desarrollada con el objetivo de: (i) obtener expresión funcional en levaduras, (ii) diseñar una aril-alcohol oxidasa activa con alcoholes secundarios, y (iii) explorar la conversión enzimática de derivados del furfural. Para obtener expresión funcional en Saccharomyces cerevisiae, el gen de la AAO se fusionó a diferentes péptidos señales incluyendo versiones quiméricas de las secuencias prepro del factor-α y la toxina killer K1. La plataforma para la evolución in vitro se completó con un ensayo dual de screening para la detección de H2O2 incluyendo un método basado en la reacción de Fenton. Para mejorar la secreción, se crearon varias librerías combinando evolución clásica (PCR mutagénica y DNA shuffling) con evolución focalizada con el método MORPHING. La variante final FX9, con alta estabilidad y constantes cinéticas similares a la enzima nativa, presentó cuatro mutaciones en el péptido señal y dos substituciones en la proteína madura incluyendo la consenso/ancestral H91N. FX9 se expresó en S. cerevisiae con valores de 4.5 mg/L y fue posteriormente clonada y expresada en Pichia pastoris a escala de fermentador de 5 L alcanzando niveles de secreción 25.5 mg/L y manteniendo sus propiedades bioquímicas generales. La variante FX9 fue sometida a posteriores ciclos de evolución, incluyendo el remodelado del bolsillo catalítico por mutagénesis saturada combinatorial, para la oxidación de alcoholes bencílicos secundarios. Las cinco mutaciones introducidas en la variante LanDo aumentaron la eficiencia catalítica con 1-(p-methoxyphenyl)-ethanol en 3 órdenes de magnitud con un 99 % ee. Explorando la transformación del 5-hydroxymethylfurfural (HMF) en furan-2,5-dicarboxylic acid (FDCA), FX9 adquirió la mutación F501W que mejoró 3 veces la eficiencia catalítica con HMF y demostró por primera vez la catálisis de 3 oxidaciones consecutivas para la AAO., Optimized oxidoreductases for medium and large scale industrial biotransformations (INDOX FP7-KBBE-2013-7-613549)” y “New enzymatic oxidation/oxyfunctionalization technologies for added value bio-based products. (ENZOX2 H2020-BBI-PPP-2015-2-720297)”. Los proyectos nacionales “Evolución dirigida de oxidoreductasas ligninolíticas modernas y ancestrales para el diseño de una levadura de podredumbre blanca (DEWRY BIO2013-43407-R)”, “Evolución dirigida y computacional de ligninasas (LIGNOLUTION BIO2016-79106-R)“ y “Química sintética mediante enzimas quiméricas de fusión diseñadas por evolución dirigida y computacional (EVOCHIMERA Y2018/BIO-4738)”. También agradecerle apoyo de la red Europea COST (http://www.cost.eu/)

[EN] Aryl alcohol oxidase (AAO) is a fungal flavoenzyme capable of oxidizing aromatic primary alcohols into their correspondent aldehydes through a stereoselective hydride abstraction. Unfortunately, this enzyme does not act on secondary benzyl alcohols in racemic mixtures due to the strict control of substrate diffusion and positioning at the active site restricted to primary benzyl alcohols. Here we describe the engineering of AAO from Pleurotus eryngii to oxidize chiral benzyl alcohols with high enantioselectivity. The secondary benzyl alcohol oxidase was remodeled at the active site through four cycles of structure‐guided evolution, including a final step of in vivo site‐directed recombination to address the positive epistatic interactions between mutations. The final variant, with five substitutions and a renovated active site, was characterized at biochemical and computational level. The mutational sculpting helped position the bulkier (S)‐1‐(p‐methoxyphenyl)‐ethanol, improving the mutant's catalytic efficiency by three orders of magnitude relative to the native enzyme while showing a high enantioselectivity (ee >99%). As a promising candidate for racemic resolution, this evolved secondary benzyl alcohol oxidase maintained its natural stereoselective mechanism while displaying activity on several secondary benzyl alcohols., This research was supported by the EU project FP7‐KBBE‐2013‐7‐613549‐INDOX, by the Spanish Government projects BIO2016‐79106‐R‐Lignolution, CTQ2016‐74959‐R (MINECO/FEDER, EU) and by the Comunidad de Madrid project Y2018/BIO4738‐EVOCHIMERA.

[EN] The ligninolytic enzyme consortium is one of the most-efficient oxidative systems found in nature, playing a pivotal role during wood decay and coal formation. Typically formed by high redox-potential oxidoreductases, this array of enzymes can be used within the emerging lignocellulose biorefineries in processes that range from the production of bioenergy to that of biomaterials. To ensure that these versatile enzymes meet industry standards and needs, they have been subjected to directed evolution and hybrid approaches that surpass the limits imposed by nature. This Opinion article analyzes recent achievements in this field, including the incipient groundbreaking research into the evolution of resurrected enzymes, and the engineering of ligninolytic secretomes to create consolidated bioprocessing microbes with synthetic biology applications., European Commission projects Indox-FP7-KBBE-2013-7-613549; Bioenergy-FP7-PEOPLE-2013-ITN-607793; Cost Action CM1303 Systems Biocatalysis; and the National projects Evofacel (BIO2010-19697), Dewry (BIO201343407-R], and Cambios (RTC-2014-1777-3).

[EN] Laccases are multicopper oxidoreductases considered by many in the biotechonology field as the ultimate >green catalysts>. This is mainly due to their broad substrate specificity and relative autonomy (they use molecular oxygen from air as an electron acceptor and they only produce water as by-product), making them suitable for a wide array of applications: biofuel production, bioremediation, organic synthesis, pulp biobleaching, textiles, the beverage and food industries, biosensor and biofuel cell development. Since the beginning of the 21st century, specific features of bacterial and fungal laccases have been exhaustively adapted in order to reach the industrial demands for high catalytic activity and stability in conjunction with reduced production cost. Among the goals established for laccase engineering, heterologous functional expression, improved activity and thermostability, tolerance to non-natural media (organic solvents, ionic liquids, physiological fluids) and resistance to different types of inhibitors are all challenges that have been met, while obtaining a more comprehensive understanding of laccase structure-function relationships. In this review we examine the most significant advances in this exciting research area in which rational, semi-rational and directed evolution approaches have been employed to ultimately convert laccases into high value-added biocatalysts., EU (FP7-KBBE-2013-7-613549-INDOX, FP7-People2013-ITN-607793 and COST-Action CM1303 Systems Biocatalysis) and the Spanish Government (BIO2010-19697-EVOFACEL, BIO2013-43407-RDEWRY and CAMBIOS-RTC-2014-1777-3)

The ligninolytic enzymatic consortium produced by white-rot fungi is one of the most efficient oxidative systems found in nature, with many potential applications that range from the production of 2nd generation biofuels to chemicals synthesis. In the current study, two high redox potential oxidoreductase fusion genes (laccase -Lac and versatile peroxidase -Vp-) that had been evolved in the laboratory were re-assembled in Saccharomyces cerevisiae. First, cell viability and secretion were assessed after co-transforming the Lac and Vp genes into yeast. Several expression cassettes were inserted in vivo into episomal bi-directional vectors in order to evaluate inducible promoter/terminator pairs of different strengths in an individual and combined manner. The synthetic white-rot yeast model harboring Vp(GAL1/CYC1)-Lac(GAL10/ADH1) displayed up to 1000 and 100 Units per L of peroxidase and laccase activity, respectively, representing a suitable point of departure for future synthetic biology studies. © 2014 Landes Bioscience. Do not distribute., This work was supported by European Commission Projects (Peroxicats-FP7-KBBE-2010-4-26537; Indox-FP7-KBBE-2013-7-613549; COST-Action CM1303: Systems Biocatalysis) and the National Project (Evofacel-cel-BIO2010-19697)

Unspecific peroxygenase (UPO) is a highly efficient biocatalyst with a peroxide dependent monooxygenase activity and many biotechnological applications, but the absence of suitable heterologous expression systems has precluded its use in different industrial settings. Recently, the UPO from Agrocybe aegerita was evolved for secretion and activity in Saccharomyces cerevisiae [8]. In the current work, we describe a tandem-yeast expression system for UPO engineering and large scale production. By harnessing the directed evolution process in S. cerevisiae, the beneficial mutations for secretion enabled Pichia pastoris to express the evolved UPO under the control of the methanol inducible alcohol oxidase 1 promoter. Whilst secretion levels were found similar for both yeasts in flask fermentation (~8. mg/L), the recombinant UPO from P. pastoris showed a 27-fold enhanced production in fed-batch fermentation (217. mg/L). The P. pastoris UPO variant maintained similar biochemical properties of the S. cerevisiae counterpart in terms of catalytic constants, pH activity profiles and thermostability. Thus, this tandem-yeast expression system ensures the engineering of UPOs to use them in future industrial applications as well as large scale production., EU (FP7-KBBE-2013-7-613549-INDOX, FP7-People-2013-ITN-607793, COST-Action CM1303 Systems Biocatalysis) and the Spanish Government (BIO2010-19697-EVOFACEL, BIO2013-43407-R-DEWRY and CAMBIOS-RTC-2014-1777-3 projects).

[EN] Aryl-alcohol oxidase (AAO) is an extracellular flavoprotein that supplies ligninolytic peroxidases with H2O2 during natural wood decay. With a broad substrate specificity and highly stereoselective reaction mechanism, AAO is an attractive candidate for studies into organic synthesis and synthetic biology, and yet the lack of suitable heterologous expression systems has precluded its engineering by directed evolution. In this study, the native signal sequence of AAO from Pleurotus eryngii was replaced by those of the mating -factor and the K1 killer toxin, as well as different chimeras of both prepro-leaders in order to drive secretion in Saccharomyces cerevisiae. The secretion of these AAO constructs increased in the following order: prepro-AAO > preproK-AAO > preKpro-AAO > preproK-AAO. The chimeric preproK-AAO was subjected to focused-directed evolution with the aid of a dual screening assay based on the Fenton reaction. Random mutagenesis and DNA recombination was concentrated on two protein segments (Met[1]-Val109 and Phe392-Gln566), and an array of improved variants was identified, among which the FX7 mutant (harboring the H91N mutation) showed a dramatic 96-fold improvement in total activity with secretion levels of 2 mg/liter. Analysis of the N-terminal sequence of the FX7 variant confirmed the correct processing of the preproK hybrid peptide by the KEX2 protease. FX7 showed higher stability in terms of pH and temperature, whereas the pH activity profiles and the Kinetic parameters were maintained. The Asn91 lies in the flavin attachment loop motif, and it is a highly conserved residue in all members of the GMC superfamily, except for P. eryngii and P. pulmonarius AAO. The in vitro involution of the enzyme by restoring the consensus ancestor Asn91 promoted AAO expression and stability., This study was supported by the European Commission projects Indox FP7-KBBE-2013-7-613549 and Cost-Action CM1303-Systems Biocatalysis and by the National Projects Dewry (BIO201343407-R) and Cambios (RTC-2014-1777-3).

Approaches that depend on directed evolution require reliable methods to generate DNA diversity so that mutant libraries can focus on specific target regions. We took advantage of the high frequency of homologous DNA recombination in Saccharomyces cerevisiae to develop a strategy for domain mutagenesis aimed at introducing and in vivo recombining random mutations in defined segments of DNA. Mutagenic Organized Recombination Process by Homologous IN vivo Grouping (MORPHING) is a one-pot random mutagenic method for short protein regions that harnesses the in vivo recombination apparatus of yeast. Using this approach, libraries can be prepared with different mutational loads in DNA segments of less than 30 amino acids so that they can be assembled into the remaining unaltered DNA regions in vivo with high fidelity. As a proof of concept, we present two eukaryotic-ligninolytic enzyme case studies: i) the enhancement of the oxidative stability of a H2O2-sensitive versatile peroxidase by independent evolution of three distinct protein segments (Leu28-Gly57, Leu149-Ala174 and Ile199-Leu268); and ii) the heterologous functional expression of an unspecific peroxygenase by exclusive evolution of its native 43-residue signal sequence. © 2014 Gonzalez-Perez et al., This work was supported by the European Comission Projects Peroxicats-FP7-KBBE-2010-4-26537 and Indox-FP7-KBBE-2013-7-613549 and the National Project (Evofacel) [BIO2010-19697]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Unspecific peroxygenase (UPO) represents a new type of heme-thiolate enzyme with self-sufficient mono(per)oxygenase activity and many potential applications in organic synthesis. With a view to taking advantage of these properties, we subjected the Agrocybe aegerita UPO1-encoding gene to directed evolution in Saccharomyces cerevisiae. To promote functional expression, several different signal peptides were fused to the mature protein, and the resulting products were tested. Over 9,000 clones were screened using an ad hoc dual-colorimetric assay that assessed both peroxidative and oxygen transfer activities. After 5 generations of directed evolution combined with hybrid approaches, 9 mutations were introduced that resulted in a 3,250-fold total activity improvement with no alteration in protein stability. A breakdown between secretion and catalytic activity was performed by replacing the native signal peptide of the original parental type with that of the evolved mutant; the evolved leader increased functional expression 27-fold, whereas an 18-fold improvement in the kcat/Km value for oxygen transfer activity was obtained. The evolved UPO1 was active and highly stable in the presence of organic cosolvents. Mutations in the hydrophobic core of the signal peptide contributed to enhance functional expression up to 8 mg/liter, while catalytic efficiencies for peroxidative and oxygen transfer reactions were increased by several mutations in the vicinity of the heme access channel. Overall, the directed-evolution platform described is a valuable point of departure for the development of customized UPOs with improved features and for the study of structure-function relationships. © 2014, American Society for Microbiology., This work was supported by European Commission Projects (Peroxicats-FP7-KBBE-2010-4-26537 and Indox-FP7-KBBE-2013-7-613549) and the National Project (Evofacel) (BIO2010-19697).

[EN] Versatile peroxidases (VP) are promiscuous biocatalysts with the highest fragility to hydroperoxides yet reported due to a complex molecular architecture, with three catalytic sites and several oxidation pathways. To improve the VP resistance to H2O2, an evolved version of this enzyme was subjected to a range of directed evolution and hybrid strategies in Saccharomyces cerevisiae. After five generations of random, saturation, and domain mutagenesis, together with in vivo DNA recombination, several structural determinants behind the oxidative destabilization of the enzyme were unmasked. To establish a balance between activity and stability, selected beneficial mutations were introduced into novel mutational environments by the in vivo exchange of sequence blocks, promoting epistatic interactions. The best variant of this process accumulated 8 mutations that increased the half-life of the protein from 3 (parental type) to 35 min in the presence of 3000 equiv of H2O2 and with a 6 °C upward shift in thermostability. Multiple structural alignment with other H2O2-tolerant heme peroxidases help to understand the possible roles played by the new mutations in the overall oxidative stabilization of these enzymes., European Commission Projects (Peroxicats-FP7-KBBE-2010-4-26537; Indox-FP7-KBBE-2013-7-613549; COST-Action CM1303: Systems Biocatalysis) and the National Projects (Evofacel) [BIO2010-19697], (Dewry) [BIO2013-43407-R] and Hipop (BIO2011-26694). F.J.R.-D. is grateful for the award of a “Ramón y Cajal” contract of the Spanish MINECO.