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New Trends in Industrial Biocatalysis
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New Trends in Industrial Biocatalysis

A special issue of Catalysts (ISSN 2073-4344). This special issue belongs to the section "Biocatalysis".

Deadline for manuscript submissions: closed (20 December 2023) | Viewed by 17469

Special Issue Editors

Prof. Dr. Rosa María Oliart-Ros

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Guest Editor
Unidad de Investigación y Desarrollo en Alimentos, Tecnológico Nacional de México/Instituto Tecnológico de Veracruz, Veracruz 91897, Mexico
Interests: extremozymes; extremophiles; biocatalysis; lipolytic enzymes; metagenomics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. María Guadalupe Sánchez-Otero

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Guest Editor
Facultad de Bioanálisis, Universidad Veracruzana, Veracruz 91000, Mexico
Interests: extremophiles; extremozymes; biocatalysis; lipases; enzyme immobilization
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Today, industrial biocatalysis is particularly important for industrial biotechnology because it uses environmentally friendly, cost-effective and sustainable processes. The improvement of those processes involves the screening and isolation of novel biocatalysts with new properties and capacities, which can be undertaken by metagenomic approaches or classical isolation techniques, as well as the improvement of their performance by emerging techniques such as the production of immobilized and co-immobilized preparations on new matrices, the enhancement of enzymatic capacities through mutagenesis and directed evolution, accompanied by in silico prediction studies and structural elucidation of biomolecules. Other areas of interest are the finding of new reactions/products or the optimization of the existing ones by the use of non-conventional substrates and/or solvents, with application in pharmaceutical and food industries as prominent examples.

This Special Issue, “New Trends in Industrial Biocatalysis” intends to compile the most recent developments, techniques, and practices in the field of industrial biocatalysis. We encourage scientists working in biocatalysis, enzymatic biotechnology, and extremophilic enzymes applied in biocatalysis to publish their recent findings and results in areas such as enzyme, protein, and medium engineering for the improvement or establishment of biocatalytic processes; new nanomaterials, nanofibers, polymers and mesoporous materials such as MOFs to immobilize enzymes and improve catalytic functions; novel modifications in immobilization solid supports; new biocatalytic strategies to treat effluents; new strategies for cofactors recycling; or design and use of flow reactors or solid-state reactors in biocatalysis.

Prof. Dr. Rosa María Oliart-Ros
Prof. Dr. María Guadalupe Sánchez-Otero
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Catalysts is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Biocatalysis
  • Extremozymes
  • Immobilization
  • Metal–organic frameworks
  • Covalent–organic frameworks
  • Protein engineering
  • Mutagenesis

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Related Special Issue

Published Papers (7 papers)

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Research

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16 pages, 7158 KiB  
Article
Selection of Putative Polyester Hydrolases from the Metagenome of Los Humeros Geothermal Field by Means of In Silico Probes
by Rocio Solis-Palacios, Graciela Espinosa-Luna, Carolina Peña-Montes, Rodolfo Quintana-Castro, María Guadalupe Sánchez-Otero and Rosa María Oliart-Ros
Catalysts 2024, 14(6), 379; https://doi.org/10.3390/catal14060379 - 14 Jun 2024
Viewed by 1065
Abstract
Hydrolases are the most popular enzymes, and among the most valuable in biotechnological applications. Some hydrolases, such as lipases, esterases, proteases, cellulases and amylases, are used in the food industry and the production of biopharmaceuticals, biofuels, biopolymers and detergents. Of special interest are [...] Read more.
Hydrolases are the most popular enzymes, and among the most valuable in biotechnological applications. Some hydrolases, such as lipases, esterases, proteases, cellulases and amylases, are used in the food industry and the production of biopharmaceuticals, biofuels, biopolymers and detergents. Of special interest are those obtained from thermophilic microorganisms. Although there is great microbial diversity in extreme environments, the investigations aimed at detecting and isolating enzymes with potential for polyester degradation such as polyethylene terephthalate (PET) are limited. In this work, we explored the metagenomic library of an oil-enriched soil sample from the “Los Humeros” geothermal field by means of in silico probes in search for enzymes potentially able to degrade polyesters. Using conserved motifs and activity-relevant sites of reported polyester hydrolases, we designed probes that allowed us to identify 6 potential polyester hydrolases in the metagenome. Three-dimensional structure prediction revealed a canonical α/β fold and a cap covering the active site of the enzymes. The catalytic triads were composed of Ser, His and Asp. Structural comparison, substrate binding site analysis and molecular docking suggested their potential as polyester hydrolases, particularly cutinases and PETases. An enzyme, REC98271, was cloned, expressed and characterized, showing thermophilic properties and preference for short-chain substrates. These findings contribute to our understanding of enzyme diversity in “Los Humeros” metagenome and their potential applications in biodegradation and recycling processes. Full article
(This article belongs to the Special Issue New Trends in Industrial Biocatalysis)
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19 pages, 2357 KiB  
Article
Production of Prebiotic Galacto-Oligosaccharides from Acid Whey Catalyzed by a Novel β-Galactosidase from Thermothielavioides terrestris and Commercial Lactases: A Comparative Study
by Athanasios Limnaios, Maria Tsevdou, Elena Tsika, Nausika Korialou, Anastasia Zerva, Evangelos Topakas and Petros Taoukis
Catalysts 2023, 13(10), 1360; https://doi.org/10.3390/catal13101360 - 11 Oct 2023
Cited by 3 | Viewed by 1657
Abstract
The steadily increasing global popularity of Greek strained yoghurt has necessitated alternative valorization approaches for acid whey, the major straining process effluent. In this context, prebiotic galacto-oligosaccharides can be enzymatically synthesized from acid whey lactose, via either commercial or novel β-galactosidases. A comparative [...] Read more.
The steadily increasing global popularity of Greek strained yoghurt has necessitated alternative valorization approaches for acid whey, the major straining process effluent. In this context, prebiotic galacto-oligosaccharides can be enzymatically synthesized from acid whey lactose, via either commercial or novel β-galactosidases. A comparative study of galacto-oligosaccharide production from acid whey was carried out, employing two commercial β-galactosidases (from Kluyveromyces lactis and Aspergillus oryzae) and one novel, in-house produced (from Thermothielavioides terrestris), as a function of the initial lactose content and enzyme load. Selected reaction conditions for β-galactosidases from K. lactis, A. oryzae, and T. terrestris were 35 °C at pH 7.2, 45 °C at pH 4.5, and 50 °C at pH 4.0, respectively. Maximum galacto-oligosaccharide yields equal to 23.7, 23.4, and 25.7% were achieved with, respectively, 0.13 U/mL of K. lactis β-galactosidase in non-concentrated acid whey, 4 U/mL of A. oryzae β-galactosidase, and 8 U/mL of T. terrestris β-galactosidase in acid whey concentrated to 20% w/v initial lactose content. The increased galacto-oligosaccharide productivity of the thermophilic β-galactosidase from T. terrestris can be a determining asset in a combined concentration and oligomerization industrial process. This will allow for high galacto-oligosaccharide yields for efficient, cost-effective production of valuable prebiotics from acid whey. Full article
(This article belongs to the Special Issue New Trends in Industrial Biocatalysis)
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19 pages, 1992 KiB  
Article
Metabolic Biodegradation Pathway of Fluoranthene by Indigenous Trichoderma lixii and Talaromyces pinophilus spp.
by Samson O. Egbewale, Ajit Kumar, Mduduzi P. Mokoena and Ademola O. Olaniran
Catalysts 2023, 13(5), 791; https://doi.org/10.3390/catal13050791 - 23 Apr 2023
Cited by 5 | Viewed by 2149
Abstract
Two indigenous ascomycetes fungi, Trichoderma lixii strain FLU1 (TlFLU1) and Talaromyces pinophilus strain FLU12 (TpFLU12), were isolated from benzo(b)fluoranthene-enriched activated sludge and tested for bio-catalytically degrade fluoranthene as a sole carbon source. TlFLU1 and TpFLU12 degraded 98 [...] Read more.
Two indigenous ascomycetes fungi, Trichoderma lixii strain FLU1 (TlFLU1) and Talaromyces pinophilus strain FLU12 (TpFLU12), were isolated from benzo(b)fluoranthene-enriched activated sludge and tested for bio-catalytically degrade fluoranthene as a sole carbon source. TlFLU1 and TpFLU12 degraded 98 and 99% of 400 mg/L of fluoranthene after 16 and 12 d incubation period, respectively. Degradation correlated with the upregulation of expression of ligninolytic enzymes. The GC-MS and FTIR analysis of the degradation products suggest that the degradation is initiated at the C1-C2 position of the compound ring via oxygenation and ring cleavage to form 9-oxo-9H-fluorene-1-carboxylic acid before undergoing ring cleavage to yield fluorenone, which then proceeds through the ß-Ketoadipate pathway via benzene-1,2,3-tricarboxylic acid. The degradation rate is better fitted in the first-order and zero-order kinetic model for TlFLU1 and TpFLU12, respectively. The metabolites from the TlFLU1 degradation media are shown to be toxic in Vibryo parahaemolyticus after 6 h of exposure with effective concentration (EC50) and toxicity unit (TU) values of 14.25 mg/L and 7.018%, respectively, while also being observed as non-toxic from TpFLU12 degradation media with an EC50 and TU values of 197.1 mg/L and 0.507%, respectively. Results from this study show efficient metabolism of fluoranthene into an innocuous state by TlFLU1 and TpFLU12. Full article
(This article belongs to the Special Issue New Trends in Industrial Biocatalysis)
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14 pages, 9291 KiB  
Article
High Internal Phase Pickering Emulsion Stabilized by Lipase-Coated ZIF-8 Nanoparticles towards Recyclable Biphasic Biocatalyst
by Chuanbang Xu, Yan Sun, Yuanyuan Sun, Ruiyun Cai and Shengmiao Zhang
Catalysts 2023, 13(2), 383; https://doi.org/10.3390/catal13020383 - 10 Feb 2023
Cited by 8 | Viewed by 2585
Abstract
High internal phase Pickering emulsion (Pickering HIPE) stabilized by enzyme-decorated metal-organic frameworks (MOFs) nanoparticles is developed for biphasic biocatalysts to enhance lipase catalysis and recycling. Specifically, enzyme decorated nanoparticles are prepared via ZIF-8 physisorption of a model lipase Candida antarctica Lipase B (CALB), [...] Read more.
High internal phase Pickering emulsion (Pickering HIPE) stabilized by enzyme-decorated metal-organic frameworks (MOFs) nanoparticles is developed for biphasic biocatalysts to enhance lipase catalysis and recycling. Specifically, enzyme decorated nanoparticles are prepared via ZIF-8 physisorption of a model lipase Candida antarctica Lipase B (CALB), named ZIF-8@CALB, to be both Pickering stabilizer and catalytic sites. An oil-in-water (o/w) Pickering HIPE with oil/water volume ratio of 3 could then be fabricated by homogenizing p-nitrophenyl palmitate (p-NPP) n-heptane solution into the ZIF-8@CALB aqueous dispersion. The biocatalytic hydrolysis of p-NPP is conducted by just standing the biphasic system at room temperature. The Pickering HIPE system achieves a product conversion of up to 48.9% within 0.5 h, whereas the p-NPP n-heptane solution system containing free CALB only achieves a stable product conversion of 6.8% for the same time. Moreover, the ZIF@CALB could be recovered by a simple centrifugation at 800 rpm, and then reused in the next cycle. The hydrolysis equilibrium conversion rate of p-NPP keeps over 40% for all 8 cycles, reflecting the high catalytic efficiency and recyclability of the Pickering HIPE. This study provides a new opportunity in designing Enzyme-MOFs-based Pickering interfacial biocatalyst for practical applications. Full article
(This article belongs to the Special Issue New Trends in Industrial Biocatalysis)
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14 pages, 4646 KiB  
Article
Enhanced Thermal Stability of Polyphosphate-Dependent Glucomannokinase by Directed Evolution
by Heming Sun, Wenlong Zhu, Qinfei Zhang, Ruonan Zheng, Luo Liu and Hui Cao
Catalysts 2022, 12(10), 1112; https://doi.org/10.3390/catal12101112 - 26 Sep 2022
Cited by 1 | Viewed by 1667
Abstract
Polyphosphate-dependent glucomannokinase (PPGMK) is able to utilize inorganic polyphosphate to synthesize mannose-6-phosphate (M6P) instead of highly costly ATP. This enzyme was modified and designed by combining error-prone PCR (EP-PCR) and site-directed saturation mutagenesis. Two mutants, H92L/A138V and E119V, were screened out from the [...] Read more.
Polyphosphate-dependent glucomannokinase (PPGMK) is able to utilize inorganic polyphosphate to synthesize mannose-6-phosphate (M6P) instead of highly costly ATP. This enzyme was modified and designed by combining error-prone PCR (EP-PCR) and site-directed saturation mutagenesis. Two mutants, H92L/A138V and E119V, were screened out from the random mutation library, and we used site-specific saturation mutations to find the optimal amino acid at each site. Finally, we found the optimal combination mutant, H92K/E119R. The thermal stability of H92K/E119R increased by 5.4 times at 50 °C, and the half-life at 50 °C increased to 243 min. Moreover, the enzyme activity of H92K/E119R increased to 16.6 U/mg, and its enzyme activity is twice that of WT. We analyzed the structure of the mutant using molecular dynamics simulation. We found that the shortening of the hydrogen bond distance and the formation of salt bridges can firmly connect the α-helix and β-sheet and improve the stability of the PPGMK structure. Full article
(This article belongs to the Special Issue New Trends in Industrial Biocatalysis)
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Review

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20 pages, 19051 KiB  
Review
Engineering of GH11 Xylanases for Optimal pH Shifting for Industrial Applications
by In Jung Kim, Soo Rin Kim, Uwe T. Bornscheuer and Ki Hyun Nam
Catalysts 2023, 13(11), 1405; https://doi.org/10.3390/catal13111405 - 30 Oct 2023
Cited by 11 | Viewed by 2676
Abstract
Endo-1,4-β-xylanases belonging to the glycoside hydrolase (GH) 11 family hydrolyze the β-1,4-glycosidic linkages in the xylan backbone to convert polymeric xylan into xylooligosaccharides. GH11 xylanases play an essential role in sugar metabolism and are one of the most widely used enzymes in various [...] Read more.
Endo-1,4-β-xylanases belonging to the glycoside hydrolase (GH) 11 family hydrolyze the β-1,4-glycosidic linkages in the xylan backbone to convert polymeric xylan into xylooligosaccharides. GH11 xylanases play an essential role in sugar metabolism and are one of the most widely used enzymes in various industries, such as pulp and paper, food and feed, biorefinery, textile, and pharmaceutical industries. pH is a crucial factor influencing the biochemical properties of GH11 xylanase and its application in bioprocessing. For the optimal pH shifting of GH11 xylanase in industrial applications, various protein engineering studies using directed evolution, rational engineering, and in silico approaches have been adopted. Here, we review the functions, structures, and engineering methods developed for the optimal pH shifting of GH11 xylanases. The various GH11 engineering techniques and key residues involved in pH shifting are discussed based on their crystal and modeled structure. This review provides an overview of recent advancements in the characterization and engineering of GH11 xylanases, providing a guide for future research in this field. Full article
(This article belongs to the Special Issue New Trends in Industrial Biocatalysis)
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24 pages, 2064 KiB  
Review
Determinants for an Efficient Enzymatic Catalysis in Poly(Ethylene Terephthalate) Degradation
by José Augusto Castro-Rodríguez, Rogelio Rodríguez-Sotres and Amelia Farrés
Catalysts 2023, 13(3), 591; https://doi.org/10.3390/catal13030591 - 15 Mar 2023
Cited by 5 | Viewed by 4305
Abstract
The enzymatic degradation of the recalcitrant poly(ethylene terephthalate) (PET) has been an important biotechnological goal. The present review focuses on the state of the art in enzymatic degradation of PET, and the challenges ahead. This review covers (i) enzymes acting on PET, (ii) [...] Read more.
The enzymatic degradation of the recalcitrant poly(ethylene terephthalate) (PET) has been an important biotechnological goal. The present review focuses on the state of the art in enzymatic degradation of PET, and the challenges ahead. This review covers (i) enzymes acting on PET, (ii) protein improvements through selection or engineering, (iii) strategies to improve biocatalyst–polymer interaction and monomer yields. Finally, this review discusses critical points on PET degradation, and their related experimental aspects, that include the control of physicochemical parameters. The search for, and engineering of, PET hydrolases, have been widely studied to achieve this, and several examples are discussed here. Many enzymes, from various microbial sources, have been studied and engineered, but recently true PET hydrolases (PETases), active at moderate temperatures, were reported. For a circular economy process, terephtalic acid (TPA) production is critical. Some thermophilic cutinases and engineered PETases have been reported to release terephthalic acid in significant amounts. Some bottlenecks in enzyme performance are discussed, including enzyme activity, thermal stability, substrate accessibility, PET microstructures, high crystallinity, molecular mass, mass transfer, and efficient conversion into reusable fragments. Full article
(This article belongs to the Special Issue New Trends in Industrial Biocatalysis)
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