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Catalysts
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Recent Advances in Biocatalysis and Enzyme Engineering
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Recent Advances in Biocatalysis and Enzyme Engineering

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

Deadline for manuscript submissions: 15 May 2025 | Viewed by 4829

Special Issue Editors

Dr. Kaili Nie

E-Mail Website
Guest Editor
Beijing Key Laboratory of Bioprocess, National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
Interests: enzymes; biocatalysis; enzyme engineering; directed evolution; rational design; metabolic engineering
Special Issues, Collections and Topics in MDPI journals
Dr. Junfeng Liu

E-Mail Website
Guest Editor Assistant
Beijing Key Laboratory of Bioprocess, National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
Interests: biocatalysis; enzyme engineering; metabolic engineering

Special Issue Information

Dear Colleagues,

Biocatalysis refers to the utilization of enzymes, or whole cells, to catalyze a single- or multi-step chemical reaction, converting synthetic molecules or natural metabolites into value-added products. However, the industrial applications of biocatalysis are modest, perhaps in part because of the limitations of biocatalysts, such as limited enzyme availability, substrate scope, and operational stability. In recent decades, with the progress of new enzyme discovery, the engineering and evolution of proteins, machine learning for biocatalyst and route design, and metabolic pathway optimization, the limitations of biocatalysis have been greatly improved. With the rapid development of enzyme engineering and metabolic engineering, biocatalysis has been firmly established as a tool for synthesizing valuable products and performing chemically challenging reactions.

This Special Issue focuses on recent advances in biocatalysis and enzyme engineering, including enzyme design and evolution, metabolic pathway optimization, and biosynthetic route discovery. Methodological and theoretical approaches to biocatalysis design and the development of high-throughput screening methods for biocatalysis are also welcome.

If you would like to submit papers to this Special Issue or have any questions, please contact the in-house editor, Ms. Rita Lin ([email protected]).

Dr. Kaili Nie
Dr. Junfeng Liu
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

  • enzyme
  • biocatalysis
  • enzyme discovery
  • enzyme engineering
  • enzyme evolution
  • multienzymatic synthesis
  • metabolic engineering
  • metabolic pathway

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Published Papers (5 papers)

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Research

15 pages, 4052 KiB  
Article
Engineering of an Alkaline Feruloyl Esterase PhFAE for Enhanced Thermal Stability and Catalytic Efficiency Through Molecular Dynamics and FireProt
by Sheng Yang, Miaofang Lin, Jiyang Chen, Min Liu and Qi Chen
Catalysts 2025, 15(1), 92; https://doi.org/10.3390/catal15010092 - 19 Jan 2025
Viewed by 605
Abstract
Feruloyl esterases (FAEs) play critical roles in industrial applications such as food processing, pharmaceuticals, and paper production by breaking down plant cell walls and releasing ferulic acid. However, most bacterial FAEs function optimally in acidic environments, limiting their use in alkaline industrial processes. [...] Read more.
Feruloyl esterases (FAEs) play critical roles in industrial applications such as food processing, pharmaceuticals, and paper production by breaking down plant cell walls and releasing ferulic acid. However, most bacterial FAEs function optimally in acidic environments, limiting their use in alkaline industrial processes. Additionally, FAEs with alkaline activity often lack the thermal stability required for demanding industrial conditions. In this study, an alkaline feruloyl esterase, PhFAE, from Pandoraea horticolens was identified that exhibits high catalytic activity but suffers from thermal instability, restricting its broader industrial applications. To address this limitation, molecular dynamics simulations were used to analyze enzyme stability, and FireProt, an automated computational tool, was employed to design stabilizing mutations. The engineered S155F mutant demonstrated a 7.8-fold increase in half-life at 60 °C and a 1.72-fold improvement in catalytic efficiency (Kcat/Km), corresponding to 680% and 72% enhancements, respectively, compared to the wild-type enzyme. Molecular docking and dynamics simulations revealed that these enhancements were likely due to increased hydrophobic interactions and altered surface charge, which stabilized the enzyme’s structure. This study provides an effective strategy for improving the functional properties of FAEs and other industrial enzymes, broadening their applicability in diverse industrial processes. Full article
(This article belongs to the Special Issue Recent Advances in Biocatalysis and Enzyme Engineering)
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15 pages, 1682 KiB  
Article
High-Level Expression and Engineering of Candida antarctica Lipase B in a Non-Methanol-Induced Pichia pastoris System
by Xinkun Lu, Bin Chen, Xiaowei Shen, Ziheng Cui and Biqiang Chen
Catalysts 2025, 15(1), 27; https://doi.org/10.3390/catal15010027 - 30 Dec 2024
Viewed by 616
Abstract
The efficient expression and excellent thermal stability of Candida antarctica lipase B (CALB) are crucial for its industrial production. In this study, through genetic engineering and rational design, while preserving the superior catalytic properties of CALB, we optimized the induction pathway using glycerol [...] Read more.
The efficient expression and excellent thermal stability of Candida antarctica lipase B (CALB) are crucial for its industrial production. In this study, through genetic engineering and rational design, while preserving the superior catalytic properties of CALB, we optimized the induction pathway using glycerol as the sole carbon source; moreover, the thermal stability sites of CALB were predicted and optimized. The results revealed that the level of CALB expression in this expression system reached 2.27 g/L under the condition of a 5 L fermenter. The Tm value of the CALB-Q231F increased by 10 °C. Moreover, after thermal inactivation at 80 °C for 1 h, the retention rate of esterification enzymatic activity over 24 h was 2.99 times that of wild-type (WT) CALB, whereas the retention rate of hydrolytic enzymatic activity was 2.23 times that of WT CALB. In this study, a non-methanol-induced Pichia pastoris expression system was successfully designed and constructed; a non-methanol-induced CALB-producing strain, X33-pGAPZ(Mα) A-CalB-Q231F, with high thermal stability and a high expression level was obtained, which can be used for the development of industrial enzymes. Full article
(This article belongs to the Special Issue Recent Advances in Biocatalysis and Enzyme Engineering)
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10 pages, 3760 KiB  
Article
An Enzyme Mimicking Dendritic Platinum–Iron Oxide Catalyzes the Production of Reactive Oxygen Species
by Feng Feng, Yajing Liu, Li Yao and Xiuyu Wang
Catalysts 2024, 14(12), 858; https://doi.org/10.3390/catal14120858 - 26 Nov 2024
Viewed by 674
Abstract
Creatine catalase (CAT), superoxide dismutase (SOD), and NADPH oxidase (NOX) are natural enzyme molecules that play a crucial role in regulating reactive oxygen species (ROS) in biological systems. They maintain life activities and eliminate pathogens by catalyzing various biochemical reactions. However, natural enzymes [...] Read more.
Creatine catalase (CAT), superoxide dismutase (SOD), and NADPH oxidase (NOX) are natural enzyme molecules that play a crucial role in regulating reactive oxygen species (ROS) in biological systems. They maintain life activities and eliminate pathogens by catalyzing various biochemical reactions. However, natural enzymes have some drawbacks in ROS control; they may lose activity under certain environmental conditions, such as high temperatures, extreme pH values, or the presence of organic solvents, which affects their stability and reliability in different applications. The construction of artificial nanozymes is an emerging technology that could probably solve the problems existing in natural enzymes. This study introduces a type of dendritic platinum–iron oxide (DPIO) nanozyme. The unique dendritic structure of this DPIO nanozyme provides a high surface area-to-volume ratio, and the addition of a platinum layer on the surface offers stability, thereby effectively enhancing the catalytic efficiency of producing reactive oxygen species (ROS). The combination of iron-based Fenton reactions and platinum-based Fenton-like reactions in this DPIO nanozyme drastically improves ROS catalytic efficiency. This artificial nanozyme has a high level of biosafety and displays no cytotoxicity. The development of DPIO nanozymes marks a significant advancement in the technology of artificial nanozymes. Full article
(This article belongs to the Special Issue Recent Advances in Biocatalysis and Enzyme Engineering)
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11 pages, 1431 KiB  
Article
Efficient Catalytic Conversion of Acetate to Citric Acid and Itaconic Acid by Engineered Yarrowia lipolytica
by Yuchen Ning, Renwei Zhang, Huan Liu, Yue Yu, Li Deng and Fang Wang
Catalysts 2024, 14(10), 710; https://doi.org/10.3390/catal14100710 - 10 Oct 2024
Viewed by 1220
Abstract
The bioconversion of agricultural and industrial wastes is considered a green and sustainable alternative method for producing high-value biochemicals. As a major catalytic product of greenhouse gases and a by-product in the fermentation and lignocellulose processing industries, acetate is a promising bioconversion raw [...] Read more.
The bioconversion of agricultural and industrial wastes is considered a green and sustainable alternative method for producing high-value biochemicals. As a major catalytic product of greenhouse gases and a by-product in the fermentation and lignocellulose processing industries, acetate is a promising bioconversion raw material. In this work, endogenous and heterologous enzymes were manipulated in Yarrowia lipolytica to achieve the conversion of acetate to high-value citric acid and itaconic acid, respectively. After the combinational expression of the key enzymes in the acetate metabolic pathway, the citric acid synthesis pathway, and the mitochondrial transport system, acetate could be efficiently converted to citric acid. Coupled with the down-regulation of fatty acid synthase expression in the competitive pathway, more acetyl-CoA flowed into the synthesis of citric acid, and the titer reached 15.11 g/L with a productivity of 0.51 g/g acetate by the engineered Y. lipolytica, which is comparable to the results using glucose as the substrate. On this basis, the heterologous cis-aconitate decarboxylase from Aspergillus terreus was introduced into the engineered Y. lipolytica to achieve the catalytic synthesis of itaconic acid from acetate. Combined with investigating the effects of multiple enzymes in the synthesis pathway, the titer of itaconic acid reached 1.87 g/L with a yield of 0.43 g/g DCW by the final engineered strain, which is the highest reported titer of itaconic acid derived from acetate by engineered microbes in shake flasks. It is demonstrated that acetate has the potential to replace traditional starch-based raw materials for the synthesis of high-value organic acids and our work lays a foundation for the rational utilization of industrial wastes and the catalytic products of greenhouse gases. Full article
(This article belongs to the Special Issue Recent Advances in Biocatalysis and Enzyme Engineering)
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14 pages, 6507 KiB  
Article
Enhanced Catalytic Synthesis of Flavonoid by UV-B Radiation in Artemisia argyi
by Haike Gu, Shuang Liu, Guoyu Li, Li Hou, Tengyuan Shen, Meifang Song and Junfeng Liu
Catalysts 2024, 14(8), 504; https://doi.org/10.3390/catal14080504 - 5 Aug 2024
Cited by 1 | Viewed by 1000
Abstract
Enzymatic synthesis of specific active substances is an important foundation for biological adaptations to various stresses. In this study, we investigated the metabolic response of the medicinal herb Artemisia argyi to UV-B radiation through transcriptome and metabolome analysis. In all tested samples, there [...] Read more.
Enzymatic synthesis of specific active substances is an important foundation for biological adaptations to various stresses. In this study, we investigated the metabolic response of the medicinal herb Artemisia argyi to UV-B radiation through transcriptome and metabolome analysis. In all tested samples, there were 544 shared differentially expressed genes, most of which were linked to the metabolism of flavonoids and fatty acids. A total of 283 differential metabolites were identified and classified into 10 categories, with flavonoids being the largest category. Through an integrated analysis of genes and metabolites involved in flavonoid biosynthesis, flavonoids were predicted to be critical for the adaptation of A. argyi to UV radiation. The increased plant hormones methyl jasmonate and salicylic acid were considered as key regulatory approaches for catalyzing the large-scale synthesis of flavonoids. We explored this by investigating the flavonoid production of A. argyi grown at different altitudes. It showed that total flavonoid content of A. argyi planted in high-altitude areas was 45% higher than that in low-altitude areas. These findings not only deepen our understanding of flavonoid anabolism and its regulation but also provide a reliable strategy for improving flavonoid content in the genus Artemisia. Full article
(This article belongs to the Special Issue Recent Advances in Biocatalysis and Enzyme Engineering)
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