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Emerging Trends in Food Enzyme Catalysis and Food Synthetic Biology
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Emerging Trends in Food Enzyme Catalysis and Food Synthetic Biology

A special issue of Foods (ISSN 2304-8158). This special issue belongs to the section "Food Engineering and Technology".

Deadline for manuscript submissions: 30 September 2026 | Viewed by 3992

Special Issue Editors

Dr. Dongdong Mu

E-Mail Website
Guest Editor
College of Food and Biological engineering, Hefei University of Technology, Hefei 230009, China
Interests: food enzyme; food hydrocolloid; enzyme secretion; food protein modification; fermented food; food microbiology
Special Issues, Collections and Topics in MDPI journals
Dr. Xin Zhao

E-Mail Website
Guest Editor
Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
Interests: gut microbiota and microbial ecology; medicinal food and microbiome regulation; food microbiology
Prof. Dr. Yanglei Yi

E-Mail Website
Guest Editor
College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
Interests: molecular microbiology; synthetic biology; food safety; probiotics; food biotechnology; antimicrobials

Special Issue Information

Dear Colleagues,

Enzyme catalysis and synthetic biology have garnered increasing attention in food production and processing, driven by the demand for sustainable and efficient solutions. Conventional food processing methods often rely on chemical or physical approaches that may compromise nutritional quality, generate undesirable byproducts, or face consumer skepticism. In contrast, enzyme catalysis offers high specificity and mild reaction conditions, while synthetic biology enables the design of novel biosynthetic pathways for tailored food ingredients. Together, these technologies present a powerful approach to enhancing food quality, safety, and functionality while aligning with clean-label trends.

Despite their promise, challenges such as enzyme stability, scalability, regulatory acceptance, and public perception of bioengineered foods must be addressed for widespread adoption. Recent advances in protein engineering, CRISPR-based genome editing, and computational biology are accelerating innovation in this field. Emerging applications include precision fermentation for alternative proteins, enzymatic modification of food textures, and microbial cell factories for bioactive compound production. This Special Issue explores cutting-edge developments in food enzyme catalysis and synthetic biology, highlighting their potential to revolutionize food systems while addressing current limitations for future industrial implementation.

Dr. Dongdong Mu
Dr. Xin Zhao
Prof. Dr. Yanglei Yi
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 250 words) can be sent to the Editorial Office for assessment.

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. Foods is an international peer-reviewed open access semimonthly 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 2900 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
  • synthetic biology
  • food processing
  • food production
  • fermentation
  • enzymatic catalysis
  • modification

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Published Papers (6 papers)

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Research

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19 pages, 3300 KB  
Article
Molecular Engineering of Nicotinamide Riboside Kinase and Process Optimization for Efficient Nicotinamide Mononucleotide Production
by Dai Ma, Rui Liu, Tong Bao, Jingwen Yang, Hongbin Zhang and Xueqin Hu
Foods 2026, 15(11), 1838; https://doi.org/10.3390/foods15111838 - 22 May 2026
Viewed by 134
Abstract
Nicotinamide mononucleotide (NMN) plays vital physiological roles as a vitamin B derivative, with nicotinamide riboside kinase (NRK) serving as a key enzyme for its efficient and environmentally friendly synthesis. In this study, semi-rational design was employed to modify the Hi-NRK enzyme at [...] Read more.
Nicotinamide mononucleotide (NMN) plays vital physiological roles as a vitamin B derivative, with nicotinamide riboside kinase (NRK) serving as a key enzyme for its efficient and environmentally friendly synthesis. In this study, semi-rational design was employed to modify the Hi-NRK enzyme at the molecular level, leading to the identification of a critical mutant, Hi-NRKG8S. This variant exhibited a twofold increase in enzymatic activity and significantly enhanced thermal stability, extending its half-life at 40 °C from 4 to 8 h. By optimizing reaction conditions, NMN yield reached 94.17% at a nicotinamide riboside (NR) substrate concentration of 50 g/L. Further addition of adenylate kinase (ADK) to facilitate ATP recycling increased the yield to 97.24% at 75 g/L NR. This study establishes a foundation for industrial-scale, efficient, and green NMN production. Full article
(This article belongs to the Special Issue Emerging Trends in Food Enzyme Catalysis and Food Synthetic Biology)
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15 pages, 3523 KB  
Article
Impact of Tetragenococcus halophilus CICC 10286 Inoculation on the Fermentation Dynamics of Soybean Paste
by Jing Cai, Ling Zhang, Hao Zhou, Xingjiang Li and Shaotong Jiang
Foods 2026, 15(10), 1744; https://doi.org/10.3390/foods15101744 - 15 May 2026
Viewed by 270
Abstract
Fermented soybean paste, a traditional high-salt condiment, faces challenges in standardization and quality control due to its reliance on natural fermentation. This study systematically evaluated the effects of a defined starter culture, Tetragenococcus halophilus CICC 10286, on soybean paste fermentation by comparing natural [...] Read more.
Fermented soybean paste, a traditional high-salt condiment, faces challenges in standardization and quality control due to its reliance on natural fermentation. This study systematically evaluated the effects of a defined starter culture, Tetragenococcus halophilus CICC 10286, on soybean paste fermentation by comparing natural fermentation (NF) and fortified fermentation (FF). Compared with NF, FF maintained a higher moisture in the later stage (NF-LS: 50.30%; FF-LS: 60.08%) and lower total acid levels in the middle and later stages (NF-MS: 1.58 g/100 g; FF-MS: 0.96 g/100 g; NF-LS: 2.23 g/100 g; FF-LS: 1.11 g/100 g). Although protein degradation was more pronounced in the FF group at the midpoint (p < 0.0001), the lower accumulation of amino acid nitrogen suggests a potential shift in nitrogen metabolism, possibly toward enhanced transamination or deamination processes. Free amino acid profiling indicated that FF facilitated earlier accumulation of umami and sweet amino acids, but the total free amino acid content in the later stage was lower. Specifically, Glu and Asp reached 724.47 nmol/L and 305.52 nmol/L, respectively, in NF-LS, whereas the corresponding values in FF-LS were 397.16 nmol/L and 275.46 nmol/L. Meanwhile, Pro reached 337.81 nmol/L in FF-MS, indicating earlier accumulation of some amino acids under FF. Notably, the proportion of bitter amino acids in the FF group was reduced in the later stage. Microbial community analysis showed that FF promoted the enrichment of Tetragenococcus and halotolerant bacteria, such as Halomonas, at the midpoint, and increased the relative abundance of the aroma-producing yeast Zygosaccharomyces (NF-MS: 37.73%; FF-MS: 65.11%). Functional prediction based on PICRUSt2 suggested a higher predicted abundance of genes involved in pyruvate metabolism and branched-chain amino acid degradation in the FF group. These findings demonstrate that T. halophilus CICC 10286, as a starter culture, can effectively modulate the fermentation of soybean paste, providing a scientific basis for developing standardized and quality-controlled fermentation processes. Full article
(This article belongs to the Special Issue Emerging Trends in Food Enzyme Catalysis and Food Synthetic Biology)
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14 pages, 959 KB  
Article
Computational Design of a Thermo-Acidostable Endo-Polygalacturonase for Efficient Juice Extraction
by Zhong Cheng, Guobin Hou, Ting Zhang, Dongping Feng, Yanwen Zhang, Xingyue Wang, Liyan Yang, Maoyang Luo and Lixia Pan
Foods 2026, 15(6), 980; https://doi.org/10.3390/foods15060980 - 10 Mar 2026
Viewed by 419
Abstract
The development of thermostable and pH-robust endo-polygalacturonases (endo-PGases) is crucial for industrial applications such as food processing. This study aimed to engineer the thermostability of an acidic, thermophilic endo-PGase (PoxaEnPG28B) by rigidifying its flexible regions. We employed an integrated computational strategy combining molecular [...] Read more.
The development of thermostable and pH-robust endo-polygalacturonases (endo-PGases) is crucial for industrial applications such as food processing. This study aimed to engineer the thermostability of an acidic, thermophilic endo-PGase (PoxaEnPG28B) by rigidifying its flexible regions. We employed an integrated computational strategy combining molecular dynamics (MD) simulations at elevated temperatures with in silico analyses of unfolding free-energy changes to identify and design stabilizing mutations. This approach successfully yielded the mutant D249K, which exhibited a 5 °C higher optimal temperature (70 °C) and a 68.8% longer half-life at 55 °C, and it retained over 76.8% activity at 75 °C. Notably, D249K maintained the wild-type’s optimal pH (5.0) and broad pH stability (3.0–8.0). Although it is not the absolute top performer in every single metric, D249K achieves the best overall balance between thermostability and pH robustness among all reported thermophilic endo-PGases. MD simulations revealed that its enhanced stability sems from reduced global and local flexibility and a more compact structure. In juice extraction applications, D249K increased yields by up to 98.5%, significantly surpassing the wild-type. This study demonstrates the efficacy of MD-guided flexible region engineering for the GH28 family and presents D249K as a highly promising industrial biocatalyst. Full article
(This article belongs to the Special Issue Emerging Trends in Food Enzyme Catalysis and Food Synthetic Biology)
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17 pages, 4196 KB  
Article
Phenotypic Characterization and Genomic Mining of Uric Acid Catabolism Genes in Lactiplantibacillus plantarum YC
by Yuqing Zhao, Sen Yang, Miao He, Peihan Chai, Zhenou Sun, Qiaomei Zhu, Zhenjing Li, Qingbin Guo and Huanhuan Liu
Foods 2025, 14(24), 4343; https://doi.org/10.3390/foods14244343 - 17 Dec 2025
Cited by 1 | Viewed by 1132
Abstract
This study presents the phenotypic characterization and genomic mining of uric acid catabolism genes in Lactiplantibacillus plantarum YC, a novel food-grade lactic acid bacterium isolated from traditional fermented vegetables with potent uric acid-lowering activity. YC is non-hemolytic, catalase- and gelatinase-negative, exhibits strong adhesion [...] Read more.
This study presents the phenotypic characterization and genomic mining of uric acid catabolism genes in Lactiplantibacillus plantarum YC, a novel food-grade lactic acid bacterium isolated from traditional fermented vegetables with potent uric acid-lowering activity. YC is non-hemolytic, catalase- and gelatinase-negative, exhibits strong adhesion and broad antibacterial activity, and degrades 29.22% of uric acid in vitro, along with complete (100%) degradation of inosine and guanosine. Whole-genome sequencing revealed a 3,214,448 bp chromosome encoding 3026 protein-coding genes. Comparative genomics-based functional annotation highlighted abundant CAZy-related genes and antimicrobial factors, including lysozyme and monooxygenase. Crucially, genomic mining identified a complete uric acid degradation gene cluster, comprising pucK (uric acid permease), hpxO (uric acid hydroxylase), eight copies of hiuH (5-hydroxyisourate hydrolase), allB (allantoinase), and purine nucleoside transport/metabolism genes (rihA, rihB, rihC, pbuG). This work provides the first comparative genomic insight into the genetic architecture and distribution of uric acid metabolism in L. plantarum, elucidating YC’s dual urate-lowering mechanism and delivering key molecular markers for developing enzyme-based functional foods and microbial therapeutics against hyperuricemia. Full article
(This article belongs to the Special Issue Emerging Trends in Food Enzyme Catalysis and Food Synthetic Biology)
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Review

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21 pages, 4402 KB  
Review
Galactooligosaccharides Based on β-Galactosidase-Catalyzed Synthesis: Function, Biosynthesis and Optimization Strategy
by Bingyi Tao, Yiping Chen, Ren He, Tingting Huang, Shaoxiong Liang, Hongkun Chen, Xiaoping Rao, Xuchong Tang and Jianchun Jiang
Foods 2026, 15(10), 1803; https://doi.org/10.3390/foods15101803 - 19 May 2026
Viewed by 437
Abstract
Galactooligosaccharides (GOS) are one of the internationally recognized prebiotic products, which have become a hot research focus in the field of biofoods because of their strong prebiotic, sugar substitution and inflammation alleviation functions. β-galactosidase (Bgal) of different microorganisms is utilized industrially in order [...] Read more.
Galactooligosaccharides (GOS) are one of the internationally recognized prebiotic products, which have become a hot research focus in the field of biofoods because of their strong prebiotic, sugar substitution and inflammation alleviation functions. β-galactosidase (Bgal) of different microorganisms is utilized industrially in order to achieve the biosynthesis of GOS. Although the biosynthesis of GOS has been supported by certain technologies, there is still room for further improvement of its synthetic yield. This paper mainly introduces the function and biosynthesis of GOS and its research progress in recent years to enhance the yield of biosynthesis. This paper also combines the research progress in related fields in recent years, based on the basic theories of molecular biology and bioinformatics, discusses the research progress of green, innovative approaches including enzyme engineering, enzyme immobilization, surface display, and microbial fermentation on the synthesis of GOS. Full article
(This article belongs to the Special Issue Emerging Trends in Food Enzyme Catalysis and Food Synthetic Biology)
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27 pages, 2360 KB  
Review
α-Amylase: Its Structure, Molecular Modification, and Application in the Food Field
by Gang Liu, Manuel Montalbán-López, Dehua Wei, Lei Wang, Xuefeng Wu, Xingjiang Li and Dongdong Mu
Foods 2026, 15(9), 1555; https://doi.org/10.3390/foods15091555 - 30 Apr 2026
Viewed by 493
Abstract
This review comprehensively examines the structural architecture, catalytic mechanisms, and targeted molecular engineering of α-amylase (primarily the GH13 family), a pivotal biocatalyst in the food industry. We highlight diverse microbial sources of α-amylases and their cost-effective heterologous expression in well-characterized hosts like Bacillus [...] Read more.
This review comprehensively examines the structural architecture, catalytic mechanisms, and targeted molecular engineering of α-amylase (primarily the GH13 family), a pivotal biocatalyst in the food industry. We highlight diverse microbial sources of α-amylases and their cost-effective heterologous expression in well-characterized hosts like Bacillus subtilis and Escherichia coli. To overcome extreme operational bottlenecks—such as elevated temperatures and acidic environments—recent advances in protein engineering are critically evaluated. These strategies, including directed evolution, semi-rational design, and advanced immobilization on nanomaterials, synergistically enhance the enzyme’s thermostability, catalytic efficiency, and reusability. Furthermore, this paper synthesizes the state-of-the-art applications of engineered α-amylases across key food processing sectors, including baking, sugar refining, and brewing. By integrating structural biology with advanced material science, this review provides a targeted roadmap for developing next-generation, high-performance α-amylases to address current and future challenges in sustainable food processing. Full article
(This article belongs to the Special Issue Emerging Trends in Food Enzyme Catalysis and Food Synthetic Biology)
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