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Fermentation
Special Issues
Applications of Enzymes in Biosynthesis
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Applications of Enzymes in Biosynthesis

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Microbial Metabolism, Physiology & Genetics".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 4740

Special Issue Editor

Prof. Dr. Xian Zhang

E-Mail Website
Guest Editor
School of Biotechnology, Jiangnan University, Wuxi 214122, China
Interests: cell metabolism; enzymaticization; protein engineering; fermentation process; fermentation control
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Enzymes play an essential role in many key technologies and manufacturing processes in life sciences. Enzymes are widely used in various fields, including food, drug, feed, and chemical industries. These ubiquitous catalysts in living organisms efficiently and selectively catalyze various biochemical reactions under mild conditions, finely regulating the complex metabolic processes in living organisms.

The use of enzymes in fermentation has a long history dating back to ancient times when humans first discovered the transformative power of microorganisms. Enzymes can break down complex substrates into simpler molecules, convert one molecule into another, or modify the properties of the final product. With the rapid development of modern biotechnology and the emergence of new technologies and engineering design ideas of synthetic biology, enzyme design and application fields have rapidly advanced. This has deepened scientists’ understanding of enzymes, from searching for natural enzymes to creating artificial enzymes, and has led to “Environmentally Conscious Manufacturing” that not only improves human life but also opens the door to designing life.

The goal of this Special Issue is to publish recent innovative research results and review papers on applications of enzymes in biosynthesis. We encourage you to submit Research Articles or Review papers to this special issue.

Prof. Dr. Xian Zhang
Guest Editor

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. Fermentation 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 2600 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
  • biosynthesis
  • synthetic biology
  • protein engineering
  • host cells
  • protein expression
  • high throughput screening
  • enzyme immobilization

Published Papers (3 papers)

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Research

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13 pages, 2612 KiB  
Article
Engineering an Artificial Pathway to Improve the Bioconversion of Lysine into Chiral Amino Alcohol 2-Hydroxycadaverine Using a Semi-Rational Design
by Jie Cheng, Shujian Xiao, Qing Luo, Bangxu Wang, Rumei Zeng, Liming Zhao and Jiamin Zhang
Fermentation 2024, 10(1), 56; https://doi.org/10.3390/fermentation10010056 - 13 Jan 2024
Viewed by 1144
Abstract
Amino alcohols are important compounds that are widely used in the polymer and pharmaceutical industry, particularly when used as chiral scaffolds in organic synthesis. The hydroxylation of polyamide polymers may allow crosslinking between molecular chains through the esterification reactions of hydroxyl and carboxyl [...] Read more.
Amino alcohols are important compounds that are widely used in the polymer and pharmaceutical industry, particularly when used as chiral scaffolds in organic synthesis. The hydroxylation of polyamide polymers may allow crosslinking between molecular chains through the esterification reactions of hydroxyl and carboxyl groups. Therefore, this may alter the functional properties of polyamide polymers. 2-hydroxycadaverine (2HyC), as a new type of chiral amino alcohol, has potential applications in the pharmaceutical, chemical, and polymer industries. Currently, 2HyC production has only been realized via pure enzyme catalysis or two-stage whole-cell biocatalysis, which faces great challenges for scale-up production. However, the use of a cell factory is very promising for the production of 2HyC in industrial applications. Here, we designed and constructed a promising artificial pathway in Escherichia coli for producing 2HyC from biomass-derived lysine. This biosynthesis route expands the lysine catabolism pathway and employs two enzymes to sequentially convert lysine into 2HyC. However, the catalytic activity of wild-type pyridoxal phosphate-dependent decarboxylase from Chitinophage pinensis (DCCp) toward 3-hydroxylysine is lower, resulting in the lower production of 2HyC. Thus, the higher catalytic activity of DCCp is desired for low-cost and expanded industrial applications of 2HyC. To improve the catalytic activity of DCCp, a mutant library of DCCp was first built using a semi-rational design. The Kcat/Km of mutant DCCp (R53D/V94I) increased by 63%. A titer of 359 mg/L 2HyC was produced in shake flasks, with a 2HyC titer increase of 54% compared to control strain ML101. The results show that the production of 2HyC was effectively increased through a semi-rational design strategy. These findings lay the foundation for the development and utilization of renewable resources to produce 2HyC in microorganisms via an efficient, green, and sustainable biosynthetic strategy for further industrial application. Full article
(This article belongs to the Special Issue Applications of Enzymes in Biosynthesis)
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16 pages, 3438 KiB  
Article
High Production of Nattokinase via Fed-Batch Fermentation of the γ-PGA-Deficient Strain of Bacillus licheniformis
by Xin Li, Jing Yang, Jun Liu, Xiaohui Zhang, Wei Wu, Dazhong Yan, Lihong Miao, Dongbo Cai, Xin Ma and Shouwen Chen
Fermentation 2023, 9(12), 1018; https://doi.org/10.3390/fermentation9121018 - 13 Dec 2023
Viewed by 1524
Abstract
During the production of nattokinase (NK) by Bacillus species, certain by-products such as poly-γ-glutamic acid (γ-PGA) are simultaneously synthesized. The impact of γ-PGA synthesis on NK production remains unclear. In this study, we knocked out the pgsC gene, a component of the γ-PGA [...] Read more.
During the production of nattokinase (NK) by Bacillus species, certain by-products such as poly-γ-glutamic acid (γ-PGA) are simultaneously synthesized. The impact of γ-PGA synthesis on NK production remains unclear. In this study, we knocked out the pgsC gene, a component of the γ-PGA synthetase cluster (pgsBCA), and constructed a novel recombinant strain, Bacillus licheniformis BL11. Next, we compared the fed-batch fermentation profiles of BL11 and its parental strain BL10, conducted transcriptional analysis, and measured intracellular ATP content. We also optimized glucose-feeding strategies under varying oxygen supply conditions. Our results indicated that the utilization rates of glucose and soybean meal were both improved in the pgsC-deficient strain BL11, and NK activity was enhanced. Furthermore, the transcriptional levels of genes involved in glycolysis and the TCA cycle were relatively upregulated in BL11. The maximal NK activity reached 2522.2 FU/mL at 54 h of fermentation using a constant glucose-feeding rate of 5.0 g/(L·h) under high oxygen supply conditions. The newly developed recombinant strain B. licheniformis BL11, along with the optimized feeding strategy, shows promise for large-scale NK production. Full article
(This article belongs to the Special Issue Applications of Enzymes in Biosynthesis)
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Review

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23 pages, 3789 KiB  
Review
Historical Aspects of Restriction Endonucleases as Intelligent Scissors for Genetic Engineering
by Irina V. Alekseeva and Nikita A. Kuznetsov
Fermentation 2023, 9(10), 874; https://doi.org/10.3390/fermentation9100874 - 28 Sep 2023
Viewed by 1692
Abstract
Restriction endonucleases are a component of restriction–modification systems, where the main biological function is to protect bacterial cells from incoming foreign DNA molecules. There are four main types of restriction enzymes (types I, II, III, and IV), which differ in protein composition, cofactor [...] Read more.
Restriction endonucleases are a component of restriction–modification systems, where the main biological function is to protect bacterial cells from incoming foreign DNA molecules. There are four main types of restriction enzymes (types I, II, III, and IV), which differ in protein composition, cofactor requirements, and mode of action. The most studied are representatives of type II, which specifically recognize DNA sequences of 4–8 bp and catalyze DNA cleavage within these sequences or not far from them. The exceptional precision of type II enzymes has made them indispensable for DNA manipulations. Although hundreds of DNA restriction enzymes are currently known, there is still a need for enzymes that recognize new DNA targets. For this reason, the discovery of new natural restriction endonucleases and rational design of their properties (to obtain enzymes with high specificity for a unique nucleotide sequence at a restriction site and without nonspecific activity) will expand the list of enzymes for use in biotechnology and genetic engineering. This review briefly touches upon the main types of restriction endonucleases, their classification, nomenclature, and typical properties, and it concisely describes approaches to the construction of enzymes with altered properties. Full article
(This article belongs to the Special Issue Applications of Enzymes in Biosynthesis)
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