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Fermentation
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New Insights into Amino Acid Biosynthesis
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New Insights into Amino Acid 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 (29 February 2024) | Viewed by 11802

Special Issue Editors

Dr. Dan Wang

E-Mail Website
Guest Editor
School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China
Interests: fundamental metabolic regulation; biomass utilization; synthetic biology; high efficient separation and purification, functional materials; artificial intelligence based chemical engineering and synthetic biology
Dr. Jie Cheng

E-Mail Website
Guest Editor
Key Laboratory of Meat Processing of Sichuan Province, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
Interests: chemical engineer; biochemistry; metabolic engineering; biological catalysis

Special Issue Information

Dear Colleagues,

Amino acid biosynthesis has been extensively studied in a variety of microorganisms, fungi and plants. Furthermore, the involvement of the amino acid biosynthesis pathways in central and specialized metabolism still raises major questions regarding the genes and enzymes involved, and their control, their evolutionary origins and coordinated regulation with genes of associated pathways in response to altered environmental conditions and diverse developmental programs. Metabolic engineering, which is based on the acknowledgement of the biological mechanisms of the synthesis of amino acids, is a novel strategy of artificial pathway design and manufacture. Additionally, its combination with synthetic biology has led to the creation of a promising field in chemicals and food science research and industry. The strategy of co-culturing strains or co-producing chemicals can also be used to maximize the use of fermentation raw materials. In addition, it is necessary to explore more mature fermentation modes and pay attention to the substrate/product inhibition of strains according to the conditions for amino acid production. Today, some chemical synthesis methods, such as electrocatalytic reduction, photocatalytic reaction, etc., are also integrated into bio-systems to enhance amino acid production, including synthetic amino acids.

This Special Issue comprises new studies and reviews addressing the biosynthesis of amino acids by fermentation, especially the pathway regulation mechanism of the natural pathways and artificial pathways, and yield improvement through metabolic engineering and synthetic biology, and even related novel chemical synthetic methods, and separation and purification technologies.

Dr. Dan Wang
Dr. Jie Cheng
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. 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.

Published Papers (6 papers)

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Research

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19 pages, 5185 KiB  
Article
Improving the Synthesis Efficiency of Amino Acids by Analyzing the Key Sites of Intracellular Self-Assembly of Artificial Cellulosome
by Nan Li, Lu Yang, Xiankun Ren, Peng Du, Piwu Li, Jing Su, Jing Xiao, Junqing Wang and Ruiming Wang
Fermentation 2024, 10(5), 229; https://doi.org/10.3390/fermentation10050229 - 25 Apr 2024
Abstract
To explore the key sites affecting the intracellular assembly of key components of cellulosomes and obtain DocA mutants independent of Ca2+, Swiss-model, GROMACS, PyMOL, and other molecular dynamics simulation software were used for modeling and static and dynamic combination analysis. Site-specific [...] Read more.
To explore the key sites affecting the intracellular assembly of key components of cellulosomes and obtain DocA mutants independent of Ca2+, Swiss-model, GROMACS, PyMOL, and other molecular dynamics simulation software were used for modeling and static and dynamic combination analysis. Site-specific mutation technology was used to mutate DocA, and Biacore was used to test the dependence of Ca2+ on the binding ability of protein DocA mutants and protein Coh, and to analyze the interaction and binding effect of mutant proteins in vitro. Forward intracellular mutant screening was performed based on semi-rational design and high throughput screening techniques. The orientation of mutations suitable for intracellular assembly was determined, and three directional mutant proteins, DocA-S1, DocA-S2, and DocA-S3, were obtained. Ca2+ independent DocA mutants were obtained gradually and their potential interaction mechanisms were analyzed. In the present study, intracellular self-assembly of key components of cellulosomes independent of Ca2+ was achieved, and DocA-S3 was applied to the assembly of key enzymes of L-lysine biosynthesis, in which DapA and DapB intracellular assembly increased L-lysine accumulation by 29.8% when compared with the control strains, providing a new strategy for improving the intracellular self-assembly of cellulosomes and amino acid fermentation efficiency. Full article
(This article belongs to the Special Issue New Insights into Amino Acid Biosynthesis)
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19 pages, 4353 KiB  
Article
Improved Glutamic Acid Production Capacity of Corynebacterium glutamicum by the ARTP Mutagenesis Method
by Lingling Shangguan, Huiyan Zhang, Zixiong Liu, Feiran An, Qiao Yang, Xiaoling Zhang, Lan Yao, Shihui Yang, Jun Dai and Xiong Chen
Fermentation 2023, 9(7), 599; https://doi.org/10.3390/fermentation9070599 - 27 Jun 2023
Cited by 2 | Viewed by 2530
Abstract
Glutamic acid is an important amino acid that is used widely in the fields of food, medicine, and agriculture. One of the methods of glutamic acid production is direct microbial fermentation, so the genetic stability and glutamic-acid-producing capacity of the producing strain are [...] Read more.
Glutamic acid is an important amino acid that is used widely in the fields of food, medicine, and agriculture. One of the methods of glutamic acid production is direct microbial fermentation, so the genetic stability and glutamic-acid-producing capacity of the producing strain are the keys to improving glutamic acid concentration. Experiments were carried out using Corynebacterium glutamicum GL−6 as the parental strain, with two iterations of mutagenesis by atmospheric and room temperature plasma (ARTP) and screening with agar plates tolerant to high sugar and malonic acid, and the best strains with stable phenotypes were verified by fermentation in 20 L tanks. The results show that the optimal mutagenesis time of ARTP was 140 s, with lethality and positive mutation rates of 93.0% and 15.6%, respectively. The concentrations of the high-sugar and malonic acid agar plates were 240 g/L and 35 g/L, respectively. A mutant strain, P−45, with improved glutamic acid production capacity and genetic stability, was obtained through two rounds of iterative mutagenesis screening. The concentration of this strain in the Erlenmeyer flasks was 17.7 g/L, which was 18.8% higher than that of the parental strain, GL−6, and could be inherited stably for 10 generations. In the glutamic acid synthesis pathway, the upregulation of the gene encoding citrate synthase (cs), gene encoding isocitrate dehydrogenase (icdh), and gene encoding glutamate dehydrogenase (gdh), and the downregulation of the gene encoding oxoglutarate dehydrogenase complex (odhc) increased the carbon flows of the TCA cycle and its branch metabolic flow to glutamic acid synthesis. P−45 showed a glutamic acid concentration of 147.0 g/L under fed-batch fermentation conditions in 20 L tanks, which was 81.5% higher than the starting strain, GL−6. This study provides a new technical solution for improving microbial metabolites and genetic stability. Full article
(This article belongs to the Special Issue New Insights into Amino Acid Biosynthesis)
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Review

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13 pages, 985 KiB  
Review
Recent Advances, Challenges, and Metabolic Engineering Strategies in L-Cysteine Biosynthesis
by Wenwei Li, Zhen Zhou and Dan Wang
Fermentation 2023, 9(9), 802; https://doi.org/10.3390/fermentation9090802 - 31 Aug 2023
Viewed by 1552
Abstract
L-Cysteine is a widely used unique sulfur-containing amino acid with wide application in the food, pharmaceutical, and agricultural industries. This paper concludes the advantages and disadvantages of chemical hydrolysis, enzymatic biotransformation, and fermentation for the synthesis of L-cysteine. Meanwhile, a detailed introduction is [...] Read more.
L-Cysteine is a widely used unique sulfur-containing amino acid with wide application in the food, pharmaceutical, and agricultural industries. This paper concludes the advantages and disadvantages of chemical hydrolysis, enzymatic biotransformation, and fermentation for the synthesis of L-cysteine. Meanwhile, a detailed introduction is given to the biosynthesis of L-cysteine, metabolic engineering strategies, and the latest progress in reported L-cysteine fermentation bacteria. Finally, insights are provided on the development direction of increasing the production of biosynthetic L-cysteine in the future. This review provides ideas for the future development of more efficient L-cysteine biosynthetic pathways. Full article
(This article belongs to the Special Issue New Insights into Amino Acid Biosynthesis)
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18 pages, 1758 KiB  
Review
Advances in Synthetic Biology Techniques and Industrial Applications of Corynebacterium glutamicum
by Yujue Wang, Qiang Wang, Aobo Sha, Kexin Ren, Mengkai Hu, Meijuan Xu, Xian Zhang and Zhiming Rao
Fermentation 2023, 9(8), 729; https://doi.org/10.3390/fermentation9080729 - 04 Aug 2023
Viewed by 1728
Abstract
Corynebacterium glutamicum is a Gram-positive bacterium (non-spore-forming) that has been wildly used for amino acid production. Due to its stable protein secretion, low extracellular hydrolase activity, and non-toxicity, the application field of C. glutamicum has been greatly expanded. Currently, gene editing technology based [...] Read more.
Corynebacterium glutamicum is a Gram-positive bacterium (non-spore-forming) that has been wildly used for amino acid production. Due to its stable protein secretion, low extracellular hydrolase activity, and non-toxicity, the application field of C. glutamicum has been greatly expanded. Currently, gene editing technology based on synthetic biology has great potential for synthetic biology research and genetic modification in C. glutamicum because of its ability to efficiently regulate the physiological and metabolic networks of the strain. Therefore, we summarize the gene editing tools and strategies of C. glutamicum from the aspects of genetic modification and expression elements, and we also describe the effects of gene editing techniques on a variety of products such as amino acids and their derivatives, recombinant proteins, and functional sugars, which provide a certain theoretical basis for the research on the modification of C. glutamicum strains and industrial applications. Finally, we prospect the design and industrial application of C. glutamicum genetic modification from multiple perspectives based on gene editing techniques. Full article
(This article belongs to the Special Issue New Insights into Amino Acid Biosynthesis)
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19 pages, 3506 KiB  
Review
Application of Synthetic Biology Approaches to High-Yield Production of Mycosporine-like Amino Acids
by Varsha K. Singh, Sapana Jha, Palak Rana, Amit Gupta, Ashish P. Singh, Neha Kumari, Sonal Mishra, Prashant R. Singh, Jyoti Jaiswal and Rajeshwar P. Sinha
Fermentation 2023, 9(7), 669; https://doi.org/10.3390/fermentation9070669 - 17 Jul 2023
Cited by 2 | Viewed by 1991
Abstract
Ultraviolet (UV) radiation reaching the Earth’s surface is a major societal concern, and therefore, there is a significant consumer demand for cosmetics formulated to mitigate the harmful effects of UV radiation. Synthetic sunscreens being formulated to block UV penetration include inorganic metal oxide [...] Read more.
Ultraviolet (UV) radiation reaching the Earth’s surface is a major societal concern, and therefore, there is a significant consumer demand for cosmetics formulated to mitigate the harmful effects of UV radiation. Synthetic sunscreens being formulated to block UV penetration include inorganic metal oxide particles and organic filters. Lately, organic UV-absorbing compounds are manufactured from non-renewable petrochemicals and, as a result, there is a need to develop a sustainable manufacturing process for efficient, high-level production of a naturally occurring group of UV-absorbing compounds, namely mycosporine-like amino acids (MAAs), for use as a sunscreen additive to skincare products. Currently, the commercial production of MAAs for use in sunscreens is not a viable proposition due to the low yield and the lack of fermentation technology associated with native MAA-producing organisms. This review summarizes the biochemical properties of MAAs, the biosynthetic gene clusters and transcriptional regulations, the associated carbon-flux-driving processes, and the host selection and biosynthetic strategies, with the aim to expand our understanding on engineering suitable cyanobacteria for cost-effective production of natural sunscreens in future practices. Full article
(This article belongs to the Special Issue New Insights into Amino Acid Biosynthesis)
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13 pages, 4986 KiB  
Review
Recent Advances in the Hydroxylation of Amino Acids and Its Derivatives
by Bangxu Wang, Shujian Xiao, Xingtao Zhao, Liming Zhao, Yin Zhang, Jie Cheng and Jiamin Zhang
Fermentation 2023, 9(3), 285; https://doi.org/10.3390/fermentation9030285 - 14 Mar 2023
Cited by 3 | Viewed by 3113
Abstract
Hydroxy amino acids (HAAs) are of unique value in the chemical and pharmaceutical industry with antiviral, antifungal, antibacterial, and anticancer properties. At present, the hydroxylated amino acids most studied are tryptophan, lysine, aspartic acid, leucine, proline, etc., and some of their derivatives. The [...] Read more.
Hydroxy amino acids (HAAs) are of unique value in the chemical and pharmaceutical industry with antiviral, antifungal, antibacterial, and anticancer properties. At present, the hydroxylated amino acids most studied are tryptophan, lysine, aspartic acid, leucine, proline, etc., and some of their derivatives. The hydroxylation of amino acids is inextricably linked to the catalysis of various biological enzymes, such as tryptophan hydroxylase, L-pipecolic acid trans-4-hydroxylase, lysine hydroxylase, etc. Hydroxylase conspicuously increases the variety of amino acid derivatives. For the manufacture of HAAs, the high regioselectivity biocatalytic synthesis approach is favored over chemical synthesis. Nowadays, the widely used method is to transcribe the hydroxylation pathway of various amino acids, including various catalytic enzymes, into Corynebacterium glutamicum or Escherichia coli for heterologous expression and then produce hydroxyamino acids. In this paper, we systematically reviewed the biosynthetic hydroxylation of aliphatic, heterocyclic, and aromatic amino acids and introduced the basic research and application of HAAs. Full article
(This article belongs to the Special Issue New Insights into Amino Acid Biosynthesis)
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