Research on Microbial Protein Synthesis: 2nd Edition

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Fermentation Process Design".

Deadline for manuscript submissions: closed (29 April 2025) | Viewed by 4347

Special Issue Editor


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Guest Editor
College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
Interests: continuous fermentation; microbiological physiology; metabolic engineering; cofactor engineering; protein secretion; biofilm; cell morphology; edible fungi; plant cell culture
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Special Issue Information

Dear Colleagues,

Protein is among the most important kinds of biomolecules to have evolved in the process of sustaining life. These days, with the unleashing of their functional potential, proteins are becoming increasingly important to our world, serving as industrial biocatalysts, food and nutrients, therapeutic agents, biomaterial, and a variety of other uses. Additionally, an increasing number of protein-derived products are being developed for new application. To cope with this emerging trend, efficient and low-cost synthesis of protein is in high demand. Microbial synthesis is a prevalent way to produce proteins of broad interest that have numerous advantages. Microbes can synthesize a diverse array of proteins, both natural or unnatural, featuring intricate structures and long chains that surpass those achievable through chemical synthesis. Microbial cells are generally easier and more cost-effective to grow compared to other cells such as plant and animal cells. Despite these factors, microbial protein synthesis still faces challenges. Continuous efforts have been made to improve the production efficiency of microbial proteins and reduce cost. This includes fine-tuning the translation machinery, enhancing protein transport or secretion pathways, applying dynamic control to global metabolic fluxes, and developing cost-effective fermentation processes.

The goal of this Special Issue is to publish recent research results as well as review papers on synthesis machinery, fermentation production, function characterization, and product development of various proteins (e.g., enzyme, pharmaceutical protein, food ingredient, protein material) from microbial systems (e.g., bacterium, yeast, filamentous fungus, mushroom culture). Methodologies employed for the extraction and processing (cell-free extracts, phase separation, aggregation, etc.) of microbial proteins and the engineering of protein behaviours are also of interest.

Prof. Dr. Dong Liu
Guest Editor

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Keywords

  • protein expression
  • protein secretion
  • molecular chaperone
  • recombinant protein
  • heterologous expression
  • alternative protein
  • precision fermentation
  • continuous fermentation
  • microbial cell factories

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Published Papers (3 papers)

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Research

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27 pages, 4772 KiB  
Article
Optimized Amino Acid-Enhanced Medium for Efficient L-Asparaginase II Production in E. coli: From Shake Flask to Bioreactor
by Nicolás Lefin, Javiera Miranda, Iris Munhoz Costa, Alejandro Pedroso Reynaldo, Gisele Monteiro, Mauricio Zamorano, Adalberto Pessoa, Jr. and Jorge G. Farias
Fermentation 2025, 11(5), 239; https://doi.org/10.3390/fermentation11050239 - 23 Apr 2025
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Abstract
L-asparaginase (L-ASNase) is a key enzyme in the treatment of leukemia and lymphoma, with high demand in cancer therapies. Advances in recombinant protein production have improved yields and reduced costs, enabling large-scale production. However, optimizing culture conditions remains crucial for maximizing production. This [...] Read more.
L-asparaginase (L-ASNase) is a key enzyme in the treatment of leukemia and lymphoma, with high demand in cancer therapies. Advances in recombinant protein production have improved yields and reduced costs, enabling large-scale production. However, optimizing culture conditions remains crucial for maximizing production. This study focused on optimizing the production of double mutant L-ASNase expressed in Escherichia coli BL21 (DE3) by supplementing media with amino acids. Five amino acids were evaluated at a shake flask scale using the design of experiments, with arginine and aspartate showing the most positive effects. Under optimized conditions (14.5 mM arginine, 12.7 mM aspartate, and 0 mM cysteine), the activity model reached 12,513 U L−1, experimentally validated at 10,089 U L−1. The maximum specific cell growth rate was µx,max = 0.74 h−1, with substrate–biomass conversion factor Yx/s = 1.16 g/g and cell–product conversion factor Yp/x = 13,891 U/gcell. Amino acid supplementation resulted in a ten-fold increase in L-ASNase activity. Finally, at the bioreactor scale, adding amino acids and the inducer at the end of the exponential phase increased activity by 135% compared to conventional MD, demonstrating its potential for industrial-scale production. Full article
(This article belongs to the Special Issue Research on Microbial Protein Synthesis: 2nd Edition)
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13 pages, 4032 KiB  
Article
Biofilm-Based Immobilization Fermentation for Continuous hEGF Production in Saccharomyces cerevisiae
by Kaiqi Zhi, Zhiguo An, Mingyang Zhang, Kehan Liu, Yafan Cai, Zhenyu Wang, Di Zhang, Jinle Liu, Zhi Wang, Chenjie Zhu, Dong Liu, Sheng Yang and Hanjie Ying
Fermentation 2024, 10(12), 661; https://doi.org/10.3390/fermentation10120661 - 21 Dec 2024
Cited by 1 | Viewed by 1201
Abstract
Biofilms can enhance industrial fermentation efficiency by increasing cell density, stability, and metabolic activity and have been successfully applied to the continuous production of many small-molecule chemicals. However, the continuous production of proteins by biofilms has been less studied. This study used secretory [...] Read more.
Biofilms can enhance industrial fermentation efficiency by increasing cell density, stability, and metabolic activity and have been successfully applied to the continuous production of many small-molecule chemicals. However, the continuous production of proteins by biofilms has been less studied. This study used secretory human epidermal growth factor (hEGF) as a representative product to evaluate and optimize biofilm-based continuous protein production. First, by deleting the protease and overexpressing eight key genes involved in protein secretion in Saccharomyces cerevisiae, the yield of hEGF was improved by 82.6% from 77.4 to 141.3 mg/L in shake flasks. Subsequently, the flocculation genes FLO11 and ALS3 were introduced to facilitate the establishment of a biofilm-based continuous immobilization fermentation model. The optimal strain SIC-ALS3-PDI1 produced 583.8 mg/L of hEGF, with a productivity of 4.9 mg/L/h during traditional free-cell fermentation, while it produced an average of 300.0 mg/L of hEGF in 10 continuous batches of biofilm-based fermentation, with a productivity of 6.3 mg/L/h. Although the hEGF production in biofilms was lower than that in free-cell fermentation, biofilm fermentation demonstrated greater productivity, with the advantage of not requiring seed culture for each batch of fermentation. This study provided a valuable reference for the biofilm-based production of other peptides. Full article
(This article belongs to the Special Issue Research on Microbial Protein Synthesis: 2nd Edition)
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Review

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27 pages, 3299 KiB  
Review
Advances in Biotechnological Strategies for Sustainable Production of Non-Animal Proteins: Challenges, Innovations, and Applications
by Emanuel do Nascimento Muniz, Rebeca Teixeira de Queiroz Montenegro, Daniel Nascimento da Silva, Alan Portal D’Almeida, Luciana Rocha Barros Gonçalves and Tiago Lima de Albuquerque
Fermentation 2024, 10(12), 638; https://doi.org/10.3390/fermentation10120638 - 13 Dec 2024
Cited by 5 | Viewed by 2852
Abstract
This review explores recent advances in the design of fermentation processes for producing alternative proteins, focusing on utilizing agro-industrial waste and renewable substrates. New bioprocess strategies, such as experimental designs, optimizing bioreactors, bioprocesses, and applying precision fermentation can improve the protein yields and [...] Read more.
This review explores recent advances in the design of fermentation processes for producing alternative proteins, focusing on utilizing agro-industrial waste and renewable substrates. New bioprocess strategies, such as experimental designs, optimizing bioreactors, bioprocesses, and applying precision fermentation can improve the protein yields and nutritional value. Also, unconventional substrates, such as hydrolysates derived from agro-industrial residues conversion may result in cost reduction and enhanced feasibility. The application of enzymes to produce protein-rich foods with high bioaccessibility that improve digestibility and nutritional value are also highlighted. This article addresses the importance of developing cost-effective fermentation solutions that minimize the environmental impact while addressing technical challenges such as scalability and contamination control. Furthermore, it emphasizes the growing need for innovations in fermentation process design to ensure the sustainability of industrial protein production. The review concludes that improvements in process design are fundamental in overcoming technological and regulatory barriers, particularly in increasing the efficiency and competitiveness of non-meat proteins in the global market. Full article
(This article belongs to the Special Issue Research on Microbial Protein Synthesis: 2nd Edition)
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