Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
6.4
4.5
Journals
Microorganisms
Special Issues
Advances in Microbial Cell Factories, 2nd Edition
share announcement

Advances in Microbial Cell Factories, 2nd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: 30 April 2024 | Viewed by 5060

Special Issue Editors

Prof. Dr. Thomas Brück

E-Mail Website
Guest Editor
Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), D-85748 Garching bei München, Germany
Interests: biocatalysis; system biology; enzyme and metabolic engineering; synthetic biology; sustainable bioprocess engineering
Special Issues, Collections and Topics in MDPI journals
Dr. Dania Awad

E-Mail Website
Guest Editor
Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), D-85748 Garching bei München, Germany
Interests: synthetic biotechnology; bioprocess development; proteomics; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue continues our previous Special Issue, "Advances in Microbial Cell Factories”.

In the “cell factory” concept, microorganisms convert substrates into desirable products. Well-established fermentation products include beer, antibiotics and insulin. Recent developments enabled by native and engineered microbial cell factories include oleochemicals, biopolymers, biofuels, animal feed, biopesticides, nutraceuticals and flavors. Currently, the availability of standardized and newly developed cloning and expression vectors, the accessibility and affordability of de novo DNA synthesis, the advancement in bioinformatics tools and the expansion of biological databases have allowed cells to become more programmable. In this revolutionized era, the design and modeling of bioprocesses, AI-guided automation and high-throughput process monitoring significantly reduce bioprocess development time and costs. Despite all this progress, only a few biotechnological processes have been adopted at an industrial level outside the confines of laboratory settings. Challenges and bottlenecks still need to be addressed at several levels, including feedstock flexibility, bioreactor design, metabolic burdens and downstream processing and iterative scale-up.

This Special Issue of Microorganisms provides a platform for authors to present novel tools and scientific concepts on Microbial Cell Factories through research articles, reviews and editorials. We invite you to send contributions relating to the development of microbial production platforms—of eukaryotic and prokaryotic origin.

Prof. Dr. Thomas Brück
Dr. Dania Awad
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. Microorganisms 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 2700 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

  • sustainability
  • biotechnology
  • bioengineering
  • biocatalysis
  • fermentation

Related Special Issue

Published Papers (5 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

16 pages, 4739 KiB  
Article
Expanding the CRISPR Toolbox for Engineering Lycopene Biosynthesis in Corynebacterium glutamicum
by Zhimin Zhan, Xiong Chen, Zhifang Ye, Ming Zhao, Cheng Li, Shipeng Gao, Anthony J. Sinskey, Lan Yao, Jun Dai, Yiming Jiang and Xueyun Zheng
Microorganisms 2024, 12(4), 803; https://doi.org/10.3390/microorganisms12040803 - 16 Apr 2024
Viewed by 366
Abstract
Lycopene represents one of the central compounds in the carotenoid pathway and it exhibits a potent antioxidant ability with wide potential applications in medicine, food, and cosmetics. The microbial production of lycopene has received increasing concern in recent years. Corynebacterium glutamicum (C. [...] Read more.
Lycopene represents one of the central compounds in the carotenoid pathway and it exhibits a potent antioxidant ability with wide potential applications in medicine, food, and cosmetics. The microbial production of lycopene has received increasing concern in recent years. Corynebacterium glutamicum (C. glutamicum) is considered to be a safe and beneficial industrial production platform, naturally endowed with the ability to produce lycopene. However, the scarcity of efficient genetic tools and the challenge of identifying crucial metabolic genes impede further research on C. glutamicum for achieving high-yield lycopene production. To address these challenges, a novel genetic editing toolkit, CRISPR/MAD7 system, was established and developed. By optimizing the promoter, ORI and PAM sequences, the CRISPR/MAD7 system facilitated highly efficient gene deletion and exhibited a broad spectrum of PAM sites. Notably, 25 kb of DNA from the genome was successfully deleted. In addition, the CRISPR/MAD7 system was effectively utilized in the metabolic engineering of C. glutamicum, allowing for the simultaneous knockout of crtEb and crtR genes in one step to enhance the accumulation of lycopene by blocking the branching pathway. Through screening crucial genes such as crtE, crtB, crtI, idsA, idi, and cg0722, an optimal carotenogenic gene combination was obtained. Particularly, cg0722, a membrane protein gene, was found to play a vital role in lycopene production. Therefore, the CBIEbR strain was obtained by overexpressing cg0722, crtB, and crtI while strategically blocking the by-products of the lycopene pathway. As a result, the final engineered strain produced lycopene at 405.02 mg/L (9.52 mg/g dry cell weight, DCW) in fed-batch fermentation, representing the highest reported lycopene yield in C. glutamicum to date. In this study, a powerful and precise genetic tool was used to engineer C. glutamicum for lycopene production. Through the modifications between the host cell and the carotenogenic pathway, the lycopene yield was stepwise improved by 102-fold as compared to the starting strain. This study highlights the usefulness of the CRISPR/MAD7 toolbox, demonstrating its practical applications in the metabolic engineering of industrially robust C. glutamicum. Full article
(This article belongs to the Special Issue Advances in Microbial Cell Factories, 2nd Edition)
►▼ Show Figures

Figure 1

16 pages, 3985 KiB  
Article
Enhanced Expression of Alcohol Dehydrogenase I in Pichia pastoris Reduces the Content of Acetaldehyde in Wines
by Kun Geng, Ying Lin, Xueyun Zheng, Cheng Li, Shuting Chen, He Ling, Jun Yang, Xiangyu Zhu and Shuli Liang
Microorganisms 2024, 12(1), 38; https://doi.org/10.3390/microorganisms12010038 - 25 Dec 2023
Viewed by 898
Abstract
Acetaldehyde is an important carbonyl compound commonly detected in wines. A high concentration of acetaldehyde can affect the flavor of wines and result in adverse effects on human health. Alcohol dehydrogenase I (ADH1) in Saccharomyces cerevisiae catalyzes the reduction reaction of acetaldehyde into [...] Read more.
Acetaldehyde is an important carbonyl compound commonly detected in wines. A high concentration of acetaldehyde can affect the flavor of wines and result in adverse effects on human health. Alcohol dehydrogenase I (ADH1) in Saccharomyces cerevisiae catalyzes the reduction reaction of acetaldehyde into ethanol in the presence of cofactors, showing the potential to reduce the content of acetaldehyde in wines. In this study, ADH1 was successfully expressed in Pichia pastoris GS115 based on codon optimization. Then, the expression level of ADH1 was enhanced by replacing its promoter with optimized promoters and increasing the copy number of the expression cassette, with ADH1 being purified using nickel column affinity chromatography. The enzymatic activity of purified ADH1 reached 605.44 ± 44.30 U/mg. The results of the effect of ADH1 on the content of acetaldehyde in wine revealed that the acetaldehyde content of wine samples was reduced from 168.05 ± 0.55 to 113.17 ± 6.08 mg/L with the addition of 5 mM NADH and the catalysis of ADH1, and from 135.53 ± 4.08 to 52.89 ± 2.20 mg/L through cofactor regeneration. Our study provides a novel approach to reducing the content of acetaldehyde in wines through enzymatic catalysis. Full article
(This article belongs to the Special Issue Advances in Microbial Cell Factories, 2nd Edition)
►▼ Show Figures

Figure 1

19 pages, 2364 KiB  
Article
Exploring and Engineering Novel Strong Promoters for High-Level Protein Expression in Bacillus subtilis DB104 through Transcriptome Analysis
by Ji-Su Jun, Hyang-Eun Jeong and Kwang-Won Hong
Microorganisms 2023, 11(12), 2929; https://doi.org/10.3390/microorganisms11122929 - 06 Dec 2023
Cited by 1 | Viewed by 1229
Abstract
Bacillus subtilis is widely employed for recombinant protein expression. B. subtilis DB104 offers a distinct advantage as a protein expression host because it is an extracellular protease-deficient derivative of B. subtilis 168. We have conducted a time-course transcriptome analysis of B. subtilis DB104 [...] Read more.
Bacillus subtilis is widely employed for recombinant protein expression. B. subtilis DB104 offers a distinct advantage as a protein expression host because it is an extracellular protease-deficient derivative of B. subtilis 168. We have conducted a time-course transcriptome analysis of B. subtilis DB104 in a prior study. In the present study, we identified 10 genes that exhibited strong expression at each time point or all, based on transcriptome data. Subsequently, we assessed the strength of 12 promoters that transcribe these genes using enhanced green fluorescent protein (eGFP) as a reporter. Among these promoters, Psdp and PskfA had the highest expression levels. At 24 h, these two promoters exhibited 34.5- and 38.8-fold higher strength, respectively, than the strength of P43, the control promoter. Consequently, these two promoters were selected for further development. We enhanced these promoters by optimizing spacer length, promoter sequence, Shine–Dalgarno sequence, regulator binding sites, and terminator sequences. As a result, we successfully engineered the most potent protein expression cassette, Psdp-4, which exhibited a 3.84-fold increase in strength compared to the original Psdp promoter. Furthermore, we constructed an expression cassette for a human epidermal growth factor (hEGF) using Psdp-4 to evaluate its general application. The expression level of His tagged hEGF, quantified using ImageJ analysis and applied to SDS-PAGE, reached the highest yield of 103.9 μg/mL under the control of Psdp-4 at 24 h. The expressed hEGF protein was purified, and its bioactivity was confirmed through a cell proliferation assay using HT-29 cells. Our work demonstrates the construction of a highly efficient expression system for B. subtilis DB104 based on transcriptome data and promoter engineering. This system enables rapid, inducer-free protein expression within 24 h. It can be used as a valuable tool for various industrial applications. Full article
(This article belongs to the Special Issue Advances in Microbial Cell Factories, 2nd Edition)
►▼ Show Figures

Figure 1

14 pages, 1844 KiB  
Article
Bivariate One Strain Many Compounds Designs Expand the Secondary Metabolite Production Space in Corallococcus coralloides
by Anton Lindig, Jenny Schwarz, Georg Hubmann, Katrin Rosenthal and Stephan Lütz
Microorganisms 2023, 11(10), 2592; https://doi.org/10.3390/microorganisms11102592 - 20 Oct 2023
Cited by 1 | Viewed by 939
Abstract
The scarcely investigated myxobacterium Corallococcus coralloides holds a large genome containing many uncharacterized biosynthetic gene clusters (BGCs) that potentially encode the synthesis of entirely new natural products. Despite its promising genomic potential, suitable cultivation conditions have not yet been found to activate the [...] Read more.
The scarcely investigated myxobacterium Corallococcus coralloides holds a large genome containing many uncharacterized biosynthetic gene clusters (BGCs) that potentially encode the synthesis of entirely new natural products. Despite its promising genomic potential, suitable cultivation conditions have not yet been found to activate the synthesis of new secondary metabolites (SMs). Finding the right cultivation conditions to activate BGCs in the genome remains a major bottleneck, and its full biosynthetic potential has so far not been determined. We therefore applied a bivariate “one strain many compounds” (OSMAC) approach, using a combination of two elicitor changes at once, for the activation of BGCs and concomitant SM production by C. coralloides. The screening was carried out in Duetz-System 24-well plates, applying univariate and bivariate OSMAC conditions. We combined biotic additives and organic solvents with a complex growth medium for univariate conditions and with minimal medium for bivariate conditions. The success in the activation of BGCs was evaluated by determining the number of new mass features detected in the respective extracts. We found synergistic effects in the bivariate OSMAC designs, evidenced by the detection of completely new mass features in the bivariate OSMAC experiments, which were not detected in the univariate OSMAC designs with only one elicitor. Overall, the bivariate OSMAC screening led to 55 new mass features, which were not detected in the univariate OSMAC design. Molecular networks revealed that these new mass features embody potential novel natural compounds and chemical derivatives like the N-acyl fatty amine N-pentyloctadecanamide and possibly sulfur-containing natural products. Hence, the presence of multiple elicitors in the bivariate OSMAC designs successfully activated the biosynthetic potential in C. coralloides. We propose bivariate OSMAC designs with a complex combination of elicitors as a straightforward strategy to robustly expand the SM space of microorganisms with large genomes. Full article
(This article belongs to the Special Issue Advances in Microbial Cell Factories, 2nd Edition)
►▼ Show Figures

Figure 1

19 pages, 2491 KiB  
Article
Optimization of Rhodococcus erythropolis JCM3201T Nutrient Media to Improve Biomass, Lipid, and Carotenoid Yield Using Response Surface Methodology
by Selina Engelhart-Straub, Martina Haack, Dania Awad, Thomas Brueck and Norbert Mehlmer
Microorganisms 2023, 11(9), 2147; https://doi.org/10.3390/microorganisms11092147 - 24 Aug 2023
Cited by 1 | Viewed by 1099
Abstract
The oleaginous bacterium Rhodococcus erythropolis JCM3201T offers various unique enzyme capabilities, and it is a potential producer of industrially relevant compounds, such as triacylglycerol and carotenoids. To develop this strain into an efficient production platform, the characterization of the strain’s nutritional requirement [...] Read more.
The oleaginous bacterium Rhodococcus erythropolis JCM3201T offers various unique enzyme capabilities, and it is a potential producer of industrially relevant compounds, such as triacylglycerol and carotenoids. To develop this strain into an efficient production platform, the characterization of the strain’s nutritional requirement is necessary. In this work, we investigate its substrate adaptability. Therefore, the strain was cultivated using nine nitrogen and eight carbon sources at a carbon (16 g L−1) and nitrogen (0.16 g L−1) weight ratio of 100:1. The highest biomass accumulation (3.1 ± 0.14 g L−1) was achieved using glucose and ammonium acetate. The highest lipid yield (156.7 ± 23.0 mg g−1DCW) was achieved using glucose and yeast extract after 192 h. In order to enhance the dependent variables: biomass, lipid and carotenoid accumulation after 192 h, for the first time, a central composite design was employed to determine optimal nitrogen and carbon concentrations. Nine different concentrations were tested. The center point was tested in five biological replicates, while all other concentrations were tested in duplicates. While the highest biomass (8.00 ± 0.27 g L−1) was reached at C:N of 18.87 (11 g L−1 carbon, 0.583 g L−1 nitrogen), the highest lipid yield (100.5 ± 4.3 mg g−1DCW) was determined using a medium with 11 g L−1 of carbon and only 0.017 g L−1 of nitrogen. The highest carotenoid yield (0.021 ± 0.001 Abs454nm mg−1DCW) was achieved at a C:N of 12 (6 g L−1 carbon, 0.5 g L−1 nitrogen). The presented results provide new insights into the physiology of R. erythropolis under variable nutritional states, enabling the selection of an optimized media composition for the production of valuable oleochemicals or pigments, such as rare odd-chain fatty acids and monocyclic carotenoids. Full article
(This article belongs to the Special Issue Advances in Microbial Cell Factories, 2nd Edition)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-5
Back to TopTop