Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
8.1
4.9
Journals
IJMS
Special Issues
Genetic Engineering in Microbial Biotechnology
ijms-logo
Submit to Special Issue Submit Abstract to Special Issue Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Genetic Engineering in Microbial Biotechnology

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: 20 May 2025 | Viewed by 12252

Special Issue Editor

Dr. Fernando Santos-Beneit

E-Mail Website
Guest Editor
1. Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
2. Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
Interests: molecular biology; microbiology; degradation; bioplastics; biotechnology; secondary metabolites; antibiotics; antimicrobial resistance; Streptomyces; Bacillus

Special Issue Information

Dear Colleagues,

The scope of this Special Issue involves genetic engineering and microbial biotechnology, including biotech activities (which are color-coded according to their common uses and applications, “Red”, “White”, “Yellow”, “Green”, etc.), with a special focus on gene-based technologies. We welcome papers (reviews and original research articles) reporting knowledge, bioinformatic analyses, and/or experimental studies using a genetic approach followed in order to achvieve biotechnological advances in the microorganisms of interest.

The aim of this Special Issue is to respond to the challenges of today’s society through sustainability, innovation, and research on the simplest forms of life, i.e., microorganisms. A considerable amount of research is still required for a real industrial biotechnological revolution, and genetic approaches are the most useful strategies for achieving this goal; therefore, we welcome studies focused on this.

Dr. Fernando Santos-Beneit
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • white biotechnology
  • red biotechnology
  • green biotechnology
  • yellow biotechnology
  • genetic engineering
  • microorganisms
  • bacteria
  • enzymes
  • genetics
  • bioproducts

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (7 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

Jump to: Review

20 pages, 4631 KiB  
Article
Mining Translation Inhibitors by a Unique Peptidyl-Aminonucleoside Synthetase Reveals Cystocin Biosynthesis and Self-Resistance
by Vera A. Alferova, Polina A. Zotova, Anna A. Baranova, Elena B. Guglya, Olga A. Belozerova, Sofiya O. Pipiya, Arsen M. Kudzhaev, Stepan E. Logunov, Yuri A. Prokopenko, Elisaveta A. Marenkova, Valeriya I. Marina, Evgenia A. Novikova, Ekaterina S. Komarova, Irina P. Starodumova, Olga V. Bueva, Lyudmila I. Evtushenko, Elena V. Ariskina, Sergey I. Kovalchuk, Konstantin S. Mineev, Vladislav V. Babenko, Petr V. Sergiev, Dmitrii A. Lukianov and Stanislav S. Terekhovadd Show full author list remove Hide full author list
Int. J. Mol. Sci. 2024, 25(23), 12901; https://doi.org/10.3390/ijms252312901 - 30 Nov 2024
Viewed by 1052
Abstract
Puromycin (Puro) is a natural aminonucleoside antibiotic that inhibits protein synthesis by its incorporation into elongating peptide chains. The unique mechanism of Puro finds diverse applications in molecular biology, including the selection of genetically engineered cell lines, in situ protein synthesis monitoring, and [...] Read more.
Puromycin (Puro) is a natural aminonucleoside antibiotic that inhibits protein synthesis by its incorporation into elongating peptide chains. The unique mechanism of Puro finds diverse applications in molecular biology, including the selection of genetically engineered cell lines, in situ protein synthesis monitoring, and studying ribosome functions. However, the key step of Puro biosynthesis remains enigmatic. In this work, pur6-guided genome mining is carried out to explore the natural diversity of Puro-like antibiotics. The diversity of biosynthetic gene cluster (BGC) architectures suggests the existence of distinct structural analogs of puromycin encoded by pur-like clusters. Moreover, the presence of tRNACys in some BGCs, i.e., cst-like clusters, leads us to the hypothesis that Pur6 utilizes aminoacylated tRNA as an activated peptidyl precursor, resulting in cysteine-based analogs. Detailed metabolomic analysis of Streptomyces sp. VKM Ac-502 containing cst-like BGC revealed the production of a cysteinyl-based analog of Puro—cystocin (Cst). Similar to puromycin, cystocin inhibits both prokaryotic and eukaryotic translation by the same mechanism. Aminonucleoside N-acetyltransferase CstC inactivated Cst, mediating antibiotic resistance in genetically modified bacteria and human cells. The substrate specificity of CstC originated from the steric hindrance of its active site. We believe that novel aminonucleosides and their inactivating enzymes can be developed through the directed evolution of the discovered biosynthetic machinery. Full article
(This article belongs to the Special Issue Genetic Engineering in Microbial Biotechnology)
►▼ Show Figures

Figure 1

15 pages, 10945 KiB  
Article
ARTP/NTG Compound Mutagenesis Improved the Spinosad Production and the Insecticidal Virulence of Saccharopolyspora Spinosa
by Zirong Zhu, Wangqiong Chen, Li Cao, Ziyuan Xia, Jie Rang, Shengbiao Hu and Liqiu Xia
Int. J. Mol. Sci. 2024, 25(22), 12308; https://doi.org/10.3390/ijms252212308 - 16 Nov 2024
Cited by 1 | Viewed by 1025
Abstract
Spinosad is an efficient and broad-spectrum environmentally friendly biopesticide, but its low yield in wild-type Saccharopolyspora spinosa limits its further application. ARTP/NTG compound mutagenesis was used in this study to improve the spinosad titer of S. spinosa and obtain a high-yield mutant—NT24. Compared [...] Read more.
Spinosad is an efficient and broad-spectrum environmentally friendly biopesticide, but its low yield in wild-type Saccharopolyspora spinosa limits its further application. ARTP/NTG compound mutagenesis was used in this study to improve the spinosad titer of S. spinosa and obtain a high-yield mutant—NT24. Compared with the wild-type strain, the fermentation cycle of NT24 was shortened by 2 days and its maximum titer of spinosad reached 858.3 ± 27.7 mg/L, which is 5.12 times more than for the same-period titer of the wild-type strain. In addition, RT-qPCR, resequencing, and targeted metabolomics showed that the upregulation of the key differential genes accD6, fadD, sdhB, oadA, and gntZ caused increased metabolic flux in the tricarboxylic acid cycle and pentose phosphate pathway, suggesting that the accumulation of pyruvate and short-chain acyl-CoA was the primary cause of spinosad accumulation in NT24. This study demonstrates the effectiveness of ARTP mutagenesis in S. spinosa, and provides new insights for the mechanism of spinosad biosynthesis and metabolic engineering in S. spinosa. Full article
(This article belongs to the Special Issue Genetic Engineering in Microbial Biotechnology)
►▼ Show Figures

Graphical abstract

16 pages, 2786 KiB  
Article
Inactivation of sacB Gene Allows Higher 2,3-Butanediol Production by Bacillus licheniformis from Inulin
by Emanoel Gergov, Penka Petrova, Alexander Arsov, Ina Ignatova, Lidia Tsigoriyna, Nadya Armenova and Kaloyan Petrov
Int. J. Mol. Sci. 2024, 25(22), 11983; https://doi.org/10.3390/ijms252211983 - 7 Nov 2024
Cited by 1 | Viewed by 854
Abstract
Bacillus licheniformis 24 (BL24) is an efficient, non-pathogenic producer of 2,3-butanediol (2,3-BD). However, during inulin fermentation, the strain produces large amounts of exopolysaccharides (EPS), which interfere with the process’ performance. The present study aims to investigate the effect that inactivation of the sacB [...] Read more.
Bacillus licheniformis 24 (BL24) is an efficient, non-pathogenic producer of 2,3-butanediol (2,3-BD). However, during inulin fermentation, the strain produces large amounts of exopolysaccharides (EPS), which interfere with the process’ performance. The present study aims to investigate the effect that inactivation of the sacB gene, encoding levansucrase in BL24, has on 2,3-BD production efficiency. Knockout of the sacB gene was accomplished via insertional inactivation. The sacB-knockout variant formed 0.57 g/L EPS from sucrose and 0.7–0.8 g/L EPS from glucose and fructose, a 15- and 2.5-fold reduction relative to the wild type, respectively. Likewise, during batch fermentation with soluble inulin Frutafit® CLR, the mutant BLΔsacB produced significantly less EPS than the wild type, allowing the maintenance of pH at values favoring 2,3-BD synthesis. At pH 6.50, BLΔsacB reached a record titer of 128.7 g/L 2,3-BD, with productivity of 1.65 g/L/h, and a yield of 85.8% of the theoretical maximum. The obtained concentration of 2,3-BD is two-fold higher compared to that of the wild type. Subsequent RT-qPCR assays confirmed a successful sacB knockout. Three of the genes involved in inulin hydrolysis (sacA, sacC, and fruA) maintained their expression levels compared to the wild type, while that of levB increased. Although total EPS accumulation could not be completely eliminated via sacB gene knockout alone, the overall reduction in EPS content has enabled the highest yield of 2,3-BD from inulin to date, a promising result for the industrial production from inulin-rich substrates. Full article
(This article belongs to the Special Issue Genetic Engineering in Microbial Biotechnology)
►▼ Show Figures

Figure 1

12 pages, 1516 KiB  
Article
Efficient Production of 9,22-Dihydroxy-23,24-bisnorchol-4-ene-3-one from Phytosterols by Modifying Multiple Genes in Mycobacterium fortuitum
by Suwan Han, Xiangcen Liu, Beiru He, Xinghui Zhai, Chenyang Yuan, Yixin Li, Weichao Lin, Haoyu Wang and Baoguo Zhang
Int. J. Mol. Sci. 2024, 25(7), 3579; https://doi.org/10.3390/ijms25073579 - 22 Mar 2024
Cited by 3 | Viewed by 1275
Abstract
C19 steroids and C22 steroids are vital intermediates for the synthesis of steroid drugs. Compared with C19 steroids, C22 steroids are more suitable for synthesizing progesterone and adrenocortical hormones, albeit less developed. 9,22-dihydroxy-23,24-bisnorchol-4-ene-3-one(9-OHBA), due to its substituents at positions C-9 and C-22, is [...] Read more.
C19 steroids and C22 steroids are vital intermediates for the synthesis of steroid drugs. Compared with C19 steroids, C22 steroids are more suitable for synthesizing progesterone and adrenocortical hormones, albeit less developed. 9,22-dihydroxy-23,24-bisnorchol-4-ene-3-one(9-OHBA), due to its substituents at positions C-9 and C-22, is a beneficial and innovative steroid derivative for synthesizing corticosteroids. We focused on the C22 pathway in Mycobacterium fortuitum ATCC 35855, aiming to develop a productive strain that produces 9-OHBA. We used a mutant strain, MFΔkstD, that knocked out kstds from Mycobacterium fortuitum ATCC 35855 named MFKD in this study as the original strain. Hsd4A and FadA5 are key enzymes in controlling the C19 metabolic pathway of steroids in Mycobacterium fortuitum ATCC 35855. After knocking out hsd4A, MFKDΔhsd4A accumulated 81.47% 9-OHBA compared with 4.13% 9-OHBA in the strain MFKD. The double mutant MFKDΔhsd4AΔfadA5 further improved the selectivity of 9-OHBA to 95.13%, and 9α-hydroxy-4-androstenedione (9-OHAD) decreased to 0.90% from 4.19%. In the end, we obtained 6.81 g/L 9-OHBA from 10 g/L phytosterols with a molar yield of 80.33%, which showed the best performance compared with formerly reported strains. Full article
(This article belongs to the Special Issue Genetic Engineering in Microbial Biotechnology)
►▼ Show Figures

Figure 1

22 pages, 2187 KiB  
Article
Gut Microbiota and Inflammation Modulation in a Rat Model for Ulcerative Colitis after the Intraperitoneal Administration of Apigenin, Luteolin, and Xanthohumol
by Patricia Magadán-Corpas, Álvaro Pérez-Valero, Suhui Ye, Sandra Sordon, Ewa Huszcza, Jarosław Popłoński, Claudio J. Villar and Felipe Lombó
Int. J. Mol. Sci. 2024, 25(6), 3236; https://doi.org/10.3390/ijms25063236 - 12 Mar 2024
Cited by 9 | Viewed by 2478
Abstract
Ulcerative colitis (UC) is a chronic inflammatory disorder affecting the colon, with symptomatology influenced by factors including environmental, genomic, microbial, and immunological interactions. Gut microbiota dysbiosis, characterized by bacterial population alterations, contributes to intestinal homeostasis disruption and aberrant immune system activation, thereby exacerbating [...] Read more.
Ulcerative colitis (UC) is a chronic inflammatory disorder affecting the colon, with symptomatology influenced by factors including environmental, genomic, microbial, and immunological interactions. Gut microbiota dysbiosis, characterized by bacterial population alterations, contributes to intestinal homeostasis disruption and aberrant immune system activation, thereby exacerbating the inflammatory state. This study assesses the therapeutic efficacy of intraperitoneal (IP) injected flavonoids (apigenin, luteolin, and xanthohumol) in the reduction of inflammatory parameters and the modulation of the gut microbiota in a murine model of ulcerative colitis. Flavonoids interact with gut microbiota by modulating their composition and serving as substrates for the fermentation into other anti-inflammatory bioactive compounds. Our results demonstrate the effectiveness of luteolin and xanthohumol treatment in enhancing the relative abundance of anti-inflammatory microorganisms, thereby attenuating pro-inflammatory species. Moreover, all three flavonoids exhibit efficacy in the reduction of pro-inflammatory cytokine levels, with luteolin strongly demonstrating utility in alleviating associated physical UC symptoms. This suggests that this molecule is a potential alternative or co-therapy to conventional pharmacological interventions, potentially mitigating their adverse effects. A limited impact on microbiota is observed with apigenin, and this is attributed to its solubility constraints via the chosen administration route, resulting in its accumulation in the mesentery. Full article
(This article belongs to the Special Issue Genetic Engineering in Microbial Biotechnology)
►▼ Show Figures

Figure 1

14 pages, 1589 KiB  
Article
Use of 3-Deoxy-D-arabino-heptulosonic acid 7-phosphate Synthase (DAHP Synthase) to Enhance the Heterologous Biosynthesis of Diosmetin and Chrysoeriol in an Engineered Strain of Streptomyces albidoflavus
by Álvaro Pérez-Valero, Juan Serna-Diestro, Claudio J. Villar and Felipe Lombó
Int. J. Mol. Sci. 2024, 25(5), 2776; https://doi.org/10.3390/ijms25052776 - 28 Feb 2024
Cited by 1 | Viewed by 1576
Abstract
Flavonoids are a large family of polyphenolic compounds with important agro-industrial, nutraceutical, and pharmaceutical applications. Among the structural diversity found in the flavonoid family, methylated flavonoids show interesting characteristics such as greater stability and improved oral bioavailability. This work is focused on the [...] Read more.
Flavonoids are a large family of polyphenolic compounds with important agro-industrial, nutraceutical, and pharmaceutical applications. Among the structural diversity found in the flavonoid family, methylated flavonoids show interesting characteristics such as greater stability and improved oral bioavailability. This work is focused on the reconstruction of the entire biosynthetic pathway of the methylated flavones diosmetin and chrysoeriol in Streptomyces albidoflavus. A total of eight different genes (TAL, 4CL, CHS, CHI, FNS1, F3′H/CPR, 3′-OMT, 4′-OMT) are necessary for the heterologous biosynthesis of these two flavonoids, and all of them have been integrated along the chromosome of the bacterial host. The biosynthesis of diosmetin and chrysoeriol has been achieved, reaching titers of 2.44 mg/L and 2.34 mg/L, respectively. Furthermore, an additional compound, putatively identified as luteolin 3′,4′-dimethyl ether, was produced in both diosmetin and chrysoeriol-producing strains. With the purpose of increasing flavonoid titers, a 3-Deoxy-D-arabino-heptulosonic acid 7-phosphate synthase (DAHP synthase) from an antibiotic biosynthetic gene cluster (BGC) from Amycolatopsis balhimycina was heterologously expressed in S. albidoflavus, enhancing diosmetin and chrysoeriol production titers of 4.03 mg/L and 3.13 mg/L, which is an increase of 65% and 34%, respectively. To the best of our knowledge, this is the first report on the de novo biosynthesis of diosmetin and chrysoeriol in a heterologous host. Full article
(This article belongs to the Special Issue Genetic Engineering in Microbial Biotechnology)
►▼ Show Figures

Figure 1

Review

Jump to: Research

22 pages, 1572 KiB  
Review
Genetic Modifications in Bacteria for the Degradation of Synthetic Polymers: A Review
by Diego Martín-González, Carlos de la Fuente Tagarro, Andrea De Lucas, Sergio Bordel and Fernando Santos-Beneit
Int. J. Mol. Sci. 2024, 25(10), 5536; https://doi.org/10.3390/ijms25105536 - 19 May 2024
Cited by 3 | Viewed by 2879
Abstract
Synthetic polymers, commonly known as plastics, are currently present in all aspects of our lives. Although they are useful, they present the problem of what to do with them after their lifespan. There are currently mechanical and chemical methods to treat plastics, but [...] Read more.
Synthetic polymers, commonly known as plastics, are currently present in all aspects of our lives. Although they are useful, they present the problem of what to do with them after their lifespan. There are currently mechanical and chemical methods to treat plastics, but these are methods that, among other disadvantages, can be expensive in terms of energy or produce polluting gases. A more environmentally friendly alternative is recycling, although this practice is not widespread. Based on the practice of the so-called circular economy, many studies are focused on the biodegradation of these polymers by enzymes. Using enzymes is a harmless method that can also generate substances with high added value. Novel and enhanced plastic-degrading enzymes have been obtained by modifying the amino acid sequence of existing ones, especially on their active site, using a wide variety of genetic approaches. Currently, many studies focus on the common aim of achieving strains with greater hydrolytic activity toward a different range of plastic polymers. Although in most cases the depolymerization rate is improved, more research is required to develop effective biodegradation strategies for plastic recycling or upcycling. This review focuses on a compilation and discussion of the most important research outcomes carried out on microbial biotechnology to degrade and recycle plastics. Full article
(This article belongs to the Special Issue Genetic Engineering in Microbial Biotechnology)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-7
Back to TopTop