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Microbial Enzymes for Biotechnological Applications: 2nd Edition
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Microbial Enzymes for Biotechnological Applications: 2nd Edition

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

Deadline for manuscript submissions: 20 August 2025 | Viewed by 7365

Special Issue Editor

Dr. Salvatore Fusco

E-Mail Website
Guest Editor
Department of Biotechnology, University of Verona, 37134 Verona, Italy
Interests: industrial enzymology; extremozymes; biocatalysis; biorefinery; biomass valorisation; enzymatic recycling of plastics; protein engineering; CRISPR-based applications; virus biotechnology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue “Microbial Enzymes for Biotechnological Applications”. Microbial biocatalysts account for about 90% of the enzyme market shares. This mainly depends on the rapid multiplication, easy manipulation, and handling of the microbial cell factories if compared to other biocatalysts sources (i.e., animal, and vegetal tissues). Unlike chemical catalysts, enzymes show wider application potentials that are revolutionizing the agricultural, chemical, energy, and pharmaceutical industries.

The aim is to collect original research articles, review articles, and short communications dealing with the study of microbial biocatalysts (both isolated enzymes and whole-cell biocatalysts). We welcome fundamental studies about design and optimization of microbial enzymes as well as those addressed to the exploitation of microbial enzymes for biotechnological applications (industrial, diagnostic, environmental, etc.).

Topics of interest include, but are not limited to, the following:

  • Discovery and/or characterization of new microbial enzymes (including commodity, specialty, extremophilic and polyextremophilic enzymes);
  • Functional and/or structural characterization of microbial enzymes;
  • Microbial enzymes for circular economy applications;
  • Design, optimization, and/or exploitation of whole-cell microbial biocatalysts;
  • Bioprospecting of microbial enzymes.

Dr. Salvatore Fusco
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

  • microbial enzymes
  • whole-cell biocatalysts
  • extremozyme
  • enzyme assays
  • protein engineering

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Related Special Issue

Published Papers (3 papers)

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Research

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20 pages, 2307 KiB  
Article
Improved Enzymatic Properties of Chitosanase CsnMY002 from Bacillus subtilis via Computational Design
by Jie Xie, Jingwei Liu, Si Wang and Ganggang Wang
Int. J. Mol. Sci. 2025, 26(4), 1588; https://doi.org/10.3390/ijms26041588 - 13 Feb 2025
Viewed by 654
Abstract
Chitooligosaccharides (COSs) are a class of functional carbohydrates with significant application prospects in food and medicine. Chitosanase CsnMY002 from the GH46 family has been used to prepare COS with controlled degrees of polymerization. To enhance the industrial applicability of CsnMY002, molecular dynamics (MD) [...] Read more.
Chitooligosaccharides (COSs) are a class of functional carbohydrates with significant application prospects in food and medicine. Chitosanase CsnMY002 from the GH46 family has been used to prepare COS with controlled degrees of polymerization. To enhance the industrial applicability of CsnMY002, molecular dynamics (MD) simulations were applied to investigate the structure–property relationship. Guided by the simulation results, the beneficial mutants were screened through a synergistic strategy using a residue-folding free energy calculation and consensus sequence analysis. Iterative combinations constructed the mutant Mut6 (A49G/K70A/S84A/N89G/D199R/N221G) with significantly improved thermal stability, which had a half-life (t1/2 value) at 55 °C and 75 °C that was 1.80 and 1.62 times higher than that of the wild type, respectively. A highly active mutant, Mut2, was created, exhibiting a 1.52 times catalytic efficiency of the wild type. An MD simulation analysis of the mutants suggested that the improved enzymatic properties were highly correlated with changes in the dynamic behaviours of the enzyme structure. This study generated more suitable CsnMY002 variants for COS production and provided a comprehensive strategy for the optimization of other industrial enzymes with application potential. Full article
(This article belongs to the Special Issue Microbial Enzymes for Biotechnological Applications: 2nd Edition)
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17 pages, 1491 KiB  
Article
Plastic-Degrading Microbial Consortia from a Wastewater Treatment Plant
by Andrea Salini, Luca Zuliani, Paolo Matteo Gonnelli, Marco Orlando, Andrea Odoardo, Daniele Ragno, Martina Aulitto, Claudio Zaccone and Salvatore Fusco
Int. J. Mol. Sci. 2024, 25(23), 12747; https://doi.org/10.3390/ijms252312747 - 27 Nov 2024
Viewed by 2365
Abstract
Plastic waste pollution has become a global crisis, with millions of tons of plastic expected to accumulate in landfills and in natural environments, posing a serious threat to wildlife and human health. As current recycling methods remain inefficient, there is an urgent need [...] Read more.
Plastic waste pollution has become a global crisis, with millions of tons of plastic expected to accumulate in landfills and in natural environments, posing a serious threat to wildlife and human health. As current recycling methods remain inefficient, there is an urgent need for innovative enzymatic solutions to break down plastics and enable a circular economy approach. In this study, we explore the plastic-degrading potential of microorganisms enriched from activated sludge (AS) sourced from a municipal wastewater treatment plant (WWTP)—a known microplastic-contaminated industrial niche. Five microbial consortia (i.e., microbiomes) were enriched under selective pressure using low-carbon conditions and high concentrations of polyester polymers, including post-consumer PET, post-consumer PLA, and virgin PLA. Enrichment was performed for 100 days at 37 °C and 50 °C, followed by microbiomes isolation and metagenomic analysis to identify plastic-active bacteria and their enzymes. The results revealed that PLA polymers, but not post-consumer PET, were effectively degraded by the microbiomes, as confirmed by nuclear magnetic resonance (NMR) and gel permeation chromatography (GPC), showing significant molecular weight reduction compared to the abiotic controls. Microbial community analysis highlighted a distinct enrichment profile driven by the polymer composition and the temperature. At 50 °C, the Bacillales order became the predominant population, whereas at 37 °C, a more diverse community within the Proteobacteria and Actinobacteria phyla were selected. Nonetheless, the enriched microbial communities at both temperatures included phyla with members known for polyester degradation. Moreover, at 50 °C, enrichment of putative PET/PLA hydrolases was also observed. These findings suggest that AS microorganisms are a reservoir of polyester-active enzymes, particularly PLA-depolymerases, and hold promise for advancing biotechnological strategies to mitigate plastic pollution through re- and up-cycling. Full article
(This article belongs to the Special Issue Microbial Enzymes for Biotechnological Applications: 2nd Edition)
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Review

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51 pages, 6029 KiB  
Review
Microbial Immobilized Enzyme Biocatalysts for Multipollutant Mitigation: Harnessing Nature’s Toolkit for Environmental Sustainability
by Mohamed A. A. Abdelhamid, Hazim O. Khalifa, Hyo Jik Yoon, Mi-Ran Ki and Seung Pil Pack
Int. J. Mol. Sci. 2024, 25(16), 8616; https://doi.org/10.3390/ijms25168616 - 7 Aug 2024
Cited by 8 | Viewed by 3250
Abstract
The ever-increasing presence of micropollutants necessitates the development of environmentally friendly bioremediation strategies. Inspired by the remarkable versatility and potent catalytic activities of microbial enzymes, researchers are exploring their application as biocatalysts for innovative environmental cleanup solutions. Microbial enzymes offer remarkable substrate specificity, [...] Read more.
The ever-increasing presence of micropollutants necessitates the development of environmentally friendly bioremediation strategies. Inspired by the remarkable versatility and potent catalytic activities of microbial enzymes, researchers are exploring their application as biocatalysts for innovative environmental cleanup solutions. Microbial enzymes offer remarkable substrate specificity, biodegradability, and the capacity to degrade a wide array of pollutants, positioning them as powerful tools for bioremediation. However, practical applications are often hindered by limitations in enzyme stability and reusability. Enzyme immobilization techniques have emerged as transformative strategies, enhancing enzyme stability and reusability by anchoring them onto inert or activated supports. These improvements lead to more efficient pollutant degradation and cost-effective bioremediation processes. This review delves into the diverse immobilization methods, showcasing their success in degrading various environmental pollutants, including pharmaceuticals, dyes, pesticides, microplastics, and industrial chemicals. By highlighting the transformative potential of microbial immobilized enzyme biocatalysts, this review underscores their significance in achieving a cleaner and more sustainable future through the mitigation of micropollutant contamination. Additionally, future research directions in areas such as enzyme engineering and machine learning hold immense promise for further broadening the capabilities and optimizing the applications of immobilized enzymes in environmental cleanup. Full article
(This article belongs to the Special Issue Microbial Enzymes for Biotechnological Applications: 2nd Edition)
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