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Fermentation
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Fermentation: Screening, Enzyme Induction and Production
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Fermentation: Screening, Enzyme Induction and Production

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Microbial Metabolism, Physiology & Genetics".

Deadline for manuscript submissions: 15 May 2024 | Viewed by 8700

Special Issue Editor

Dr. Antonella Costantini

E-Mail Website
Guest Editor
Council for Agricultural Research and Agricultural Economy Analysis-Research Centre for Viticulture and Enology (CREA-VE), Via Pietro Micca 35, 14100 Asti, Italy
Interests: microbiology; biotechnology; lactic acid bacteria; yeasts; beverages; fermentation; microbial biodiversity; molecular biology; biogenic amines; ochratoxin
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microorganisms play a dominant role in many processes thanks to their enzymes, and their ability to act on these proteins by selecting strains and increasing or silencing their activity can be advantageous.

This Special Issue aims to discuss and enhance current knowledge on this matter by highlighting studies on both the screening of specific activities and their induction using mutation, genetic engineering, and new technologies. Submissions can be on the application of microorganisms for improving the quality or obtaining the organoleptic profiles of food and beverages, but also to biomass, waste and bioenergy, where enzymes are fundamental in the transformation of specific substrates to produce useful compounds or reduce waste.

Finally, analysis of the proteome in complex environments is an emerging topic in this field; new technologies such as meta-proteomics analysis can enable researchers to identify the main proteins and understand the main microbial activities involved in ecosystems.

This Special Issue invites specialists, researchers, and students to contribute original and review articles concerning (or related to):

  • Microorganisms’ enzymatic activities;
  • Enzymes useful for quality improvement;
  • The effects of substrates or molecules on enzymes;
  • Mutation induction using different methods;
  • Enzyme applications in a circular economy, waste management, and food;
  • Methods to screen specific activities;
  • Methods for the detection and control of proteins;
  • Proteomics and proteome analysis;
  • Enzymes that increase bioactive compounds and can have beneficial effects on health.

Dr. Antonella Costantini
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. 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.

Keywords

  • beverages
  • food
  • biomass
  • waste
  • enzymes
  • microorganisms
  • screening
  • induction
  • mutation
  • genes
  • proteome

Published Papers (4 papers)

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Research

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25 pages, 3635 KiB  
Article
Induction and Characterisation of Lignocellulolytic Activities from Novel Deep-Sea Fungal Secretomes
by Bronwyn Dowd and Maria G. Tuohy
Fermentation 2023, 9(9), 780; https://doi.org/10.3390/fermentation9090780 - 23 Aug 2023
Viewed by 1321
Abstract
Fungi are increasingly recognised as being able to inhabit extreme environments. The deep sea is considered an extreme environment because of its low temperatures, high hydrostatic and lithostatic pressures, 3.5% salinity, and low oxygen, nutrient and light availability. Fungi inhabiting the deep sea [...] Read more.
Fungi are increasingly recognised as being able to inhabit extreme environments. The deep sea is considered an extreme environment because of its low temperatures, high hydrostatic and lithostatic pressures, 3.5% salinity, and low oxygen, nutrient and light availability. Fungi inhabiting the deep sea may have evolved to produce proteins that allow them to survive these conditions. Investigation and characterisation of fungal lignocellulolytic enzymes from extreme environments like the deep sea is needed, as they may have unusual adaptations that would be useful in industry. This work, therefore, aimed to profile in detail the lignocellulolytic capabilities of fungi isolated from deep-sea sediments in the Atlantic Ocean, and a comparative lignocellulolytic terrestrial isolate. The isolates were strains of Emericellopsis maritima, Penicillium chrysogenum, P. antarcticum and Talaromyces stollii. Lignocellulolytic enzyme induction was achieved using liquid-state fermentation (LSF) with wheat bran as the main carbon source, while enzyme characteristics were evaluated using biochemical assays and gel-based proteomics. This study revealed that the isolates were halotolerant, produced xylanase over wide pH and temperature ranges, and produced a variety of glycoside hydrolase and feruloyl esterase activities. The T. stollii secretome demonstrated remarkable levels of exo-glycoside hydrolase activity, with xylanase activity optimum between pH 1.5–6.0 and temperatures between 1–60 °C, making this isolate an ideal candidate for biotechnological applications. This study is the first to quantitatively characterise xylanase activities and exo-glycoside hydrolase activities secreted by E. maritima, P. antarcticum and a marine T. stollii strain. This study is also the first to quantitatively characterise xylanase activities by a marine strain of P. chrysogenum during LSF. Full article
(This article belongs to the Special Issue Fermentation: Screening, Enzyme Induction and Production)
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12 pages, 1563 KiB  
Communication
Cloning, Expression, and Characterization of Family A DNA Polymerase from Massilia aurea
by Aleksandra A. Kuznetsova, Ksenia S. Bedritskikh, Anatoly A. Bulygin and Nikita A. Kuznetsov
Fermentation 2023, 9(7), 650; https://doi.org/10.3390/fermentation9070650 - 10 Jul 2023
Viewed by 1061
Abstract
Mau DNA polymerase is a family A DNA polymerase isolated from Massilia aurea. In this study, a recombinant plasmid, His6-tagged Mau-pET28c, was constructed. His-tagged Mau was expressed in Escherichia coli Rosseta 2 (DE3) competent cells and, after optimization of purification conditions, [...] Read more.
Mau DNA polymerase is a family A DNA polymerase isolated from Massilia aurea. In this study, a recombinant plasmid, His6-tagged Mau-pET28c, was constructed. His-tagged Mau was expressed in Escherichia coli Rosseta 2 (DE3) competent cells and, after optimization of purification conditions, was successfully isolated via a two-step purification system by Ni2+-chelating affinity chromatography followed by heparin affinity chromatography. The biochemical properties of Mau DNA polymerase were investigated next. This polymerase showed maximal polymerase activity at 30 °C, pH 8.4–8.8, 2–10 mM MgCl2, and 10–40 mM KCl. Kinetic parameters of correct and incorrect dNTP incorporation as well as DNA-binding affinity were determined too. KdNTPd,app values were found to be 16 µM for correct dNTP and 200–500 µM for incorrect dNTP. The kinetic parameter kcat turned out to be 0.2 s−1 for correct dNTP incorporation and an order of magnitude less for incorrect dNTP incorporation. It was demonstrated that Mau DNA polymerase has 5′→3′ and 3′→5′ exonuclease activities associated with the main activity. Full article
(This article belongs to the Special Issue Fermentation: Screening, Enzyme Induction and Production)
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Review

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15 pages, 1124 KiB  
Review
Advances in Droplet-Based Microfluidic High-Throughput Screening of Engineered Strains and Enzymes Based on Ultraviolet, Visible, and Fluorescent Spectroscopy
by Shunyang Hu, Bangxu Wang, Qing Luo, Rumei Zeng, Jiamin Zhang and Jie Cheng
Fermentation 2024, 10(1), 33; https://doi.org/10.3390/fermentation10010033 - 30 Dec 2023
Viewed by 1604
Abstract
Genetic engineering and directed evolution are effective methods for addressing the low yield and poor industrialization level of microbial target products. The current research focus is on how to efficiently and rapidly screen beneficial mutants from constructed large-scale mutation libraries. Traditional screening methods [...] Read more.
Genetic engineering and directed evolution are effective methods for addressing the low yield and poor industrialization level of microbial target products. The current research focus is on how to efficiently and rapidly screen beneficial mutants from constructed large-scale mutation libraries. Traditional screening methods such as plate screening and well-plate screening are severely limited in their development and application due to their low efficiency and high costs. In the past decade, microfluidic technology has become an important high-throughput screening technology due to its fast speed, low cost, high automation, and high screening throughput, and it has developed rapidly. Droplet-based microfluidic high-throughput screening has been widely used in various fields, such as strain/enzyme activity screening, pathogen detection, single-cell analysis, drug discovery, and chemical synthesis, and has been widely applied in industries such as those involving materials, food, chemicals, textiles, and biomedicine. In particular, in the field of enzyme research, droplet-based microfluidic high-throughput screening has shown excellent performance in discovering enzymes with new functions as well as improved catalytic efficiency or stability, acid-base tolerance, etc. Currently, droplet-based microfluidic high-throughput screening technology has achieved the high-throughput screening of enzymes such as glycosidase, lipase, peroxidase, protease, amylase, oxidase, and transaminase as well as the high-throughput detection of products such as riboflavin, coumarin, 3-dehydroquinate, lactic acid, and ethanol. This article reviews the application of droplet-based microfluidics in high-throughput screening, with a focus on high-throughput screening strategies based on UV, visible, and fluorescence spectroscopy, including labeled optical signal detection screening, as well as label-free electrochemical detection, mass spectrometry, Raman spectroscopy, nuclear magnetic resonance, etc. Furthermore, the research progress and development trends of droplet-based microfluidic technology in enzyme modification and strain screening are also introduced. Full article
(This article belongs to the Special Issue Fermentation: Screening, Enzyme Induction and Production)
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20 pages, 4116 KiB  
Review
Microbial and Commercial Enzymes Applied in the Beverage Production Process
by Fernanda Cosme, António Inês and Alice Vilela
Fermentation 2023, 9(4), 385; https://doi.org/10.3390/fermentation9040385 - 17 Apr 2023
Cited by 5 | Viewed by 4065
Abstract
Enzymes are highly effective biocatalysts used in various industrial processes, playing a key role in winemaking and in other fermented beverages. Many of the enzymes used in fermentation processes have their origin in fruits, in the indigenous microbiota of the fruit, and in [...] Read more.
Enzymes are highly effective biocatalysts used in various industrial processes, playing a key role in winemaking and in other fermented beverages. Many of the enzymes used in fermentation processes have their origin in fruits, in the indigenous microbiota of the fruit, and in the microorganisms present during beverage processing. Besides naturally occurring enzymes, commercial preparations that usually blend different activities are used (glucosidases, glucanases, pectinases, and proteases, among others). Over the years, remarkable progress has been made in enhancing enzyme performance under operating conditions. The winemaking industry has observed a significant improvement in production levels, stimulating the introduction of technological innovations that aim to enhance efficiency and wine quality. Enzymes have traditionally been used in the beverage industry; however, others have been introduced more recently, with numerous studies aimed at optimizing their performance under processing conditions, including the use of immobilized enzymes. Therefore, one major goal of the current review is to give a detailed overview of the endogenous enzyme potential of wine microorganisms, as well as of enzymes obtained from grapes or even commercial preparations, studied and already in use in the beverage industry, and to present the future trends in enzyme production and application. Full article
(This article belongs to the Special Issue Fermentation: Screening, Enzyme Induction and Production)
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