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Fermentation
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Metabolic Engineering of Yeast for the Production of Fuels and...
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Metabolic Engineering of Yeast for the Production of Fuels and Chemicals

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

Deadline for manuscript submissions: 28 June 2025 | Viewed by 3963

Special Issue Editors

Prof. Dr. Akinori Matsushika

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Guest Editor
Department of Biotechnology and Chemistry, Faculty of Engineering, Kindai University, Higashi-Hiroshima 739-2116, Hiroshima, Japan
Interests: life sciences; applied microbiology; co-fermentation; ethanol
Dr. Hironaga Akita

E-Mail Website
Guest Editor
Department of Basic Science, College of Industrial Technology, Nihon University, 2-11-1 Shinei, Narashino 275-8575, Chiba, Japan
Interests: biomass conversion; fermentation; synthetic biology; environmental microbiology; microbial isolation; enzymes
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over the past decade, synthetic biology has flourished, and metabolic engineering approaches have been developed for the production of different bio-products through biotechnology (i.e., bio-manufacturing) using microorganisms. On the other hand, circular economies are becoming more important, and there is a need to reduce the burden on the environment by circulating raw materials and products while keeping their value as high as possible. Expectations are high for biorefineries and recycling technologies that produce products using sustainable biomass as raw materials, and investment in research and development is accelerating.

Microbial production of fuels and chemicals from renewable resources such as lignocellulosic biomass provides sustainable and economically attractive alternatives to their petrochemical-based production by conventional oil refineries. The yeast Saccharomyces cerevisiae is the most promising candidate for the industrial-scale production of fuels, particularly bioethanol, and chemicals, while non-conventional yeasts are emerging as suitable hosts for industrial applications. It is also important that yeasts are tolerant to extreme fermentation conditions, biomass-derived inhibitors, and their target products and by-products.

This Special Issue focuses on the breeding of yeast, which is the core of bio-manufacturing, and provides an overview of elemental technologies and examples of manufacturing. Yeast is highly diverse, and its products are varied and used for a variety of purposes, but breeding methods differ depending on the yeast species, so extensive research is essential. Furthermore, progress is being made in the development of manufacturing technology for bio-products that are not originally produced by yeast, in which the introduction of novel pathways and the optimization of its native cellular processes via metabolic engineering are rapidly expanding its range of cell-factory applications.

In this Special Issue, we aim to introduce recent scientific progress in metabolic engineering strategies of various yeasts for the production of bioethanol, advanced biofuels, and chemicals.

Prof. Dr. Akinori Matsushika
Dr. Hironaga Akita
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 2100 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

  • metabolic engineering
  • fuels
  • chemicals
  • Saccharomyces cerevisiae
  • non-conventional yeasts
  • lignocellulosic biomass

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Published Papers (3 papers)

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Research

17 pages, 4281 KiB  
Article
Optimizing Bacterial Protectant Composition to Enhance Baijiu Yeast Survival and Productivity During Spray Drying
by Jingyu Li, Fengkui Xiong, Zhongbin Liu, Jia Zheng, Guangzhong Hu and Zheng Feng
Fermentation 2025, 11(1), 29; https://doi.org/10.3390/fermentation11010029 - 13 Jan 2025
Viewed by 763
Abstract
The flavor substances produced by the division of baijiu yeast during the winemaking process often determine the quality of white wine, and the difficulty of storing and transporting high-quality baijiu yeast is a bottleneck that restricts the development of China’s baijiu industry. It [...] Read more.
The flavor substances produced by the division of baijiu yeast during the winemaking process often determine the quality of white wine, and the difficulty of storing and transporting high-quality baijiu yeast is a bottleneck that restricts the development of China’s baijiu industry. It is widely accepted that drying microorganisms such as baijiu yeast is the best way to improve its storage and transport performance. Spray drying, as one of the most widely used microbial drying processes, with a high efficiency and low cost, is the hot spot of current research in the field of microbial drying, but it has the inherent defect of a low drying survival rate. In order to address this inherent defect, the present study was carried out with a high-quality white wine yeast, Modified Sporidiobolus Johnsonii A (MSJA), as the target. Firstly, an orthogonal experiment, Steep Hill Climbing experiment, and response surface experiment were sequentially designed to optimize the type and amount of protective agent added in the spray-drying process of MSJA. Then, the effects of glutamyl transaminase (TGase) treatment on the drying process of MSJA were revealed with the help of advanced equipment, such as laser particle sizer, environmental scanning electron microscope (ESEM), and Fourier-transform infrared scanner (FTIR). The results showed that the addition of “TGase-treated soybean isolate protein (SPI) + lactic protein (LP)” as an in vitro bacterial protectant and “14.15% trehalose + 7.10% maltose + 14.04% sucrose” TGase treatment can promote the cross-linking of protective proteins, reduce the distance between MSJA bacteria and protective proteins, and increase the glass transition temperature to enhance the protective effect of protective proteins, so as to improve the survival rate of MSJA during spray drying. Full article
(This article belongs to the Special Issue Metabolic Engineering of Yeast for the Production of Fuels and Chemicals)
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21 pages, 2723 KiB  
Article
Production, Purification, and Characterization of Extracellular Lipases from Hyphopichia wangnamkhiaoensis and Yarrowia deformans
by Misael Romo-Silva, Emanuel Osmar Flores-Camargo, Griselda Ma. Chávez-Camarillo and Eliseo Cristiani-Urbina
Fermentation 2024, 10(12), 595; https://doi.org/10.3390/fermentation10120595 - 21 Nov 2024
Viewed by 1034
Abstract
The efficient production of microbial lipases from organic wastes has garnered great interest because of the diverse and potential biotechnological applications of these enzymes. However, the extracellular lipases from the novel yeast strains Hyphopichia wangnamkhiaoensis and Yarrowia deformans remain uncharacterized. Thus, this study [...] Read more.
The efficient production of microbial lipases from organic wastes has garnered great interest because of the diverse and potential biotechnological applications of these enzymes. However, the extracellular lipases from the novel yeast strains Hyphopichia wangnamkhiaoensis and Yarrowia deformans remain uncharacterized. Thus, this study aimed to investigate the characteristics and production of lipases from both yeasts. Lipases from H. wangnamkhiaoensis and Y. deformans were purified and biochemically characterized, and their production was measured in batch cultures with olive oil (reference), waste cooking oil, and glycerol as substrates. The purified lipases from H. wangnamkhiaoensis and Y. deformans had molecular weights of approximately 33 and 45 kDa, respectively. Their activities on p-nitrophenyl palmitate were optimal at pH 8.0 and 40 °C. Moreover, the activities of the lipases were inhibited by ethylenediaminetetraacetic acid, phenylmethylsulfonyl fluoride, and 4-(2-aminoethyl)benzenesulfonyl fluoride, and were reactivated by Ca2+ and Mg2+, indicating that both lipases are metalloenzymes and serine-type enzymes. The lipases were more tolerant to hydrophilic solvents than to hydrophobic solvents, and they followed Michaelis–Menten kinetics. Among the various substrates used, waste cooking oil yielded the highest lipase production and productivity. These results indicate that H. wangnamkhiaoensis and Y. deformans are suitable and potential candidates for lipase production. Full article
(This article belongs to the Special Issue Metabolic Engineering of Yeast for the Production of Fuels and Chemicals)
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12 pages, 1829 KiB  
Article
Inhibitor Tolerance Capacity of Pichia kudriavzevii NBRC1279 and NBRC1664
by Hironaga Akita and Akinori Matsushika
Fermentation 2024, 10(7), 331; https://doi.org/10.3390/fermentation10070331 - 25 Jun 2024
Cited by 1 | Viewed by 1487
Abstract
The thermotolerant yeast Pichia kudriavzevii (previously known as Issatchenkia orientalis), can produce ethanol from a variety of carbon sources and grows at around 45 °C. Thus, this yeast is considered a useful biocatalyst for producing ethanol from lignocellulose through simultaneous saccharification and [...] Read more.
The thermotolerant yeast Pichia kudriavzevii (previously known as Issatchenkia orientalis), can produce ethanol from a variety of carbon sources and grows at around 45 °C. Thus, this yeast is considered a useful biocatalyst for producing ethanol from lignocellulose through simultaneous saccharification and fermentation (SSF). SSF has several advantages, such as a simplified manufacturing process, ease of operation and reduced energy input. Using P. kudriavzevii NBRC1279 and NBRC1664, we previously succeeded in producing ethanol through SSF; however, the extent to which inhibitors by-produced from lignocellulose hydrolysis affect the growth and ethanol productivity of the two strains remains to be investigated. In this study, to better understand the inhibitor tolerance capacity of the two strains, spot assay, growth experiment, real-time quantitative PCR (RT-qPCR) analysis and multiple sequence alignment analysis were carried out. When P. kudriavzevii NBRC1279 and NBRC1664, as well as Saccharomyces cerevisiae BY4742 as a control, were cultured on SCD plates containing 17% ethanol, 42 mM furfural, 56 mM 5-hydroxymethylfurfural (HMF) or 10 mM vanillin, only P. kudriavzevii NBRC1664 was able to grow under all conditions. Moreover, the inhibitor tolerance capacity of P. kudriavzevii NBRC1664 was greater than those of other strains using SCD medium containing the same concentrations of various inhibitors. When an RT-qPCR analysis of seven gene sequences from aldehyde dehydrogenase and the aldehyde dehydrogenase family protein (ADHF) was performed using P. kudriavzevii NBRC1664 cultivated in the presence of 56 mM HMF, ADHF1 and ADHF2 were up-regulated in the early logarithmic growth phase. Moreover, a multiple sequence alignment of the amino acid sequences of ADHF1, ADHF2 and the known ADH suggested that ADHF1 and ADHF2 may catalyze the reversible NAD+-dependent oxidation of HMF. Our data may be useful for future studies on the metabolic engineering of more useful strains for ethanol production from lignocellulose. Full article
(This article belongs to the Special Issue Metabolic Engineering of Yeast for the Production of Fuels and Chemicals)
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