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Yeast Metabolic Engineering for Bio-Based Fuels, Chemicals and Materials
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Yeast Metabolic Engineering for Bio-Based Fuels, Chemicals and Materials

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Genomics, Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (1 December 2023) | Viewed by 7683

Special Issue Editors

Dr. Violeta Sànchez i Nogué

E-Mail Website
Guest Editor
Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
Interests: bio-based molecules for fuels; chemicals and materials production; non-conventional organisms; non-conventional substrates; bioprocess development and optimization
Dr. João Ricardo M. Almeida

E-Mail Website
Guest Editor
1. Graduate Program of Microbial Biology, Institute of Biology, University of Brasília, Brasília 70770-901, Brazil
2. Microbial Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasília 70770-901, Brazil
Interests: renewable fuels and chemicals; yeast metabolic engineering; bioprospecting and bioprocesses development

Special Issue Information

Dear Colleagues,

Biofuels and bioproducts are characterized as products obtained from renewable biomass. Yeasts have been employed in the industrial production of bioethanol and other bioproducts for decades. However, the substitution of fossil routes for advanced bio-based processes is still limited due to constraints of process titer, yield, and productivity. In the post-genome era, advances in metabolic engineering tools have allowed for the identification and construction of new yeast strains to meet the increased demand for renewable products and the diversification of feedstocks used in bioprocesses. Indeed, several yeast species have been metabolically engineered to produce organic acids, alcohols, and other compounds using, among other substrates, sugars, methanol, glycerol, and even CO2.

This Special Issue aims to present the recent advances in yeast metabolic engineering and bioprocess development for the production of biofuels and bioproducts. Works on tools for yeast metabolic engineering, and yeast metabolic engineering targeting the production of bio-based molecules for fuel, chemical, and material production, and substrate usage optimization are specially suited to this Special Issue. Additionally, studies addressing the development and optimization of these bioprocesses are encouraged.

Dr. Violeta Sànchez i Nogué
Dr. João Ricardo M. Almeida
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. Journal of Fungi 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

  • renewable chemicals
  • bioeconomy
  • organic acids
  • alcohols
  • fermentative process
  • bioprocess development
  • bioprocess optimization
  • lignocellulosic biomass
  • non-conventional feedstocks
  • non-conventional yeasts
  • metabolic engineering tools

Published Papers (5 papers)

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Research

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13 pages, 3126 KiB  
Article
Characterization of Three Types of Elongases from Different Fungi and Site-Directed Mutagenesis
by Yuxin Wang, Lulu Chang, Hao Zhang, Yong Q. Chen, Wei Chen and Haiqin Chen
J. Fungi 2024, 10(2), 129; https://doi.org/10.3390/jof10020129 - 03 Feb 2024
Viewed by 1319
Abstract
Fatty acid elongases play crucial roles in synthesizing long-chain polyunsaturated fatty acids. Identifying more efficient elongases is essential for enhancing oleaginous microorganisms to produce high yields of target products. We characterized three elongases that were identified with distinct specificities: McELO from Mucor circinelloides [...] Read more.
Fatty acid elongases play crucial roles in synthesizing long-chain polyunsaturated fatty acids. Identifying more efficient elongases is essential for enhancing oleaginous microorganisms to produce high yields of target products. We characterized three elongases that were identified with distinct specificities: McELO from Mucor circinelloides, PrELO from Phytophthora ramorum, and PsELO from Phytophthora sojae. Heterologous expression in Saccharomyces cerevisiae showed that McELO preferentially elongates C16 to C18 fatty acids, PrELO targets Δ6 polyunsaturated fatty acids, and PsELO uses long chain saturated fatty acids as substrates. McELO and PrELO exhibited more homology, potentially enabling fatty acid composition remodeling and enhanced LC-PUFAs production in oleaginous microorganisms. Site-directed mutagenesis of conserved amino acids across elongase types identified residues essential for activity, supported by molecular docking. Alanine substitution of conserved polar residues led to enzyme inactivation, underscoring their importance in the condensation reaction. Our findings offer promising elongase candidates for polyunsaturated fatty acid production, contributing to the bioindustry’s sustainable development. Full article
(This article belongs to the Special Issue Yeast Metabolic Engineering for Bio-Based Fuels, Chemicals and Materials)
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17 pages, 5078 KiB  
Article
Assessment of the TRX2p-yEGFP Biosensor to Monitor the Redox Response of an Industrial Xylose-Fermenting Saccharomyces cerevisiae Strain during Propagation and Fermentation
by Raquel Perruca Foncillas, Miguel Sanchis Sebastiá, Ola Wallberg, Magnus Carlquist and Marie F. Gorwa-Grauslund
J. Fungi 2023, 9(6), 630; https://doi.org/10.3390/jof9060630 - 30 May 2023
Viewed by 1236
Abstract
The commercial production of bioethanol from lignocellulosic biomass such as wheat straw requires utilizing a microorganism that can withstand all the stressors encountered in the process while fermenting all the sugars in the biomass. Therefore, it is essential to develop tools for monitoring [...] Read more.
The commercial production of bioethanol from lignocellulosic biomass such as wheat straw requires utilizing a microorganism that can withstand all the stressors encountered in the process while fermenting all the sugars in the biomass. Therefore, it is essential to develop tools for monitoring and controlling the cellular fitness during both cell propagation and sugar fermentation to ethanol. In the present study, on-line flow cytometry was adopted to assess the response of the biosensor TRX2p-yEGFP for redox imbalance in an industrial xylose-fermenting strain of Saccharomyces cerevisiae during cell propagation and the following fermentation of wheat-straw hydrolysate. Rapid and transient induction of the sensor was recorded upon exposure to furfural and wheat straw hydrolysate containing up to 3.8 g/L furfural. During the fermentation step, the induction rate of the sensor was also found to correlate to the initial ethanol production rate, highlighting the relevance of redox monitoring and the potential of the presented tool to assess the ethanol production rate in hydrolysates. Three different propagation strategies were also compared, and it was confirmed that pre-exposure to hydrolysate during propagation remains the most efficient method for high ethanol productivity in the following wheat-straw hydrolysate fermentations. Full article
(This article belongs to the Special Issue Yeast Metabolic Engineering for Bio-Based Fuels, Chemicals and Materials)
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19 pages, 2185 KiB  
Article
Engineering 3-Hydroxypropionic Acid Production from Glucose in Yarrowia lipolytica through Malonyl-CoA Pathway
by Shiyu Liu, Yao Sun, Tianhui Wei, Dianliang Gong, Qi Wang, Zhe Zhan and Jinzhu Song
J. Fungi 2023, 9(5), 573; https://doi.org/10.3390/jof9050573 - 15 May 2023
Cited by 1 | Viewed by 1571
Abstract
3-Hydroxypropionic acid (3-HP) is an important intermediate compound in the chemical industry. Green and environmentally friendly microbial synthesis methods are becoming increasingly popular in a range of industries. Compared to other chassis cells, Yarrowia lipolytica possesses advantages, such as high tolerance to organic [...] Read more.
3-Hydroxypropionic acid (3-HP) is an important intermediate compound in the chemical industry. Green and environmentally friendly microbial synthesis methods are becoming increasingly popular in a range of industries. Compared to other chassis cells, Yarrowia lipolytica possesses advantages, such as high tolerance to organic acid and a sufficient precursor required to synthesize 3-HP. In this study, gene manipulations, including the overexpression of genes MCR-NCa, MCR-CCa, GAPNSm, ACC1 and ACSSeL641P and knocking out bypass genes MLS1 and CIT2, leading to the glyoxylate cycle, were performed to construct a recombinant strain. Based on this, the degradation pathway of 3-HP in Y. lipolytica was discovered, and relevant genes MMSDH and HPDH were knocked out. To our knowledge, this study is the first to produce 3-HP in Y. lipolytica. The yield of 3-HP in recombinant strain Po1f-NC-14 in shake flask fermentation reached 1.128 g·L−1, and the yield in fed-batch fermentation reached 16.23 g·L−1. These results are highly competitive compared to other yeast chassis cells. This study creates the foundation for the production of 3-HP in Y. lipolytica and also provides a reference for further research in the future. Full article
(This article belongs to the Special Issue Yeast Metabolic Engineering for Bio-Based Fuels, Chemicals and Materials)
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Review

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22 pages, 1346 KiB  
Review
Just around the Corner: Advances in the Optimization of Yeasts and Filamentous Fungi for Lactic Acid Production
by Nadielle Tamires Moreira Melo, Ana Caroline de Oliveira Junqueira, Letícia Ferreira Lima, Kamila Botelho Sampaio de Oliveira, Micaela Cristiane Gomes dos Reis, Octávio Luiz Franco and Hugo Costa Paes
J. Fungi 2024, 10(3), 207; https://doi.org/10.3390/jof10030207 - 09 Mar 2024
Viewed by 1152
Abstract
Lactic acid (LA) production has seen significant progress over the past ten years. LA has seen increased economic importance due to its broadening use in different sectors such as the food, medicine, polymer, cosmetic, and pharmaceutical industries. LA production bioprocesses using microorganisms are [...] Read more.
Lactic acid (LA) production has seen significant progress over the past ten years. LA has seen increased economic importance due to its broadening use in different sectors such as the food, medicine, polymer, cosmetic, and pharmaceutical industries. LA production bioprocesses using microorganisms are economically viable compared to chemical synthesis and can benefit from metabolic engineering for improved productivity, purity, and yield. Strategies to optimize LA productivity in microorganisms on the strain improvement end include modifying metabolic routes, adding gene coding for lactate transporters, inducing tolerance to organic acids, and choosing cheaper carbon sources as fuel. Many of the recent advances in this regard have involved the metabolic engineering of yeasts and filamentous fungi to produce LA due to their versatility in fuel choice and tolerance of industrial-scale culture conditions such as pH and temperature. This review aims to compile and discuss metabolic engineering innovations in LA production in yeasts and filamentous fungi over the 2013–2023 period, and present future directions of research in this area, thus bringing researchers in the field up to date with recent advances. Full article
(This article belongs to the Special Issue Yeast Metabolic Engineering for Bio-Based Fuels, Chemicals and Materials)
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26 pages, 1603 KiB  
Review
From Saccharomyces cerevisiae to Ethanol: Unlocking the Power of Evolutionary Engineering in Metabolic Engineering Applications
by Alican Topaloğlu, Ömer Esen, Burcu Turanlı-Yıldız, Mevlüt Arslan and Zeynep Petek Çakar
J. Fungi 2023, 9(10), 984; https://doi.org/10.3390/jof9100984 - 29 Sep 2023
Cited by 2 | Viewed by 1857
Abstract
Increased human population and the rapid decline of fossil fuels resulted in a global tendency to look for alternative fuel sources. Environmental concerns about fossil fuel combustion led to a sharp move towards renewable and environmentally friendly biofuels. Ethanol has been the primary [...] Read more.
Increased human population and the rapid decline of fossil fuels resulted in a global tendency to look for alternative fuel sources. Environmental concerns about fossil fuel combustion led to a sharp move towards renewable and environmentally friendly biofuels. Ethanol has been the primary fossil fuel alternative due to its low carbon emission rates, high octane content and comparatively facile microbial production processes. In parallel to the increased use of bioethanol in various fields such as transportation, heating and power generation, improvements in ethanol production processes turned out to be a global hot topic. Ethanol is by far the leading yeast output amongst a broad spectrum of bio-based industries. Thus, as a well-known platform microorganism and native ethanol producer, baker’s yeast Saccharomyces cerevisiae has been the primary subject of interest for both academic and industrial perspectives in terms of enhanced ethanol production processes. Metabolic engineering strategies have been primarily adopted for direct manipulation of genes of interest responsible in mainstreams of ethanol metabolism. To overcome limitations of rational metabolic engineering, an alternative bottom-up strategy called inverse metabolic engineering has been widely used. In this context, evolutionary engineering, also known as adaptive laboratory evolution (ALE), which is based on random mutagenesis and systematic selection, is a powerful strategy to improve bioethanol production of S. cerevisiae. In this review, we focus on key examples of metabolic and evolutionary engineering for improved first- and second-generation S. cerevisiae bioethanol production processes. We delve into the current state of the field and show that metabolic and evolutionary engineering strategies are intertwined and many metabolically engineered strains for bioethanol production can be further improved by powerful evolutionary engineering strategies. We also discuss potential future directions that involve recent advancements in directed genome evolution, including CRISPR-Cas9 technology. Full article
(This article belongs to the Special Issue Yeast Metabolic Engineering for Bio-Based Fuels, Chemicals and Materials)
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