Review
Biotechnology & Applied Microbiology
Yang Zhang, Xiao Guo, Huaiyi Yang, Shuobo Shi
Summary: Fatty acid alkyl esters have various applications, but traditional production methods are unsustainable and energy-intensive. Microbial production using renewable feedstocks provides a promising alternative, with yeasts being ideal hosts due to their fermentation capabilities and resistance to inhibitors. This review summarizes recent developments in the biosynthesis of alkyl esters, focusing on enzyme engineering strategies and pathway engineering strategies employed in yeast cell factories. Bottlenecks limiting productivity and potential solutions are also discussed.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Review
Biochemical Research Methods
Yiming Zhang, Jens Nielsen, Zihe Liu
Summary: Researchers have extensively studied and engineered yeast cell factories to produce a variety of oleochemicals from renewable feedstocks. Recent progress includes exploring alternative renewable feedstocks like xylose and L-arabinose, as well as investigating the utilization of C1 compounds for third generation yeast based biorefineries for oleochemical production.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Gehad G. Ibrahim, Jinyong Yan, Li Xu, Min Yang, Yunjun Yan
Summary: Resveratrol, a plant secondary metabolite, has various therapeutic applications and is in high demand. Recent efforts have focused on using yeast as a host for resveratrol production through metabolic engineering, showing promising results in increasing yields.
Article
Biotechnology & Applied Microbiology
Sasa Liu, Mengyao Zhang, Yuyao Ren, Guojie Jin, Yongsheng Tao, Liting Lyu, Zongbao K. Zhao, Xiaobing Yang
Summary: In this study, Rhodosporidium toruloides was engineered to produce limonene, with a maximum titer of 393.5 mg/L. The results provide insights into microbial production of valuable monoterpenes. This is the first report on engineering R. toruloides toward limonene production based on NPP and a fusion protein SltNPPS-CltLS.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Article
Biotechnology & Applied Microbiology
Kostyantyn V. Dmytruk, Justyna Ruchala, Liubov R. Fayura, Grzegorz Chrzanowski, Olena V. Dmytruk, Andriy O. Tsyrulnyk, Yuliia A. Andreieva, Daria V. Fedorovych, Olena I. Motyka, Diethard Mattanovich, Hans Marx, Andriy A. Sibirny
Summary: Recombinant strains of yeast capable of producing bacterial antibiotics aminoriboflavin and roseoflavin were constructed and evaluated.
MICROBIAL CELL FACTORIES
(2023)
Article
Biotechnology & Applied Microbiology
Francesca V. Gambacorta, Joshua J. Dietrich, Justin J. Baerwald, Stephanie J. Brown, Yun Su, Brian F. Pfleger
Summary: This study aimed to identify an isobutanol pathway cassette that can support the growth of a non-ethanol producing S. cerevisiae. By screening a combinatorial library of pathway enzymes, the researchers isolated a cassette that was able to produce 364 mg/L isobutanol under aerobic conditions. This approach shows promise for rewiring the metabolism of S. cerevisiae to produce other fermentation products.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Kirsty Black, Graeme Walker
Summary: The production of neutral distilled spirits, such as vodka and gin, is growing globally. This paper discusses the differences between the yeast strains used in neutral spirits and those used in whisky, rum, and brandy fermentation. It also describes the raw materials, yeasts, and fermentation conditions involved in neutral spirit production and explores challenges and opportunities in the technology, including advancements in improving yeast strains.
APPLIED SCIENCES-BASEL
(2023)
Review
Biotechnology & Applied Microbiology
Siyuan Gao, Yang Liao, Hao He, Huiling Yang, Xuewei Yang, Sheng Xu, Xin Wang, Kequan Chen, Pingkai Ouyang
Summary: Industrial microbes, as cell factories, face extreme stress conditions during production, making it essential to enhance their robustness for better tolerance. Improving cell robustness can be achieved through irrational and rational engineering strategies, including reshaping regulatory networks, modifying cell membranes, and other stress responses. This review provides a summary of metabolic engineering technologies for enhancing the tolerance of microbes to industrial conditions, and discusses the emerging ideas related to the development of biological instruments and synthetic biology.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Min Chen, Tingting Xie, Huan Li, Yingping Zhuang, Jianye Xia, Jens Nielsen
Summary: Supply and regulation of Gibbs free energy and precursors in cellular metabolism are essential for cellular function. In this study, we used multi-omics data under different conditions to investigate the regulation of central carbon metabolism (CCM) in yeast. We identified a metabolism-specific CCM flux regulation mechanism, which is affected by posttranslational modification and allosteric regulation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biotechnology & Applied Microbiology
Marc Scherer, Sarel J. Fleishman, Patrik R. Jones, Thomas Dandekar, Elena Bencurova
Summary: In order to ensure a sustainable supply of chemicals, innovative biotechnological solutions are essential to replace reliance on fossil resources. The lack of efficient and specific biocatalysts has hindered the commercialization of biotechnological processes for renewable chemical manufacturing. To address this challenge, researchers propose utilizing computational tools to streamline the identification and optimization of enzyme variants for use in the biotechnological industry.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Steven A. van der Hoek, Matej Rusnak, Guokun Wang, Lyubomir Dimitrov Stanchev, Luana de Fatima Alves, Mathew M. Jessop-Fabre, Kalaivani Paramasivan, Irene Hjorth Jacobsen, Nikolaus Sonnenschein, Jose L. Martinez, Behrooz Darbani, Douglas B. Kell, Irina Borodina
Summary: Ergothioneine is a rare sulfur-containing amino acid with potent antioxidant properties. Engineered yeast strains can be used to produce high levels of ergothioneine using glucose as the carbon source. Metabolic engineering and medium optimization are effective strategies to improve ergothioneine production.
METABOLIC ENGINEERING
(2022)
Review
Biochemistry & Molecular Biology
Vassiliki A. Boumba
Summary: This article discusses the challenges faced by forensic toxicologists in identifying the source of ethanol in postmortem blood and interpreting the corresponding blood alcohol concentration (BAC) results. The study investigates the role of higher alcohols as biomarkers of microbial ethanol production and emphasizes the importance of microbial ethanol production models in interpreting the origin of ethanol concentrations in postmortem cases.
Article
Agricultural Engineering
Mengsu Liu, Chao Wang, Xuefeng Ren, Song Gao, Shiqin Yu, Jingwen Zhou
Summary: Resveratrol, a polyphenol with various applications, has low production yield. Researchers were able to increase resveratrol production through pathway engineering and enzyme assembly, achieving high yields.
BIORESOURCE TECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Zhihu You, Zijie Zhao, Qiankun Zhang, Chuanhui Zhang, Xiaojing Long, Daohao Li, Yanzhi Xia
Summary: This study successfully modulates the electronic state of Pd electrocatalysts by anchoring Pd nanoparticles to conjugated microporous polymers with different heterocycles. The Pd catalyst with S, N-containing thiazole heterocyclic polymer exhibits the highest catalytic activity in alcohol oxidation reactions, surpassing commercial catalysts.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Biotechnology & Applied Microbiology
Hang Qi, Yuanzi Li, Miao Cai, Jiaze He, Jiayu Liu, Xiaofei Song, Zhongqiang Ma, Haijin Xu, Mingqiang Qiao
Summary: This study achieved high-copy genome integration and stable heterologous production of p-coumaric acid (p-CA) in Saccharomyces cerevisiae. By using episomal plasmids and genetic integration, a high-level p-CA-producing strain with superior genetic stability and production stability was obtained, which has significant implications for future production of p-CA derivatives.
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Ryutaro Kawai, Yoshihiro Toya, Kenta Miyoshi, Manami Murakami, Teppei Niide, Takaaki Horinouchi, Tomoya Maeda, Atsushi Shibai, Chikara Furusawa, Hiroshi Shimizu
Summary: Co-culture is a promising approach to alleviate metabolic burden by dividing metabolic pathways into multiple modules and sharing conversion processes with different strains. Enhancing intermediate consumption rate is crucial for increasing target productivity. Adaptive laboratory evolution can improve mevalonate consumption in E. coli, leading to increased isoprenol production in a co-culture system.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Biotechnology & Applied Microbiology
Yoshihiro Toya, Yoko Hirono-Hara, Hidenobu Hirayama, Kentaro Kamata, Ryo Tanaka, Mikoto Sano, Sayaka Kitamura, Kensuke Otsuka, Rei Abe-Yoshizumi, Satoshi P. Tsunoda, Hiroshi Kikukawa, Hideki Kandori, Hiroshi Shimizu, Fumio Matsuda, Jun Ishii, Kiyotaka Y. Hara
Summary: In microbial fermentative production, harnessing the power of microbial rhodopsins with light-driven proton pumping activity to supplement ATP can improve the efficiency of target chemical biosynthesis.
METABOLIC ENGINEERING
(2022)
Article
Biology
Yoichiro Ito, Misa Ishigami, Goro Terai, Yasuyuki Nakamura, Noriko Hashiba, Teruyuki Nishi, Hikaru Nakazawa, Tomohisa Hasunuma, Kiyoshi Asai, Mitsuo Umetsu, Jun Ishii, Akihiko Kondo
Summary: This study presents a method to improve protein production in the non-conventional yeast Komagataella phaffii. The method involves gene knockout screening, combining gene disruptions, and adaptive evolution to recover growth reduction. The researchers used a multiwell-formatted screening system to evaluate a large number of mutant strains and identified multiple gene disruptions that increased antibody production. They also found that the target protein and promoter could be interchangeable for the effects of gene knockouts. Adaptive evolution was used to recover reduced cell growth caused by multiple gene knockouts and explore the possibility of further enhancing protein secretion. The overall approach holds promise for improving protein production in non-conventional microorganisms.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Kensuke Otsuka, Taisuke Seike, Yoshihiro Toya, Jun Ishii, Yoko Hirono-Hara, Kiyotaka Y. Hara, Fumio Matsuda
Summary: This study presents an approach to enhance the proton-pumping activity of rhodopsin through mutation and evolutionary engineering. Two strains with twice the proton pumping activity were successfully identified in E. coli, which will contribute to the industrial application of rhodopsin.
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2022)
Article
Biotechnology & Applied Microbiology
Tatsumi Imada, Chiaki Yamamoto, Masakazu Toyoshima, Yoshihiro Toya, Hiroshi Shimizu
Summary: In this study, the metabolic response of Synechocystis sp. PCC 6803 to light fluctuations was investigated using C-13-metabolic flux analysis. The results showed that the metabolic flux distributions and cofactor production rates were not affected by the light fluctuations. Furthermore, it was found that NADPH-consuming electron dissipation occurs under fluctuating light conditions.
BIOTECHNOLOGY PROGRESS
(2023)
Article
Biotechnology & Applied Microbiology
Kenta Miyoshi, Ryutaro Kawai, Teppei Niide, Yoshihiro Toya, Hiroshi Shimizu
Summary: In microbial bioproduction, CO2 emissions from pyruvate dehydrogenase pose a challenge in enhancing carbon yield. The non-oxidative glycolysis (NOG) pathway has the potential to overcome this challenge by converting glucose into acetyl-CoA without CO2 emissions. This study experimentally evaluated the metabolic flow of the NOG pathway in E. coli and demonstrated its feasibility during stationary phase. The results showed a significantly higher carbon yield of acetate using the engineered strain compared to the control strain.
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2023)
Article
Biochemical Research Methods
Musashi Takekana, Takanobu Yoshida, Erika Yoshida, Sumika Ono, Shinnosuke Horie, Christopher J. Vavricka, Moe Hiratani, Kenji Tsuge, Jun Ishii, Yoshihiro Hayakawa, Akihiko Kondo, Tomohisa Hasunuma
Summary: Conventional analysis of microbial bioproducers using liquid cultures is time consuming and limits productivity. This study introduces a new method, SFE-SFC-MS/MS, which allows for direct evaluation of microbial bioproduction colonies. Compared to traditional analysis, this method offers faster and more convenient screening of highly productive strains.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2023)
Article
Biochemical Research Methods
Mikoto Sano, Ryo Tanaka, Kentaro Kamata, Yoko Hirono-Hara, Jun Ishii, Fumio Matsuda, Kiyotaka Y. Hara, Hiroshi Shimizu, Yoshihiro Toya
Summary: This study demonstrated the ATP-consuming conversion of mevalonate to isoprenol using rhodopsin-expressing E. coli cells as a whole-cell catalyst, without energy cosubstrates in the medium. The conversion efficiency was enhanced under light conditions, indicating that ATP regenerated by rhodopsin under light energy can drive the ATP-consuming reactions.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Nanoscience & Nanotechnology
Kenta Morita, Yuya Nishimura, Jun Ishii, Tatsuo Maruyama
Summary: In this study, a short-peptide hydrogelator P1 was used to solubilize and enhance the antifungal selectivity of a conventional antifungal drug AmB. The nanoassembly of P1 successfully formed a nanocomplex with AmB, which showed remarkably low toxicity and suppressed the antifungal activity of AmB. The coassembly strategy could selectively kill fungi and has potential applications in drug repositioning.
ACS APPLIED NANO MATERIALS
(2022)
Article
Microbiology
Taisuke Seike, Hiroki Takekata, Yui Uchida, Natsue Sakata, Chikara Furusawa, Fumio Matsuda
Summary: Two novel yeast species, NBRC 115686T and NBRC 115687, were isolated from flowers and insects in Japan. These strains represent a new species of the genus Wickerhamiella based on sequence analysis and physiological characteristics. The proposed name for this species is Wickerhamiella bidentis sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Toshiharu Arai, Mayumi Wada, Hiroki Nishiguchi, Yasushi Takimura, Jun Ishii
Summary: The filamentous fungi Trichoderma reesei, commonly used for lignocellulosic biomass-degrading enzymes production, has not been widely utilized for heterologous recombinant protein production. This study demonstrates a novel inducer-free biomass-degrading enzyme expression system that allows the high secretory production of protein of interest (POI) in T. reesei using glucose as the sole carbon source. By replacing major cellulase genes with genes encoding enzymes and nanobodies, the occupancy of recombinant proteins in the secreted proteins was significantly increased.
MICROBIAL CELL FACTORIES
(2023)
Article
Evolutionary Biology
Yui Uchida, Hiroyuki Takeda, Chikara Furusawa, Naoki Irie
Summary: Phenotypes with greater developmental stability tend to have stronger evolutionary conservation. Experimental results showed that genes and developmental stages with lower variations led to lower diversity in subsequent generations, suggesting a causal relationship between stability and evolutionary conservation.
Article
Biochemical Research Methods
Yuji Omachi, Nen Saito, Chikara Furusawa
Summary: This study investigates the fitness landscape of the genetic code and finds four major fitness peaks, with one being the standard genetic code. Genetic algorithm analysis suggests that evolution under this multi-peaked fitness landscape is biased towards a narrow peak and is dependent on the evolutionary path.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Futa Yatabe, Taisuke Seike, Nobuyuki Okahashi, Jun Ishii, Fumio Matsuda
Summary: This study aimed to enhance the production of ethanol and 2,3-butanediol in S. cerevisiae strains by inducing ATP dissipation through the expression of FBPase and ATPase genes. The results showed increased ethanol and 2,3-butanediol production in the engineered strains, suggesting that ATP wasting may be an effective strategy for improving the fermentative biosynthetic capacity of S. cerevisiae.
MICROBIAL CELL FACTORIES
(2023)
Article
Mathematical & Computational Biology
Masato Tsutsumi, Nen Saito, Daisuke Koyabu, Chikara Furusawa
Summary: This article introduces a deep learning method called Morpho-VAE, which can analyze biological shape features without the need for manual annotations. The method was applied to primate mandible image data and successfully extracted morphological features that reflected the characteristics of different biological families, as well as reconstructed missing segments from incomplete images.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2023)