Review
Microbiology
Sonia Salazar-Cerezo, Ronald P. de Vries, Sandra Garrigues
Summary: The use of microorganisms in industry allows for the mass production of various compounds relevant to antibiotics, food, beverages, cosmetics, chemicals, and biofuels. Traditional strain improvement and random screening are commonly used to obtain industrial strains, but recombinant DNA technology has enabled the improvement of microbial strains by gene manipulation. Genetic engineering, genome editing, and other techniques are contributing to the development of fungal production strains. This review discusses classical and recent methods, tools, and technologies used to develop fungal production strains for industrial applications, as well as the use of functional genomics and other omics technologies in combination with genetic manipulation techniques.
Article
Materials Science, Multidisciplinary
Yujie Tu, Zheng Zhao, Jacky W. Y. Lam, Ben Zhong Tang
Summary: As scientists assemble microscopic molecules into macroscopic substances, new properties may emerge while original properties may disappear. Studying mesoscopic aggregates can help us better understand these processes.
Article
Biotechnology & Applied Microbiology
Valentina Goldfinger, Marius Spohn, Jens-Peter Rodler, Melanie Sigle, Andreas Kulik, Max J. Cryle, Johanna Rapp, Hannes Link, Wolfgang Wohlleben, Evi Stegmann
Summary: The control of precursor delivery is crucial for the assembly of glycopeptide antibiotics (GPA). The cross-regulation between the tyrosine and phenylalanine pathways plays an important role in GPA production. Overexpression of the key enzyme gene involved in the tyrosine pathway significantly increased antibiotic yield, while overexpression of the key enzyme gene in the phenylalanine pathway had no positive effects.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Yang Tan, Changzheng Gao, Wei Song, Wanqing Wei, Jia Liu, Cong Gao, Liang Guo, Xiulai Chen, Liming Liu, Jing Wu
Summary: In this study, a tri-enzyme cascade pathway was designed for the efficient industrial production of d-HPG from racemate DL-HPG. The rate-limiting step, amination activity of PtDAPDH toward HPGA, was improved by solving the crystal structure of PtDAPDH and developing a binding pocket and conformation remodeling strategy. The best variant, PtDAPDH(M4), showed a catalytic efficiency 26.75-fold higher than the wild type, leading to the synthesis of 19.8 g/L d-HPG with high conversion and enantiomeric excess.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Environmental Sciences
J. Germain, M. Raveton, M. N. Binet, B. Mouhamadou
Summary: The study shows that native fungal strains isolated from PCB contaminated sites have significant biodegradation and detoxification capabilities, with only a few strains able to reduce the toxicity associated with PCBs and their metabolites. The enzymatic activities induced by PCBs vary among strains.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Biotechnology & Applied Microbiology
Aafke C. A. van Aalst, Igor S. van der Meulen, Mickel L. A. Jansen, Robert Mans, Jack T. Pronk
Summary: This study explores the potential advantages of co-cultivating engineered S. cerevisiae strains in anaerobic bioreactor batch cultures. Co-cultivating these strains can reduce byproduct formation and improve ethanol yields, and the co-cultures can completely remove acetate in the medium that mimics industrial feedstocks.
METABOLIC ENGINEERING
(2023)
Article
Multidisciplinary Sciences
Jiancheng Zhao, Miao Liu, Jun Xu, Zhenya Yang, Qin Li, Chunju Cai
Summary: This study aimed to investigate the response of soil fauna communities to agroforestry management in a bamboo-fungus agroforestry system. The results showed that planting Stropharia rugosoannulata in moso bamboo forest increased the diversity and abundance of soil fauna communities, which were associated with the abundance of organic matter and supply of nutrients in the soil.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Jiajia Wu, Zhaoai Shi, Jiahong Zhu, Aocheng Cao, Wensheng Fang, Dongdong Yan, Qiuxia Wang, Yuan Li
Summary: The study found that biofertilizers significantly improve cucumber growth and reduce the number of soil-borne pathogens. Different biofertilizers have different effects on soil microbial communities, which leads to changes in microbial diversity and taxonomic structure during different growing seasons. The use of biofertilizers allows for cost-effective continuous production of high-quality crops from the same soil each year, while controlling soil-borne diseases.
SCIENTIFIC REPORTS
(2022)
Review
Biology
Xiunan Yi, Hal S. Alper
Summary: The metabolic capacity of yeast strains can vary within the same species, which affects their performance in metabolic engineering. Understanding the characteristics of different strains is crucial for successful metabolic engineering applications.
Article
Plant Sciences
Xingli Zhao, Dianyun Hou, Jiaqi Xu, Kaixuan Wang, Zhenjie Hu
Summary: This study screened and identified antagonistic strains against Fusarium pseudograminearum (Fp), the dominant pathogen associated with the crown rot of wheat in China, and evaluated their biosynthetic potential. The results demonstrated potential strains for the biocontrol of the crown rot of wheat, with T. trachyspermus R-17 showing promising antibacterial properties.
Article
Agricultural Engineering
Xiaolan Li, Yufei Zhang, Hossain M. Zabed, Junhua Yun, Guoyan Zhang, Mei Zhao, Yuvaraj Ravikumar, Xianghui Qi
Summary: Metabolic engineering and process optimization were used to improve the production of D-arabitol in Zygosaccharomyces rouxii. The engineered strain ZR-5A achieved a production of 29.01 g/L, 59.31% higher than the parent strain. With the optimal medium composition and fed-batch fermentation, the strain ZR-5A produced 149.10 g/L of D-arabitol with a productivity of 1.04 g/L/h, the highest reported in Z. rouxii system.
BIORESOURCE TECHNOLOGY
(2023)
Article
Chemistry, Physical
Kaori Hiraga, Tetsuji Itoh, Deeptak Verma, Wei Wang, Chen Huang, Michael Ardolino, Yong-Li Zhong, Grant Murphy
Summary: Chiral vicinal diols are important intermediates in pharmaceutical synthesis. Epoxide hydrolases can catalyze the hydrolytic ring opening of epoxides, providing an attractive and efficient method to access these building blocks. In this study, an engineered epoxide hydrolase was able to produce (3S,4S)-tetrahydrofurandiol with high optical purity. Through directed evolution, the enzyme's stereopreference was reversed and its activity was significantly improved. Computational modelling provided insights into the changes in enzyme-substrate interaction resulting in divergent enantioselectivities.
Review
Biotechnology & Applied Microbiology
Xiangfeng Meng, Yu Fang, Mingyang Ding, Yanyu Zhang, Kaili Jia, Zhongye Li, Jerome Collemare, Weifeng Liu
Summary: Natural products from fungi are important for therapeutic agent development, but many fungal biosynthetic gene clusters (BGCs) are not expressed under laboratory conditions, necessitating the development of new expression platforms. Therefore, increasing heterologous expression of BGCs is a current research focus.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Biotechnology & Applied Microbiology
Wenting Gao, Ying Yin, Pan Wang, Wei Tan, Mingliang He, Jianping Wen
Summary: In this study, the genes of the Dahms xylose-utilization pathway were integrated into Bacillus subtilis and a metabolic control module was designed, resulting in an increased yield of fengycin. Metabonomic analysis revealed the underlying factors for the increase of fengycin titer.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Environmental Sciences
Quratulain Maqsood, Aleena Sumrin, Rafia Waseem, Maria Hussain, Mehwish Imtiaz, Nazim Hussain
Summary: Industrialization and other human activities pose significant environmental risks, but bioremediation using microbes or their active metabolites is a successful approach to remove hazardous compounds. Restoring soil health is critical, and genetically modified organisms can speed up the breakdown process. This review focuses on enzymatic removal of hazardous pollutants and assesses current findings and future plans.
ENVIRONMENTAL RESEARCH
(2023)
Article
Plant Sciences
Yagut Allahverdiyeva, Eva-Mari Aro, Bert van Bavel, Carlos Escudero, Christiane Funk, Jarna Heinonen, Lars Herfindal, Peter Lindblad, Sari Makinen, Merja Penttila, Kaarina Sivonen, Matilde Skogen Chauton, Hanne Skomedal, Jorunn Skjermo
Summary: NordAqua is a Nordic Center of Excellence focused on promoting Blue Bioeconomy and reforming the use of natural resources sustainably. Their key research includes improving photosynthesis, developing novel photosynthetic cell factories, promoting diversity of Nordic cyanobacteria and algae, and improving bio-based wastewater purification technologies.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Biotechnology & Applied Microbiology
Anna Ylinen, Hannu Maaheimo, Adina Anghelescu-Hakala, Merja Penttila, Laura Salusjarvi, Mervi Toivari
Summary: In this study, PDLA and P(LA-3HB) were successfully produced and characterized in yeast for the first time. The engineered enzymes resulted in accumulation of 3.6% P(LA-3HB) and 0.73% PDLA, showing the potential of yeast for producing 2-hydroxy acid containing PHAs.
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Javier Garrigos-Martinez, Kiira Vuoristo, Miguel Angel Nieto-Taype, Juha Taehtiharju, Jaana Uusitalo, Pauliina Tukiainen, Christian Schmid, Ilya Tolstorukov, Knut Madden, Merja Penttila, Jose Luis Montesinos-Segui, Francisco Valero, Anton Glieder, Xavier Garcia-Ortega
Summary: Through a comparative analysis of the dynamic characteristics of P-PDF and P-UPP, it was found that these two expression systems exhibit higher efficiency in CalB production compared to P-GAP, with higher specific production rates and transcription levels. Both systems are considered to be highly efficient alternatives for P. pastoris-based RPP bioprocesses.
MICROBIAL CELL FACTORIES
(2021)
Article
Chemistry, Multidisciplinary
Pezhman Mohammadi, Julie-Anne Gandier, Nonappa, Wolfgang Wagermaier, Ali Miserez, Merja Penttila
Summary: Inspired by the dactyl club of the stomatopod, a mineralized biocomposite with high strength, stiffness, and fracture toughness is designed and produced using cellulose nanocrystals and genetically engineered proteins. The material's structural properties are controlled through self-assembly and phase separation of protein components, offering an innovative platform for the synthesis of multifunctional biocomposites.
ADVANCED MATERIALS
(2021)
Article
Immunology
Andrea Aebischer, Kerstin Wernike, Patricia Koenig, Kati Franzke, Paul J. Wichgers Schreur, Jeroen Kortekaas, Marika Vitikainen, Marilyn Wiebe, Markku Saloheimo, Ronen Tchelet, Jean-Christophe Audonnet, Martin Beer
Summary: This study developed a novel self-assembling multimeric protein scaffold particle (MPSP) vaccine platform, with designed vaccines showing effective protection against virus infection in both mice and cattle, and demonstrating relatively high immunogenicity. The MPSP rapidly induced high levels of immunity, showing great potential in combating viral infections.
Article
Biotechnology & Applied Microbiology
Andreea Perpelea, Andy Wiranata Wijaya, Luis C. Martins, Dorthe Rippert, Mathias Klein, Angel Angelov, Kaisa Peltonen, Attila Teleki, Wolfgang Liebl, Peter Richard, Johan M. Thevelein, Ralf Takors, Isabel Sa-Correia, Elke Nevoigt
Summary: This study successfully demonstrated the co-fermentation of D-GalUA and glycerol by introducing the fungal D-GalUA pathway into yeast strain S. cerevisiae, resulting in the production of ethanol at a high rate in synthetic minimal medium. The fast and complete consumption of D-GalUA in crude sugar beet pulp hydrolysate was also confirmed, indicating potential for industrial application.
METABOLIC ENGINEERING
(2022)
Article
Biotechnology & Applied Microbiology
Anna Ylinen, Jorg C. de Ruijter, Paula Jouhten, Merja Penttila
Summary: This study demonstrated the production of poly(hydroxybutyrate) (PHB) in yeast Saccharomyces cerevisiae using cellobiose as a sole carbon source. Utilizing different cellobiose utilization routes led to increased PHB production and accumulation percentage, offering a promising solution for sustainable polymer production using microbial cells.
MICROBIAL CELL FACTORIES
(2022)
Article
Biochemical Research Methods
Maryam Sabzevari, Sandor Szedmak, Merja Penttila, Paula Jouhten, Juho Rousu
Summary: This paper presents an AI approach using multi-agent reinforcement learning to guide the strain optimization of engineered microbial cells. The method learns from experiments to improve production by tuning metabolic enzyme levels. The results show that multi-agent reinforcement learning holds promise for guiding strain optimization and achieving industrially attractive production levels.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Natalia Kakko, Anssi Rantasalo, Tino Koponen, Virve Vidgren, Matti Kannisto, Natalia Maiorova, Heli Nygren, Dominik Mojzita, Merja Penttila, Paula Jouhten
Summary: We achieved inducible synthetic resource-use control overSaccharomyces cerevisiae by expressing a bacterial ClpXP proteasome from an inducible promoter. This control method efficiently repressed cell growth, improved product yields, and did not compromise biomass accumulation. The study provides a new approach to tackle uncertainties in strain optimization and address strain stability and low productivity challenges.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Robert Pylkkanen, Daniel Werner, Ajit Bishoyi, Dominik Weil, Ernesto Scoppola, Wolfgang Wagermaier, Adil Safeer, Salima Bahri, Marc Baldus, Arja Paananen, Merja Penttila, Geza R. Szilvay, Pezhman Mohammadi
Summary: We demonstrate that Fomes fomentarius is a unique material with exceptional mechanical properties due to its structural design. It consists of three distinct layers with different microstructures and adhesive properties, resulting in its high strength and toughness.
Article
Agriculture, Multidisciplinary
Markus Laurel, Dominik Mojzita, Tuulikki Seppanen-Laakso, Kirsi-Marja Oksman-Caldentey, Heiko Rischer
Summary: Raspberry ketone has gained attention as a flavor agent and health supplement. The fusion of certain enzymes allows for efficient production of raspberry ketone in plants and yeast. This study successfully expressed key pathway genes for raspberry ketone formation in N. benthamiana, achieving high production levels.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Anna Ylinen, Laura Salusjarvi, Mervi Toivari, Merja Penttila
Summary: In this study, a precise synthetic biology method was used to adjust the composition of polymers by controlling gene expression. The results demonstrate the ability to tune polymer properties by adjusting the monomer content.
METABOLIC ENGINEERING COMMUNICATIONS
(2022)
Correction
Chemistry, Multidisciplinary
Robert Pylkkanen, Pezhman Mohammadi, Ville Liljestrom, Wojciech Plazinski, Gregory Beaune, Jaakko V. I. Timonen, Merja Penttila
Article
Chemistry, Multidisciplinary
Robert Pylkkanen, Pezhman Mohammadi, Ville Liljestrom, Wojciech Plazinski, Gregory Beaune, Jaakko V. Timonen, Merja Penttila
Summary: This study provides the first evidence of supramolecular complexation of beta-1,3-glucans and explains their formation of intricate hierarchical architectures at multiple length scales. The findings expand our understanding of beta-1,3-glucan molecular organization and offer a new approach for the synthesis of materials for diverse medical and industrial applications.
