Review
Biochemistry & Molecular Biology
Kacper Zbieralski, Donata Wawrzycka
Summary: Alpha-arrestins are a conserved family of proteins that selectively identify membrane proteins for ubiquitination and degradation, playing a crucial role in maintaining membrane protein homeostasis and global cellular metabolisms. Although the functions and regulation mechanisms of alpha-arrestins are not fully understood, their roles in redox homeostasis regulation, innate immune response regulation, and tumor suppression have been characterized in animal models.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Izmari Jasel Alvarez Gaona, Mariela Vanesa Assof, Viviana Patricia Jofre, Mariana Combina, Ivan Francisco Ciklic
Summary: A mutant screening method was designed to isolate B. bruxellensis mutants with reduced 4-EP production, leading to the selection of a strain with significantly lower 4-EP production and higher diversity and concentration of ethyl esters. This selected mutant strain shows promise as a candidate for producing wines and beers with novel aromatic properties.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Davier Gutierrez-Gongora, Fouad Raouf-Alkadhimi, Ryan S. S. Prosser, Jennifer Geddes-McAlister
Summary: Extracts from mollusk species showed inhibitory effects on the growth and virulence factor production of Cryptococcus neoformans. The compounds derived from natural sources have the potential to inhibit virulence factor production in this fungal pathogen.
SCIENTIFIC REPORTS
(2023)
Article
Food Science & Technology
Elizabeth C. Hann, Sean Overa, Marcus Harland-Dunaway, Andres F. Narvaez, Dang N. Le, Martha L. Orozco-Cardenas, Feng Jiao, Robert E. Jinkerson
Summary: Artificial photosynthesis systems can capture CO2 and produce a highly concentrated acetate stream, which can be used for heterotrophic cultivation of yeast, mushroom-producing fungus, and photosynthetic green algae. Coupling this approach with photovoltaic systems can significantly improve solar-to-food energy conversion efficiency and reduce the required solar footprint. This technology allows for a reimagining of food production in controlled environments.
Article
Biochemical Research Methods
Kai Peng, Heinrich Kroukamp, Isak S. Pretorius, Ian T. Paulsen
Summary: The unfolded protein response (UPR) is a crucial cellular response to ER stress in eukaryotic cells, with implications for human diseases and recombinant protein production. By constructing and evaluating high-throughput UPR sensors, it is possible to predict strains' protein production capacity, understand protein properties affecting secretion, and guide optimal engineering strategies for heterologous protein production.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemical Research Methods
Suman Pal, Ina F. de la Fuente, Shraddha S. Sawant, Jenna N. Cannata, Wu He, Jessica L. Rouge
Summary: In this study, the mechanisms and effects of serum on the uptake of DNA-functionalized micelles by cells were investigated. It was found that scavenger receptor-mediated, caveolae-dependent endocytosis is the major uptake pathway. Additionally, energy-independent pathways and clathrin-mediated endocytosis were involved in the uptake of particles degraded by enzymes. This study provides insights into the cytosolic delivery and therapeutic activity of DNA-functionalized nanomaterials, and highlights the stability of nucleic acids delivered by the micellular NAN platform in the presence of serum.
BIOCONJUGATE CHEMISTRY
(2023)
Article
Biology
Chong Zhang, Jiaguang Li, Imran Tarique, Yizhuang Zhang, Tong Lu, Jiasheng Wang, Aijun Chen, Fenfen Wen, Zhuoyu Zhang, Yanjun Zhang, Ming Shao
Summary: Maternal products, including mRNAs and proteins deposited during oogenesis, play vital roles in controlling oocyte formation, fertilization, and early embryonic development. A new conditional knockout strategy has been successfully used to overcome the current challenges in studying genes with multiple functionally redundant paralogs.
Article
Biotechnology & Applied Microbiology
Fidan Erden-Karaoglan, Mert Karaoglan
Summary: This study investigated the applicability of heterologous yeast promoters in Pichia pastoris, and found inducible and constitutive regulation modes as well as the optimal carbon sources for these promoters. The study also determined the DNA region with the highest activity for all promoters through promoter deletion analysis.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Rebecca Mercier, Danielle Yama, Paul LaPointe, Jill L. Johnson
Summary: Molecular chaperones, such as Hsp90, play a crucial role in maintaining protein stability and cellular health. Hsp90 facilitates the folding and activation of numerous client proteins through an ATP-dependent pathway. The interaction between Hsp90 and cochaperones, such as Hch1 and Cpr6, tightly regulate Hsp90 function and the conformational changes it undergoes during the folding cycle. Understanding these interactions and conformational changes may lead to new strategies for modulating Hsp90 function.
Article
Biotechnology & Applied Microbiology
Bo Tian, Tianxin Fu, Yang Wan, Yun Ma, Yanbo Wang, Zhibiao Feng, Zhanmei Jiang
Summary: In this study, B- and N-doped carbon dots (BN-CDs) were prepared and used to label yeast cells, allowing for quick identification of cell viability and growth status. The study also investigated the effects of different lethal methods on yeast cell morphology, as well as the endocytosis mechanism of BN-CDs.
JOURNAL OF NANOBIOTECHNOLOGY
(2021)
Article
Cell Biology
Andrew King On Wong, Barry Paul Young, Christopher J. R. Loewen
Summary: Our study demonstrates that Ist2 plays a crucial role in recruiting PS transport proteins and ORP family members Osh6 and Osh7 to ER-PM contacts, facilitating nonvesicular PS transport for PE synthesis in the endosomes/Golgi/vacuoles. This molecular link between the ORP and TMEM16 families highlights the specific role of Ist2 and Osh6/7 in the endocytosis of PS for PE production.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Biochemical Research Methods
David Romero-Suarez, Tune Wulff, Yixin Rong, Tadas Jakociunas, Satoshi Yuzawa, Jay D. Keasling, Michael K. Jensen
Summary: Protein misfolding and aggregation are associated with neurodegenerative diseases and suboptimal protein expression in biotechnology. A promoter-reporter system based on yeast response to misfolded protein was developed to monitor protein aggregates, showing a 12-fold output dynamic range and the ability to distinguish different protein states. Optimization of promoters and culture conditions improved the performance of the reporter system.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Nai-Xin Lin, Rui-Zhen He, Yan Xu, Xiao-Wei Yu
Summary: The robust P. pastoris mutant demonstrates higher expression levels of not only lipase but also other heterogeneous proteins under methanol induction conditions. The mutant shows lower intracellular ROS levels compared to the WT. RNA-seq analysis revealed upregulation of key pathways related to antioxidant, MAPK pathway, ergosterol synthesis pathway, transcription factors, and the peroxisome pathway in the robust mutant, contributing to its enhanced oxidative stress tolerance and high heterologous protein expression efficiency.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Article
Biochemistry & Molecular Biology
Jeong-Ho Kim, Rebeca Rodriguez
Summary: The glucose sensing receptors Rgt2 and Snf3 in yeast Saccharomyces cerevisiae are expressed at different levels in response to different glucose concentrations, regulated through distinct mechanisms. While Rgt2 is highly regulated at the level of protein stability, Snf3 is mainly regulated at the level of transcription. The difference in their roles in glucose sensing is attributed to their cell surface abundance rather than having different functions.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2021)
Article
Multidisciplinary Sciences
Louis-Philippe Bergeron-Sandoval, Sandeep Kumar, Hossein Khadivi Heris, Catherine L. A. Chang, Caitlin E. Cornell, Sarah L. Keller, Paul Francois, Adam G. Hendricks, Allen J. Ehrlicher, Rohit Pappu, Stephen W. Michnick
Summary: Endocytic coat proteins with prion-like domains form hemispherical puncta in budding yeast, which act as biomolecular condensates to organize proteins at the membrane for actin-dependent endocytosis. These endocytic condensates are reversible, forming and dissolving in response to temperature and solution conditions, and are organized around dynamic protein-protein interaction networks.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Alexandra M. de Paz, Thaddeus R. Cybulski, Adam H. Marblestone, Bradley M. Zamft, George M. Church, Edward S. Boyden, Konrad P. Kording, Keith E. J. Tyo
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
Andrew K. D. Younger, Peter Y. Su, Andrea J. Shepard, Shreya V. Udani, Thaddeus R. Cybulski, Keith E. J. Tyo, Joshua N. Leonard
PROTEIN ENGINEERING DESIGN & SELECTION
(2018)
Article
Biochemical Research Methods
Adebola Adeniran, Sarah Stainbrook, John W. Bostick, Keith E. J. Tyo
ACS SYNTHETIC BIOLOGY
(2018)
Correction
Biochemical Research Methods
Adebola Adeniran, Sarah Stainbrook, John W. Bostick, Keith E. J. Tyo
ACS SYNTHETIC BIOLOGY
(2018)
Article
Biotechnology & Applied Microbiology
Jennifer Greene, James Daniell, Michael Kopke, Linda Broadbelt, Keith E. J. Tyo
BIOCHEMICAL ENGINEERING JOURNAL
(2019)
Article
Biotechnology & Applied Microbiology
Sarah C. Stainbrook, Keith E. J. Tyo
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2019)
Review
Biochemical Research Methods
Jonathan Strutz, Jacob Martin, Jennifer Greene, Linda Broadbelt, Keith Tyo
CURRENT OPINION IN BIOTECHNOLOGY
(2019)
Article
Biochemical Research Methods
Peter C. St John, Jonathan Strutz, Linda J. Broadbelt, Keith E. J. Tyo, Yannick J. Bomble
PLOS COMPUTATIONAL BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Bradley W. Biggs, Stacy R. Bedore, Erika Arvay, Shu Huang, Harshith Subramanian, Emily A. McIntyre, Chantel Duscent-Maitland, Ellen L. Neidle, Keith E. J. Tyo
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biotechnology & Applied Microbiology
Zhuofu Ni, Andrew E. Stine, Keith E. J. Tyo, Linda J. Broadbelt
Summary: Enzyme substrate promiscuity is important for metabolic engineering, and predicting possible enzymatic side reactions is crucial for understanding underground metabolic networks in microorganisms and producing desired chemicals.
METABOLIC ENGINEERING
(2021)
Review
Chemistry, Applied
Nick Fackler, Bjorn D. Heijstra, Blake J. Rasor, Hunter Brown, Jacob Martin, Zhuofu Ni, Kevin M. Shebek, Rick R. Rosin, Sean D. Simpson, Keith E. Tyo, Richard J. Giannone, Robert L. Hettich, Timothy J. Tschaplinski, Ching Leang, Steven D. Brown, Michael C. Jewett, Michael Kopke
Summary: Rising levels of greenhouse gases have led to significant environmental, economic, and social challenges globally. Technology that converts greenhouse gases into useful products can help mitigate climate change by enabling a circular carbon economy. Gas fermentation using carbon-fixing microorganisms is a commercially viable and scalable solution which offers unique feedstock and product flexibility.
ANNUAL REVIEW OF CHEMICAL AND BIOMOLECULAR ENGINEERING, VOL 12, 2021
(2021)
Article
Biochemical Research Methods
Cameron J. Glasscock, Bradley W. Biggs, John T. Lazar, Jack H. Arnold, Lisa A. Burdette, Aliki Valdes, Min-Kyoung Kang, Danielle Tullman-Ercek, Keith E. J. Tyo, Julius B. Lucks
Summary: One major challenge in synthetic biology is the deleterious impacts of cellular stress caused by expression of heterologous pathways. Feedback control and dynamic regulation are proposed strategies to mitigate this stress. rSFPs provide additional control over gene expression output through multiple activation mechanisms, allowing control over timing, magnitude, and autonomy of expression.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Erika Arvay, Bradley W. Biggs, Laura Guerrero, Virginia Jiang, Keith Tyo
Summary: Utilization of lignin as a renewable resource is limited by its complex structure and heterogenous composition. Biological valorization of lignin presents advantages over traditional chemical processing, but faces limitations due to lack of relevant metabolic networks and low tolerance to degradation products in traditional engineered model organisms.
METABOLIC ENGINEERING COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Li Wang, Chenchen Liang, Jing Wu, Liming Liu, Keith E. J. Tyo
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2017)
Article
Biophysics
Jennifer L. Greene, Andreas Waechter, Keith E. J. Tyo, Linda J. Broadbelt
BIOPHYSICAL JOURNAL
(2017)