Article
Biochemistry & Molecular Biology
Yuanyuan Huang, Yanfei Wu, Han Hu, Bangzhuo Tong, Jie Wang, Siyu Zhang, Yanyi Wang, Jicong Zhang, Yue Yin, Shengkun Dai, Wenjuan Zhao, Bolin An, Jiahua Pu, Yaomin Wang, Chao Peng, Nan Li, Jiahai Zhou, Yan Tan, Chao Zhong
Summary: This study describes a technological workflow that facilitates the design and development of engineered living materials (ELMs) through the integration of bioinformatics, structural biology, and synthetic biology technologies. By developing a bioinformatics software called Bacteria Biopolymer Sniffer (BBSniffer), the researchers are able to identify bacteria and biopolymers of interest. Using genetic manipulation and structural characterization, a programmable bacterium was identified in the industrial workhorse Corynebacterium glutamicum, enabling the design of ELMs.
NATURE CHEMICAL BIOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Chenmeng Zhang, Hongyu Chen, Yiping Zhu, Yu Zhang, Xun Li, Fei Wang
Summary: Microbial cell surface display technology is a powerful platform for engineering proteins/peptides with improved properties. Saccharomyces cerevisiae is an ideal cell factory for this technology due to its large cell size, Generally Regarded As Safe (GRAS) status, and post-translational processing capabilities. This technology has various applications in industrial processes, including biofuels and chemical production, environmental pollution treatment, and immunization processes.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Tea Martinic Cezar, Mateja Lozancic, Ana Novacic, Ana Maticevic, Dominik Matijevic, Beatrice Vallee, Vladimir Mrsa, Renata Teparic, Bojan Zunar
Summary: By studying yeast surface display, we have developed a new tool that can efficiently convert enzymes of interest into their surface-displayed forms and anchor them near the cell wall. Through rational engineering, we have designed multiple fusion proteins and discovered guidelines for efficient surface display. Additionally, we have developed a small peptide tag that promotes efficient surface display.
MICROBIAL CELL FACTORIES
(2023)
Article
Thermodynamics
Joana T. Cunha, Daniel G. Gomes, Aloia Romani, Kentaro Inokuma, Tomohisa Hasunuma, Akihiko Kondo, Lucilia Domingues
Summary: This study engineered industrial strains of Saccharomyces cerevisiae with improved thermotolerance and stress resistance for cell surface display of cellulolytic enzymes, enabling high ethanol titers through consolidated bioprocessing. Additionally, beta-galactosidase was displayed for lactose consumption, resulting in high ethanol production from the simultaneous use of cheese whey and pretreated corn cob as substrate. The multi-feedstock valorization approach and lactose-consuming cellulolytic yeast led to a 60% reduction in materials costs and a 2.5-fold increase in annual ethanol production, contributing to the establishment of economically viable ethanol processes.
ENERGY CONVERSION AND MANAGEMENT
(2021)
Article
Biochemistry & Molecular Biology
Petra Vande Zande, Patricia J. Wittkopp
Summary: This study uses expression and fitness data from Saccharomyces cerevisiae gene deletion strains to show that cis-acting mutations tend to have lower pleiotropy and trans-acting mutations are more deleterious. These findings provide strong support for the role of pleiotropy in the preferential fixation of cis-regulatory alleles over evolutionary time.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Infectious Diseases
Wei Sun, Liyan Ma, Yana Li, Ying Xu, Jingjuan Wei, Lei Sa, Xinxin Chen, Jianrong Su
Summary: This study investigated the antimicrobial susceptibilities, drug resistance mechanisms, and biofilm formation capacities of non-diphtheriae Corynebacterium strains isolated from urine samples of hospitalized patients with urinary tract infections. The results showed that C. striatum, C. glucuronolyticum, and C. urealyticum were the most prevalent species associated with UTIs. The high occurrence of multidrug-resistant isolates and the ability to form biofilms highlighted the importance of identifying and understanding the drug resistance profiles of these bacteria in order to improve antibiotic therapy and reduce resistance transmission.
INFECTION AND DRUG RESISTANCE
(2022)
Article
Agriculture, Multidisciplinary
Weiguo Li, Xiaoguang Yan, Yuting Zhang, Dongmei Liang, Qinggele Caiyin, Jianjun Qiao
Summary: This study investigated the biosynthesis of volatile terpenoids in Celastrus angulatus, identified two trans-nerolidol synthases and successfully constructed a Saccharomyces cerevisiae cell factory for high-level production of trans-nerolidol. The results demonstrate the potential for industrial production of trans-nerolidol in S. cerevisiae and shed light on terpenoid biosynthesis in C. angulatus.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Yu Chen, Jens Nielsen
Summary: In this study, the in vivo catalytic rates of the yeast Saccharomyces cerevisiae under various conditions were estimated and compared with in vitro enzyme activity, revealing a weak correlation and considerable deviations between in vivo and in vitro enzyme activities. The correlation was improved after removing enzymes obtained through heterologous expression, but still not as strong as for bacteria. Parameterizing an enzyme-constrained metabolic model with the kapp dataset showed better performance in predicting proteomics data compared to using in vitro kcat, highlighting the importance of the generated dataset.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biotechnology & Applied Microbiology
Nanzhu Chen, Shuo Yang, Dawei You, Junfeng Shen, Banlai Ruan, Mei Wu, Jianzhi Zhang, Xiaozhou Luo, Hongting Tang
Summary: This study systematically investigated the effect of engineering cell wall biosynthesis on the activity of cellulolytic enzymes and found that the inactivation of certain genes significantly improved the secretion and surface-display of β-glucosidase. Furthermore, combinatorial modifications of these genes, along with the use of rich medium, greatly increased the activity of the enzymes. Proteomic analysis also revealed the involvement of translation processes in improving enzyme activity through cell wall biosynthesis engineering.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Jantima Arnthong, Jatupong Ponjarat, Piyada Bussadee, Pacharawan Deenarn, Parichat Prommana, Apisan Phienluphon, Salisa Charoensri, Verawat Champreda, Xin-Qing Zhao, Surisa Suwannarangsee
Summary: This study explored the effects of two cell wall protein genes, CWP2 and YGP1, on beta-glucosidase activity on the yeast cell surface. The disruption of YGP1 and CWP2 increased beta-glucosidase activity, and further transcriptional analysis revealed changes in the expression of genes related to cell wall structure, biogenesis, and integrity.
BIOCHEMICAL ENGINEERING JOURNAL
(2022)
Article
Microbiology
Shuo Yang, Junfeng Shen, Jiliang Deng, Hongxing Li, Jianzhi Zhao, Hongting Tang, Xiaoming Bao
Summary: This study focuses on improving the production of recombinant proteins in yeast cell factories by modifying cell polarization. Overexpression of genes related to cell polarization can enhance the surface display and secretion of recombinant proteins. Combinatorial modification of gene expression can increase protein production in a dose-dependent manner.
Article
Engineering, Chemical
Boitumelo F. Mashangoane, Evans N. Chirwa
Summary: Platinum group metals (PGMs) are elements that are concentrated in the earth's core and mantle, with low natural abundances. Due to their limited supply, there is economic value in recovering and reusing PGMs from waste solutions. Conventional methods for removing PGMs from wastewater have drawbacks, leading to a search for new technologies such as biosorption. This research project successfully developed a genetically modified strain of Saccharomyces cerevisiae EBY100 for biosorption of Pd (II) in aqueous solutions, with a maximum adsorption capacity of 125 mg/g.
MINERALS ENGINEERING
(2022)
Article
Multidisciplinary Sciences
Vinh G. Tran, Somesh Mishra, Sarang S. Bhagwat, Saman Shafaei, Yihui Shen, Jayne L. Allen, Benjamin A. Crosly, Shih-I Tan, Zia Fatma, Joshua D. Rabinowitz, Jeremy S. Guest, Vijay Singh, Huimin Zhao
Summary: In this study, we successfully engineered yeast to produce succinic acid at high efficiency under low pH conditions. The high titers of succinic acid obtained in the experiments, as well as the economic and environmental benefits demonstrated in the techno-economic and life cycle assessments, indicate the potential of scaling up this process for industrial applications.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Mi-Jin Kim, Bong Hyun Sung, Hyun-Jin Kim, Jung-Hoon Sohn, Jung-Hoon Bae
Summary: Protein expression with a fusion partner followed by the removal of the fusion partner via in vitro processing with a specific endoprotease is a favored method for efficient production of intact recombinant proteins. This study developed an autolysis-proof Kex2p endoprotease, facilitating the large-scale production of recombinant proteins.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Vinh G. Tran, Somesh Mishra, Sarang S. Bhagwat, Saman Shafaei, Yihui Shen, Jayne L. Allen, Benjamin A. Crosly, Shih- Tan, Zia Fatma, Joshua D. Rabinowitz, Jeremy S. Guest, Vijay Singh, Huimin Zhao
Summary: This study presents a metabolic engineering approach to enhance the production of succinic acid (SA) by acid-tolerant yeast, achieving high titers at low pH conditions. The pilot-scale fermentation using sugarcane juice medium resulted in a SA titer of 63.1g/L with a high crystallization yield. Techno-economic analysis and life cycle assessment indicate the financial viability and significant reduction in greenhouse gas emissions of the proposed low-pH SA production process.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Seonghun Kim
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2018)
Article
Biochemistry & Molecular Biology
Seonghun Kim
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2018)
Article
Biotechnology & Applied Microbiology
Seonghun Kim
BIOMED RESEARCH INTERNATIONAL
(2018)
Article
Biotechnology & Applied Microbiology
Seonghun Kim, Jinhyuk Lee, Bong Hyun Sung
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Seonghun Kim
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2020)
Article
Green & Sustainable Science & Technology
Seonghun Kim, Sang-Dae Kim, Seok Young Sohn
Article
Food Science & Technology
Seonghun Kim
Review
Chemistry, Multidisciplinary
Seonghun Kim
Summary: Mushroom ligninolytic enzymes are powerful biocatalysts that can degrade complex lignin structures, with laccase-mediated grafting being used to modify lignin and other polymers to obtain novel functional groups. These enzymes have potential applications in catalytic reactions involving lignin and its derivatives for obtaining value-added chemicals and materials in lignin valorization.
APPLIED SCIENCES-BASEL
(2021)
Article
Biochemistry & Molecular Biology
Seonghun Kim, Jinhyuk Lee, Doo-Byoung Oh, Ohsuk Kwon
Summary: The invertebrate sialyltransferase cST3Gal-I from the sea squirt Ciona savignyi shows a preference for O-glycans as substrates, effectively transferring Neu5Ac to core 1 O-glycan compared to its human orthologue. Structural modeling suggests that the active sites of cST3Gal-I are similar to a mammalian enzyme, porcine ST3Gal-I, indicating a potential ancestral preference for O-glycans in C. savignyi.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Review
Microbiology
Sang-Myung Jung, Seonghun Kim
Summary: This review discusses the models used to simulate normal and diseased states of the small intestine, including ex vivo, 2D culture, organoid, lab-on-a-chip, and 3D culture models. The focus is on current techniques and potential applications, summarizing the main features and future developments of intestine models.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Food Science & Technology
Seonghun Kim
Summary: This study analyzed the enzymatic hydrolysates of porcine whole blood and found that it contained abundant peptides and free amino acids. The proteolysis reaction converted proteins into peptides and increased the content of free amino acids. Furthermore, the study found diverse bacterial species in the hydrolyzed whole blood. These findings suggest that animal blood byproducts could be utilized to produce bioactive food supplements.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Energy & Fuels
Seonghun Kim
FRONTIERS IN ENERGY RESEARCH
(2019)
Article
Engineering, Biomedical
Sun-Young Kim, Young-Woock Noh, Tae Heung Kang, Jung-Eun Kim, Sohyun Kim, Soong Ho Um, Doo-Byoung Oh, Yeong-Min Park, Yong Taik Lim
Article
Biotechnology & Applied Microbiology
Yeong Hun Kim, Ji-Yeon Kang, Jin Young Gil, Sang-Yoon Kim, Keun Koo Shin, Hyun Ah Kang, Jeong-Yoon Kim, Ohsuk Kwon, Doo-Byoung Oh
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2017)
Article
Multidisciplinary Sciences
Ji-Yeon Kang, Ohsuk Kwon, Jin Young Gil, Doo-Byoung Oh