Article
Biotechnology & Applied Microbiology
Jasvinder Kaur, Anupam Singh, Amulya K. Panda, Rup Lal
Summary: LinB is an important haloalkane dehalogenase mainly involved in degrading the notorious 13-HCH in the isomers of hexachlorocyclohexane (HCH). Studies found that the enzyme activity on 13-HCH is significantly affected by a mutation in the active site.
ENZYME AND MICROBIAL TECHNOLOGY
(2021)
Article
Chemistry, Physical
Eva D. Schuiten, Christoffel P. S. Badenhorst, Gottfried J. Palm, Leona Berndt, Michael Lammers, Jan Mican, David Bednar, Jiri Damborsky, Uwe T. Bornscheuer
Summary: The study identified an epoxide hydrolase called CorEH that exhibits dehalogenase activity, suggesting a rare example of a protein with dual enzymatic functions. Despite the much lower dehalogenase activity compared to epoxide hydrolase activity, the presence of multiple activities in one naturally occurring protein demonstrates significant diversity.
Article
Environmental Sciences
Marco C. Knobloch, Lena Schinkel, Iris Schilling, Hans-Peter E. Kohler, Peter Lienemann, Davide Bleiner, Norbert V. Heeb
Summary: Short-chain chlorinated paraffins (SCCPs) are persistent organic pollutants listed under the Stockholm Convention. Certain bacterial strains can degrade SCCPs, with the enzyme LinB catalyzing the conversion of chlorinated tridecanes to hydroxylated compounds. LC-MS analysis revealed the formation of various hydroxylated products after exposure to LinB, suggesting its potential for environmental remediation.
Article
Chemistry, Physical
Jianxiong Chen, Xiaodong Ming, Zitao Guo, Yi Shi, Moying Li, Zhongpeng Guo, Yu Xin, Zhenghua Gu, Liang Zhang, Xuan Guo
Summary: In this study, an iron-based hybrid nanocomposite biocatalyst FeHN@DhaA was successfully constructed to enhance the environmental tolerability of DhaA. FeHN@DhaA exhibited excellent immobilized enzymatic properties, better tolerance to extreme acid and alkali, and satisfactory reusability.
Article
Chemistry, Physical
Iuliia Iermak, Oksana Degtjarik, Petra Havlickova, Michal Kuty, Radka Chaloupkova, Jiri Damborsky, Tatyana Prudnikova, Ivana Kuta Smatanova
Summary: Enzyme activity relies on efficient transport of substrates and products, with access to active sites affecting catalytic specificity. Understanding the structural basis of altered activity in mutant variants, such as LinB D147C+L177C, presents challenges due to changes in access tunnels and protein crystallization. The crystal structure of the LinB D147C+L177C variant was characterized after significant delays and deposited to the Protein Data Bank.
Article
Engineering, Environmental
Analia Alvarez, Beatriz Rodriguez-Garrido, Andrea Cerdeira-Perez, Alba Tome-Perez, Petra Kidd, Angeles Prieto-Fernandez
Summary: This study investigated the expression of genes encoding enzymes involved in HCH degradation in the bacterium Sphingobium sp. D4, selected strains able to mobilize HCHs from contaminated soil, and analyzed the biodegradation of HCHs by strain D4. The results showed that the degradation of HCH isomers by strain D4 was enhanced when co-inoculated with HCH mobilizing strains or when cultivated with root exudates.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Green & Sustainable Science & Technology
Kenta Sato, Seiryu Take, Siti Aqlima Ahmad, Claudio Gomez-Fuentes, Azham Zulkharnain
Summary: The Antarctic region is at a heightened risk of hydrocarbon pollution due to increased human activities. Polycyclic aromatic hydrocarbons (PAHs) and heterocyclic compounds from fuel can persist in the environment for a long time if not treated. To tackle this issue, native strains need to be isolated for the development of suitable bioremediation applications. Strain BS19, identified as a carbazole-degrading bacterium, was isolated from Antarctic soil and showed high efficiency in removing carbazole.
Article
Biotechnology & Applied Microbiology
Yasuyuki Nakamura, Ririka Asama, Takuya Tabata, Kenta Morita, Tatsuo Maruyama, Akihiko Kondo, Jun Ishii
Summary: Researchers utilized a yeast-based biosensor to analyze signal activation of melatonin receptors, finding that most mutations significantly affected the function of these receptors. This system holds promise for revealing the functions of melatonin receptors.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Microbiology
Emily C. Hoedt, Francesca Bottacini, Nora Cash, Roger S. Bongers, Kees van Limpt, Kaouther Ben Amor, Jan Knol, John MacSharry, Douwe van Sinderen
Summary: Members of the genus Bifidobacterium are difficult to genetically manipulate due to their extensive and variable Restriction-Modification systems. A modified suicide vector, pFREM28, was developed to target specific genes in B. breve by removing known restriction sites, reducing the time, effort, and resources required for generating site-directed mutants. This approach could be applied to other (bifido)bacterial species as well.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Su-Jin Jun, Jung-A Lee, Young-Wan Kim, Sang-Ho Yoo
Summary: Through site-directed mutagenesis, a robust mutant Bifidobacterium thermophilum (BtAS) strain BtAS(Y414F/P200R) with enhanced turanose productivity was successfully developed, showing an increase in turanose yield by two times compared to the wild type BtAS and completing the reaction in half the time.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Soroosh Pouyan, Milad Lagzian, Mohammad Hossein Sangtarash
Summary: This study characterized a new alpha-amylase from Bacillus cereus GL96 and used an in-silico approach to redesign the enzyme for improved thermal stability. The engineered enzyme showed higher stability and activity at elevated temperatures compared to the wild-type enzyme. Specifically, the D162K mutation resulted in the best performance, with increased optimum temperature and improved stability. This mutant enzyme holds promise for further investigation and industrial applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Plant Sciences
Xia Li, Geng Chen, Qing-Qing Gao, Chun-Fan Xiang, Cheng-Xiao Yuan, Xiao-Ning Li, Yan-Yu Shu, Guang-Hui Zhang, Yan-Li Liang, Sheng-Chao Yang, Chen-Xi Zhai, Yan Zhao
Summary: This study explored the key enzymes involved in cucurbitacins biosynthesis in the Chinese traditional medicinal plant Hemsleya chinensis. Using AlphaFold2 and molecular docking, the researchers successfully predicted the 3D structure of HcOSC6 and its binding features to 2,3-oxidosqualene. Mutagenesis experiments identified three key amino acid residues, E246, M261, and D490, which significantly affected the activity of HcOSC6. This study not only characterized three potential key residues for producing cucurbitacins, but also provided insights into their significant role in metabolic engineering.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Lena Goshayeshi, Sara Yousefi Taemeh, Nima Dehdilani, Mohammadreza Nasiri, Mohammad M. Ghahramani Seno, Hesam Dehghani
Summary: The study demonstrates the use of an RNA-guided piggyBac transposase and dual sgRNAs for site-directed integrations in the human ROSA26 safe harbor region. This methodology shows promise for targeting specific genomic regions, such as in cancer cells for inserting sequences into target regions or activating tumor suppressor genes.
Article
Microbiology
Jesica M. Soder-Walz, Kenneth Wasmund, Darja Deobald, Teresa Vicent, Lorenz Adrian, Ernest Marco-Urrea
Summary: This study sequenced the genome of Dehalobacter sp. strain 8M and analyzed its protein expression. It discovered evidence of interactions among respiratory proteins and discussed implications for the respiratory architecture and advances in understanding this unique respiratory chain.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Agriculture, Multidisciplinary
Cheng-Hua Wang, Wu-Ping Xiong, Cheng Huang, Xiao-Ming Li, Qing-Yan Wang, Ri-Bo Huang
Summary: This study successfully increased the catalytic activity and efficiency of an exoinulinase under acidic conditions through rational site-directed mutagenesis. The mutants showed improved substrate preference for inulin and may serve as promising candidates for industrial inulin hydrolysis. The study demonstrates the potential of mutating non-conserved substrate recognition residues for industrial enzyme improvements.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2021)
Article
Engineering, Chemical
Qi Gao, Jia-Nan Chen, Jian-Chao Zhang, Chun-Ju Liu, Da-Jing Li, Chun-Quan Liu, Masaru Tanokura, You-Lin Xue
Summary: Different drying methods, such as freeze drying and explosion puffing drying, resulted in yam chips with distinct physicochemical properties, including nutrition retention and texture quality. Freeze-dried and explosion puffing-dried chips showed higher levels of these characteristics compared to other drying methods.
Article
Multidisciplinary Sciences
Keita Negishi, Kenichi Aizawa, Takayuki Shindo, Toru Suzuki, Takayuki Sakurai, Yuichiro Saito, Takuya Miyakawa, Masaru Tanokura, Yosky Kataoka, Mitsuyo Maeda, Shota Tomida, Hiroyuki Morita, Norifumi Takeda, Issei Komuro, Kazuomi Kario, Ryozo Nagai, Yasushi Imai
Summary: Pathogenic variants in the Myh11 gene cause familial thoracic aortic aneurysms and dissections (FTAAD). This study established a mouse model carrying the Myh11 K1256del variant, which was found in two FTAAD families. The Myh11(K/K) aorta showed increased wall thickness and ultrastructural abnormalities, including weakened cell adhesion. Interestingly, the Myh11(K/+) mice developed aortic dissections and intramural hematomas when stimulated with angiotensin II. Mechanistically, the downregulation of integrin subunit alpha2 (Itga2) was observed in the Myh11(K/K) aorta and smooth muscle cells differentiated from Myh11(K/K) induced pluripotent stem cells. The contractility of the Myh11(K/K) aorta in response to phenylephrine was also reduced. These findings suggest that the suboptimal cell adhesion caused by Itga2 downregulation leads to a defect in aortic contraction, potentially contributing to the development of aortic dissections.
SCIENTIFIC REPORTS
(2022)
Article
Food Science & Technology
Rong Wang, Haruyo Nakajima-Adachi, Yimei Wang, Yingyu Zhou, Wenting Gu, Erika Hiraide, Mamiko Morinaga, Ryogo Nakagawa, Shotaro Nakamura, Tomohiro Takano, Xuyang Li, Mayumi Saeki, Osamu Kaminuma, Takachika Hiroi, Kenji Uchida, Hidemasa Motoshima, Masaru Tanokura, Takuya Miyakawa, Satoshi Hachimura
Summary: Lactococcus lactis subsp. cremoris YRC3780 isolated from kefir has anti-allergic effects in humans. The oral administration of L. cremoris YRC3780 enhanced IFN-gamma and IL-12 production, inhibited IL-4 production, and attenuated symptoms in an atopic dermatitis mouse model by regulating cytokine expression.
JOURNAL OF FUNCTIONAL FOODS
(2022)
Article
Multidisciplinary Sciences
Takuya Miyakawa, Jian Yang, Masato Kawasaki, Naruhiko Adachi, Ayumu Fujii, Yumiko Miyauchi, Tomonari Muramatsu, Toshio Moriya, Toshiya Senda, Masaru Tanokura
Summary: This study solves the cryo-EM structures of CphA1 and reveals the aspartate binding mode and protein dynamics required for cyanophycin elongation. The research also suggests a potential role of protein dynamics in the catalytic efficiency of the arginine condensation reaction.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Chao Li, Xin Gao, Hongbin Qi, Wei Zhang, Lei Li, Cancan Wei, Meijing Wei, Xiaoxuan Sun, Shusen Wang, Liyan Wang, Yingbin Ji, Shuhong Mao, Zhangliang Zhu, Masaru Tanokura, Fuping Lu, Hui-Min Qin
Summary: In this study, a genetically encoded biosensor based on a D-allulose-responsive transcriptional regulator was redesigned for real-time monitoring of D-allulose. Furthermore, an ultrahigh-throughput droplet-based microfluidic screening platform was constructed for the directed evolution of ketose 3-epimerases (KEases). Structural analysis revealed a lid conformation in Sinorhizobium fredii D-allulose 3-epimerase (SfDAE) that regulates substrate recognition, and through rational design and directed evolution, a mutant M3-2 with 17-fold enhanced catalytic efficiency was identified. This research provides a paradigm for the design and optimization of biosensor-based microdroplet screening platforms.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Multidisciplinary Sciences
Satoshi Kidokoro, Izumi Konoura, Fumiyuki Soma, Kazuo Shinozaki, Takamasa Suzuki, Masaru Tanokura, Takuya Miyakawa, Takato Imaizumi, Kazuko Yamaguchi-Shinozaki
Summary: Plants respond to severe temperature changes by inducing the expression of numerous genes whose products enhance stress tolerance and responses. DREB1 genes are rapidly and strongly induced by cold stress and their molecular mechanisms are vital for recognizing the initial responses to cold stress in plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Immunology
Yimei Wang, Tomohiro Takano, Yingyu Zhou, Rong Wang, Takayuki Toshimitsu, Toshihiro Sashihara, Masaru Tanokura, Takuya Miyakawa, Haruyo Nakajima-Adachi, Satoshi Hachimura
Summary: This study investigated the effects of Lactiplantibacillus plantarum OLL2712 on obesity-induced inflammation. It was found that the LAB strain regulated gut microbiota, suppressed intestinal inflammation, and improved gut barrier function, thereby reducing obesity-related inflammation.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Microbiology
Mizuki Watanabe, Tomoya Kitamura, Koji Nagata, Mitsutaka Ikezawa, Ken-ichiro Kameyama, Kentaro Masujin, Takehiro Kokuho
Summary: African swine fever is a highly fatal viral disease in pigs, and its control and eradication depend on good biosecurity management and accurate diagnosis. A new serological ELISA using recombinant p11.5 protein from ASFV as a target has been developed, showing high sensitivity and specificity. This assay has the ability to detect anti-ASFV antibodies earlier after virus inoculation, making it a valuable tool for the diagnosis of African swine fever.
Article
Biology
Akira Nozawa, Ryoko Miyazaki, Yoshinao Aoki, Reina Hirose, Ryosuke Hori, Chihiro Muramatsu, Yukinori Shigematsu, Keiichirou Nemoto, Yoshinori Hasegawa, Keiko Fujita, Takuya Miyakawa, Masaru Tanokura, Shunji Suzuki, Tatsuya Sawasaki
Summary: A new gibberellin receptor agonist, diphegaractin, has been identified in this study, which shows gibberellin-like activity in the growth and maturation of grapes, lettuce, Arabidopsis, and citrus fruit. This is the first successful identification of a GA receptor agonist with GA-like activity in agricultural plants using an in vitro molecular-targeted drug screening system.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Konosuke Takemoto, Akiho Tsurugi-Sakurada, Ryota Moriuchi, Yuko Yoneda, Shingo Kawai
Summary: Diarylheptanoids are secondary metabolites of plants that can be classified into linear-type and cyclic-type based on their chemical structures. This study focuses on the isolation and characterization of two double-bond reductases (AsDBR1 and AsDBR2) from Alnus sieboldiana that catalyze the reduction of bisdemethoxycurcumin and curcumin. The study provides valuable insights into the biosynthesis of cyclic diarylheptanoids and their potential roles in nodule symbiosis.
Article
Multidisciplinary Sciences
Satoshi Yamanaka, Hirotake Furihata, Yuta Yanagihara, Akihito Taya, Takato Nagasaka, Mai Usui, Koya Nagaoka, Yuki Shoya, Kohei Nishino, Shuhei Yoshida, Hidetaka Kosako, Masaru Tanokura, Takuya Miyakawa, Yuuki Imai, Norio Shibata, Tatsuya Sawasaki
Summary: Lenalidomide is an effective drug for treating hematological cancers, but has teratogenic effects on fetuses. This study identifies modifications that enhance the selectivity and effectiveness of lenalidomide as a standalone molecular glue or integrated in PROTACs.
NATURE COMMUNICATIONS
(2023)
Article
Food Science & Technology
Wanyi Chiu, Tomonari Muramatsu, Yingyu Zhou, Takuya Miyakawa, Masaru Tanokura
Summary: This study investigated the changes in compounds in Virginia-type peanut seeds and peels during roasting. The results showed an increase in taste and aroma compounds, as well as functional benefits of roasted peanuts.
ACS FOOD SCIENCE & TECHNOLOGY
(2022)
Article
Biology
Masahiko Okai, Rintaro Endo, Masachika Takashio, Masami Ishida, Naoto Urano
Summary: In this study, a simple and rapid method for the detection of ESBL bla(SHV) gene was developed and successfully amplified. The LAMP method showed higher sensitivity and great potential for applications in hospital, soil and water environment, food, and livestock.
BIOCONTROL SCIENCE
(2022)
Article
Plant Sciences
Shohei Nosaki, Nobutaka Mitsuda, Shingo Sakamoto, Kazuki Kusubayashi, Ayumi Yamagami, Yuqun Xu, Thi Bao Chau Bui, Tohru Terada, Kenji Miura, Takeshi Nakano, Masaru Tanokura, Takuya Miyakawa
Summary: The transcription factor BIL1/BZR1 is involved in regulating gene expression in response to brassinosteroid hormones in plants. This study reveals that BIL1/BZR1 can repress the transcription of certain genes by binding tightly to specific regions on the DNA. Furthermore, the study demonstrates that BIL1/BZR1 achieves selectivity for particular DNA sequences by reading the shape of the DNA rather than directly recognizing the nucleobases. These findings provide valuable insights into the molecular and structural basis of transcriptional repression by BIL1/BZR1 and its role in gene regulation.
Article
Food Science & Technology
Peng Lu, Saki Takiguchi, Yuka Honda, Yi Lu, Taichi Mitsui, Shingo Kato, Rina Kodera, Kazuo Furihata, Mimin Zhang, Ken Okamoto, Hideaki Itoh, Michio Suzuki, Hiroyuki Kono, Koji Nagata
Summary: This study analyzed 11 samples of bee pollen from Spain, China, and Australia using metabolomic analysis, and found variations in the concentrations of different components among samples from different countries, which can be used to identify the country of origin.
FOOD CHEMISTRY: MOLECULAR SCIENCES
(2022)
