Article
Biochemistry & Molecular Biology
Eugenio Ferrario, Riccardo Miggiano, Menico Rizzi, Davide M. Ferraris
Summary: Computational methods, such as AlphaFold, have improved protein structure prediction. In this study, we combined AlphaFold with crystal structures to investigate the structure of a previously unreported enzyme. We identified a functionally important structural element that was missing in the AlphaFold model but present in the crystal structure. We were able to reconstruct the protein oligomer using computational approaches and successfully solve the protein structure by phasing the diffraction data with the AlphaFold model. This work demonstrates the integration of AlphaFold with experimental data and its significance in protein analysis, crystallographic phasing, and structure solution.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Review
Biotechnology & Applied Microbiology
Zhenyu Zhang, Pengfu Liu, Weike Su, Huawei Zhang, Wenqian Xu, Xiaohe Chu
Summary: Trans-4-hydroxy-L-proline is an important amino acid used in medicinal and industrial applications, mainly produced through microbial fermentation. Recent advances in metabolic engineering have improved the biosynthetic pathway of trans-4-hydroxy-L-proline, aiming to enhance its production. New strategies and tools are needed to further explore the potential of microorganisms for trans-4-hydroxy-L-proline production.
MICROBIAL CELL FACTORIES
(2021)
Article
Chemistry, Applied
Elena S. Filatova, Olga V. Fedorova, Irina G. Ovchinnikova, Konstantin A. Chistyakov, Ilya N. Ganebnykh, Mikhail A. Uimin, Gennady L. Rusinov
Summary: The stereoselective Biginelli reaction involving nanosized metal oxides, Bronsted acid, and chiral inductors was studied. The use of nanooxide NiO and 4-hydroxy-L-proline resulted in the synthesis of a dihydropyrimidinethione-containing podand with a 70% enantiomeric excess. The study showed that nanosized metal oxides have an activating and coordinating effect, increasing the chemoselectivity and stereoselectivity of the reaction.
APPLIED ORGANOMETALLIC CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Liangzhen Jiang, Jing Pang, Lixia Yang, Wei Li, Lili Duan, Guolin Zhang, Yinggang Luo
Summary: The study focuses on enhancing t4HYP production in E. coli through metabolic engineering by manipulating the endogenous L-proline biosynthetic pathway. Knocking out genes responsible for by-product formation and enhancing the expression of genes related to L-proline biosynthesis resulted in a significant increase in t4HYP production.
JOURNAL OF BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Cristina C. Clement, Angelo D'Alessandro, Sangeetha Thangaswamy, Samantha Chalmers, Raquel Furtado, Sheila Spada, Giada Mondanelli, Federica Ianni, Sarah Gehrke, Marco Gargaro, Giorgia Manni, Luisa Carlota Lopez Cara, Peter Runge, Wanxia Li Tsai, Sinem Karaman, Jorge Arasa, Ruben Fernandez-Rodriguez, Amanda Beck, Antonio Macchiarulo, Massimo Gadina, Cornelia Halin, Francesca Fallarino, Mihaela Skobe, Marc Veldhoen, Simone Moretti, Silvia Formenti, Sandra Demaria, Rajesh K. Soni, Roberta Galarini, Roccaldo Sardella, Gregoire Lauvau, Chaim Putterman, Kari Alitalo, Ursula Grohmann, Laura Santambrogio
Summary: 3-hydroxy-L-kynurenamine (3-HKA) is a metabolite deriving from a lateral pathway of tryptophan catabolism. The authors identify 3-HKA as a biogenic amine with anti-inflammatory properties, showing its protective effects against psoriasis and nephrotoxic nephritis in mice.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Fanfan Zhang, Shiwen Xia, Hui Lin, Jiao Liu, Wenxin Huang
Summary: An efficient proline racemase-proline dehydrogenase cascade has been developed for the enantioselective production of d-proline and N-boc-5-hydroxy-l-proline from l-proline.
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Physical
J. Carlos Jimenez-Cruz, Ramon Guzman-Mejia, Pedro Navarro-Santos, Stephanie Garcia-Zavala, Rafael Herrera-Bucio, Hugo A. Garcia-Gutierrez, Judit A. Avina-Verduzco
Summary: This work describes the synthesis and structural characterization of two palladium (II) complexes using various analytical techniques. The study focuses on a chiral complex derived from L-proline amino acid and a complex derived from glycine methyl ester. The structural features and reactivity properties of these complexes were explored using experimental and computational methods.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Agriculture, Multidisciplinary
Ruichen Gao, Zhimin Li
Summary: This study utilized a biocatalytic approach to achieve efficient production of HMB by rational design and optimization of reaction conditions, overcoming the limitations of traditional chemical synthesis and fermentation methods.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Alexandra N. Bogner, Kyle M. Stiers, Cole M. McKay, Donald F. Becker, John J. Tanner
Summary: ALDH4A1 is a dual substrate enzyme involved in the final steps of proline and hydroxyproline catabolism. The study found that trans-4-hydroxy-L-proline is the strongest inhibitor of ALDH4A1, with a competitive inhibition constant of 0.7 mM.
Article
Biochemistry & Molecular Biology
Danni Yang, Ruize Ni, Shihai Yang, Yanan Pu, Min Qian, Yunqiang Yang, Yongping Yang
Summary: This study cloned and identified the P5CS gene from Stipa purpurea, finding that overexpression of SpP5CS in Arabidopsis thaliana led to increased proline content and better growth under drought stress. SpP5CS-overexpressing A. thaliana showed higher resistance to drought stress compared to the wild type, suggesting that SpP5CS may be a potential target gene for enhancing plant resistance to drought.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Kaiying Wei, Liangkun Long, Qunying Lin, Shaojun Ding
Summary: Protocatechuic acid (PCA) is an important phenolic compound and can be efficiently produced through the conversion of 3-dehydroshikimate (DHS) by dehydroshikimate dehydratase (DSD). A new DSD from fungus Eupenicillium parvum was functionally studied after expression in Escherichia coli. The recombinant protein showed catalytic activity against DHS, with optimal temperature and pH of 40 degrees C and 7.5, respectively. Metal ions (Mg2+ or Mn2+) played a critical role in the enzymatic activity and thermal stability of the protein. The expression of the protein in E. coli resulted in the production of 491 mg/L PCA in a modified M9 medium with glycerol as the carbon source.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Zhenyu Zhang, Weike Su, Yunyun Bao, Qianqian Huang, Kai Ye, Pengfu Liu, Xiaohe Chu
Summary: This study optimized a microbial cell factory for efficient production of t4Hyp using a modular engineering approach. By reducing α-KG attrition, inhibiting L-proline consumption, and optimizing gene overexpression, promoter, copy number, and fusion system, a high yield of t4Hyp was achieved.
MICROBIAL CELL FACTORIES
(2022)
Article
Multidisciplinary Sciences
Meiyun Niu, Haifeng Yan, Yuping Xiong, Yueya Zhang, Xinhua Zhang, Yuan Li, Jaime A. Teixeira da Silva, Guohua Ma
Summary: In this study, two genes related to the biosynthesis of sandalwood terpenoids, SaAACT and SaHMGS, were cloned and characterized. These genes were found to be constitutively expressed in all tissues of sandalwood, with the highest expression in roots. The expression levels of these genes increased after treatment with methyl jasmonate, indicating their responsiveness to external stimuli.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Matteo Gaglianone, Maria Elena Laugieri, Adriana Lucely Rojas, Maria Rosaria Coppola, Francesco Piacente, Pier Luigi Fiori, Michela Giulia Tonetti
Summary: In this study, the first committed and limiting step of the L-rhamnose biosynthetic pathway in Trichomonas vaginalis was identified and characterized. The L-rhamnose synthesis in T. vaginalis proceeds through a mechanism different from typical eukaryotic pathways and involves separate enzymes for epimerase and reductase activities. Understanding the L-rhamnose biosynthetic pathway can provide insights into the formation of complex glycan structures and the development of selective inhibitors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Xiulai Chen, Juyang Yi, Jia Liu, Qiuling Luo, Liming Liu
Summary: This study presents a green and efficient production process for Hyp by overexpressing DsP4H enzyme and optimizing culture parameters, achieving high yields and conversion rates.
MICROBIAL BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Ryotaro Hara, Ryohei Suzuki, Kuniki Kino
ANALYTICAL BIOCHEMISTRY
(2015)
Article
Biotechnology & Applied Microbiology
Ryotaro Hara, Saki Kitatsuji, Kai Yamagata, Kuniki Kino
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2016)
Article
Biotechnology & Applied Microbiology
Shin Suzuki, Ryotaro Hara, Kuniki Kino
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2018)
Article
Multidisciplinary Sciences
Ryotaro Hara, Kengo Hirai, Shin Suzuki, Kuniki Kino
SCIENTIFIC REPORTS
(2018)
Article
Biotechnology & Applied Microbiology
Soichiro Kano, Shin Suzuki, Ryotaro Hara, Kuniki Kino
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Ryotaro Hara, Takeyuki Nishikawa, Takuya Okuhara, Kento Koketsu, Kuniki Kino
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2019)
Review
Biotechnology & Applied Microbiology
Ryotaro Hara, Kuniki Kino
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Ryotaro Hara, Yuta Nakajima, Hiroaki Yanagawa, Ryo Gawasawa, Izumi Hirasawa, Kuniki Kino
Summary: Enzymatic synthesis of beta-Hydroxy-alpha-amino acids using the newly discovered enzyme AEP14369 from Sulfobacillus thermotolerans Y0017 has shown regioselectivity and stereoselectivity, producing high yields of the desired compounds. This achievement opens the way for practical production of beta-hydroxy-alpha-amino acids and contributes to the diversification of pharmaceutical structures, providing a sustainable and economical industrial application for these important compounds.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Shota Kimoto, Michiki Takeuchi, Shigenobu Kishino, Yudai Itagaki, Ryotaro Hara, Nahoko Kitamura, Natsumi Okada, Si -Bum Park, Akinori Ando, Makoto Ueda, Jun Ogawa
Summary: This study discovered that Rhizobium pusense JCM 16209T has the ability to catalyze regioselective glycosylation. By cloning and expressing two α-glucosidases, it was found that RpG I exhibited high glycosylation activity towards resveratrol. The research suggests that RpG I can glycosylate a wide range of substrates, which is significant for precise synthesis of glycosides.
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2022)
Article
Biotechnology & Applied Microbiology
Taku Mizutani, Ryotaro Hara, Takayuki Iihoshi, Shoko Kozono, Michiki Takeuchi, Makoto Hibi, Satomi Takahashi, Makoto Ueda, Jun Ogawa
Summary: This study found that E. coli has the ability to synthesize S-allyl-L-cysteine (SAC) through the enzyme tryptophanase (TnaA). TnaA also showed the ability to synthesize a wide range of S-substituted cysteines with various chains or rings. These findings have important implications for the development of new processes for synthesizing valuable S-substituted cysteine derivatives.
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Taku Mizutani, Ryotaro Hara, Michiki Takeuchi, Kazuo Yamagishi, Yoshinori Hirao, Kenichi Mori, Makoto Hibi, Makoto Ueda, Jun Ogawa
Summary: This study developed a culturing method for synthesizing S-Allyl-L-cysteine (SAC) from readily available materials and screened microorganisms with high SAC-synthesizing activity. Food-related Klebsiella pneumoniae and Pantoea agglomerans showed significantly increased SAC-synthesizing activity. The study provides a shorter duration process for SAC production and proposes a promising alternative strategy using microorganisms for food-grade SAC production.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Tatsuya Suzuki, Miyu Fukaya, Kazuki Takahashi, Michiki Takeuchi, Ryotaro Hara, Jun Ogawa, Makoto Ueda
BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Kuniki Kino, Yasutaka Hirokawa, Ryo Gawasawa, Ryota Murase, Ryohei Tsuchihashi, Ryotaro Hara
JOURNAL OF BIOTECHNOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Ryotaro Hara, Kai Yamagata, Ryoma Miyake, Hiroshi Kawabata, Hisatoshi Uehara, Kuniki Kino
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2017)