Article
Biochemistry & Molecular Biology
Huanhuan Ma, Yuanlong Wu, Ruiling Lv, Huabin Chi, Yunlong Zhao, Yanlong Li, Hongbo Liu, Yizan Ma, Longfu Zhu, Xiaoping Guo, Jie Kong, Jianyong Wu, Chaozhu Xing, Xianlong Zhang, Ling Min
Summary: Researchers identified two key genes in the salicylic acid methyl ester synthesis pathway. These genes are highly expressed in stages 7-9 anthers and play important roles in pollen development and sporopollenin formation. Decreased enzyme activity in the mutants leads to pollen degradation and male sterility.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Article
Chemistry, Physical
Lea R. Rapp, Sergio M. Marques, Erna Zukic, Benjamin Rowlinson, Mahima Sharma, Gideon Grogan, Jiri Damborsky, Bernhard Hauer
Summary: The cytochrome P450 CYP153A(M.aq) enzyme from Marinobacter aquaeolei was engineered to hydroxylate octanoic acid with significantly improved catalytic efficiency and substrate binding. The modifications in tunnel structures and loop regions were key in stabilizing the enzyme-substrate complex and enhancing catalytic efficiency. Previous fatty acid anchor interactions were also found to boost the enzyme activity towards octanoic acid.
Article
Chemistry, Physical
Yiheng Liu, Zhongyu Li, Chenqi Cao, Xianzhi Zhang, Shuaiqi Meng, Mehdi D. Davari, Haijun Xu, Yu Ji, Ulrich Schwaneberg, Luo Liu
Summary: To overcome the complexity of protein sequence space, a study employed a machine learning approach combined with iterative generation and experimental data implementation, successfully identifying and validating multiple improved recombinant variants as well as comparing regression models. The research demonstrates the feasibility of integrating machine learning with experimental methods and proves effective in exploring potential variations within the protein sequence space.
Article
Biochemistry & Molecular Biology
Paula Bracco, Hein J. Wijma, Bastian Nicolai, Jhon Alexander Rodriguez Buitrago, Thomas Kluenemann, Agustina Vila, Patrick Schrepfer, Wulf Blankenfeldt, Dick B. Janssen, Anett Schallmey
Summary: By utilizing protein engineering and substrate modifications based on the crystal structure of CYP154C5, researchers were able to alter the regioselectivity of the enzyme in steroid hydroxylation. This change in selectivity was attributed to an alternative binding mode of the steroid in the active site of the mutant enzyme. Additionally, molecular dynamics simulations indicated that higher uncoupling in the mutant enzyme may have been caused by the entrance of water to the active site.
Article
Biochemistry & Molecular Biology
Christopher S. Campomizzi, George E. Ghanatios, D. Fernando Estrada
Summary: Cytochromes P450 are versatile enzymes involved in endogenous and exogenous metabolism, undergoing structural changes related to function. This study demonstrates the utility of fluorine (19F)-NMR spectroscopy in monitoring structural changes in CYP121A1, revealing insights into its role in substrate recognition and mechanistic details of this essential enzyme from Mycobacterium tuberculosis.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Chemistry, Physical
Pradeep Subedi, Jong Kook Park, Tae-Jin Oh
Summary: This study reported the catalytic capabilities of a bacterial cytochrome P450 enzyme, CYP105A5, towards different flavonoids and enhanced the product formation rate through rational design. The double mutant L100A/I302A showed significant improvement in flavonoid hydroxylation. These findings may facilitate the application of CYP105A5 in whole-cell biocatalysts for the production of valuable polyphenols.
Article
Biotechnology & Applied Microbiology
Ying Huang, Dan Jiang, Guangxi Ren, Yan Yin, Yifan Sun, Tengfei Liu, Chunsheng Liu
Summary: In this study, de novo biosynthesis of the rare compound Glycyrrhetic acid 3-O-mono-beta-D-glucuronide (GAMG) was achieved in engineered Saccharomyces cerevisiae strains using CRISPR/Cas9 genome editing technology. The engineered yeast strains provided a new approach for the production of glycosylated triterpenoids in pharmaceutical, cosmetic, and food industries, with significantly increased production yield through pathway optimization and environmental conditions enhancement.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Chenghai Sun, Bao-Di Ma, Guangjun Li, Wenya Tian, Lu Yang, Haidong Peng, Zhi Lin, Zixin Deng, Xu-Dong Kong, Xudong Qu
Summary: Through genome mining and study of the sequence-product relationship, we identified three key residues (F387, F388, and E73) that play pivotal roles in selecting different diketopiperazine (DKP) substrates. Engineering these residues in Nas(F5053) greatly expanded its substrate specificity, enabling the biosynthesis of 12 self-dimerized and at least 81 cross-dimerized HTDKPs. Structural and molecular dynamics analysis of F387G and E73S revealed that they control substrate specificity by reducing steric hindrance and regulating substrate tunnels.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biotechnology & Applied Microbiology
Jutapat Romsuk, Shuhei Yasumoto, Hikaru Seki, Ery Odette Fukushima, Toshiya Muranaka
Summary: This study investigates the catalytic mechanism of CYP716A subfamily enzymes in triterpenoid biosynthesis by combining bioinformatics approaches with data from other CYP families. Key amino acid residues that influence the catalytic activity and substrate specificity of the enzymes are identified and validated through homology modeling, site-directed mutagenesis, and functional analysis. The research has the potential to improve the production of desired triterpenoids in engineered yeast by enhancing the catalytic activity and substrate specificity of CYP716A subfamily enzymes.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Shuaiqi Meng, Yu Ji, Luo Liu, Mehdi D. Davari, Ulrich Schwaneberg
Summary: This study demonstrates that engineering the tunnels of cytochrome P450 can improve coupling efficiency by controlling water diffusion. The reduced water molecules around the active site lead to higher coupling efficiency. This research provides valuable insights for improving coupling efficiency through tunnel engineering.
Article
Biotechnology & Applied Microbiology
Shuaiqi Meng, Ruipeng An, Zhongyu Li, Ulrich Schwaneberg, Yu Ji, Mehdi D. Davari, Fang Wang, Meng Wang, Meng Qin, Kaili Nie, Luo Liu
Summary: The study demonstrates how tunnel engineering can modulate substrate preference and improve decarboxylation activity of enzymes, resulting in significantly increased conversion rates for specific fatty acids.
BIORESOURCES AND BIOPROCESSING
(2021)
Article
Chemistry, Physical
Zhongyu Li, Shuaiqi Meng, Kaili Nie, Ulrich Schwaneberg, Mehdi D. Davari, Haijun Xu, Yu Ji, Luo Liu
Summary: This study reports a loop engineering strategy to improve the stability of substrate access tunnels, revealing the molecular mechanism between loops and tunnels. The best variant identified through saturation mutagenesis showed considerably increased activity in dealkylation and hydroxylation reactions.
Review
Food Science & Technology
Mahmuda Akter Mele, Ho-Min Kang, Young-Tack Lee, Mohammad Zahirul Islam
Summary: Terpenes play a significant role in the flavor and quality of grapes and wine. Genetic and metabolic engineering can be utilized to modify terpenoid metabolism and potentially enhance the flavor of wine through transgenic grapevines. Strategies to improve grape breeding technology for enhanced wine aroma quality are also discussed in this review.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2021)
Article
Biochemistry & Molecular Biology
Melanie Nolden, Mark J. Paine, Ralf Nauen
Summary: Cytochrome P450 monooxygenases play a crucial role in the oxidative metabolism of xenobiotics in insects and their duplication and upregulation can lead to insecticide resistance. The interaction between P450s and other enzymes like NADPH cytochrome P450 oxidoreductase and cytochrome b5 is complex and can impact metabolic capacity. Recombinant expression of P450s in insect cells with cytochrome b5 can significantly enhance their ability to metabolize certain substrates, but not necessarily insecticides like deltamethrin.
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Yifeng Zhang, Lin Ma, Ping Su, Luqi Huang, Wei Gao
Summary: Terpenoids, as the largest family of natural products, play significant roles in medicine, agriculture, cosmetics, and food. Traditional extraction methods have low yields, waste resources, and are not suitable for endangered species. Modern biotech approaches are promising in discovering and characterizing plant terpenoid-related P450 enzymes, and metabolic engineering strategies can be employed to increase terpenoid production.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2023)
Article
Microbiology
Brian Shing, Seema Singh, Larissa M. Podust, James H. McKerrow, Anjan Debnath
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2020)
Meeting Abstract
Biochemistry & Molecular Biology
Vandna Sharma, Brian Shing, Anjan Debnath, Larissa Podust
Article
Chemistry, Multidisciplinary
Girish C. Sati, Joshua L. Martin, Yishu Xu, Tanmay Malakar, Paul M. Zimmerman, John Montgomery
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Article
Chemistry, Physical
Alexander W. Rand, Hongfei Yin, Liang Xu, Jessica Giacoboni, Raul Martin-Montero, Ciro Romano, John Montgomery, Ruben Martin
Article
Chemistry, Organic
Wesley L. Pein, Eric M. Wiensch, John Montgomery
Summary: This study describes the conversion of silyloxyarenes to boronic acid pinacol esters via nickel catalysis, showing competence in activating carbon-oxygen bonds of silyloxyarenes in isolated aromatic systems lacking a directing group. Additionally, catalytic functionalization of benzyl silyl ethers was achieved under these conditions, and sequential cross-coupling reactions were realized by leveraging the orthogonal reactivity of silyloxyarenes.
Article
Chemistry, Physical
Rosa Espinoza, Kersti Caddell Haatveit, S. Wald Grossman, Jin Yi Tan, Caylie A. McGlade, Yogan Khatri, Sean A. Newmister, Jennifer J. Schmidt, Marc Garcia-Borras, John Montgomery, K. N. Houk, David H. Sherman
Summary: Iterative P450 enzymes are powerful biocatalysts for selective late-stage C-H oxidation of complex natural product scaffolds. The study reports the structure of the multifunctional bacterial P450 TamI and the design of a toolbox of TamI biocatalysts, including a variant capable of catalyzing a four-step oxidative cascade without assistance. These tuned enzymes enable catalyst-controlled C-H functionalization and alkene epoxidation, leading to the synthesis of bioactive tirandamycin derivatives. Quantum mechanics calculations and MD simulations provide insights into the altered selectivity and enhanced oxidation mechanisms of the iterative P450 TamI.
Article
Chemistry, Multidisciplinary
Jichao Xiao, Zhenning Li, John Montgomery
Summary: This study demonstrates a method using nickel catalysis and BiOx ligand for the reductive coupling of redox-active esters with aliphatic aldehydes to obtain silyl-protected secondary alcohols. The protocol is simple, mild, and tolerates a variety of functional groups, with potential mechanistic insights pointing towards a radical chain pathway.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Physical
Jichao Xiao, John Montgomery
Summary: A simple procedure for the nickel-catalyzed defluorinative alkylation of unactivated aliphatic aldehydes is reported. The protocol exhibits broad substrate scope, mild conditions, and a simple catalytic setup.
Article
Chemistry, Organic
Joshua L. Martin, Girish C. Sati, Tanmay Malakar, Jessica Hatt, Paul M. Zimmerman, John Montgomery
Summary: A novel mode of reactivity involving a dioxolenium ion as a key intermediate that promotes both glycosylation and glycosyl exchange pathways has been discovered through experimental and computational mechanistic studies. By modifying the catalyst structure, it is possible to selectively favor one pathway, leading to improved multicomponent iterative couplings and glycosyl exchange processes.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Physical
Rosa Espinoza, Mark A. Maskeri, Aneta Turlik, Anjanay Nangia, Yogan Khatri, John Montgomery, K. N. Houk, David H. Sherman
Summary: This study reports the ability of bacterial P450 TamI L295A to switch between different oxidizing species in the synthesis of new tirandamycin antibiotics. By providing experimental evidence and theoretical calculations, new insights into the active oxidant species used by P450 TamI are revealed, providing new understanding of the oxidative decorations of tirandamycin.
Article
Chemistry, Inorganic & Nuclear
Michael T. Robo, Amie R. Frank, Ellen Butler, Alex J. Nett, Santiago Canellas, Paul M. Zimmerman, John Montgomery
Summary: This study delves into the activation mechanism of an IMes-nickel(0) catalyst, stabilized by covalent modification of the stabilizing ligand, revealing an unexpected catalyst activation pathway when ligand exchange is thermodynamically unfavorable.
Article
Chemistry, Physical
Mo Chen, John Montgomery
Summary: Regio- and enantioselective functionalization of heteroarene C-H bonds in the absence of directing groups has been a long-standing challenge. In this study, we developed a new approach for intermolecular enantioselective C-H alkylation of heteroarenes using nickel catalysts. The reaction can be carried out under mild conditions without the need for Lewis acid co-catalysts. Synthesis of NHC nickel complexes stabilized with 1,5-hexadiene improved the functional group tolerance and heteroarene scope. Mechanistic investigations revealed a ligand-to-ligand hydrogen transfer pathway.
Article
Chemistry, Multidisciplinary
Mo Chen, Austin M. Ventura, Soumik Das, Ammar F. Ibrahim, Paul M. Zimmerman, John Montgomery
Summary: Current methodologies for metal-catalyzed cross-couplings require the installation of reactive functional groups on both reaction partners in advance. In contrast, C-H functionalization approaches show potential in simplifying the substrates required; however, challenges such as low reactivity and similar reactivity of different C-H bonds add complexity. This study describes an oxidative cross dehydrogenative coupling of α-amino C(sp(3))-H bonds and aldehydes to produce ketone derivatives using an unusual reaction medium that simultaneously utilizes di-tert-butyl peroxide as an oxidant and zinc metal as a reductant. The method has a broad substrate scope and offers an attractive approach for accessing α-amino ketones through the formal acylation of C-H bonds adjacent to nitrogen in N-heterocycles. Experimental investigation and computational modeling provide evidence for a mechanistic pathway involving cross-selective nickel-mediated cross-coupling of α-amino radicals and acyl radicals.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Cole L. Cruz, John Montgomery
Summary: A mild and convenient coupling reaction between aliphatic aldehydes and unactivated alkyl bromides has been developed using a common Ni(II) precatalyst and a readily available bioxazoline ligand, affording silyl-protected secondary alcohols. The reaction is operationally simple, utilizes Mn as a stoichiometric reductant, and tolerates a wide range of functional groups. The presence of 1,5-hexadiene as an additive plays a crucial role in optimizing yields.
Article
Chemistry, Organic
Annabel Q. Ansel, John Montgomery