Article
Biotechnology & Applied Microbiology
Meng Chen, Chunyang Xu, Xu Wang, Yanan Wu, Li Li
Summary: Microcystis, a prevalent bloom-forming cyanobacterial genus, can synthesize a variety of toxic cyanopeptides via nonribosomal peptide synthetase (NRPS) pathways. The toxicity and enzyme-inhibiting activities of cyanopeptides are mainly determined by the molecules' structure and composition, which can be predicted based on the order and specificity of NRPS modules in NRPS gene clusters using bioinformatics approaches.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2021)
Article
Biochemistry & Molecular Biology
Joshua C. Corpuz, Ashay Patel, Tony D. Davis, Larissa M. Podust, J. Andrew McCammon, Michael D. Burkart
Summary: This study reveals the binding specificities between peptidyl carrier proteins (PCPs) and adenylation (A) domains in non-ribosomal peptide synthetases (NRPSs) using chemical biology approaches. The research also demonstrates the possibility of controlling PCP binding specificity through modifying interfacial interactions.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Zhiyong Wu, Youran Li, Yakun Fang, Ji Zhang, Tian Yang, Huilin Zhu, Guanjun Tao, Zhongyang Ding, Liang Zhang, Guiyang Shi
Summary: Dipeptides and their derivatives are important functional compounds that can be used in medicine and food. The adenylation domains of nonribosomal peptide synthetase (NRPS) can recognize and activate various building blocks, such as amino acids, for biosynthesis. This study explores the substrate selectivity and nucleophilic reactions of adenylation domains, and successfully synthesizes L-alanyl-L-glutamine and aspartame. The research expands on the synthesis of functional dipeptides and their derivatives based on the chemoenzymatic process.
ENZYME AND MICROBIAL TECHNOLOGY
(2022)
Review
Chemistry, Medicinal
Zhenhua Lu, Xiao-Huan Liu, Xinsong Yuan, Fei Liu, Tao Wang
Summary: Nonribosomal peptide synthetases, comprised of multiple catalytic domains, are crucial for the biosynthesis of bioactive natural products. Among these domains, adenylation domains are responsible for recognizing carboxylic acid building blocks and synthesizing aminoacyl adenylates. This review highlights recent developments on A-domains from NRPSs, exploring their structures, functions, and molecular interactions, as well as discussing their potential in A-domain engineering. It provides a framework for the production of novel nonribosomal peptides through combinatorial biosynthesis or synthetic biology-driven microbial production.
CURRENT TOPICS IN MEDICINAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Fumihiro Ishikawa, Shinya Nakamura, Isao Nakanishi, Genzoh Tanabe
Summary: Nonribosomal peptide synthetases (NRPSs) are responsible for synthesizing peptide-based natural products with great potential for drug discovery and development due to their wide range of biological activities. Reprogramming the NRPS machinery to enable the biosynthesis of new peptides is a major challenge in this field. This article highlights the recent progress in NRPS machinery reprogramming and its application in peptide synthesis.
JOURNAL OF PEPTIDE SCIENCE
(2023)
Article
Microbiology
Eunji Kim, Young Eun Du, Yeon Hee Ban, Yern-Hyerk Shin, Dong-Chan Oh, Yeo Joon Yoon
Summary: OMS A displays greater potency against Mycobacterium tuberculosis and human cancer cells compared to OMS B, with substrate promiscuous adenylation domain in the second module of OMS synthetase playing a key role in the synthesis process.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Plant Sciences
Han Wang, Huan Qi, Hui Zhang, Shao-Yong Zhang, Cheng-Hong Zhang, Li -Qin Zhang, Wen-Sheng Xiang, Ji-Dong Wang
Summary: Bioinformatics analysis and HPLC-DAD analysis of a whole genome sequence revealed the ability of Streptomyces sp. Hu103 to produce skyllamycin analogues. Chemical investigation of this strain led to the discovery of four new cinnamoyl-containing cyclo-peptides, anulamycins A-D (1-4), two new cinnamoyl-containing linear peptides, anulamycins E and F (5 and 6), and two known cyclopeptides, skyllamycins A (7) and B (8). Their structures and absolute configurations were determined by detailed analysis of NMR and HRESIMS/MS spectroscopic data and the advanced Marfey's method. Compounds 1-4 exhibited antibacterial activity comparable to skyllamycins A and B.
JOURNAL OF NATURAL PRODUCTS
(2023)
Article
Biochemical Research Methods
Ruolin He, Jinyu Zhang, Yuanzhe Shao, Shaohua Gu, Chen Song, Long Qian, Wen-Bing Yin, Zhiyuan Li
Summary: This research applies existing knowledge to data mining of NRPS sequences, partitions NRPS sequences into motif-intermotif architectures using known conserved motifs, and provides a comprehensive overview of NRPSs across different kingdoms. New C domain subtypes, novel conserved motifs with structural flexibility implications, and insights into why NRPSs are difficult to re-engineer are discovered. An online platform, NRPS Motif Finder, is constructed for researchers in related fields.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Engineering, Environmental
Guansong Hu, Junjian Chen, Yan Fan, Haiyan Zhou, Kunzhong Guo, Zhou Fang, Liangxu Xie, Lin Wang, Yingjun Wang
Summary: This study established a facile and efficient CuAAC-Bor system, finding that CuNCs showed stronger efficiency in immobilizing multiple peptides on titanium implants. Mechanistic insights into the significance of peptide size on CuAAC efficiency were revealed through all-atom molecular dynamics simulation and machine learning.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Biotechnology & Applied Microbiology
Panpan Han, Zhou Chen, Yangliu Liu, Aijin Ma, Siting Li, Yingmin Jia
Summary: This study revealed the reason for the production of multi-component brevilaterin in Brevibacillus laterosporus and identified key design sites to enhance specificity. The findings provide a reasonable direction for genetic engineering and contribute to a deeper understanding of the adenylation domain. This could lead to more accurate and efficient design and utilization of brevilaterins, as well as applications in biotechnology.
MICROBIAL CELL FACTORIES
(2022)
Article
Chemistry, Multidisciplinary
Zi-Wang Wei, Haruka Niikura, Kalindi D. Morgan, Condurache M. Vacariu, Raymond J. Andersen, Katherine S. Ryan
Summary: Piperazic acid is incorporated into nonribosomal peptides through adenylation, and the consensus sequences for its adenylation have been determined. This study provides valuable insights into the biosynthesis and function of Piperazic acid.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Zi-Wang Wei, Haruka Niikura, Kalindi D. Morgan, Condurache M. Vacariu, Raymond J. Andersen, Katherine S. Ryan
Summary: This study demonstrates the adenylation and incorporation mechanism of piperazic acid (Piz) into nonribosomal peptides, as well as the consensus sequences for piperazic acid adenylation. The fusion protein of piperazate synthase and adenylation domain suggests a close biosynthetic relationship between piperazic acid formation and its adenylation. These findings shed light on the evolution of biosynthetic systems for the activation of free piperazic acid.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Plant Sciences
Dipesh Dhakal, Sofia Kokkaliari, Garret M. Rubin, Valerie J. Paul, Yousong Ding, Hendrik Luesch
Summary: In this study, a biosynthetic gene cluster (BGC) for Lyngbyastatins (Lbns) was identified and characterized in a marine cyanobacterium. The BGC was found to encode enzymes responsible for the production of compounds 1 and 2, which have anti-cancer activity. Similar BGCs were also identified in the genomes of other marine cyanobacteria.
JOURNAL OF NATURAL PRODUCTS
(2022)
Article
Multidisciplinary Sciences
Wei Li Thong, Yingxin Zhang, Ying Zhuo, Katherine J. Robins, Joanna K. Fyans, Abigail J. Herbert, Brian J. C. Law, Jason Micklefield
Summary: Engineering biosynthetic assembly lines, especially megasynthases like NRPS, using CRISPR-Cas9 technology can rapidly create new natural products with altered substrate selectivity. This method allows for the generation of diverse lipopeptide variants in good yields compared to traditional homologous recombination-mediated approaches.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Gunlatida Promsuk, Supachai Vuttipongchaikij, Kamonchat Prommarit, Anongpat Suttangkakul, Colin M. Lazarus, Passorn Wonnapinij, Pakorn Wattana-Amorn
Summary: Heterologous expression of nrps33 in Saccharomyces cerevisiae resulted in the unexpected accumulation of anthranilic acid, which was found to be caused by the inhibition of Trp4 activity and the down-regulation of tryptophan biosynthesis genes.
Article
Chemistry, Multidisciplinary
Felix Trottmann, Keishi Ishida, Jakob Franke, Aleksa Stanisic, Mie Ishida-Ito, Hajo Kries, Georg Pohnert, Christian Hertweck
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
Article
Chemistry, Physical
Aleksa Stanisic, Annika Huesken, Philipp Stephan, David L. Niquille, Jochen Reinstein, Hajo Kries
Summary: Engineering of nonribosomal peptide synthetases (NRPSs) faces challenges, with specificity filters determining success and debate over the contribution of adenylation (A) and condensation (C) domains. Kinetic modeling shows that product specificity changes during reactions, with the A-domain overriding C-domain specificity when the thiolation domain loading reaches a steady state. This nonlinear modeling provides critical insights into how the interplay of the A- and C-domains determines product specificity in NRPSs.
Article
Chemistry, Multidisciplinary
Luka Raguz, Chia-Chi Peng, Florentine U. N. Rutaganira, Thomas Kruger, Aleksa Stanisic, Theresa Jautzus, Hajo Kries, Olaf Kniemeyer, Axel A. Brakhage, Nicole King, Christine Beemelmanns
Summary: The study developed a synthetic compound IOR-1A that inhibits rosette formation in S.rosetta and demonstrated the biochemical basis of cell differentiation processes within S.rosetta through the synthesis of derivatives and evaluation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Felix Trottmann, Keishi Ishida, Mie Ishida-Ito, Hajo Kries, Michael Groll, Christian Hertweck
Summary: Bacteria of the Burkholderia pseudomallei group are a global health threat, causing infectious diseases. A conserved gene cluster in these bacteria is responsible for the synthesis of polyketides, which are critical for virulence. Researchers have discovered that an enzyme called BurG is involved in the formation of a cyclopropanol ring, providing insight into the biochemical basis of this process. This finding has important implications for the development of antivirulence strategies.
Article
Biochemistry & Molecular Biology
Farzaneh Pourmasoumi, Sayantan De, Huiyun Peng, Felix Trottmann, Christian Hertweck, Hajo Kries
Summary: Nonribosomal peptide synthetases (NRPSs) are a valuable source of natural products, and re-engineering them is an attractive approach for structurally diversified active compounds. This study applied a protein splitting strategy to the gramicidin S NRPS and found that the addition of the type II thioesterase GrsT enhanced production. The researchers attribute this activity enhancement to the removal of a stalled intermediate from the split NRPS. These results highlight the usefulness of type II thioesterases in NRPS engineering.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Philipp Stephan, Chloe Langley, Daniela Winkler, Jerome Basquin, Lorenzo Caputi, Sarah E. E. O'Connor, Hajo Kries
Summary: Engineering of biosynthetic enzymes is used to synthesize antibiotics analogues. This study focuses on nonribosomal peptide synthetases (NRPSs) responsible for producing antimicrobial peptides. By directed evolution, the substrate specificity of an adenylation domain of a Pro-specific NRPS module was completely switched to a non-standard amino acid. This achievement was made through screening of mutant libraries and can be replicated with different substrates and NRPS modules. New possibilities for modifying NRPS specificity in a biosynthetically useful way are presented.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Organic
Guillaume Coin, Tuo Jiang, Samuele Bordi, Paula L. Nichols, Benedikt M. Wanner, Jeffrey W. Bode
Summary: The development of an automated process for Suzuki-Miyaura cross couplings is described, which involves automatic completion of the entire reaction, workup, and product isolation without any user involvement except for loading the starting materials and reaction capsule. This practical and simple method has been successfully demonstrated for the production of desired biaryl products using various aryl bromides and boronic acids, and it is also effective for late-stage functionalization of aryl halides in bioactive molecules.
Review
Biochemistry & Molecular Biology
Kexin Zhang, Hajo Kries
Summary: Nonribosomal peptides (NRPs) are gaining attention for their diverse biological activities and potential applications in medicine and agriculture. The natural diversity of NRPs is a result of evolutionary processes occurring over millions of years. Recent studies have uncovered the mechanisms by which NRPSs evolve, and mimicking natural evolution could be a useful strategy for engineering NRPSs to produce novel compounds. NRPs also offer promise for drug discovery, particularly in the context of antibiotic-resistant bacteria. This review discusses the engineering potential of NRPSs in light of their evolutionary history.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2023)
Article
Biochemical Research Methods
Jiayi Lan, Giorgia Greter, Bettina Streckenbach, Benedikt Wanner, Markus Arnoldini, Renato Zenobi, Emma Slack
Summary: We demonstrate the use of secondary electrospray ionization-mass spectrometry (SESI-MS) to non-invasively monitor the metabolic activity of the intestinal microbiome in a live mouse. By comparing the metabolites released by gut bacteria in culture with those in gnotobiotic mice, we show that the volatilome is characteristic of the dominant colonizing bacteria. Combining SESI-MS with heavy-isotope-labeled microbiota-accessible sugars reveals microbial cross-feeding within the animal intestine.
CELL REPORTS METHODS
(2023)
Article
Biochemistry & Molecular Biology
Maximilian Muell, Farzaneh Pourmasoumi, Leon Wehrhan, Olena Nosovska, Philipp Stephan, Hannah Zeihe, Ivan Vilotijevic, Bettina G. Keller, Hajo Kries
Summary: Fluorine is a crucial element in medicinal chemistry, as it enhances the pharmacological properties of drugs. This study aimed to produce fluorinated analogues of the antimicrobial cyclic decapeptide gramicidin S (GS) through biosynthesis. However, results showed that the A-domain of the NRPS module GrsA rejects 4-fluorinated analogues due to an interrupted aromatic interaction. A GrsA mutant, W239S, was found to improve the incorporation of 4-fluorinated amino acids into GS. These findings provide new insights into NRPS behavior and strategies for the biosynthesis of fluorinated peptides.
RSC CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Angus E. McMillan, Wilson W. X. Wu, Paula L. Nichols, Benedikt M. Wanner, Jeffrey W. Bode
Summary: Due to the high false positive rates in virtual screening, synthesising and validating prospective hits can be time consuming and laborious. This study evaluated large virtual libraries and identified one sub-library with unique drug-like structures. By using automated synthesis and a streamlined method of relative stereochemical assignment, the preparation of virtual screening hits was accelerated and user efficiency significantly improved.
Article
Chemistry, Multidisciplinary
Jacob M. Wurlitzer, Aleksa Stanisic, Sebastian Ziethe, Paul M. Jordan, Kerstin Guenther, Oliver Werz, Hajo Kries, Markus Gressler
Summary: This study identified and characterized the nonribosomal peptide synthetase (NRPS) MalA in early diverging fungi, which catalyzes the biosynthesis of the surface-active biosurfactants malpinins. Specificity-based precursor-directed biosynthesis resulted in the production of 20 new congeners, and the study demonstrated the importance of fungi as a source of chemically tractable compounds for pharmaceutical applications.
Article
Chemistry, Multidisciplinary
Tuo Jiang, Samuele Bordi, Angus E. McMillan, Kuang-Yen Chen, Fumito Saito, Paula L. Nichols, Benedikt M. Wanner, Jeffrey W. Bode
Summary: The study introduces an instrument capable of automatically executing complex organic reactions in the laboratory, successfully implementing two desirable reaction classes in the field of organic synthesis. This system provides a convenient and safe method for future developers to conduct organic synthesis.
Article
Biochemistry & Molecular Biology
Hsin-Mei Huang, Philipp Stephan, Hajo Kries
Summary: By incorporating zinc-finger tags into split NRPS modules to create DNA-templated NRPS (DT-NRPS), researchers have demonstrated that covalent intermediate channeling is possible along the DNA template for the biosynthesis of non-ribosomal peptides and other polymers. This innovative catalytic strategy outperforms previously reported DNA-templated enzyme cascades in terms of DNA acceleration, indicating its potential for sequence-controlled biosynthesis.
CELL CHEMICAL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Jacob M. Wurlitzer, Aleksa Stanisic, Ina Wasmuth, Sandra Jungmann, Dagmar Fischer, Hajo Kries, Markus Gressler
Summary: This study reports the biosynthesis of cyclic pentapeptides in Mortierella alpina, highlighting early-diverging fungi as an underestimated resource of natural products. The enzymes involved in this biosynthesis are more closely related to bacterial NRPSs, suggesting a bacterial origin of these NRPS genes in Mortierella. This discovery establishes early-diverging fungi as prolific natural compound producers and sheds light on the origin of their biosynthetic capacity.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)