Article
Chemistry, Multidisciplinary
Hanna Chen, Lin Zhong, Haibo Zhou, Tao Sun, Guannan Zhong, Qiang Tu, Yan Zhuang, Xianping Bai, Xingyan Wang, Jiaying Xu, Liqiu Xia, Yuemao Shen, Youming Zhang, Xiaoying Bian
Summary: Nonribosomal peptide synthetases (NRPSs) can incorporate nonproteinogenic amino acids into peptidyl backbones to increase structural diversity. This study identified a class of linear lipoheptapeptides featuring two unusual residues and revealed the β-hydroxylation mechanisms of Asp and His, which require the concerted action of specific enzymes and domains.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Myoun-Su Kim, Munhyung Bae, Ye-Eun Jung, Jung Min Kim, Sunghoon Hwang, Myoung Chong Song, Yeon Hee Ban, Eun Seo Bae, Suckchang Hong, Sang Kook Lee, Sun-Shin Cha, Dong-Chan Oh, Yeo Joon Yoon
Summary: The biosynthesis of cyclodepsipeptide WS9326A in Streptomyces sp. SNM55 involves unprecedented nonlinear NRPS assembly processes, including the shuttling of activated amino acids mediated by TE enzymes, the independent operation of C-T didomain modules, and the first example of module skipping.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Xiaolin Zou, Zhen Hui, Robert A. Shepherd, Shuaiqiang Zhao, Yanfei Wu, Zhuanglin Shen, Cuiping Pang, Shipeng Zhou, Zehai Yu, Jiahai Zhou, Bradly S. Moore, Laura M. Sanchez, Xiaoyu Tang
Summary: This study provides a comprehensive exploration of the genetic and biochemical aspects of the enzymes responsible for the assembly and cleavage of the acylated peptide prodrug scaffolds in the assembly line biosynthesis of didemnin cyclic peptides. The findings shed light on the complex prodrug release mechanism underlying the synthesis and secretion of didemnin compounds and offer novel insights into the expanded role of CAAX hydrolases in microbes. This knowledge can be used for the strategic design of genome mining approaches to discover new bioactive natural products that employ similar prodrug biochemical strategies.
Article
Biochemistry & Molecular Biology
Milda Kaniusaite, Julien Tailhades, Tiia Kittila, Christopher D. Fage, Robert J. A. Goode, Ralf B. Schittenhelm, Max J. Cryle
Summary: The biosynthesis of glycopeptide antibiotics demonstrates the exceptional ability of nonribosomal peptide synthesis to generate diverse and complex structures. An important study on the NRPS assembly lines involved in synthesizing GPAs revealed that they function as dynamic peptide assembly lines, allowing for flexible control over amino acid modifications and peptide formation, which is beneficial for the redesign of important biosynthetic systems.
Article
Biochemistry & Molecular Biology
Xueyang Ma, Zhijun Tang, Wenping Ding, Tan Liu, Donghui Yang, Wen Liu, Ming Ma
Summary: Recruitment of trans-acting enzymes by non ribosomal peptide synthetase (NRPS) assembly line is rare. In collismycin biosynthesis, ColB1, a flavin-dependent dehydrogenase, is recruited by an NRPS terminal condensation domain (Ct domain) and catalyzes peptidyl carrier protein (PCP)-tethered cysteine dehydrogenation. The crystal structure of ColB1 complexed with FAD reveals distinct structural features from acyl-CoA dehydrogenases (ACADs) in substrate recognition. A Glu393-mediated catalytic mechanism is established, where the cysteine substrate is sandwiched between Glu393 and FAD. A ColB1-PCP-Ct complex model provides insights into the unique recruitment interactions between ColB1 and associated NRPS.
ACS CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Physical
Qiyao Shen, Haibo Zhou, Guangzhi Dai, Guannan Zhong, Liujie Huo, Aiying Li, Yang Liu, Ming Yang, Vinothkannan Ravichandran, Zhihui Zheng, Ya-Jie Tang, Nianzhi Jiao, Youming Zhang, Xiaoying Bian
Summary: The biosynthetic mechanism of polythiazole in microbial nonribosomal peptides (NRPs) has been uncovered, revealing the involvement of a cryptic NRPS gene cluster. The study also showed that the oxidation of polythiazole in NRPs is not catalyzed by integrated oxidase domains as previously believed, but by a standalone oxidase.
Review
Biochemistry & Molecular Biology
Akimasa Miyanaga, Fumitaka Kudo, Tadashi Eguchi
Summary: Adenylation (A) domains are essential for the biosynthesis of nonribosomal peptides and related natural products. They selectively transfer acyl substrates onto cognate carrier proteins, expanding the structural diversity of natural products. Interrupted A domains with embedded auxiliary domains can modify the incorporated acyl units.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Akimasa Miyanaga, Kenji Nagata, Joji Nakajima, Taichi Chisuga, Fumitaka Kudo, Tadashi Eguchi
Summary: Adenylation enzymes activate amino acid substrates and transfer them onto carrier proteins for selective incorporation in natural product biosynthesis. VinM, an amide-forming adenylation enzyme, transfers an l-alanyl group onto the amino group of the aminoacyl unit attached to the carrier protein VinL in vicenistatin biosynthesis. Structural and biochemical analyses reveal that interactions with both the phosphopantetheine arm and VinL are critical for VinM's amide-forming activity.
ACS CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Yongwei Zhao, Edward Marschall, Maxine Treisman, Alasdair McKay, Leo Padva, Max Crusemann, David R. Nelson, David L. Steer, Ralf B. Schittenhelm, Julien Tailhades, Max J. Cryle
Summary: This study investigates the use of peptide crosslinking cytochrome P450 enzymes in generating cyclic tripeptides from simple synthons. The enzymes produced both tyrosine-histidine and tyrosine-tryptophan crosslinked tripeptides, the latter being a rare example of phenolic crosslinking to an indole moiety. The tripeptides can be easily isolated after removing the leader peptide and can include a wide range of amino acids. This research suggests that P450 enzymes have the potential to play a significant role in the synthesis of high-value cyclic tripeptides, which can be further diversified using selective chemical techniques.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Cell Biology
Hanne Hendrix, Maria Zimmermann-Kogadeeva, Michael Zimmermann, Uwe Sauer, Jeroen De Smet, Laurens Muchez, Maries Lissens, Ines Staes, Marleen Voet, Jeroen Wagemans, Pieter-Jan Ceyssens, Jean-Paul Noben, Abram Aertsen, Rob Lavigne
Summary: This study reveals the role of the Pseudomonas quinolone signal (PQS) in bacterial virus infection. The virus LUZ19 targets the PQS system by expressing the quorum sensing targeting protein (Qst), which interacts with key enzymes in the PQS biosynthesis pathway. This interaction leads to a decrease in PQS levels and impairs the virus infection, but can be restored by external supplementation of a PQS precursor. Qst represents a potential tool for combating antibiotic resistance in bacterial pathogens.
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
Chemistry, Physical
Christopher D. Fage, Simone Kosol, Matthew Jenner, Carl Oster, Angelo Gallo, Milda Kaniusaite, Roman Steinbach, Michael Staniforth, Vasilios G. Stavros, Mohamed A. Marahiel, Max J. Cryle, Jozef R. Lewandowski
Summary: Nonribosomal peptides are a type of natural products constructed by nonribosomal peptide synthetases (NRPSs), and the communication between donor epimerization (E) and acceptor condensation (C) domains found at the termini of NRPS subunits is mediated by COM domains. Biophysical studies using X-ray crystallography, circular dichroism spectroscopy, NMR spectroscopy, and molecular dynamics simulations show that the donor COM region is intrinsically disordered and folds into a helical motif upon binding to an acceptor, suggesting a dynamic interaction interface. Further experiments demonstrate the importance of donor COM region in binding the acceptor C domain, pointing towards potential noncognate domain crosstalk.
Review
Biochemistry & Molecular Biology
Yongwei Zhao, Y. T. Candace Ho, Julien Tailhades, Max Cryle
Summary: Researchers are intrigued by the complex biosynthesis of glycopeptide antibiotics, particularly the role of the X-domain in recruiting P450 enzymes. In vitro studies have provided insights into the tolerances and limitations of the GPA cyclisation cascade, paving the way for future reengineering of this important antibiotic class.
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
Multidisciplinary Sciences
Michael J. Wheadon, Craig A. Townsend
Summary: Nonribosomal peptide synthetases (NRPSs) are large, multidomain enzymes involved in the assembly-line-like synthesis of peptide natural products, including clinically useful antibiotics. The condensation (C) domains in NRPSs catalyze peptide bond formation during synthesis. Research has shown that in certain cases, the function of C domains can be altered, providing insights into beta-lactam synthesis and canonical peptide synthesis mechanisms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Letter
Microbiology
Roderich D. Sussmuth, Alexandra Lensch, Stefan Pelzer
Summary: A recent study claims that a newly isolated Bacillus velezensis strain RP137 from the Persian Gulf can produce an aminoglycoside compound called S-137-R. However, the provided data does not prove its structure and purity, and lacks proper comparison with other aminoglycosides. Therefore, it is scientifically unjustified to confirm the production of aminoglycosides by this strain, and it should not be regarded as a probiotic.
CURRENT MICROBIOLOGY
(2022)
Article
Microbiology
Nicole Hugouvieux-Cotte-Pattat, Monique Royer, Erwan Gueguen, Paul Le Guen, Roderich D. Suessmuth, Sylvie Reverchon, Stephane Cociancich
Summary: The Vfm quorum sensing system is important for the virulence of Dickeya bacteria, with a strain-specific polymorphism in the biosynthesis genes vfmO and vfmP potentially leading to the production of different analogues of the QS signal.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Timur Bulatov, Sebastian Gensel, Andi Mainz, Tam Dang, Timm O. Koller, Kerstin Voigt, Julia Ebeling, Daniel N. Wilson, Elke Genersch, Roderich D. Suessmuth
Summary: The study reports the total synthesis and structural revision of paenilamicin B2, highlighting the N-terminal fragment as an important pharmacophore, and conducts biological activity evaluation and competition experiments with bacterial competitors in the ecological niche. It also presents data classifying paenilamicins as potential ribosome inhibitors, contributing to a better understanding of the pathogenicity of P. larvae and paving the way for future structure-activity relationship and mode-of-action studies.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biotechnology & Applied Microbiology
Joana C. Barbosa, Itala C. Silva, Tania Caetano, Eva Mosker, Maria Seidel, Joana Lourenco, Roderich D. Suessmuth, Nuno C. Santos, Sonia Goncalves, Sonia Mendo
Summary: Lichenicidin is a promising natural antimicrobial peptide with strong bactericidal activity and no cytotoxicity towards human cells.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Romina Schnegotzki, Jeroen Koopman, Stefan Grimme, Roderich D. Suessmuth
Summary: In organic mass spectrometry, quantum chemical calculations can be used to predict ion fragment structures, particularly for large molecules, and discover previously unknown fragmentation pathways.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Organic
Romina Schnegotzki, Vincent Wiebach, Marina Sanchez-Hidalgo, Marcel Tietzmann, Andreas B. zur Bonsen, Olga Genilloud, Roderich D. Suessmuth
Summary: Phenylglycines are crucial components in the synthesis of non-ribosomally synthesized peptides. The cyclodepsipeptide cochinmicin I, which contains dihydroxyphenylglycine, acts as an endothelin receptor antagonist. In this study, we accomplished the total synthesis of cochinmicin I and its non-natural derivative cochinmicin VI. Additionally, we identified and assigned the gene cluster responsible for cochinmicin biosynthesis, which encodes a non-ribosomal peptide synthetase.
Article
Chemistry, Multidisciplinary
Christian E. Stieger, Yerin Park, Mark A. R. de Geus, Dongju Kim, Christiane Huhn, J. Sophia Slenczka, Philipp Ochtrop, Judith M. Muechler, Roderich D. Suessmuth, Johannes Broichhagen, Mu-Hyun Baik, Christian P. R. Hackenberger
Summary: We have discovered ethynyl-triazolyl-phosphinates (ETPs) as a new class of electrophilic warheads with cysteine selectivity for bioconjugation. Through Cu-I-catalyzed azide alkyne cycloaddition (CuAAC), various functional electrophilic building blocks, including proteins, were obtained from diethynyl-phosphinate. ETP-reagents were used to create fluorescent peptide-conjugates for receptor labeling on live cells and stable and biologically active antibody-drug conjugates. The excellent cysteine selectivity of ETP-electrophiles was demonstrated in mass spectrometry-based, proteome-wide cysteine profiling, highlighting their potential for homogeneous bioconjugation strategies to connect complex biomolecules.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Letter
Biochemistry & Molecular Biology
Daniel L. Machell, Mathias H. Hansen, Max J. Cryle
Summary: Detection of pyrophosphate is crucial for quantifying enzyme activity, especially adenylation domain activity in non-ribosomal peptide synthesis. After screening, viable replacement enzymes with higher activity have been identified, allowing the continued use of the established online assay for pyrophosphate detection.
Article
Biochemistry & Molecular Biology
Y. T. Candace Ho, Ralf B. Schittenhelm, Dumitrita Iftime, Evi Stegmann, Julien Tailhades, Max J. Cryle
Summary: Glycopeptide antibiotics inhibit bacterial cell-wall biosynthesis by sequestration of precursor lipid II. The oxidative crosslinking of the core peptide during GPA biosynthesis is essential and challenging. Understanding the activity and selectivity of Oxy enzymes is important for future engineering of this compound class.
Article
Chemistry, Multidisciplinary
Rania A. A. Hashad, Edwina Jap, Joanne L. L. Casey, Y. T. Candace Ho, Alexander Wright, Claudia Thalmann, Mark Sleeman, David W. W. Lupton, Christoph E. E. Hagemeyer, Max J. J. Cryle, Remy Robert, Karen Alt
Summary: A highly effective 2-step system using engineered methionine residues was used for site-specific antibody modification and conjugation. This system offers a novel way to fundamentally change the process of antibody bioconjugation. The versatility of this system was demonstrated by incorporating a fluorescent dye and can be applied to a wide variety of conjugation partners.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Songya Zhang, Yunliang Chen, Jing Zhu, Qiujie Lu, Max J. Cryle, Youming Zhang, Fu Yan
Summary: Streptomyces bacteria are widely distributed in terrestrial and marine environments and are a rich source of active natural products due to their metabolic diversity. This review highlights the importance of nonribosomal lipopeptides as important natural products with diverse biological activities that play crucial roles in the lifestyle of Streptomyces. Recent advances in the biosynthesis of lipopeptide antibiotics produced by Streptomyces have greatly contributed to our understanding of their structures, properties, biosynthetic mechanisms, chemical and chemoenzymatic synthesis, and biological functions. The use of genome mining techniques has led to the discovery of many novel lipopeptides, further demonstrating their potential for future development in modern medicine.
NATURAL PRODUCT REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Sylvester Hoffmann, Maik Damm, Leonard Roth, Roderich D. Suessmuth
Summary: This study investigates the activation mechanism of hydroxy acid substrates in non-ribosomal peptide synthetases (NRPSs). By homology modelling and molecular docking, it was found that the selection of hydroxy acid is determined by its interaction with the backbone carbonyls rather than a specific side chain. These findings contribute to the understanding of non-amino acid substrate activation and have implications for the engineering of depsipeptide synthetases.
Article
Food Science & Technology
Ignazio Avella, Maik Damm, Ines Freitas, Wolfgang Wuster, Nahla Lucchini, Oscar Zuazo, Roderich D. Suessmuth, Fernando Martinez-Freiria
Summary: This study analyzed the venom of Vipera seoanei snakes from different locations and found that there is little variation in venom composition, which may be due to recent population expansion or other factors.
Article
Chemistry, Multidisciplinary
Y. T. Candace Ho, Joe A. Kaczmarski, Julien Tailhades, Thierry Izore, David L. Steer, Ralf B. Schittenhelm, Manuela Tosin, Colin J. Jackson, Max J. Cryle
Summary: Nonribosomal peptide synthetases play a significant role in producing essential peptide natural products, with carrier proteins as their core component. By replacing the CP substrate thioesters with stabilized ester analogues, active condensation domain complexes are formed, while amide stabilization leads to non-functional complexes.
CHEMICAL COMMUNICATIONS
(2023)
Review
Multidisciplinary Sciences
Roland Hellinger, Arnar Sigurdsson, Wenxin Wu, Elena V. Romanova, Lingjun Li, Jonathan V. Sweedler, Roderich D. Suessmuth, Christian W. Gruber
Summary: Peptidomics combines genomics, modern proteomics, analytical chemistry, and computational biology techniques for peptide discovery and characterization. Peptides are biopolymers composed of 2-50 amino acids, often produced by cellular machinery or enzymes. They play important physiological roles as signaling molecules and toxins, and have emerging applications in biomarker discovery and therapeutics. Peptidomics involves qualitative and quantitative analysis of peptides in biological samples using a specialized set of tools and workflows.
NATURE REVIEWS METHODS PRIMERS
(2023)