Review
Chemistry, Multidisciplinary
Uli Kazmaier
Summary: Bottromycins, discovered in the mid-20th century, represent a unique class of natural products that have posed challenges in terms of structure elucidation and synthesis. Recent studies suggest that they belong to ribosomally synthesized and posttranslationally modified peptides, with a biosynthetic pathway that deviates from the norm.
ISRAEL JOURNAL OF CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Natasha DesRochers, Justin B. Renaud, Joey B. Tanney, Ashraf Ibrahim, Ken K. -C. Yeung, Mark W. Sumarah
Summary: This study identified many species of endophytic fungi in plants, most of which produce secondary metabolites with diverse structures and biological activities. Through LC-HRMS/MS analysis, 60 known compounds and 7 new compounds were identified. These previously unknown compounds are potential targets for further purification, characterization, and bioactivity testing in future studies.
Article
Microbiology
Haoyu Liang, Zhi-Man Song, Zheng Zhong, Dengwei Zhang, Wei Yang, Le Zhou, Ethan A. Older, Jie Li, Huan Wang, Zhirui Zeng, Yong-Xin Li
Summary: In this study, two new lanthipeptides with distinct ring topologies were discovered from a halophilic archaeon. One of these lanthipeptides, called archalan a, exhibited anti-archaeal activities against halophilic archaea, potentially mediating the archaeal antagonistic interactions in the halophilic niche. This is the first lantibiotic and anti-archaeal secondary metabolite discovered from the archaea domain.
Article
Chemistry, Analytical
Ayako Takemori, Philipp T. Kaulich, Liam Cassidy, Nobuaki Takemori, Andreas Tholey
Summary: The combination of liquid chromatography (LC) and gas-phase separation by field-asymmetric ion mobility spectrometry (FAIMS) is a powerful proteoform separation system for top-down proteomics. In this study, an in-depth top-down proteomics workflow, GeLC-FAIMS-MS, was presented, which utilized a molecular-weight-based proteome fractionation approach using SDS-poly-acrylamide gel electrophoresis. The authors optimized the MS parameters for each gel band and compensating voltage (CV) to improve the identification of proteoforms. They also developed a simple and cost-effective method, combining the PEPPI protocol with an AnExSP method, for stain and SDS removal. Results showed that this method was better suited for low-molecular-weight proteoforms, while a methanol-chloroform-water (MCW)-based protocol showed advantages for higher-molecular-weight proteoforms.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Erik Saparbaev, Andrei Zviagin, Oleg Boyarkin
Summary: We propose a universal approach for the quantitative identification of different isomeric biomolecules using infrared fragment cold ion spectroscopy. The method utilizes solvent molecules as natural tags, eliminating the need for any special compounds and allowing for the measurement of relative concentrations of isomers.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Kaho Sogahata, Taro Ozaki, Yuya Igarashi, Yuka Naganuma, Chengwei Liu, Atsushi Minami, Hideaki Oikawa
Summary: UstYa family proteins are widely distributed in fungi and are involved in the biosynthesis of peptides. Three UstYa homologues were found to be crucial for desaturation of amino acid moieties, displaying unique functions. Further research could lead to the discovery of novel fungal metabolites with unique modifications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Applied
Carmen Dominguez-Castillo, Maria Jimenez-Hidalgo, Jose Lopez-Gamez, Ana Rodriguez-Hortal, Milagros Alzaga-Garcia, Mercedes Gallardo-Abarzuza, Jose Manuel Higueras-Milena, Auxiliadora Gomez-Moron, Esteban Garcia-Vinas, Eloisa Bernaldez-Sanchez, Bruno Martinez-Haya
Summary: This study used liquid chromatography and high-resolution tandem mass spectrometry to assess the degradation products of cochineal dyes from a 16th century sunken wreck. It found that under harsh environmental conditions, the original structures of cochineal dyes are prone to chemical transformation, typically losing certain groups. Comparison with modern cochineal samples allows for an updated chart of dye compounds and degradation products.
Article
Chemistry, Multidisciplinary
Xiaojun Li, Ryo Shimaya, Tohru Dairi, Wei-chen Chang, Yasushi Ogasawara
Summary: The study identified the biosynthetic pathways of peptide natural products Hormaomycins and Belactosins, revealing a novel pathway for cyclopropane ring construction and exemplifying new chemistry involving metalloenzymes in natural product biosynthesis.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Sara Perez-Polo, Md Abdus Shukur Imran, Sonia Dios, Jaime Perez, Lorena Barros, Monica Carrera, Camino Gestal
Summary: This study conducted the first proteomic analysis of the common octopus skin mucus proteome, identifying proteins related to defense and discussing the potential application of bioactive peptides in biomedicine, pharmaceutical, and nutraceutical industry.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Analytical
Amanda Helms, Edwin E. E. Escobar, Saulius Vainauskas, Christopher H. H. Taron, Jennifer S. S. Brodbelt
Summary: The complete characterization of O-glycopeptides, including identification of peptides, localization of glycosites, and mapping of glycans, has been a challenging task in O-glycoproteomics. This study successfully applied a strategy combining the use of O-glycoprotease IMPa and HCD-triggered UVPD to achieve the complete characterization of O-glycopeptides. This approach allowed the localization of multiple adjacent or proximal O-glycosites and the identification of a previously unknown glycosite on etanercept.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Deseree J. Reid, Tapasyatanu Dash, Zhihan Wang, Craig A. Aspinwall, Michael T. Marty
Summary: In this study, native mass spectrometry (MS) and fast photochemical oxidation of peptides (FPOP) were used to investigate the interactions between the antibiotic daptomycin and different lipid bilayer nanodiscs. The results showed that daptomycin incorporates randomly into bilayers and has stronger interactions with rigid membranes. Pore formation may occur in fluid membranes, exposing daptomycin to oxidation. These findings demonstrate the complementarity of native MS, FPOP, and membrane conductance experiments in understanding antibiotic peptide-membrane interactions.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Florian Hubrich, Nina M. Bosch, Clara Chepkirui, Brandon Morinaka, Michael Rust, Muriel Gugger, Serina L. Robinson, Anna L. Vagstad, Jorn Piel
Summary: Lipopeptides are a group of microbial natural products that are important for their antibacterial and antifungal properties, as well as their strong biosurfactant effects. Most lipopeptides consist of cyclic peptides with various fatty acyl groups at the N-terminus. In this study, ribosomally derived lipopeptides called selidamides were discovered through genome-guided approaches. These selidamides were found to be widely distributed across different bacterial phyla and have cyclic peptide moieties with fatty acyl units attached to ornithine or lysine side chains. Unlike nonribosomal lipopeptides, selidamides are selectively acylated with different fatty acids. This study highlights the ability of ribosomal pathways to produce diverse lipopeptides and expands the potential for peptide drug development and targeted discovery.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Jia-Xuan Yan, Qihao Wu, Mitasree Maity, Doug R. Braun, Imraan Alas, Xiao Wang, Xing Yin, Yanlong Zhu, Bailey A. Bell, Scott R. Rajski, Ying Ge, Douglas D. Richardson, Wendy Zhong, Tim S. Bugni
Summary: Cyclic peptides are a promising source of drug leads, but their structural complexity poses challenges for structure elucidation. Isotopic fine structure analysis, NMR, and mass spectrometry techniques were used to determine the sequence and stereochemistry of streptnatamide A, a cyclic peptide from a marine-derived Streptomyces sp. The analysis also tentatively identified and annotated a biosynthetic gene cluster for streptnatamide A based on genomic sequencing data. These analytical tools are valuable for overcoming the challenges of cyclic peptide structure elucidation and accelerating the development of bioactive cyclic peptides.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Analytical
Yongyi Li, Shuai Zhao, Yunpeng Sun, Jixin Li, Yongyue Wang, Wenjun Xu, Jun Luo, Lingyi Kong
Summary: In this study, a program called LindenaneExtractor was developed to automatically extract the features of target natural products in plants using characteristic MS/MS ions. Through the study of characteristic ions and coding, a total of 96 target compounds were discovered, with 37 of them potentially being new natural products.
ANALYTICAL CHEMISTRY
(2022)
Review
Chemistry, Multidisciplinary
Jin-jun Hou, Zi-jia Zhang, Wen-yong Wu, Qing-qing He, Teng-qian Zhang, Ya-wen Liu, Zhao-jun Wang, Lei Gao, Hua-li Long, Min Lei, Wan-ying Wu, De-an Guo
Summary: Natural products and their structural analogs play a major role in novel drug development, but few molecular imaging technologies can detect multiple compounds simultaneously. Mass spectrometry imaging has been instrumental in discovering natural products and evaluating their applications, providing a visualization tool for drug development.
ACTA PHARMACOLOGICA SINICA
(2022)
Article
Biochemistry & Molecular Biology
Javier Santos-Aberturas, Govind Chandra, Luca Frattaruolo, Rodney Lacret, Thu H. Pham, Natalia M. Vior, Tom H. Eyles, Andrew W. Truman
NUCLEIC ACIDS RESEARCH
(2019)
Article
Microbiology
Yolanda Martinez-Burgo, Javier Santos-Aberturas, Antonio Rodriguez-Garcia, Eva G. Barreales, Jose Ruben Tormo, Andrew W. Truman, Fernando Reyes, Jesus F. Aparicio, Paloma Liras
FRONTIERS IN MICROBIOLOGY
(2019)
Editorial Material
Microbiology
Matthew I. Hutchings, Andrew W. Truman, Barrie Wilkinson
CURRENT OPINION IN MICROBIOLOGY
(2019)
Review
Microbiology
Matthew I. Hutchings, Andrew W. Truman, Barrie Wilkinson
CURRENT OPINION IN MICROBIOLOGY
(2019)
Article
Cell Biology
Luca Frattaruolo, Marco Fiorillo, Matteo Brindisi, Rosita Curcio, Vincenza Dolce, Rodney Lacret, Andrew W. Truman, Federica Sotgia, Michael P. Lisanti, Anna Rita Cappello
Review
Biotechnology & Applied Microbiology
Oleksandr Yushchuk, Bohdan Ostash, Andrew W. Truman, Flavia Marinelli, Victor Fedorenko
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2020)
Article
Biochemical Research Methods
Allegra T. Aron, Emily C. Gentry, Kerry L. McPhail, Louis-Felix Nothias, Melissa Nothias-Esposito, Amina Bouslimani, Daniel Petras, Julia M. Gauglitz, Nicole Sikora, Fernando Vargas, Justin J. J. van Der Hooft, Madeleine Ernst, Kyo Bin Kang, Christine M. Aceves, Andres Mauricio Caraballo-Rodriguez, Irina Koester, Kelly C. Weldon, Samuel Bertrand, Catherine Roullier, Kunyang Sun, Richard M. Tehan, Cristopher A. Boya P, Martin H. Christian, Marcelino Gutierrez, Aldo Moreno Ulloa, Javier Andres Tejeda Mora, Randy Mojica-Flores, Johant Lakey-Beitia, Victor Vasquez-Chaves, Yilue Zhang, Angela Calderon, Nicole Tayler, Robert A. Keyzers, Fidele Tugizimana, Nombuso Ndlovu, Alexander A. Aksenov, Alan K. Jarmusch, Robin Schmid, Andrew W. Truman, Nuno Bandeira, Mingxun Wang, Pieter C. Dorrestein
Article
Microbiology
Natalia M. Vior, Eva Cea-Torrescassana, Tom H. Eyles, Govind Chandra, Andrew W. Truman
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Asfandyar Sikandar, Laura Franz, Sebastian Adam, Javier Santos-Aberturas, Liliya Horbal, Andriy Luzhetskyy, Andrew W. Truman, Olga Kalinina, Jesko Koehnke
NATURE CHEMICAL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Oleksandr Yushchuk, Natalia M. Vior, Andres Andreo-Vidal, Francesca Berini, Christian Rueckert, Tobias Busche, Elisa Binda, Joern Kalinowski, Andrew W. Truman, Flavia Marinelli
Summary: The study describes a novel GPA producer Nonomuraea coxensis DSM 45129, which produces a GPA similar to A40926 but lacking a carboxyl group. By introducing the dbv29 factor, N. coxensis successfully produced A40926, demonstrating potential tools for GPA production. This work highlights genus Nonomuraea as an untapped source of novel GPAs.
ACS CHEMICAL BIOLOGY
(2021)
Article
Oncology
Flaviu Bulat, Friederike Hesse, Bala Attili, Chandra Solanki, Iosif A. Mendichovszky, Franklin Aigbirhio, Finian J. Leeper, Kevin M. Brindle, Andre A. Neves
Summary: There is a clinical demand for imaging agents that can detect tumor cell death after treatment. We present a gallium-68-labeled derivative of Synaptotagmin-I for imaging tumor cell death using PET. Ga-68-C2Am could be a valuable tool for rapidly assessing tumor responses to treatment.
Article
Chemistry, Multidisciplinary
Alicia H. Russell, Natalia M. Vior, Edward S. Hems, Rodney Lacret, Andrew W. Truman
Summary: RiPPs are a structurally diverse class of natural products, and a new and diverse family of RiPP BGCs has been identified using the RiPPER tool, spanning over 230 species of Actinobacteria and Firmicutes. The discovery of a novel amidine-containing RiPP streptamidine from Streptomyces albidoflavus J1074 highlights the breadth of unexplored natural products with structurally rare features in these clusters.
Article
Chemistry, Multidisciplinary
Tom H. Eyles, Natalia M. Vior, Rodney Lacret, Andrew W. Truman
Summary: Thiostreptamide S4 is a thioamitide belonging to the RiPPs family, with complex structure and incompletely elucidated biosynthetic steps. By engineering the BGC, coupled with metabolomics and targeted mutations, the biosynthetic pathway was revealed, a critical protein was identified, and diverse RiPP-like BGCs were bioinformatically identified for future discovery and engineering.
Article
Biochemical Research Methods
Alaster D. Moffat, Adam Elliston, Nicola J. Patron, Andrew W. Truman, Jose A. Carrasco Lopez
Summary: Biofoundries integrate high-throughput software and hardware platforms with synthetic biology approaches to enable the design, execution, and analyses of large-scale experiments. In the field of molecular microbiology, biofoundries have demonstrated their ability to accelerate screening processes and identify the genetic basis of growth inhibition.
Review
Biochemistry & Molecular Biology
Laura Franz, Uli Kazmaier, Andrew W. Truman, Jesko Koehnke
Summary: This article covers the research on Bottromycins from the 1950s to the end of 2020, highlighting their promising antibacterial activity against clinically relevant multidrug-resistant pathogens. It discusses their unique structure and recent advances in total synthesis and understanding of biosynthesis.
NATURAL PRODUCT REPORTS
(2021)