Article
Biochemistry & Molecular Biology
Don D. Nguyen, Veronika Saharuka, Vitaly Kovalev, Lachlan Stuart, Massimo Del Prete, Kinga Lubowiecka, Rene De Mot, Vittorio Venturi, Theodore Alexandrov
Summary: METASPACE is a fast and accurate tool for annotating microbial specialized metabolites from imaging MS data. It has been shown to successfully annotate a variety of microbial metabolites from data obtained from microbial colonies grown on agar.
Editorial Material
Microbiology
Joris J. R. Louwen, Justin J. J. van der Hooft
Summary: Microbial specialized metabolites play a crucial role in host-microbiome interactions, and there is a need for new methods to utilize the expanding genomic and metabolomic datasets while connecting them to structural and functional knowledge inferred from transcriptomics and proteomics experiments. This article describes current approaches for comprehensive mining of metabolomics and genomics data, as well as proposes a vision for automated linking of omics data of specialized metabolites to their structures, biosynthesis pathways, producers, and functions.
Article
Chemistry, Analytical
Daniel Eilertz, Michael Mitterer, Joerg M. Buescher
Summary: This study presents an automated tool automRm for preprocessing of liquid chromatography-mass spectrometry data, which includes features such as using machine learning for chromatographic peak detection and quality control of results. The tool is generally applicable to a wide range of analytical methods and outperforms other software solutions when applied to a HILIC-MS data set.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Narumol Jariyasopit, Suphitcha Limjiasahapong, Alongkorn Kurilung, Sitanan Sartyoungkul, Pattipong Wisanpitayakorn, Narong Nuntasaen, Chutima Kuhakarn, Vichai Reutrakul, Prasat Kittakoop, Yongyut Sirivatanauksorn, Sakda Khoomrung
Summary: The combination of ion mobility mass spectrometry and chromatography is a powerful tool for identifying compounds in natural products. In this study, a comprehensive database for plant specialized metabolites was established and validated using an ultra-performance liquid chromatography system coupled with a high-resolution quadrupole/traveling wave ion mobility spectrometry/time-of-flight mass spectrometry. The database included both commercially available compounds and those that were isolated and purified in-house, providing accurate information on molecular weight, retention times, fragment ions, and ion mobility-derived collision cross section values. The database was successfully applied to extend the metabolite coverage of Ventilago harmandiana Pierre.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Cell Biology
Andrzej Patyra, Marta Katarzyna Dudek, Anna Karolina Kiss
Summary: This study analyzed and compared the chemical profiles of wood extracts from different species in the Pinaceae family. The results showed that different species contained a variety of compounds, with Norway spruce being rich in stilbenes, European larch mostly containing flavonoids, and silver fir rich in lignans. The findings also suggested that conifer branches, a waste material from the wood industry, could be a valuable source of phytochemicals.
Article
Biochemistry & Molecular Biology
Anna Piasecka, Aneta Sawikowska, Nicolas Jedrzejczak-Rey, Mariola Pislewska-Bednarek, Pawel Bednarek
Summary: Brachypodium distachyon, a model grass species, has been extensively studied due to its fully sequenced genome. However, its metabolome, an essential component of complex biological systems, remains poorly characterized. In this study, we conducted a comprehensive metabolomic examination using LC-MS technology to analyze the metabolite profiles of roots, leaves, and spikes of this species. Our results revealed the accumulation of specialized metabolites related to various metabolic pathways, including flavonoid biosynthesis, nucleotide metabolism, sugar metabolism, and amino acid metabolism. Structural analysis based on MS fragmentation spectra identified 93 specialized metabolites, mainly phenylpropanoids and flavonoid derivatives. These findings provide insights into the metabolic profile of Brachypodium and highlight the differences in metabolite composition among different plant tissues and lines.
Article
Ecology
Alexander B. Chase, Alexander Bogdanov, Alyssa M. Demko, Paul R. Jensen
Summary: This study examines the relationship between microbial community structure and specialized metabolism in marine sediment samples collected from the LTER site in Moorea, French Polynesia. The researchers find that local scale processes, such as biotic interactions, drive the biogeographic patterns of microbial communities. The study also reveals high variation in biosynthetic potential between samples, reflecting uncharacterized chemical space associated with site-specific metabolomes.
Article
Plant Sciences
Suphitcha Limjiasahapong, Khwanta Kaewnarin, Narumol Jariyasopit, Sakchai Hongthong, Narong Nuntasaen, Jonathan L. Robinson, Intawat Nookaew, Yongyut Sirivatanauksorn, Chutima Kuhakarn, Vichai Reutrakul, Sakda Khoomrung
Summary: Pyranonaphthoquinones (PNQs) are important structural scaffolds found in natural products, and Ventilago harmandiana was found to be a rich source of PNQs. A new method using ultraperformance liquid chromatography-mass spectrometry was developed to quantitatively determine six PNQs in various parts of the plant. Different parts of the plant showed varying concentrations of PNQs, with PNQ-332 being the major compound in most parts except for the root, where PNQ-318A was the most abundant. MS/MS spectra at different collision energies were provided for structural elucidation of the PNQs.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Chemistry, Analytical
Teresa S. McMillen, Andrew Leslie, Kenneth Chisholm, Susanne Penny, Jeffrey Gallant, Alejandro Cohen, Arik Drucker, James P. Fawcett, Devanand M. Pinto
Summary: This study presents a comprehensive and quantitatively robust method for metabolomic analysis, using HILIC and RP stationary phases combined with positive and negative electrospray ionization. The method allows for complete analysis of a single sample in as little as 40 minutes and has been validated with clinical samples.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biochemical Research Methods
Olatomiwa O. Bifarin, Samyukta Sah, David A. Gaul, Samuel G. Moore, Ruihong Chen, Murugesan Palaniappan, Jaeyeon Kim, Martin M. Matzuk, Facundo M. Fernandez
Summary: Ovarian cancer is a deadly cancer that affects the female reproductive system and is often asymptomatic until later stages. Little is known about the metabolic changes in the early stages of high-grade serous ovarian cancer. This study used a mouse model and machine learning analysis to examine the temporal changes in serum lipidome. The results showed unique alterations in cell membrane stability, proliferation, and survival during cancer development and progression, providing potential targets for early detection and prognosis of ovarian cancer.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Microbiology
Rahim Rajwani, Shannon Ohlemacher, Gengxiang Zhao, Hong-Bing Liu, Carole A. Bewley
Summary: Genome mining is crucial for discovering new natural products, and long-read sequencing methods are necessary for obtaining contiguous DNA assemblies for analyzing biosynthetic gene clusters. The Flongle platform by Oxford Nanopore Technologies provides a low-cost option for such sequencing needs, allowing for multiplexing and efficient analysis of BGCs even at low sequencing depth.
Article
Chemistry, Analytical
Haosong Zhang, Mingdu Luo, Hongmiao Wang, Fandong Ren, Yandong Yin, Zheng-Jiang Zhu
Summary: The development of IM-MS has revolutionized the analysis of small molecules. The curation of comprehensive CCS databases plays a pivotal role in the successful application of IM-MS. AllCCS2, an enhanced version, achieved exceptional prediction accuracy and compatibility with different instrument platforms.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Elizabeth J. Parker, Kathryn C. Billane, Nichola Austen, Anne Cotton, Rachel M. George, David Hopkins, Janice A. Lake, James K. Pitman, James N. Prout, Heather J. Walker, Alex Williams, Duncan D. Cameron
Summary: Untargeted metabolomics is a powerful tool for measuring and understanding complex biological chemistries. This tutorial provides a workflow for connecting open-source tools to process and analyze untargeted mass spectrometry data. The authors welcome contributions and improvements to the workflow via the online repository.
Article
Biochemistry & Molecular Biology
Mayya Razgonova, Alexander Zakharenko, Konstantin Pikula, Yury Manakov, Sezai Ercisli, Irina Derbush, Evgeniy Kislin, Ivan Seryodkin, Andrey Sabitov, Tatiana Kalenik, Kirill Golokhvast
Summary: A comparative metabolomic study was conducted on wild grapes from different locations in the Primorsky and Khabarovsk territories, as well as grapes from the collection of the N.I. Vavilov All-Russian Institute of Plant Genetic Resources, using liquid chromatography and ion trap mass spectrometry. The ethanolic extracts of V. amurensis grapes contained 118 compounds, with several new metabolites identified. Samples of V. amurensis grapes collected near Vyazemsky and the Arsenyevka River showed the highest diversity of phenolic compounds compared to other wild samples and cultural grapes.
Article
Cell Biology
Franz Hadacek
Summary: This case study illustrates the challenges and limitations in identifying structurally closely related specialized metabolites, using flavonol glycosides as an example. The study emphasizes the importance of specific software tools and chemical reference databases in obtaining deeper information about the structures and characteristics of metabolites.
Article
Biochemistry & Molecular Biology
Michelle A. Schorn, Stefan Verhoeven, Lars Ridder, Florian Huber, Deepa D. Acharya, Alexander A. Aksenov, Gajender Aleti, Jamshid Amiri Moghaddam, Allegra T. Aron, Saefuddin Aziz, Anelize Bauermeister, Katherine D. Bauman, Martin Baunach, Christine Beemelmanns, J. Michael Beman, Maria Victoria Berlanga-Clavero, Alex A. Blacutt, Helge B. Bode, Anne Boullie, Asker Brejnrod, Tim S. Bugni, Alexandra Calteau, Liu Cao, Victor J. Carrion, Raquel Castelo-Branco, Shaurya Chanana, Alexander B. Chase, Marc G. Chevrette, Leticia V. Costa-Lotufo, Jason M. Crawford, Cameron R. Currie, Bart Cuypers, Tam Dang, Tristan de Rond, Alyssa M. Demko, Elke Dittmann, Chao Du, Christopher Drozd, Jean-Claude Dujardin, Rachel J. Dutton, Anna Edlund, David P. Fewer, Neha Garg, Julia M. Gauglitz, Emily C. Gentry, Lena Gerwick, Evgenia Glukhov, Harald Gross, Muriel Gugger, Dulce G. Guillen Matus, Eric J. N. Helfrich, Benjamin-Florian Hempel, Jae-Seoun Hur, Marianna Iorio, Paul R. Jensen, Kyo Bin Kang, Leonard Kaysser, Neil L. Kelleher, Chung Sub Kim, Ki Hyun Kim, Irina Koester, Gabriele M. Koenig, Tiago Leao, Seoung Rak Lee, Yi-Yuan Lee, Xuanji Li, Jessica C. Little, Katherine N. Maloney, Daniel Maennle, Christian Martin H., Andrew C. McAvoy, Willam W. Metcalf, Hosein Mohimani, Carlos Molina-Santiago, Bradley S. Moore, Michael W. Mullowney, Mitchell Muskat, Louis-Felix Nothias, Ellis C. O'Neill, Elizabeth I. Parkinson, Daniel Petras, Jorn Piel, Emily C. Pierce, Karine Pires, Raphael Reher, Diego Romero, M. Caroline Roper, Michael Rust, Hamada Saad, Carmen Saenz, Laura M. Sanchez, Soren Johannes Sorensen, Margherita Sosio, Roderich D. Sussmuth, Douglas Sweeney, Kapil Tahlan, Regan J. Thomson, Nicholas J. Tobias, Amaro E. Trindade-Silva, Gilles P. van Wezel, Mingxun Wang, Kelly C. Weldon, Fan Zhang, Nadine Ziemert, Katherine R. Duncan, Max Cruesemann, Simon Rogers, Pieter C. Dorrestein, Marnix H. Medema, Justin J. J. van der Hooft
Summary: Genomics and metabolomics are commonly used to explore the diversity of specialized metabolites. The Paired Omics Data Platform aims to systematically document the connections between metabolome and (meta)genome data to aid in the identification of natural product biosynthetic origins and metabolite structures.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Microbiology
Katherine E. Zink, Denise A. Ludvik, Phillip R. Lazzara, Terry W. Moore, Mark J. Mandel, Laura M. Sanchez
Summary: The lifelong relationship between the Hawaiian bobtail squid Euprymna scolopes and its microbial symbiont Vibrio fischeri offers a simplified model system for studying microbiome establishment and maintenance, involving precise molecular communication and the initiation of a specific relationship. The identification of a diketopiperazine as a signal molecule modulating the symbiosis highlights the importance of untargeted discovery efforts in host-microbe interactions. The study also suggests that multiple small molecules play a crucial role in establishing beneficial relationships between hosts and microbes.
Article
Plant Sciences
Jung-Ho Lee, Julia R. Austin, Joanna E. Burdette, Brian T. Murphy
Summary: The study found that a new secoiridoid, demethoxy-cornuside, along with other known secoiridoids isolated from the twigs of dogwood may potentiate progesterone signaling, affecting hormone-sensitive tissues.
JOURNAL OF NATURAL PRODUCTS
(2021)
Article
Biochemistry & Molecular Biology
Maryam Elfeki, Shrikant Mantri, Chase M. Clark, Stefan J. Green, Nadine Ziemert, Brian T. Murphy
Summary: Environmental microorganisms are a significant source of bioactive natural products, but there is no apparent geographic distribution pattern for these products across different sampling locations, indicating a high degree of chemical diversity between sediment microbial communities.
ACS CHEMICAL BIOLOGY
(2021)
Article
Plant Sciences
Kailiang Li, Djeneba Diakite, Julia Austin, Jung-Ho Lee, Daniel D. Lantvit, Brian T. Murphy, Joanna E. Burdette
Summary: Baicalein functions as a PR antagonist in vivo and attenuates the antiproliferative effect of P4 on luminal epithelium, while not changing levels of PR or GR RNA or protein in the uterus. RNA sequencing data suggest that transcripts significantly altered by baicalein are regulated in the opposite direction by P4, indicating potential opposing effects of baicalein and P4 in the uterus.
JOURNAL OF NATURAL PRODUCTS
(2022)
Article
Biochemical Research Methods
Hannah J. Lusk, Sarah E. Levy, Tova M. Bergsten, Joanna E. Burdette, Laura M. Sanchez
Summary: Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is a technique for mapping the spatial distribution of molecules in biological samples. Sample preparation is crucial, and a home-built robotic spinner can improve the quality of IMS data by accelerating drying and reducing wrinkles.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemistry & Molecular Biology
Chase M. Clark, Linh Nguyen, Van Cuong Pham, Laura M. Sanchez, Brian T. Murphy
Summary: In microbial drug discovery, reducing the redundancy of bacterial taxa in libraries through DNA sequencing and mass spectrometry is crucial. The IDBac platform helps assess and reduce overlap among environmental bacterial isolates, and developing algorithms to automate isolate selection can greatly improve efficiency in microbial strain prioritization.
Article
Biochemical Research Methods
Gordon T. Luu, Michael A. Freitas, Itzel Lizama-Chamu, Catherine S. McCaughey, Laura M. Sanchez, Mingxun Wang
Summary: In this paper, we present TIMSCONVERT, a high-throughput data conversion workflow that converts timsTOF Pro/fleX mass spectrometer raw data files to mzML and imzML formats while incorporating ion mobility data and maintaining compatibility with popular data analysis tools.
Article
Cell Biology
Tova M. Bergsten, Sarah E. Levy, Katherine E. Zink, Hannah J. Lusk, Melissa R. Pergande, Stephanie M. Cologna, Joanna E. Burdette, Laura M. Sanchez
Summary: This study discovered that a secreted protein called SPARC, produced by tumorigenic fallopian tube epithelial cells, enhances the release of norepinephrine (NE) from the ovary, influencing the primary metastasis of high grade serous ovarian cancer (HGSOC).
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Nutrition & Dietetics
Tova M. Bergsten, Kailiang Li, Daniel D. Lantvit, Brian T. Murphy, Joanna E. Burdette
Summary: This study analyzed the relationship between two natural products, the flavonoids apigenin and kaempferol, and progesterone treatment. The results showed that apigenin and kaempferol have progestogenic activity in vivo but act differently from progesterone. They have different effects on gene transcription, with kaempferol showing some unique effects.
Article
Microbiology
Vanessa M. M. Nepomuceno, Kaitlyn M. M. Tylor, Skylar Carlson, Michael J. J. Federle, Brian T. T. Murphy, Tiara Perez Morales
Summary: Streptococcus pyogenes, a human pathogen, uses quorum sensing to regulate social responses in its environment. Previous studies focused on disrupting quorum sensing to control bacterial signaling outcomes. This study identified a naturally derived compound that inhibits quorum sensing in S. pyogenes.
MICROBIOLOGY SPECTRUM
(2023)
Letter
Endocrinology & Metabolism
Tiago F. Leao, Chase M. Clark, Anelize Bauermeister, Emmanuel O. Elijah, Emily C. Gentry, Makhai Husband, Michelli F. Oliveira, Nuno Bandeira, Mingxun Wang, Pieter C. Dorrestein
Review
Biochemistry & Molecular Biology
Antonio Hernandez, Linh T. Nguyen, Radhika Dhakal, Brian T. Murphy
Summary: The viability of culturable microorganisms as a source of new drug leads is tied to sampling strategies, cultivation methods, and library creation processes. Innovations such as targeted cultivation of understudied bacterial phyla and untargeted use of mass spectrometry and bioinformatics to generate diverse microbial libraries could enhance therapeutic discovery efficiency.
NATURAL PRODUCT REPORTS
(2021)