Discovery of the Tyrobetaine Natural Products and Their Biosynthetic Gene Cluster via Metabologenomics

This article is cited by 34 publications.

1. James H. Tryon, Jennifer C. Rote, Li Chen, Matthew T. Robey, Marvin M. Vega, Wan Cheng Phua, William W. Metcalf, Kou-San Ju, Neil L. Kelleher, Regan J. Thomson. Genome Mining and Metabolomics Uncover a Rare d-Capreomycidine Containing Natural Product and Its Biosynthetic Gene Cluster. ACS Chemical Biology 2020, 15 (11) , 3013-3020. https://doi.org/10.1021/acschembio.0c00663
2. Alen Pšeničnik, Lucija Slemc, Martina Avbelj, Miha Tome, Martin Šala, Paul Herron, Maksym Shmatkov, Marko Petek, Špela Baebler, Peter Mrak, Daslav Hranueli, Antonio Starčević, Iain S. Hunter, Hrvoje Petković, . Oxytetracycline hyper-production through targeted genome reduction of Streptomyces rimosus. mSystems 2024, 1 https://doi.org/10.1128/msystems.00250-24
3. Michael W. Mullowney, Katherine R. Duncan, Somayah S. Elsayed, Neha Garg, Justin J. J. van der Hooft, Nathaniel I. Martin, David Meijer, Barbara R. Terlouw, Friederike Biermann, Kai Blin, Janani Durairaj, Marina Gorostiola González, Eric J. N. Helfrich, Florian Huber, Stefan Leopold-Messer, Kohulan Rajan, Tristan de Rond, Jeffrey A. van Santen, Maria Sorokina, Marcy J. Balunas, Mehdi A. Beniddir, Doris A. van Bergeijk, Laura M. Carroll, Chase M. Clark, Djork-Arné Clevert, Chris A. Dejong, Chao Du, Scarlet Ferrinho, Francesca Grisoni, Albert Hofstetter, Willem Jespers, Olga V. Kalinina, Satria A. Kautsar, Hyunwoo Kim, Tiago F. Leao, Joleen Masschelein, Evan R. Rees, Raphael Reher, Daniel Reker, Philippe Schwaller, Marwin Segler, Michael A. Skinnider, Allison S. Walker, Egon L. Willighagen, Barbara Zdrazil, Nadine Ziemert, Rebecca J. M. Goss, Pierre Guyomard, Andrea Volkamer, William H. Gerwick, Hyun Uk Kim, Rolf Müller, Gilles P. van Wezel, Gerard J. P. van Westen, Anna K. H. Hirsch, Roger G. Linington, Serina L. Robinson, Marnix H. Medema. Artificial intelligence for natural product drug discovery. Nature Reviews Drug Discovery 2023, 22 (11) , 895-916. https://doi.org/10.1038/s41573-023-00774-7
4. Giuliano Gattoni, Fabiana Di Costanzo, Rafael R. de la Haba, Ana B. Fernández, Shaday Guerrero-Flores, Nelly Selem-Mojica, Antonio Ventosa, Paulina Corral. Biosynthetic gene profiling and genomic potential of the novel photosynthetic marine bacterium Roseibaca domitiana. Frontiers in Microbiology 2023, 14 https://doi.org/10.3389/fmicb.2023.1238779
5. Xinyi Li, Ping Zhang, Jia Liu, Hongxin Wang, Junna Liu, Hanxue Li, Heng Xie, Qianchao Wang, Li Li, Shan Zhang, Liubin Huang, Chenghong Liu, Peng Qin. Integrated Metabolomic and Transcriptomic Analysis of the Quinoa Seedling Response to High Relative Humidity Stress. Biomolecules 2023, 13 (9) , 1352. https://doi.org/10.3390/biom13091352
6. Miguel Cuevas-Cruz, Ulises Hernández-Guzmán, Poulette Carolina Álvarez-Rosales, Meike Schnabel, Saúl Gómez-Manzo, Roberto Arreguín-Espinosa. The Role of Mass Spectrometry in the Discovery of Antibiotics and Bacterial Resistance Mechanisms: Proteomics and Metabolomics Approaches. Current Medicinal Chemistry 2023, 30 (1) , 30-58. https://doi.org/10.2174/0929867329666220329090822
7. Pulak Kumar Maiti, Sukhendu Mandal. Comprehensive genome analysis of Lentzea reveals repertoire of polymer-degrading enzymes and bioactive compounds with clinical relevance. Scientific Reports 2022, 12 (1) https://doi.org/10.1038/s41598-022-12427-7
8. Yuchen Li, Seoung Rak Lee, Esther J. Han, Mohammad R. Seyedsayamdost. Momomycin, an Antiproliferative Cryptic Metabolite from the Oxytetracycline Producer Streptomyces rimosus. Angewandte Chemie 2022, 134 (39) https://doi.org/10.1002/ange.202208573
9. Yuchen Li, Seoung Rak Lee, Esther J. Han, Mohammad R. Seyedsayamdost. Momomycin, an Antiproliferative Cryptic Metabolite from the Oxytetracycline Producer Streptomyces rimosus. Angewandte Chemie International Edition 2022, 61 (39) https://doi.org/10.1002/anie.202208573
10. Chen Wang, Dongliang Xiao, Baoqing Dun, Miaomiao Yin, Adigo Setargie Tsega, Linan Xie, Wenhua Li, Qun Yue, Sibao Wang, Han Gao, Min Lin, Liwen Zhang, István Molnár, Yuquan Xu. Chemometrics and genome mining reveal an unprecedented family of sugar acid–containing fungal nonribosomal cyclodepsipeptides. Proceedings of the National Academy of Sciences 2022, 119 (32) https://doi.org/10.1073/pnas.2123379119
11. José Rivera-Chávez, Corina-Diana Ceapă, Mario Figueroa. Biological Dark Matter Exploration using Data Mining for the Discovery of Antimicrobial Natural Products. Planta Medica 2022, 88 (09/10) , 702-720. https://doi.org/10.1055/a-1795-0562
12. Heng Xie, Qianchao Wang, Ping Zhang, Xuesong Zhang, Tingzhi Huang, Yirui Guo, Junna Liu, Li Li, Hanxue Li, Peng Qin. Transcriptomic and Metabolomic Analysis of the Response of Quinoa Seedlings to Low Temperatures. Biomolecules 2022, 12 (7) , 977. https://doi.org/10.3390/biom12070977
13. Paris S Salazar-Hamm, Jennifer J Marshall Hathaway, Ara S Winter, Nicole A Caimi, Debbie C Buecher, Ernest W Valdez, Diana E Northup. Great diversity of KS α sequences from bat-associated microbiota suggests novel sources of uncharacterized natural products. FEMS Microbes 2022, 3 https://doi.org/10.1093/femsmc/xtac012
14. Lucija Slemc, Jernej Jakše, Alessandro Filisetti, Damir Baranasic, Antonio Rodríguez-García, Francesco Del Carratore, Stefano Maria Marino, Jurica Zucko, Antonio Starcevic, Martin Šala, Mercedes Pérez-Bonilla, Marina Sánchez-Hidalgo, Ignacio González, Fernando Reyes, Olga Genilloud, Vicki Springthorpe, Dušan Goranovič, Gregor Kosec, Gavin H. Thomas, Davide De Lucrezia, Hrvoje Petković, Miha Tome, . Reference-Grade Genome and Large Linear Plasmid of Streptomyces rimosus: Pushing the Limits of Nanopore Sequencing. Microbiology Spectrum 2022, 10 (2) https://doi.org/10.1128/spectrum.02434-21
15. Bahar Behsaz, Edna Bode, Alexey Gurevich, Yan-Ni Shi, Florian Grundmann, Deepa Acharya, Andrés Mauricio Caraballo-Rodríguez, Amina Bouslimani, Morgan Panitchpakdi, Annabell Linck, Changhui Guan, Julia Oh, Pieter C. Dorrestein, Helge B. Bode, Pavel A. Pevzner, Hosein Mohimani. Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery. Nature Communications 2021, 12 (1) https://doi.org/10.1038/s41467-021-23502-4
16. Lindsay K. Caesar, Rana Montaser, Nancy P. Keller, Neil L. Kelleher. Metabolomics and genomics in natural products research: complementary tools for targeting new chemical entities. Natural Product Reports 2021, 38 (11) , 2041-2065. https://doi.org/10.1039/D1NP00036E
17. Marnix H. Medema, Tristan de Rond, Bradley S. Moore. Mining genomes to illuminate the specialized chemistry of life. Nature Reviews Genetics 2021, 22 (9) , 553-571. https://doi.org/10.1038/s41576-021-00363-7
18. Laurine Darcel, Sanjit Das, Isabelle Bonnard, Bernard Banaigs, Nicolas Inguimbert. Thirtieth Anniversary of the Discovery of Laxaphycins. Intriguing Peptides Keeping a Part of Their Mystery. Marine Drugs 2021, 19 (9) , 473. https://doi.org/10.3390/md19090473
19. Linda Sukmarini. Recent Advances in Discovery of Lead Structures from Microbial Natural Products: Genomics- and Metabolomics-Guided Acceleration. Molecules 2021, 26 (9) , 2542. https://doi.org/10.3390/molecules26092542
20. Max Crüsemann. Coupling Mass Spectral and Genomic Information to Improve Bacterial Natural Product Discovery Workflows. Marine Drugs 2021, 19 (3) , 142. https://doi.org/10.3390/md19030142
21. Satria A Kautsar, Justin J J van der Hooft, Dick de Ridder, Marnix H Medema. BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters. GigaScience 2021, 10 (1) https://doi.org/10.1093/gigascience/giaa154
22. Komal Sharma, Mohammad Rifqi Ghiffary, Hyun Uk Kim, Sang Yup Lee. Engineering Heterologous Hosts for the Enhanced Production of Non-ribosomal Peptides. Biotechnology and Bioprocess Engineering 2020, 25 (6) , 795-809. https://doi.org/10.1007/s12257-020-0080-z
23. Kaitlyn C. Belknap, Cooper J. Park, Brian M. Barth, Cheryl P. Andam. Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces bacteria. Scientific Reports 2020, 10 (1) https://doi.org/10.1038/s41598-020-58904-9
24. Ryosuke Kozakai, Takuto Ono, Shotaro Hoshino, Hidenori Takahashi, Yohei Katsuyama, Yoshinori Sugai, Taro Ozaki, Kazuya Teramoto, Kanae Teramoto, Koichi Tanaka, Ikuro Abe, Shumpei Asamizu, Hiroyasu Onaka. Acyltransferase that catalyses the condensation of polyketide and peptide moieties of goadvionin hybrid lipopeptides. Nature Chemistry 2020, 12 (9) , 869-877. https://doi.org/10.1038/s41557-020-0508-2
25. Allegra T. Aron, Emily C. Gentry, Kerry L. McPhail, Louis-Félix Nothias, Mélissa 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, Andrés Mauricio Caraballo-Rodríguez, Irina Koester, Kelly C. Weldon, Samuel Bertrand, Catherine Roullier, Kunyang Sun, Richard M. Tehan, Cristopher A. Boya P., Martin H. Christian, Marcelino Gutiérrez, Aldo Moreno Ulloa, Javier Andres Tejeda Mora, Randy Mojica-Flores, Johant Lakey-Beitia, Victor Vásquez-Chaves, Yilue Zhang, Angela I. Calderón, 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. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nature Protocols 2020, 15 (6) , 1954-1991. https://doi.org/10.1038/s41596-020-0317-5
26. Birgit Wiltschi, Tomislav Cernava, Alexander Dennig, Meritxell Galindo Casas, Martina Geier, Steffen Gruber, Marianne Haberbauer, Petra Heidinger, Enrique Herrero Acero, Regina Kratzer, Christiane Luley-Goedl, Christina A. Müller, Julia Pitzer, Doris Ribitsch, Michael Sauer, Katharina Schmölzer, Wolfgang Schnitzhofer, Christoph W. Sensen, Jung Soh, Kerstin Steiner, Christoph K. Winkler, Margit Winkler, Tamara Wriessnegger. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnology Advances 2020, 40 , 107520. https://doi.org/10.1016/j.biotechadv.2020.107520
27. Nadine Ziemert, Tilmann Weber, Marnix H. Medema. Genome Mining Approaches to Bacterial Natural Product Discovery. 2020, 19-33. https://doi.org/10.1016/B978-0-12-409547-2.14627-X
28. Jorge C. Navarro-Muñoz, Nelly Selem-Mojica, Michael W. Mullowney, Satria A. Kautsar, James H. Tryon, Elizabeth I. Parkinson, Emmanuel L. C. De Los Santos, Marley Yeong, Pablo Cruz-Morales, Sahar Abubucker, Arne Roeters, Wouter Lokhorst, Antonio Fernandez-Guerra, Luciana Teresa Dias Cappelini, Anthony W. Goering, Regan J. Thomson, William W. Metcalf, Neil L. Kelleher, Francisco Barona-Gomez, Marnix H. Medema. A computational framework to explore large-scale biosynthetic diversity. Nature Chemical Biology 2020, 16 (1) , 60-68. https://doi.org/10.1038/s41589-019-0400-9
29. Guoqing Niu, Wenli Li. Next-Generation Drug Discovery to Combat Antimicrobial Resistance. Trends in Biochemical Sciences 2019, 44 (11) , 961-972. https://doi.org/10.1016/j.tibs.2019.05.005
30. Alexander E. Fox Ramos, Laurent Evanno, Erwan Poupon, Pierre Champy, Mehdi A. Beniddir. Natural products targeting strategies involving molecular networking: different manners, one goal. Natural Product Reports 2019, 36 (7) , 960-980. https://doi.org/10.1039/C9NP00006B
31. Lakshmi Prasuna Mekala, Mujahid Mohammed, Sasikala Chintalapati, Venkata Ramana Chintalapati. Precursor-feeding and altered-growth conditions reveal novel blue pigment production by Rubrivivax benzoatilyticus JA2. Biotechnology Letters 2019, 41 (6-7) , 813-822. https://doi.org/10.1007/s10529-019-02682-6
32. Sylvia Soldatou, Grimur Hjorleifsson Eldjarn, Alejandro Huerta-Uribe, Simon Rogers, Katherine R Duncan. Linking biosynthetic and chemical space to accelerate microbial secondary metabolite discovery. FEMS Microbiology Letters 2019, 366 (13) https://doi.org/10.1093/femsle/fnz142
33. Matt McErlean, Jonathan Overbay, Steven Van Lanen. Refining and expanding nonribosomal peptide synthetase function and mechanism. Journal of Industrial Microbiology and Biotechnology 2019, 46 (3-4) , 493-513. https://doi.org/10.1007/s10295-018-02130-w
34. Robert A. Hill, Andrew Sutherland. Hot off the Press. Natural Product Reports 2018, 35 (6) , 496-500. https://doi.org/10.1039/C8NP90015A