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30 results on '"Duggan, Brendan M"'

1. Changes in Internal Structure and Dynamics upon Binding Stabilise the Nematode Anticoagulant NAPc2

Author

Woodward, Elaine, Woodward, Elaine, Duggan, Brendan M, Woodward, Elaine, Woodward, Elaine, and Duggan, Brendan M

Abstract

Abnormal blood coagulation is a major health problem and natural anticoagulants from blood-feeding organisms have been investigated as novel therapeutics. NAPc2, a potent nematode-derived inhibitor of coagulation, has an unusual mode of action that requires coagulation factor Xa but does not inhibit it. Molecular dynamics simulations of NAPc2 and factor Xa were generated to better understand NAPc2. The simulations suggest that parts of NAPc2 become more rigid upon binding factor Xa and reveal that two highly conserved residues form an internal salt bridge that stabilises the bound conformation. Clotting time assays with mutants confirmed the utility of the salt bridge and suggested that it is a conserved mechanism for stabilising the bound conformation of secondary structure-poor protease inhibitors.

Published
2024

2. A Survey of Didemnin Depsipeptide Production in Tistrella.

Author

Stankey, Robert J, Stankey, Robert J, Johnson, Don, Duggan, Brendan M, Mead, David A, La Clair, James J, Stankey, Robert J, Stankey, Robert J, Johnson, Don, Duggan, Brendan M, Mead, David A, and La Clair, James J

Abstract

As one of the first families of marine natural products to undergo clinical trials, the didemnin depsipeptides have played a significant role in inspiring the discovery of marine drugs. Originally developed as anticancer therapeutics, the recent re-evaluation of these compounds including synthetically derived dehydrodidemnin B or Aplidine, has led to their advancement towards antiviral applications. While conventionally associated with production in colonial tunicates of the family Didemnidae, recent studies have identified their biosynthetic gene clusters from the marine-derived bacteria Tistrella mobilis. While these studies confirm the production of didemnin X/Y, the low titer and general lack of understanding of their biosynthesis in Tistrella currently prevents the development of effective microbial or synthetic biological approaches for their production. To this end, we conducted a survey of known species of Tistrella and report on their ability to produce the didemnin depsipeptides. These data were used to develop conditions to produce didemnin B at titers over 15 mg/L.

Published
2023

3. Cannabinol inhibits oxytosis/ferroptosis by directly targeting mitochondria independently of cannabinoid receptors.

Author

Liang, Zhibin, Liang, Zhibin, Soriano-Castell, David, Kepchia, Devin, Duggan, Brendan M, Currais, Antonio, Schubert, David, Maher, Pamela, Liang, Zhibin, Liang, Zhibin, Soriano-Castell, David, Kepchia, Devin, Duggan, Brendan M, Currais, Antonio, Schubert, David, and Maher, Pamela

Abstract

The oxytosis/ferroptosis regulated cell death pathway recapitulates many features of mitochondrial dysfunction associated with the aging brain and has emerged as a potential key mediator of neurodegeneration. It has thus been proposed that the oxytosis/ferroptosis pathway can be used to identify novel drug candidates for the treatment of age-associated neurodegenerative diseases that act by preserving mitochondrial function. Previously, we identified cannabinol (CBN) as a potent neuroprotector. Here, we demonstrate that not only does CBN protect nerve cells from oxytosis/ferroptosis in a manner that is dependent on mitochondria and it does so independently of cannabinoid receptors. Specifically, CBN directly targets mitochondria and preserves key mitochondrial functions including redox regulation, calcium uptake, membrane potential, bioenergetics, biogenesis, and modulation of fusion/fission dynamics that are disrupted following induction of oxytosis/ferroptosis. These protective effects of CBN are at least partly mediated by the promotion of endogenous antioxidant defenses and the activation of AMP-activated protein kinase (AMPK) signaling. Together, our data highlight the potential of mitochondrially-targeted compounds such as CBN as novel oxytotic/ferroptotic inhibitors to rescue mitochondrial dysfunction as well as opportunities for the discovery and development of future neurotherapeutics.

Published
2022

4. Searching for Small Molecules with an Atomic Sort.

Author

Duggan, Brendan M, Duggan, Brendan M, Cullum, Reiko, Fenical, William, Amador, Luis A, Rodríguez, Abimael D, La Clair, James J, Duggan, Brendan M, Duggan, Brendan M, Cullum, Reiko, Fenical, William, Amador, Luis A, Rodríguez, Abimael D, and La Clair, James J

Abstract

The discovery of biologically active small molecules requires sifting through large amounts of data to identify unique or unusual arrangements of atoms. Here, we develop, test and evaluate an atom-based sort to identify novel features of secondary metabolites and demonstrate its use to evaluate novelty in marine microbial and sponge extracts. This study outlines an important ongoing advance towards the translation of autonomous systems to identify, and ultimately elucidate, atomic novelty within a complex mixture of small molecules.

Published
2020

5. Editorial to the Special Issue-'Technology for Natural Products Research'.

Author

Duggan, Brendan M, Duggan, Brendan M, Duggan, Brendan M, and Duggan, Brendan M

Abstract

Natural product research continues to be a productive source of unusual chemistry, producing novel compounds for biomedical applications and, increasingly, sustainably providing commercially useful compounds [...].

Published
2020

6. Searching for Small Molecules with an Atomic Sort

Author

Duggan, Brendan M, Duggan, Brendan M, Cullum, Reiko, Fenical, William, Amador, Luis A, Rodríguez, Abimael D, La Clair, James J, Duggan, Brendan M, Duggan, Brendan M, Cullum, Reiko, Fenical, William, Amador, Luis A, Rodríguez, Abimael D, and La Clair, James J

Abstract

The discovery of biologically active small molecules requires sifting through large amounts of data to identify unique or unusual arrangements of atoms. Here, we develop, test and evaluate an atom‐based sort to identify novel features of secondary metabolites and demonstrate its use to evaluate novelty in marine microbial and sponge extracts. This study outlines an important ongoing advance towards the translation of autonomous systems to identify, and ultimately elucidate, atomic novelty within a complex mixture of small molecules.

Published
2020

7. Author Correction: Small Molecule Accurate Recognition Technology (SMART) to Enhance Natural Products Research.

Author

Zhang, Chen, Zhang, Chen, Idelbayev, Yerlan, Roberts, Nicholas, Tao, Yiwen, Nannapaneni, Yashwanth, Duggan, Brendan M, Min, Jie, Lin, Eugene C, Gerwick, Erik C, Cottrell, Garrison W, Gerwick, William H, Zhang, Chen, Zhang, Chen, Idelbayev, Yerlan, Roberts, Nicholas, Tao, Yiwen, Nannapaneni, Yashwanth, Duggan, Brendan M, Min, Jie, Lin, Eugene C, Gerwick, Erik C, Cottrell, Garrison W, and Gerwick, William H

Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

8. Author Correction: Small Molecule Accurate Recognition Technology (SMART) to Enhance Natural Products Research.

Author

Zhang, Chen, Zhang, Chen, Idelbayev, Yerlan, Roberts, Nicholas, Tao, Yiwen, Nannapaneni, Yashwanth, Duggan, Brendan M, Min, Jie, Lin, Eugene C, Gerwick, Erik C, Cottrell, Garrison W, Gerwick, William H, Zhang, Chen, Zhang, Chen, Idelbayev, Yerlan, Roberts, Nicholas, Tao, Yiwen, Nannapaneni, Yashwanth, Duggan, Brendan M, Min, Jie, Lin, Eugene C, Gerwick, Erik C, Cottrell, Garrison W, and Gerwick, William H

Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

9. Tutuilamides A-C: Vinyl-Chloride-Containing Cyclodepsipeptides from Marine Cyanobacteria with Potent Elastase Inhibitory Properties.

Author

Keller, Lena, Keller, Lena, Canuto, Kirley Marques, Liu, Chenxi, Suzuki, Brian M, Almaliti, Jehad, Sikandar, Asfandyar, Naman, C Benjamin, Glukhov, Evgenia, Luo, Danmeng, Duggan, Brendan M, Luesch, Hendrik, Koehnke, Jesko, O'Donoghue, Anthony J, Gerwick, William H, Keller, Lena, Keller, Lena, Canuto, Kirley Marques, Liu, Chenxi, Suzuki, Brian M, Almaliti, Jehad, Sikandar, Asfandyar, Naman, C Benjamin, Glukhov, Evgenia, Luo, Danmeng, Duggan, Brendan M, Luesch, Hendrik, Koehnke, Jesko, O'Donoghue, Anthony J, and Gerwick, William H

Abstract

Marine cyanobacteria (blue-green algae) have been shown to possess an enormous capacity to produce structurally diverse natural products that exhibit a broad spectrum of potent biological activities, including cytotoxic, antifungal, antiparasitic, antiviral, and antibacterial activities. Using mass-spectrometry-guided fractionation together with molecular networking, cyanobacterial field collections from American Samoa and Palmyra Atoll yielded three new cyclic peptides, tutuilamides A-C. Their structures were established by spectroscopic techniques including 1D and 2D NMR, HR-MS, and chemical derivatization. Structure elucidation was facilitated by employing advanced NMR techniques including nonuniform sampling in combination with the 1,1-ADEQUATE experiment. These cyclic peptides are characterized by the presence of several unusual residues including 3-amino-6-hydroxy-2-piperidone and 2-amino-2-butenoic acid, together with a novel vinyl chloride-containing residue. Tutuilamides A-C show potent elastase inhibitory activity together with moderate potency in H-460 lung cancer cell cytotoxicity assays. The binding mode to elastase was analyzed by X-ray crystallography revealing a reversible binding mode similar to the natural product lyngbyastatin 7. The presence of an additional hydrogen bond with the amino acid backbone of the flexible side chain of tutuilamide A, compared to lyngbyastatin 7, facilitates its stabilization in the elastase binding pocket and possibly explains its enhanced inhibitory potency.

Published
2020

10. A Convolutional Neural Network-Based Approach for the Rapid Annotation of Molecularly Diverse Natural Products.

Author

Reher, Raphael, Reher, Raphael, Kim, Hyun Woo, Zhang, Chen, Mao, Huanru Henry, Wang, Mingxun, Nothias, Louis-Félix, Caraballo-Rodriguez, Andres Mauricio, Glukhov, Evgenia, Teke, Bahar, Leao, Tiago, Alexander, Kelsey L, Duggan, Brendan M, Van Everbroeck, Ezra L, Dorrestein, Pieter C, Cottrell, Garrison W, Gerwick, William H, Reher, Raphael, Reher, Raphael, Kim, Hyun Woo, Zhang, Chen, Mao, Huanru Henry, Wang, Mingxun, Nothias, Louis-Félix, Caraballo-Rodriguez, Andres Mauricio, Glukhov, Evgenia, Teke, Bahar, Leao, Tiago, Alexander, Kelsey L, Duggan, Brendan M, Van Everbroeck, Ezra L, Dorrestein, Pieter C, Cottrell, Garrison W, and Gerwick, William H

Abstract

This report describes the first application of the novel NMR-based machine learning tool "Small Molecule Accurate Recognition Technology" (SMART 2.0) for mixture analysis and subsequent accelerated discovery and characterization of new natural products. The concept was applied to the extract of a filamentous marine cyanobacterium known to be a prolific producer of cytotoxic natural products. This environmental Symploca extract was roughly fractionated, and then prioritized and guided by cancer cell cytotoxicity, NMR-based SMART 2.0, and MS2-based molecular networking. This led to the isolation and rapid identification of a new chimeric swinholide-like macrolide, symplocolide A, as well as the annotation of swinholide A, samholides A-I, and several new derivatives. The planar structure of symplocolide A was confirmed to be a structural hybrid between swinholide A and luminaolide B by 1D/2D NMR and LC-MS2 analysis. A second example applies SMART 2.0 to the characterization of structurally novel cyclic peptides, and compares this approach to the recently appearing "atomic sort" method. This study exemplifies the revolutionary potential of combined traditional and deep learning-assisted analytical approaches to overcome longstanding challenges in natural products drug discovery.

Published
2020

11. Commensal Oral Rothia mucilaginosa Produces Enterobactin, a Metal-Chelating Siderophore.

Author

Uranga, Carla C, Cleary, David W1, Uranga, Carla C, Arroyo, Pablo, Duggan, Brendan M, Gerwick, William H, Edlund, Anna, Uranga, Carla C, Cleary, David W1, Uranga, Carla C, Arroyo, Pablo, Duggan, Brendan M, Gerwick, William H, and Edlund, Anna

Abstract

Next-generation sequencing studies of saliva and dental plaque from subjects in both healthy and diseased states have identified bacteria belonging to the Rothia genus as ubiquitous members of the oral microbiota. To gain a deeper understanding of molecular mechanisms underlying the chemical ecology of this unexplored group, we applied a genome mining approach that targets functionally important biosynthetic gene clusters (BGCs). All 45 genomes that were mined, representing Rothia mucilaginosa, Rothia dentocariosa, and Rothia aeria, harbored a catechol-siderophore-like BGC. To explore siderophore production further, we grew the previously characterized R. mucilaginosa ATCC 25296 in liquid cultures, amended with glycerol, which led to the identification of the archetype siderophore enterobactin by using tandem liquid chromatography-mass spectrometry (LC-MS/MS), high-performance liquid chromatography (HPLC), and nuclear magnetic resonance (NMR) spectroscopy. Normally attributed to pathogenic gut bacteria, R. mucilaginosa is the first commensal oral bacterium found to produce enterobactin. Cocultivation studies including R. mucilaginosa or purified enterobactin revealed that enterobactin reduced growth of certain strains of cariogenic Streptococcus mutans and pathogenic strains of Staphylococcus aureus Commensal oral bacteria were either unaffected, reduced in growth, or induced to grow adjacent to enterobactin-producing R. mucilaginosa or the pure compound. Taken together with Rothia's known capacity to ferment a variety of carbohydrates and amino acids, our findings of enterobactin production add an additional level of explanation to R. mucilaginosa's prevalence in the oral cavity. Enterobactin is the strongest Fe(III) binding siderophore known, and its role in oral health requires further investigation.IMPORTANCE The communication language of the human oral microbiota is vastly underexplored. However, a few studies have shown that specialized small molecules encoded

Published
2020

12. Small Molecule Accurate Recognition Technology (SMART) to Enhance Natural Products Research.

Author

Zhang, Chen, Zhang, Chen, Idelbayev, Yerlan, Roberts, Nicholas, Tao, Yiwen, Nannapaneni, Yashwanth, Duggan, Brendan M, Min, Jie, Lin, Eugene C, Gerwick, Erik C, Cottrell, Garrison W, Gerwick, William H, Zhang, Chen, Zhang, Chen, Idelbayev, Yerlan, Roberts, Nicholas, Tao, Yiwen, Nannapaneni, Yashwanth, Duggan, Brendan M, Min, Jie, Lin, Eugene C, Gerwick, Erik C, Cottrell, Garrison W, and Gerwick, William H

Abstract

Various algorithms comparing 2D NMR spectra have been explored for their ability to dereplicate natural products as well as determine molecular structures. However, spectroscopic artefacts, solvent effects, and the interactive effect of functional group(s) on chemical shifts combine to hinder their effectiveness. Here, we leveraged Non-Uniform Sampling (NUS) 2D NMR techniques and deep Convolutional Neural Networks (CNNs) to create a tool, SMART, that can assist in natural products discovery efforts. First, an NUS heteronuclear single quantum coherence (HSQC) NMR pulse sequence was adapted to a state-of-the-art nuclear magnetic resonance (NMR) instrument, and data reconstruction methods were optimized, and second, a deep CNN with contrastive loss was trained on a database containing over 2,054 HSQC spectra as the training set. To demonstrate the utility of SMART, several newly isolated compounds were automatically located with their known analogues in the embedded clustering space, thereby streamlining the discovery pipeline for new natural products.

Published
2017

13. Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae.

Author

Luzzatto-Knaan, Tal, Luzzatto-Knaan, Tal, Garg, Neha, Wang, Mingxun, Glukhov, Evgenia, Peng, Yao, Ackermann, Gail, Amir, Amnon, Duggan, Brendan M, Ryazanov, Sergey, Gerwick, Lena, Knight, Rob, Alexandrov, Theodore, Bandeira, Nuno, Gerwick, William H, Dorrestein, Pieter C, Luzzatto-Knaan, Tal, Luzzatto-Knaan, Tal, Garg, Neha, Wang, Mingxun, Glukhov, Evgenia, Peng, Yao, Ackermann, Gail, Amir, Amnon, Duggan, Brendan M, Ryazanov, Sergey, Gerwick, Lena, Knight, Rob, Alexandrov, Theodore, Bandeira, Nuno, Gerwick, William H, and Dorrestein, Pieter C

Abstract

Natural product screening programs have uncovered molecules from diverse natural sources with various biological activities and unique structures. However, much is yet underexplored and additional information is hidden in these exceptional collections. We applied untargeted mass spectrometry approaches to capture the chemical space and dispersal patterns of metabolites from an in-house library of marine cyanobacterial and algal collections. Remarkably, 86% of the metabolomics signals detected were not found in other available datasets of similar nature, supporting the hypothesis that marine cyanobacteria and algae possess distinctive metabolomes. The data were plotted onto a world map representing eight major sampling sites, and revealed potential geographic locations with high chemical diversity. We demonstrate the use of these inventories as a tool to explore the diversity and distribution of natural products. Finally, we utilized this tool to guide the isolation of a new cyclic lipopeptide, yuvalamide A, from a marine cyanobacterium.

Published
2017

14. Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae.

Author

Luzzatto-Knaan, Tal, Luzzatto-Knaan, Tal, Garg, Neha, Wang, Mingxun, Glukhov, Evgenia, Peng, Yao, Ackermann, Gail, Amir, Amnon, Duggan, Brendan M, Ryazanov, Sergey, Gerwick, Lena, Knight, Rob, Alexandrov, Theodore, Bandeira, Nuno, Gerwick, William H, Dorrestein, Pieter C, Luzzatto-Knaan, Tal, Luzzatto-Knaan, Tal, Garg, Neha, Wang, Mingxun, Glukhov, Evgenia, Peng, Yao, Ackermann, Gail, Amir, Amnon, Duggan, Brendan M, Ryazanov, Sergey, Gerwick, Lena, Knight, Rob, Alexandrov, Theodore, Bandeira, Nuno, Gerwick, William H, and Dorrestein, Pieter C

Abstract

Natural product screening programs have uncovered molecules from diverse natural sources with various biological activities and unique structures. However, much is yet underexplored and additional information is hidden in these exceptional collections. We applied untargeted mass spectrometry approaches to capture the chemical space and dispersal patterns of metabolites from an in-house library of marine cyanobacterial and algal collections. Remarkably, 86% of the metabolomics signals detected were not found in other available datasets of similar nature, supporting the hypothesis that marine cyanobacteria and algae possess distinctive metabolomes. The data were plotted onto a world map representing eight major sampling sites, and revealed potential geographic locations with high chemical diversity. We demonstrate the use of these inventories as a tool to explore the diversity and distribution of natural products. Finally, we utilized this tool to guide the isolation of a new cyclic lipopeptide, yuvalamide A, from a marine cyanobacterium.

Published
2017

15. Small Molecule Accurate Recognition Technology (SMART) to Enhance Natural Products Research.

Author

Zhang, Chen, Zhang, Chen, Idelbayev, Yerlan, Roberts, Nicholas, Tao, Yiwen, Nannapaneni, Yashwanth, Duggan, Brendan M, Min, Jie, Lin, Eugene C, Gerwick, Erik C, Cottrell, Garrison W, Gerwick, William H, Zhang, Chen, Zhang, Chen, Idelbayev, Yerlan, Roberts, Nicholas, Tao, Yiwen, Nannapaneni, Yashwanth, Duggan, Brendan M, Min, Jie, Lin, Eugene C, Gerwick, Erik C, Cottrell, Garrison W, and Gerwick, William H

Abstract

Various algorithms comparing 2D NMR spectra have been explored for their ability to dereplicate natural products as well as determine molecular structures. However, spectroscopic artefacts, solvent effects, and the interactive effect of functional group(s) on chemical shifts combine to hinder their effectiveness. Here, we leveraged Non-Uniform Sampling (NUS) 2D NMR techniques and deep Convolutional Neural Networks (CNNs) to create a tool, SMART, that can assist in natural products discovery efforts. First, an NUS heteronuclear single quantum coherence (HSQC) NMR pulse sequence was adapted to a state-of-the-art nuclear magnetic resonance (NMR) instrument, and data reconstruction methods were optimized, and second, a deep CNN with contrastive loss was trained on a database containing over 2,054 HSQC spectra as the training set. To demonstrate the utility of SMART, several newly isolated compounds were automatically located with their known analogues in the embedded clustering space, thereby streamlining the discovery pipeline for new natural products.

Published
2017

16. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Author

Wang, Mingxun, Carver, Jeremy J., Phelan, Vanessa V., Sanchez, Laura M., Garg, Neha, Peng, Yao, Don Duy Nguyen, Watrous, Jeramie, Kapono, Clifford A., Luzzatto-knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V., Meehan, Michael J., Liu, Wei -ting, Criisemann, Max, Boudreau, Paul D., Esquenazi, Eduardo, Sandoval-calderon, Mario, Kersten, Roland D., Pace, Laura A., Quinn, Robert A., Duncan, Katherine R., Hsu, Cheng-chih, Floros, Dimitrios J., Gavilan, Ronnie G., Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J., Parrot, Delphine, Carlson, Erin E., Aigle, Bertrand, Michelsen, Charlotte F., Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, Mclean, Jeffrey, Piel, Jorn, Murphy, Brian T., Gerwick, Lena, Liaw, Chih-chuang, Yang, Yu-liang, Humpf, Hans-ulrich, Maansson, Maria, Keyzers, Robert A., Sims, Amy C., Johnson, Andrew R., Sidebottom, Ashley M., Sedio, Brian E., Klitgaard, Andreas, Larson, Charles B., Boya P, Cristopher A., Torres-mendoza, Daniel, Gonzalez, David J., Silva, Denise B., Marques, Lucas M., Demarque, Daniel P., Pociute, Egle, O'Neill, Ellis C., Briand, Enora, Helfrich, Eric J. N., Granatosky, Eve A., Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J., Zeng, Yi, Vorholt, Julia A., Kurita, Kenji L., Charusanti, Pep, Mcphail, Kerry L., Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F., Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B., Baric, Ralph, Silva, Ricardo R., Mascuch, Samantha J., Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G., Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodriguez, Andres M. C., Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M., Almaliti, Jehad, Allard, Pierre-marie, Phapale, Prasad, Nothias, Louis-felix, Alexandrovr, Theodore, Litaudon, Marc, Wolfender, Jean-luc, Kyle, Jennifer E., Metz, Thomas O., Peryea, Tyler, Dac-trung Nguyen, Vanleer, Danielle, Shinn, Paul, Jadhav, Ajit, Muller, Rolf, Waters, Katrina M., Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R., Palsson, Bernhard O., Pogliano, Kit, Linington, Roger G., Gutierrez, Marcelino, Lopes, Norberto P., Gerwick, William H., Moore, Bradley S., Dorrestein, Pieter C., Bandeira, Nuno, Wang, Mingxun, Carver, Jeremy J., Phelan, Vanessa V., Sanchez, Laura M., Garg, Neha, Peng, Yao, Don Duy Nguyen, Watrous, Jeramie, Kapono, Clifford A., Luzzatto-knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V., Meehan, Michael J., Liu, Wei -ting, Criisemann, Max, Boudreau, Paul D., Esquenazi, Eduardo, Sandoval-calderon, Mario, Kersten, Roland D., Pace, Laura A., Quinn, Robert A., Duncan, Katherine R., Hsu, Cheng-chih, Floros, Dimitrios J., Gavilan, Ronnie G., Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J., Parrot, Delphine, Carlson, Erin E., Aigle, Bertrand, Michelsen, Charlotte F., Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, Mclean, Jeffrey, Piel, Jorn, Murphy, Brian T., Gerwick, Lena, Liaw, Chih-chuang, Yang, Yu-liang, Humpf, Hans-ulrich, Maansson, Maria, Keyzers, Robert A., Sims, Amy C., Johnson, Andrew R., Sidebottom, Ashley M., Sedio, Brian E., Klitgaard, Andreas, Larson, Charles B., Boya P, Cristopher A., Torres-mendoza, Daniel, Gonzalez, David J., Silva, Denise B., Marques, Lucas M., Demarque, Daniel P., Pociute, Egle, O'Neill, Ellis C., Briand, Enora, Helfrich, Eric J. N., Granatosky, Eve A., Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J., Zeng, Yi, Vorholt, Julia A., Kurita, Kenji L., Charusanti, Pep, Mcphail, Kerry L., Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F., Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B., Baric, Ralph, Silva, Ricardo R., Mascuch, Samantha J., Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G., Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodriguez, Andres M. C., Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M., Almaliti, Jehad, Allard, Pierre-marie, Phapale, Prasad, Nothias, Louis-felix, Alexandrovr, Theodore, Litaudon, Marc, Wolfender, Jean-luc, Kyle, Jennifer E., Metz, Thomas O., Peryea, Tyler, Dac-trung Nguyen, Vanleer, Danielle, Shinn, Paul, Jadhav, Ajit, Muller, Rolf, Waters, Katrina M., Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R., Palsson, Bernhard O., Pogliano, Kit, Linington, Roger G., Gutierrez, Marcelino, Lopes, Norberto P., Gerwick, William H., Moore, Bradley S., Dorrestein, Pieter C., and Bandeira, Nuno

Abstract

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Published
2016
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17. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Author

Wang, Mingxun, Carver, Jeremy J., Phelan, Vanessa V., Sanchez, Laura M., Garg, Neha, Peng, Yao, Don Duy Nguyen, Watrous, Jeramie, Kapono, Clifford A., Luzzatto-knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V., Meehan, Michael J., Liu, Wei -ting, Criisemann, Max, Boudreau, Paul D., Esquenazi, Eduardo, Sandoval-calderon, Mario, Kersten, Roland D., Pace, Laura A., Quinn, Robert A., Duncan, Katherine R., Hsu, Cheng-chih, Floros, Dimitrios J., Gavilan, Ronnie G., Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J., Parrot, Delphine, Carlson, Erin E., Aigle, Bertrand, Michelsen, Charlotte F., Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, Mclean, Jeffrey, Piel, Jorn, Murphy, Brian T., Gerwick, Lena, Liaw, Chih-chuang, Yang, Yu-liang, Humpf, Hans-ulrich, Maansson, Maria, Keyzers, Robert A., Sims, Amy C., Johnson, Andrew R., Sidebottom, Ashley M., Sedio, Brian E., Klitgaard, Andreas, Larson, Charles B., Boya P, Cristopher A., Torres-mendoza, Daniel, Gonzalez, David J., Silva, Denise B., Marques, Lucas M., Demarque, Daniel P., Pociute, Egle, O'Neill, Ellis C., Briand, Enora, Helfrich, Eric J. N., Granatosky, Eve A., Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J., Zeng, Yi, Vorholt, Julia A., Kurita, Kenji L., Charusanti, Pep, Mcphail, Kerry L., Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F., Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B., Baric, Ralph, Silva, Ricardo R., Mascuch, Samantha J., Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G., Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodriguez, Andres M. C., Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M., Almaliti, Jehad, Allard, Pierre-marie, Phapale, Prasad, Nothias, Louis-felix, Alexandrovr, Theodore, Litaudon, Marc, Wolfender, Jean-luc, Kyle, Jennifer E., Metz, Thomas O., Peryea, Tyler, Dac-trung Nguyen, Vanleer, Danielle, Shinn, Paul, Jadhav, Ajit, Muller, Rolf, Waters, Katrina M., Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R., Palsson, Bernhard O., Pogliano, Kit, Linington, Roger G., Gutierrez, Marcelino, Lopes, Norberto P., Gerwick, William H., Moore, Bradley S., Dorrestein, Pieter C., Bandeira, Nuno, Wang, Mingxun, Carver, Jeremy J., Phelan, Vanessa V., Sanchez, Laura M., Garg, Neha, Peng, Yao, Don Duy Nguyen, Watrous, Jeramie, Kapono, Clifford A., Luzzatto-knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V., Meehan, Michael J., Liu, Wei -ting, Criisemann, Max, Boudreau, Paul D., Esquenazi, Eduardo, Sandoval-calderon, Mario, Kersten, Roland D., Pace, Laura A., Quinn, Robert A., Duncan, Katherine R., Hsu, Cheng-chih, Floros, Dimitrios J., Gavilan, Ronnie G., Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J., Parrot, Delphine, Carlson, Erin E., Aigle, Bertrand, Michelsen, Charlotte F., Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, Mclean, Jeffrey, Piel, Jorn, Murphy, Brian T., Gerwick, Lena, Liaw, Chih-chuang, Yang, Yu-liang, Humpf, Hans-ulrich, Maansson, Maria, Keyzers, Robert A., Sims, Amy C., Johnson, Andrew R., Sidebottom, Ashley M., Sedio, Brian E., Klitgaard, Andreas, Larson, Charles B., Boya P, Cristopher A., Torres-mendoza, Daniel, Gonzalez, David J., Silva, Denise B., Marques, Lucas M., Demarque, Daniel P., Pociute, Egle, O'Neill, Ellis C., Briand, Enora, Helfrich, Eric J. N., Granatosky, Eve A., Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J., Zeng, Yi, Vorholt, Julia A., Kurita, Kenji L., Charusanti, Pep, Mcphail, Kerry L., Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F., Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B., Baric, Ralph, Silva, Ricardo R., Mascuch, Samantha J., Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G., Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodriguez, Andres M. C., Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M., Almaliti, Jehad, Allard, Pierre-marie, Phapale, Prasad, Nothias, Louis-felix, Alexandrovr, Theodore, Litaudon, Marc, Wolfender, Jean-luc, Kyle, Jennifer E., Metz, Thomas O., Peryea, Tyler, Dac-trung Nguyen, Vanleer, Danielle, Shinn, Paul, Jadhav, Ajit, Muller, Rolf, Waters, Katrina M., Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R., Palsson, Bernhard O., Pogliano, Kit, Linington, Roger G., Gutierrez, Marcelino, Lopes, Norberto P., Gerwick, William H., Moore, Bradley S., Dorrestein, Pieter C., and Bandeira, Nuno

Abstract

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Published
2016
Full Text
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18. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

Author

Wang, Mingxun, Wang, Mingxun, Carver, Jeremy J, Phelan, Vanessa V, Sanchez, Laura M, Garg, Neha, Peng, Yao, Nguyen, Don Duy, Watrous, Jeramie, Kapono, Clifford A, Luzzatto-Knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V, Meehan, Michael J, Liu, Wei-Ting, Crüsemann, Max, Boudreau, Paul D, Esquenazi, Eduardo, Sandoval-Calderón, Mario, Kersten, Roland D, Pace, Laura A, Quinn, Robert A, Duncan, Katherine R, Hsu, Cheng-Chih, Floros, Dimitrios J, Gavilan, Ronnie G, Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J, Parrot, Delphine, Carlson, Erin E, Aigle, Bertrand, Michelsen, Charlotte F, Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, McLean, Jeffrey, Piel, Jörn, Murphy, Brian T, Gerwick, Lena, Liaw, Chih-Chuang, Yang, Yu-Liang, Humpf, Hans-Ulrich, Maansson, Maria, Keyzers, Robert A, Sims, Amy C, Johnson, Andrew R, Sidebottom, Ashley M, Sedio, Brian E, Klitgaard, Andreas, Larson, Charles B, P, Cristopher A Boya, Torres-Mendoza, Daniel, Gonzalez, David J, Silva, Denise B, Marques, Lucas M, Demarque, Daniel P, Pociute, Egle, O'Neill, Ellis C, Briand, Enora, Helfrich, Eric JN, Granatosky, Eve A, Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J, Zeng, Yi, Vorholt, Julia A, Kurita, Kenji L, Charusanti, Pep, McPhail, Kerry L, Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F, Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B, Baric, Ralph, Silva, Ricardo R, Mascuch, Samantha J, Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G, Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodríguez, Andrés MC, Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M, Almaliti, Jehad, Allard, Pierre-Marie, Phapale, Prasad, Wang, Mingxun, Wang, Mingxun, Carver, Jeremy J, Phelan, Vanessa V, Sanchez, Laura M, Garg, Neha, Peng, Yao, Nguyen, Don Duy, Watrous, Jeramie, Kapono, Clifford A, Luzzatto-Knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V, Meehan, Michael J, Liu, Wei-Ting, Crüsemann, Max, Boudreau, Paul D, Esquenazi, Eduardo, Sandoval-Calderón, Mario, Kersten, Roland D, Pace, Laura A, Quinn, Robert A, Duncan, Katherine R, Hsu, Cheng-Chih, Floros, Dimitrios J, Gavilan, Ronnie G, Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J, Parrot, Delphine, Carlson, Erin E, Aigle, Bertrand, Michelsen, Charlotte F, Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, McLean, Jeffrey, Piel, Jörn, Murphy, Brian T, Gerwick, Lena, Liaw, Chih-Chuang, Yang, Yu-Liang, Humpf, Hans-Ulrich, Maansson, Maria, Keyzers, Robert A, Sims, Amy C, Johnson, Andrew R, Sidebottom, Ashley M, Sedio, Brian E, Klitgaard, Andreas, Larson, Charles B, P, Cristopher A Boya, Torres-Mendoza, Daniel, Gonzalez, David J, Silva, Denise B, Marques, Lucas M, Demarque, Daniel P, Pociute, Egle, O'Neill, Ellis C, Briand, Enora, Helfrich, Eric JN, Granatosky, Eve A, Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J, Zeng, Yi, Vorholt, Julia A, Kurita, Kenji L, Charusanti, Pep, McPhail, Kerry L, Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F, Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B, Baric, Ralph, Silva, Ricardo R, Mascuch, Samantha J, Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G, Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodríguez, Andrés MC, Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M, Almaliti, Jehad, Allard, Pierre-Marie, and Phapale, Prasad

Abstract

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Published
2016

19. Divergent Biosynthesis Yields a Cytotoxic Aminomalonate-Containing Precolibactin

Author

Li, Zhongrui, Li, Jie, Gu, Jin-Ping, Lai, Jennifer Yuet Ha, Duggan, Brendan M., Zhang, Weipeng, Li, Zhilong, Li, Yongxin, Tong, Rongbiao, Xu, Ying, Lin, Dong-Hai, Moore, Bradley S., Qian, Peiyuan, Li, Zhongrui, Li, Jie, Gu, Jin-Ping, Lai, Jennifer Yuet Ha, Duggan, Brendan M., Zhang, Weipeng, Li, Zhilong, Li, Yongxin, Tong, Rongbiao, Xu, Ying, Lin, Dong-Hai, Moore, Bradley S., and Qian, Peiyuan

Abstract

Colibactin is an as-yet-uncharacterized genotoxic secondary metabolite produced by human gut bacteria. Here we report the biosynthetic discovery of two new precolibactin molecules from Escherichia coli, including precolibactin-886, which uniquely incorporates the highly sought genotoxicity-associated aminomalonate building block into its unprecedented macrocyclic structure. This work provides new insights into the biosynthetic logic and mode of action of this colorectal-cancer-linked microbial chemical.

Published
2016

20. Divergent Biosynthesis Yields a Cytotoxic Aminomalonate-Containing Precolibactin

Author

Li, Zhongrui, Li, Jie, Gu, Jin-Ping, Lai, Jennifer Yuet Ha, Duggan, Brendan M., Zhang, Weipeng, Li, Zhilong, Li, Yongxin, Tong, Rongbiao, Xu, Ying, Lin, Dong-Hai, Moore, Bradley S., Qian, Peiyuan, Li, Zhongrui, Li, Jie, Gu, Jin-Ping, Lai, Jennifer Yuet Ha, Duggan, Brendan M., Zhang, Weipeng, Li, Zhilong, Li, Yongxin, Tong, Rongbiao, Xu, Ying, Lin, Dong-Hai, Moore, Bradley S., and Qian, Peiyuan

Abstract

Colibactin is an as-yet-uncharacterized genotoxic secondary metabolite produced by human gut bacteria. Here we report the biosynthetic discovery of two new precolibactin molecules from Escherichia coli, including precolibactin-886, which uniquely incorporates the highly sought genotoxicity-associated aminomalonate building block into its unprecedented macrocyclic structure. This work provides new insights into the biosynthetic logic and mode of action of this colorectal-cancer-linked microbial chemical.

Published
2016

21. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

Author

Wang, Mingxun, Wang, Mingxun, Carver, Jeremy J, Phelan, Vanessa V, Sanchez, Laura M, Garg, Neha, Peng, Yao, Nguyen, Don Duy, Watrous, Jeramie, Kapono, Clifford A, Luzzatto-Knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V, Meehan, Michael J, Liu, Wei-Ting, Crüsemann, Max, Boudreau, Paul D, Esquenazi, Eduardo, Sandoval-Calderón, Mario, Kersten, Roland D, Pace, Laura A, Quinn, Robert A, Duncan, Katherine R, Hsu, Cheng-Chih, Floros, Dimitrios J, Gavilan, Ronnie G, Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J, Parrot, Delphine, Carlson, Erin E, Aigle, Bertrand, Michelsen, Charlotte F, Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, McLean, Jeffrey, Piel, Jörn, Murphy, Brian T, Gerwick, Lena, Liaw, Chih-Chuang, Yang, Yu-Liang, Humpf, Hans-Ulrich, Maansson, Maria, Keyzers, Robert A, Sims, Amy C, Johnson, Andrew R, Sidebottom, Ashley M, Sedio, Brian E, Klitgaard, Andreas, Larson, Charles B, P, Cristopher A Boya, Torres-Mendoza, Daniel, Gonzalez, David J, Silva, Denise B, Marques, Lucas M, Demarque, Daniel P, Pociute, Egle, O'Neill, Ellis C, Briand, Enora, Helfrich, Eric JN, Granatosky, Eve A, Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J, Zeng, Yi, Vorholt, Julia A, Kurita, Kenji L, Charusanti, Pep, McPhail, Kerry L, Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F, Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B, Baric, Ralph, Silva, Ricardo R, Mascuch, Samantha J, Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G, Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodríguez, Andrés MC, Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M, Almaliti, Jehad, Allard, Pierre-Marie, Phapale, Prasad, Wang, Mingxun, Wang, Mingxun, Carver, Jeremy J, Phelan, Vanessa V, Sanchez, Laura M, Garg, Neha, Peng, Yao, Nguyen, Don Duy, Watrous, Jeramie, Kapono, Clifford A, Luzzatto-Knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V, Meehan, Michael J, Liu, Wei-Ting, Crüsemann, Max, Boudreau, Paul D, Esquenazi, Eduardo, Sandoval-Calderón, Mario, Kersten, Roland D, Pace, Laura A, Quinn, Robert A, Duncan, Katherine R, Hsu, Cheng-Chih, Floros, Dimitrios J, Gavilan, Ronnie G, Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J, Parrot, Delphine, Carlson, Erin E, Aigle, Bertrand, Michelsen, Charlotte F, Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, McLean, Jeffrey, Piel, Jörn, Murphy, Brian T, Gerwick, Lena, Liaw, Chih-Chuang, Yang, Yu-Liang, Humpf, Hans-Ulrich, Maansson, Maria, Keyzers, Robert A, Sims, Amy C, Johnson, Andrew R, Sidebottom, Ashley M, Sedio, Brian E, Klitgaard, Andreas, Larson, Charles B, P, Cristopher A Boya, Torres-Mendoza, Daniel, Gonzalez, David J, Silva, Denise B, Marques, Lucas M, Demarque, Daniel P, Pociute, Egle, O'Neill, Ellis C, Briand, Enora, Helfrich, Eric JN, Granatosky, Eve A, Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J, Zeng, Yi, Vorholt, Julia A, Kurita, Kenji L, Charusanti, Pep, McPhail, Kerry L, Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F, Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B, Baric, Ralph, Silva, Ricardo R, Mascuch, Samantha J, Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G, Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodríguez, Andrés MC, Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M, Almaliti, Jehad, Allard, Pierre-Marie, and Phapale, Prasad

Abstract

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Published
2016

22. The Alga Ochromonas danica Produces Bromosulfolipids.

Author

White, Alexander R, White, Alexander R, Duggan, Brendan M, Tsai, Shiou-Chuan, Vanderwal, Christopher D, White, Alexander R, White, Alexander R, Duggan, Brendan M, Tsai, Shiou-Chuan, and Vanderwal, Christopher D

Abstract

Many halogenases interchangeably incorporate chlorine and bromine into organic molecules. On the basis of an unsubstantiated report that the alga Ochromonas danica, a prodigious producer of chlorosulfolipids, was able to produce bromosulfolipids, we have investigated the promiscuity of its halogenases toward bromine incorporation. We have found that bromosulfolipids are produced with the exact positional and stereochemical selectivity as in the chlorosulfolipid danicalipin A when this alga is grown under modified conditions containing excess bromide ion.

Published
2016

23. Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides.

Author

Nguyen, Don D, Nguyen, Don D, Melnik, Alexey V, Koyama, Nobuhiro, Lu, Xiaowen, Schorn, Michelle, Fang, Jinshu, Aguinaldo, Kristen, Lincecum, Tommie L, Ghequire, Maarten GK, Carrion, Victor J, Cheng, Tina L, Duggan, Brendan M, Malone, Jacob G, Mauchline, Tim H, Sanchez, Laura M, Kilpatrick, A Marm, Raaijmakers, Jos M, De Mot, René, Moore, Bradley S, Medema, Marnix H, Dorrestein, Pieter C, Nguyen, Don D, Nguyen, Don D, Melnik, Alexey V, Koyama, Nobuhiro, Lu, Xiaowen, Schorn, Michelle, Fang, Jinshu, Aguinaldo, Kristen, Lincecum, Tommie L, Ghequire, Maarten GK, Carrion, Victor J, Cheng, Tina L, Duggan, Brendan M, Malone, Jacob G, Mauchline, Tim H, Sanchez, Laura M, Kilpatrick, A Marm, Raaijmakers, Jos M, De Mot, René, Moore, Bradley S, Medema, Marnix H, and Dorrestein, Pieter C

Abstract

Pseudomonads are cosmopolitan microorganisms able to produce a wide array of specialized metabolites. These molecules allow Pseudomonas to scavenge nutrients, sense population density and enhance or inhibit growth of competing microorganisms. However, these valuable metabolites are typically characterized one-molecule-one-microbe at a time, instead of being inventoried in large numbers. To index and map the diversity of molecules detected from these organisms, 260 strains of ecologically diverse origins were subjected to mass-spectrometry-based molecular networking. Molecular networking not only enables dereplication of molecules, but also sheds light on their structural relationships. Moreover, it accelerates the discovery of new molecules. Here, by indexing the Pseudomonas specialized metabolome, we report the molecular-networking-based discovery of four molecules and their evolutionary relationships: a poaeamide analogue and a molecular subfamily of cyclic lipopeptides, bananamides 1, 2 and 3. Analysis of their biosynthetic gene cluster shows that it constitutes a distinct evolutionary branch of the Pseudomonas cyclic lipopeptides. Through analysis of an additional 370 extracts of wheat-associated Pseudomonas, we demonstrate how the detailed knowledge from our reference index can be efficiently propagated to annotate complex metabolomic data from other studies, akin to the way in which newly generated genomic information can be compared to data from public databases.

Published
2016

24. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Author

Wang, Mingxun, Carver, Jeremy J., Phelan, Vanessa V., Sanchez, Laura M., Garg, Neha, Peng, Yao, Don Duy Nguyen, Watrous, Jeramie, Kapono, Clifford A., Luzzatto-knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V., Meehan, Michael J., Liu, Wei -ting, Criisemann, Max, Boudreau, Paul D., Esquenazi, Eduardo, Sandoval-calderon, Mario, Kersten, Roland D., Pace, Laura A., Quinn, Robert A., Duncan, Katherine R., Hsu, Cheng-chih, Floros, Dimitrios J., Gavilan, Ronnie G., Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J., Parrot, Delphine, Carlson, Erin E., Aigle, Bertrand, Michelsen, Charlotte F., Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, Mclean, Jeffrey, Piel, Jorn, Murphy, Brian T., Gerwick, Lena, Liaw, Chih-chuang, Yang, Yu-liang, Humpf, Hans-ulrich, Maansson, Maria, Keyzers, Robert A., Sims, Amy C., Johnson, Andrew R., Sidebottom, Ashley M., Sedio, Brian E., Klitgaard, Andreas, Larson, Charles B., Boya P, Cristopher A., Torres-mendoza, Daniel, Gonzalez, David J., Silva, Denise B., Marques, Lucas M., Demarque, Daniel P., Pociute, Egle, O'Neill, Ellis C., Briand, Enora, Helfrich, Eric J. N., Granatosky, Eve A., Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J., Zeng, Yi, Vorholt, Julia A., Kurita, Kenji L., Charusanti, Pep, Mcphail, Kerry L., Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F., Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B., Baric, Ralph, Silva, Ricardo R., Mascuch, Samantha J., Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G., Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodriguez, Andres M. C., Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M., Almaliti, Jehad, Allard, Pierre-marie, Phapale, Prasad, Nothias, Louis-felix, Alexandrovr, Theodore, Litaudon, Marc, Wolfender, Jean-luc, Kyle, Jennifer E., Metz, Thomas O., Peryea, Tyler, Dac-trung Nguyen, Vanleer, Danielle, Shinn, Paul, Jadhav, Ajit, Muller, Rolf, Waters, Katrina M., Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R., Palsson, Bernhard O., Pogliano, Kit, Linington, Roger G., Gutierrez, Marcelino, Lopes, Norberto P., Gerwick, William H., Moore, Bradley S., Dorrestein, Pieter C., Bandeira, Nuno, Wang, Mingxun, Carver, Jeremy J., Phelan, Vanessa V., Sanchez, Laura M., Garg, Neha, Peng, Yao, Don Duy Nguyen, Watrous, Jeramie, Kapono, Clifford A., Luzzatto-knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V., Meehan, Michael J., Liu, Wei -ting, Criisemann, Max, Boudreau, Paul D., Esquenazi, Eduardo, Sandoval-calderon, Mario, Kersten, Roland D., Pace, Laura A., Quinn, Robert A., Duncan, Katherine R., Hsu, Cheng-chih, Floros, Dimitrios J., Gavilan, Ronnie G., Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J., Parrot, Delphine, Carlson, Erin E., Aigle, Bertrand, Michelsen, Charlotte F., Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, Mclean, Jeffrey, Piel, Jorn, Murphy, Brian T., Gerwick, Lena, Liaw, Chih-chuang, Yang, Yu-liang, Humpf, Hans-ulrich, Maansson, Maria, Keyzers, Robert A., Sims, Amy C., Johnson, Andrew R., Sidebottom, Ashley M., Sedio, Brian E., Klitgaard, Andreas, Larson, Charles B., Boya P, Cristopher A., Torres-mendoza, Daniel, Gonzalez, David J., Silva, Denise B., Marques, Lucas M., Demarque, Daniel P., Pociute, Egle, O'Neill, Ellis C., Briand, Enora, Helfrich, Eric J. N., Granatosky, Eve A., Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J., Zeng, Yi, Vorholt, Julia A., Kurita, Kenji L., Charusanti, Pep, Mcphail, Kerry L., Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F., Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B., Baric, Ralph, Silva, Ricardo R., Mascuch, Samantha J., Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G., Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodriguez, Andres M. C., Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M., Almaliti, Jehad, Allard, Pierre-marie, Phapale, Prasad, Nothias, Louis-felix, Alexandrovr, Theodore, Litaudon, Marc, Wolfender, Jean-luc, Kyle, Jennifer E., Metz, Thomas O., Peryea, Tyler, Dac-trung Nguyen, Vanleer, Danielle, Shinn, Paul, Jadhav, Ajit, Muller, Rolf, Waters, Katrina M., Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R., Palsson, Bernhard O., Pogliano, Kit, Linington, Roger G., Gutierrez, Marcelino, Lopes, Norberto P., Gerwick, William H., Moore, Bradley S., Dorrestein, Pieter C., and Bandeira, Nuno

Abstract

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Published
2016
Full Text
View/download PDF

25. Divergent biosynthesis yields a cytotoxic aminomalonate-containing precolibactin.

Author

Li, Zhong-Rui, Li, Zhong-Rui, Li, Jie, Gu, Jin-Ping, Lai, Jennifer YH, Duggan, Brendan M, Zhang, Wei-Peng, Li, Zhi-Long, Li, Yong-Xin, Tong, Rong-Biao, Xu, Ying, Lin, Dong-Hai, Moore, Bradley S, Qian, Pei-Yuan, Li, Zhong-Rui, Li, Zhong-Rui, Li, Jie, Gu, Jin-Ping, Lai, Jennifer YH, Duggan, Brendan M, Zhang, Wei-Peng, Li, Zhi-Long, Li, Yong-Xin, Tong, Rong-Biao, Xu, Ying, Lin, Dong-Hai, Moore, Bradley S, and Qian, Pei-Yuan

Abstract

Colibactin is an as-yet-uncharacterized genotoxic secondary metabolite produced by human gut bacteria. Here we report the biosynthetic discovery of two new precolibactin molecules from Escherichia coli, including precolibactin-886, which uniquely incorporates the highly sought genotoxicity-associated aminomalonate building block into its unprecedented macrocyclic structure. This work provides new insights into the biosynthetic logic and mode of action of this colorectal-cancer-linked microbial chemical.

Published
2016

26. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Author

Wang, Mingxun, Carver, Jeremy J, Phelan, Vanessa V, Sanchez, Laura M, Garg, Neha, Peng, Yao, Nguyen, Don Duy, Watrous, Jeramie, Kapono, Clifford A, Luzzatto-Knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V, Meehan, Michael J, Liu, Wei-Ting, Crüsemann, Max, Boudreau, Paul D, Esquenazi, Eduardo, Sandoval-Calderón, Mario, Kersten, Roland D, Pace, Laura A, Quinn, Robert A, Duncan, Katherine R, Hsu, Cheng-Chih, Floros, Dimitrios J, Gavilan, Ronnie G, Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J, Parrot, Delphine, Carlson, Erin E, Aigle, Bertrand, Michelsen, Charlotte F, Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, McLean, Jeffrey, Piel, Jörn, Murphy, Brian T, Gerwick, Lena, Liaw, Chih-Chuang, Yang, Yu-Liang, Humpf, Hans-Ulrich, Maansson, Maria, Keyzers, Robert A, Sims, Amy C, Johnson, Andrew R, Sidebottom, Ashley M, Sedio, Brian E, Klitgaard, Andreas, Larson, Charles B, Boya P, Cristopher A, Torres-Mendoza, Daniel, Gonzalez, David J, Silva, Denise B, Marques, Lucas M, Demarque, Daniel P, Pociute, Egle, O'Neill, Ellis C, Briand, Enora, Helfrich, Eric J N, Granatosky, Eve A, Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J, Zeng, Yi, Vorholt, Julia A, Kurita, Kenji L, Charusanti, Pep, McPhail, Kerry L, Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F, Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B, Baric, Ralph, Silva, Ricardo R, Mascuch, Samantha J, Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G, Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodríguez, Andrés M C, Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M, Almaliti, Jehad, Allard, Pierre-Marie, Phapale, Prasad, Nothias, Louis-Felix, Alexandrov, Theodore, Litaudon, Marc, Wolfender, Jean-Luc, Kyle, Jennifer E, Metz, Thomas O, Peryea, Tyler, Nguyen, Dac-Trung, VanLeer, Danielle, Shinn, Paul, Jadhav, Ajit, Müller, Rolf, Waters, Katrina M, Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R, Palsson, Bernhard Ø, Pogliano, Kit, Linington, Roger G, Gutiérrez, Marcelino, Lopes, Norberto P, Gerwick, William H, Moore, Bradley S, Dorrestein, Pieter C, Bandeira, Nuno, Wang, Mingxun, Carver, Jeremy J, Phelan, Vanessa V, Sanchez, Laura M, Garg, Neha, Peng, Yao, Nguyen, Don Duy, Watrous, Jeramie, Kapono, Clifford A, Luzzatto-Knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V, Meehan, Michael J, Liu, Wei-Ting, Crüsemann, Max, Boudreau, Paul D, Esquenazi, Eduardo, Sandoval-Calderón, Mario, Kersten, Roland D, Pace, Laura A, Quinn, Robert A, Duncan, Katherine R, Hsu, Cheng-Chih, Floros, Dimitrios J, Gavilan, Ronnie G, Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J, Parrot, Delphine, Carlson, Erin E, Aigle, Bertrand, Michelsen, Charlotte F, Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, McLean, Jeffrey, Piel, Jörn, Murphy, Brian T, Gerwick, Lena, Liaw, Chih-Chuang, Yang, Yu-Liang, Humpf, Hans-Ulrich, Maansson, Maria, Keyzers, Robert A, Sims, Amy C, Johnson, Andrew R, Sidebottom, Ashley M, Sedio, Brian E, Klitgaard, Andreas, Larson, Charles B, Boya P, Cristopher A, Torres-Mendoza, Daniel, Gonzalez, David J, Silva, Denise B, Marques, Lucas M, Demarque, Daniel P, Pociute, Egle, O'Neill, Ellis C, Briand, Enora, Helfrich, Eric J N, Granatosky, Eve A, Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J, Zeng, Yi, Vorholt, Julia A, Kurita, Kenji L, Charusanti, Pep, McPhail, Kerry L, Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F, Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B, Baric, Ralph, Silva, Ricardo R, Mascuch, Samantha J, Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G, Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodríguez, Andrés M C, Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M, Almaliti, Jehad, Allard, Pierre-Marie, Phapale, Prasad, Nothias, Louis-Felix, Alexandrov, Theodore, Litaudon, Marc, Wolfender, Jean-Luc, Kyle, Jennifer E, Metz, Thomas O, Peryea, Tyler, Nguyen, Dac-Trung, VanLeer, Danielle, Shinn, Paul, Jadhav, Ajit, Müller, Rolf, Waters, Katrina M, Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R, Palsson, Bernhard Ø, Pogliano, Kit, Linington, Roger G, Gutiérrez, Marcelino, Lopes, Norberto P, Gerwick, William H, Moore, Bradley S, Dorrestein, Pieter C, and Bandeira, Nuno

Abstract

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Published
2016
Full Text
View/download PDF

27. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Author

Wang, Mingxun, Carver, Jeremy J., Phelan, Vanessa V., Sanchez, Laura M., Garg, Neha, Peng, Yao, Don Duy Nguyen, Watrous, Jeramie, Kapono, Clifford A., Luzzatto-knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V., Meehan, Michael J., Liu, Wei -ting, Criisemann, Max, Boudreau, Paul D., Esquenazi, Eduardo, Sandoval-calderon, Mario, Kersten, Roland D., Pace, Laura A., Quinn, Robert A., Duncan, Katherine R., Hsu, Cheng-chih, Floros, Dimitrios J., Gavilan, Ronnie G., Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J., Parrot, Delphine, Carlson, Erin E., Aigle, Bertrand, Michelsen, Charlotte F., Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, Mclean, Jeffrey, Piel, Jorn, Murphy, Brian T., Gerwick, Lena, Liaw, Chih-chuang, Yang, Yu-liang, Humpf, Hans-ulrich, Maansson, Maria, Keyzers, Robert A., Sims, Amy C., Johnson, Andrew R., Sidebottom, Ashley M., Sedio, Brian E., Klitgaard, Andreas, Larson, Charles B., Boya P, Cristopher A., Torres-mendoza, Daniel, Gonzalez, David J., Silva, Denise B., Marques, Lucas M., Demarque, Daniel P., Pociute, Egle, O'Neill, Ellis C., Briand, Enora, Helfrich, Eric J. N., Granatosky, Eve A., Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J., Zeng, Yi, Vorholt, Julia A., Kurita, Kenji L., Charusanti, Pep, Mcphail, Kerry L., Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F., Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B., Baric, Ralph, Silva, Ricardo R., Mascuch, Samantha J., Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G., Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodriguez, Andres M. C., Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M., Almaliti, Jehad, Allard, Pierre-marie, Phapale, Prasad, Nothias, Louis-felix, Alexandrovr, Theodore, Litaudon, Marc, Wolfender, Jean-luc, Kyle, Jennifer E., Metz, Thomas O., Peryea, Tyler, Dac-trung Nguyen, Vanleer, Danielle, Shinn, Paul, Jadhav, Ajit, Muller, Rolf, Waters, Katrina M., Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R., Palsson, Bernhard O., Pogliano, Kit, Linington, Roger G., Gutierrez, Marcelino, Lopes, Norberto P., Gerwick, William H., Moore, Bradley S., Dorrestein, Pieter C., Bandeira, Nuno, Wang, Mingxun, Carver, Jeremy J., Phelan, Vanessa V., Sanchez, Laura M., Garg, Neha, Peng, Yao, Don Duy Nguyen, Watrous, Jeramie, Kapono, Clifford A., Luzzatto-knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V., Meehan, Michael J., Liu, Wei -ting, Criisemann, Max, Boudreau, Paul D., Esquenazi, Eduardo, Sandoval-calderon, Mario, Kersten, Roland D., Pace, Laura A., Quinn, Robert A., Duncan, Katherine R., Hsu, Cheng-chih, Floros, Dimitrios J., Gavilan, Ronnie G., Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J., Parrot, Delphine, Carlson, Erin E., Aigle, Bertrand, Michelsen, Charlotte F., Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, Mclean, Jeffrey, Piel, Jorn, Murphy, Brian T., Gerwick, Lena, Liaw, Chih-chuang, Yang, Yu-liang, Humpf, Hans-ulrich, Maansson, Maria, Keyzers, Robert A., Sims, Amy C., Johnson, Andrew R., Sidebottom, Ashley M., Sedio, Brian E., Klitgaard, Andreas, Larson, Charles B., Boya P, Cristopher A., Torres-mendoza, Daniel, Gonzalez, David J., Silva, Denise B., Marques, Lucas M., Demarque, Daniel P., Pociute, Egle, O'Neill, Ellis C., Briand, Enora, Helfrich, Eric J. N., Granatosky, Eve A., Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J., Zeng, Yi, Vorholt, Julia A., Kurita, Kenji L., Charusanti, Pep, Mcphail, Kerry L., Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F., Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B., Baric, Ralph, Silva, Ricardo R., Mascuch, Samantha J., Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G., Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodriguez, Andres M. C., Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M., Almaliti, Jehad, Allard, Pierre-marie, Phapale, Prasad, Nothias, Louis-felix, Alexandrovr, Theodore, Litaudon, Marc, Wolfender, Jean-luc, Kyle, Jennifer E., Metz, Thomas O., Peryea, Tyler, Dac-trung Nguyen, Vanleer, Danielle, Shinn, Paul, Jadhav, Ajit, Muller, Rolf, Waters, Katrina M., Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R., Palsson, Bernhard O., Pogliano, Kit, Linington, Roger G., Gutierrez, Marcelino, Lopes, Norberto P., Gerwick, William H., Moore, Bradley S., Dorrestein, Pieter C., and Bandeira, Nuno

Abstract

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Published
2016
Full Text
View/download PDF

28. Divergent Biosynthesis Yields a Cytotoxic Aminomalonate-Containing Precolibactin

Author

Li, Zhongrui, Li, Jie, Gu, Jin-Ping, Lai, Jennifer Yuet Ha, Duggan, Brendan M., Zhang, Weipeng, Li, Zhilong, Li, Yongxin, Tong, Rongbiao, Xu, Ying, Lin, Dong-Hai, Moore, Bradley S., Qian, Peiyuan, Li, Zhongrui, Li, Jie, Gu, Jin-Ping, Lai, Jennifer Yuet Ha, Duggan, Brendan M., Zhang, Weipeng, Li, Zhilong, Li, Yongxin, Tong, Rongbiao, Xu, Ying, Lin, Dong-Hai, Moore, Bradley S., and Qian, Peiyuan

Abstract

Colibactin is an as-yet-uncharacterized genotoxic secondary metabolite produced by human gut bacteria. Here we report the biosynthetic discovery of two new precolibactin molecules from Escherichia coli, including precolibactin-886, which uniquely incorporates the highly sought genotoxicity-associated aminomalonate building block into its unprecedented macrocyclic structure. This work provides new insights into the biosynthetic logic and mode of action of this colorectal-cancer-linked microbial chemical.

Published
2016

29. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Author

Wang, Mingxun, Carver, Jeremy J, Phelan, Vanessa V, Sanchez, Laura M, Garg, Neha, Peng, Yao, Nguyen, Don Duy, Watrous, Jeramie, Kapono, Clifford A, Luzzatto-Knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V, Meehan, Michael J, Liu, Wei-Ting, Crüsemann, Max, Boudreau, Paul D, Esquenazi, Eduardo, Sandoval-Calderón, Mario, Kersten, Roland D, Pace, Laura A, Quinn, Robert A, Duncan, Katherine R, Hsu, Cheng-Chih, Floros, Dimitrios J, Gavilan, Ronnie G, Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J, Parrot, Delphine, Carlson, Erin E, Aigle, Bertrand, Michelsen, Charlotte F, Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, McLean, Jeffrey, Piel, Jörn, Murphy, Brian T, Gerwick, Lena, Liaw, Chih-Chuang, Yang, Yu-Liang, Humpf, Hans-Ulrich, Maansson, Maria, Keyzers, Robert A, Sims, Amy C, Johnson, Andrew R, Sidebottom, Ashley M, Sedio, Brian E, Klitgaard, Andreas, Larson, Charles B, Boya P, Cristopher A, Torres-Mendoza, Daniel, Gonzalez, David J, Silva, Denise B, Marques, Lucas M, Demarque, Daniel P, Pociute, Egle, O'Neill, Ellis C, Briand, Enora, Helfrich, Eric J N, Granatosky, Eve A, Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J, Zeng, Yi, Vorholt, Julia A, Kurita, Kenji L, Charusanti, Pep, McPhail, Kerry L, Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F, Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B, Baric, Ralph, Silva, Ricardo R, Mascuch, Samantha J, Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G, Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodríguez, Andrés M C, Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M, Almaliti, Jehad, Allard, Pierre-Marie, Phapale, Prasad, Nothias, Louis-Felix, Alexandrov, Theodore, Litaudon, Marc, Wolfender, Jean-Luc, Kyle, Jennifer E, Metz, Thomas O, Peryea, Tyler, Nguyen, Dac-Trung, VanLeer, Danielle, Shinn, Paul, Jadhav, Ajit, Müller, Rolf, Waters, Katrina M, Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R, Palsson, Bernhard Ø, Pogliano, Kit, Linington, Roger G, Gutiérrez, Marcelino, Lopes, Norberto P, Gerwick, William H, Moore, Bradley S, Dorrestein, Pieter C, Bandeira, Nuno, Wang, Mingxun, Carver, Jeremy J, Phelan, Vanessa V, Sanchez, Laura M, Garg, Neha, Peng, Yao, Nguyen, Don Duy, Watrous, Jeramie, Kapono, Clifford A, Luzzatto-Knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V, Meehan, Michael J, Liu, Wei-Ting, Crüsemann, Max, Boudreau, Paul D, Esquenazi, Eduardo, Sandoval-Calderón, Mario, Kersten, Roland D, Pace, Laura A, Quinn, Robert A, Duncan, Katherine R, Hsu, Cheng-Chih, Floros, Dimitrios J, Gavilan, Ronnie G, Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J, Parrot, Delphine, Carlson, Erin E, Aigle, Bertrand, Michelsen, Charlotte F, Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, McLean, Jeffrey, Piel, Jörn, Murphy, Brian T, Gerwick, Lena, Liaw, Chih-Chuang, Yang, Yu-Liang, Humpf, Hans-Ulrich, Maansson, Maria, Keyzers, Robert A, Sims, Amy C, Johnson, Andrew R, Sidebottom, Ashley M, Sedio, Brian E, Klitgaard, Andreas, Larson, Charles B, Boya P, Cristopher A, Torres-Mendoza, Daniel, Gonzalez, David J, Silva, Denise B, Marques, Lucas M, Demarque, Daniel P, Pociute, Egle, O'Neill, Ellis C, Briand, Enora, Helfrich, Eric J N, Granatosky, Eve A, Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J, Zeng, Yi, Vorholt, Julia A, Kurita, Kenji L, Charusanti, Pep, McPhail, Kerry L, Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F, Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B, Baric, Ralph, Silva, Ricardo R, Mascuch, Samantha J, Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G, Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodríguez, Andrés M C, Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M, Almaliti, Jehad, Allard, Pierre-Marie, Phapale, Prasad, Nothias, Louis-Felix, Alexandrov, Theodore, Litaudon, Marc, Wolfender, Jean-Luc, Kyle, Jennifer E, Metz, Thomas O, Peryea, Tyler, Nguyen, Dac-Trung, VanLeer, Danielle, Shinn, Paul, Jadhav, Ajit, Müller, Rolf, Waters, Katrina M, Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R, Palsson, Bernhard Ø, Pogliano, Kit, Linington, Roger G, Gutiérrez, Marcelino, Lopes, Norberto P, Gerwick, William H, Moore, Bradley S, Dorrestein, Pieter C, and Bandeira, Nuno

Abstract

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Published
2016
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30. MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus.

Author

Liu, Wei-Ting, Liu, Wei-Ting, Lamsa, Anne, Wong, Weng Ruh, Boudreau, Paul D, Kersten, Roland, Peng, Yao, Moree, Wilna J, Duggan, Brendan M, Moore, Bradley S, Gerwick, William H, Linington, Roger G, Pogliano, Kit, Dorrestein, Pieter C, Liu, Wei-Ting, Liu, Wei-Ting, Lamsa, Anne, Wong, Weng Ruh, Boudreau, Paul D, Kersten, Roland, Peng, Yao, Moree, Wilna J, Duggan, Brendan M, Moore, Bradley S, Gerwick, William H, Linington, Roger G, Pogliano, Kit, and Dorrestein, Pieter C

Abstract

Most (75%) of the anti-infectives that save countless lives and enormously improve quality of life originate from microbes found in nature. Herein, we described a global visualization of the detectable molecules produced from a single microorganism, which we define as the 'molecular network' of that organism, followed by studies to characterize the cellular effects of antibacterial molecules. We demonstrate that Streptomyces roseosporus produces at least four non-ribosomal peptide synthetase-derived molecular families and their gene subnetworks (daptomycin, arylomycin, napsamycin and stenothricin) were identified with different modes of action. A number of previously unreported analogs involving truncation, glycosylation, hydrolysis and biosynthetic intermediates and/or shunt products were also captured and visualized by creation of a map through MS/MS networking. The diversity of antibacterial compounds produced by S. roseosporus highlights the importance of developing new approaches to characterize the molecular capacity of an organism in a more global manner. This allows one to more deeply interrogate the biosynthetic capacities of microorganisms with the goal to streamline the discovery pipeline for biotechnological applications in agriculture and medicine. This is a contribution to a special issue to honor Chris Walsh's amazing career.

Published
2014

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