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Hou R, Li K, Guo B, Zhao Y, Li C, Tang B, Sun W, Wang B, Chen W, Sheng C, Kan J, Zhao Y, Liu F. Antifungal Compound from the Predatory Bacterium Lysobacter enzymogenes Inhibits a Plant Pathogenic Fungus by Targeting the AAA ATPase VpVeb1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15003-15016. [PMID: 37812568 DOI: 10.1021/acs.jafc.3c06262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Heat-stable antifungal factor (HSAF) isolated from Lysobacter enzymogenes is considered a potential biocontrol agent. However, the target of HSAF in phytopathogenic fungi remains unclear. In this study, we investigated the target of HSAF in Valsa pyri that causes fatal pear Valsa canker. Thirty-one HSAF-binding proteins were captured and identified by surface plasmon resonance (SPR) and high-performance liquid chromatography-mass spectrometry (LC-MS/MS), and 11 deletion mutants were obtained. Among these mutants, only ΔVpVEB1 showed decreased sensitivity to HSAF. Additionally, ΔVpVEB1 exhibited significantly reduced virulence in V. pyri. Molecular docking and SPR results revealed that HSAF bound to threonine 569 and glycine 570 of VpVeb1, which are crucial for AAA ATPase activity. Another study showed that HSAF could decrease the ATPase activity of VpVeb1, leading to the reduced virulence of V. pyri. Taken together, this study first identified the potential target of HSAF in fungi. These findings will help us better understand the model of action of HSAF to fungi.
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Affiliation(s)
- Rongxian Hou
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Kaihuai Li
- Department of Plant Pathology/Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P. R. China
| | - Baodian Guo
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P. R. China
| | - Yangyang Zhao
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P. R. China
| | - Chaohui Li
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P. R. China
| | - Bao Tang
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P. R. China
| | - Weibo Sun
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P. R. China
| | - Bo Wang
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P. R. China
| | - Wenchan Chen
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P. R. China
| | - Cong Sheng
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P. R. China
| | - Jialiang Kan
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P. R. China
| | - Yancun Zhao
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P. R. China
| | - Fengquan Liu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Department of Plant Pathology/Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P. R. China
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P. R. China
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2
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Ngo-Mback MNL, Zeuko'o Menkem E, Marco HG. Antifungal Compounds from Microbial Symbionts Associated with Aquatic Animals and Cellular Targets: A Review. Pathogens 2023; 12:pathogens12040617. [PMID: 37111503 PMCID: PMC10142389 DOI: 10.3390/pathogens12040617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Fungal infections continue to be a serious public health problem, leading to an estimated 1.6 million deaths annually. It remains a major cause of mortality for people with a weak or affected immune system, such as those suffering from cancer under aggressive chemotherapies. On the other hand, pathogenic fungi are counted among the most destructive factors affecting crops, causing a third of all food crop losses annually and critically affecting the worldwide economy and food security. However, the limited number currently available and the cytotoxicity of the conventional antifungal drugs, which are not yet properly diversified in terms of mode of action, in addition to resistance phenomena, make the search for new antifungals imperative to improve both human health and food protection. Symbiosis has been a crucial alternative for drug discovery, through which many antimicrobials have been discovered. This review highlights some antifungal models of a defensive symbiosis of microbial symbiont natural products derived from interacting with aquatic animals as one of the best opportunities. Some recorded compounds with supposed novel cell targets such as apoptosis could lead to the development of a multitherapy involving the mutual treatment of fungal infections and other metabolic diseases involving apoptosis in their pathogenesis pathways.
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Affiliation(s)
| | | | - Heather G Marco
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
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3
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Robbins N, Ketela T, Kim SH, Cowen LE. Chemical-Genetic Approaches for Exploring Mode of Action of Antifungal Compounds in the Fungal Pathogen Candida albicans. Methods Mol Biol 2023; 2658:145-165. [PMID: 37024700 PMCID: PMC11019913 DOI: 10.1007/978-1-0716-3155-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Candida albicans is a prevalent fungal pathogen of humans that can cause both superficial and life-threatening disease, primarily in immunocompromised populations. Currently, antifungal drug classes available to treat fungal infections remain limited and the emergence of drug-resistant strains threatens antifungal efficacy, necessitating the discovery and development of additional therapeutics. The construction of the C. albicans double-barcoded heterozygous deletion collection (DBC) enables the rapid and systematic assessment of haploinsufficiency phenotypes in a pooled format. Specifically, this functional genomics resource can be used to identify heterozygous deletion mutants that are hypersensitive to compounds in order to define putative cellular targets and/or other modifiers of compound activity. Here, we describe protocols to characterize the mode of action of small molecules using the C. albicans DBC, including how to prepare compound-treated cultures, isolate genomic DNA, amplify strain-specific barcodes, and prepare DNA libraries for high-throughput sequencing. This technique provides a powerful approach to elucidate the compound mechanism of action in order to bolster the antifungal pipeline.
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Affiliation(s)
- Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Troy Ketela
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sang Hu Kim
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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4
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Vanacloig-Pedros E, Fisher KJ, Liu L, Debrauske DJ, Young MKM, Place M, Hittinger CT, Sato TK, Gasch AP. Comparative chemical genomic profiling across plant-based hydrolysate toxins reveals widespread antagonism in fitness contributions. FEMS Yeast Res 2022; 21:6650360. [PMID: 35883225 PMCID: PMC9508847 DOI: 10.1093/femsyr/foac036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/06/2022] [Accepted: 07/21/2022] [Indexed: 11/15/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae has been used extensively in fermentative industrial processes, including biofuel production from sustainable plant-based hydrolysates. Myriad toxins and stressors found in hydrolysates inhibit microbial metabolism and product formation. Overcoming these stresses requires mitigation strategies that include strain engineering. To identify shared and divergent mechanisms of toxicity and to implicate gene targets for genetic engineering, we used a chemical genomic approach to study fitness effects across a library of S. cerevisiae deletion mutants cultured anaerobically in dozens of individual compounds found in different types of hydrolysates. Relationships in chemical genomic profiles identified classes of toxins that provoked similar cellular responses, spanning inhibitor relationships that were not expected from chemical classification. Our results also revealed widespread antagonistic effects across inhibitors, such that the same gene deletions were beneficial for surviving some toxins but detrimental for others. This work presents a rich dataset relating gene function to chemical compounds, which both expands our understanding of plant-based hydrolysates and provides a useful resource to identify engineering targets.
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Affiliation(s)
- Elena Vanacloig-Pedros
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Kaitlin J Fisher
- Laboratory of Genetics, University of Wisconsin-Madison, 53706, Madison, WI, United States
- Center for Genomic Science Innovation, University of Wisconsin-Madison, 53706, Madison, WI, United States
- J.F. Crow Institute for the Study of Evolution, 53706, Madison, WI, United States
| | - Lisa Liu
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Derek J Debrauske
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Megan K M Young
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Michael Place
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
- Laboratory of Genetics, University of Wisconsin-Madison, 53706, Madison, WI, United States
- Center for Genomic Science Innovation, University of Wisconsin-Madison, 53706, Madison, WI, United States
- J.F. Crow Institute for the Study of Evolution, 53706, Madison, WI, United States
| | - Trey K Sato
- Corresponding author: Trey K. Sato, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 4117 Wisconsin Energy Institute, 1552 University Ave, Madison, WI 53726. Tel: (608) 890-2546; E-mail:
| | - Audrey P Gasch
- Corresponding author: Audrey P. Gasch, Center for Genomic Science Innovation, University of Wisconsin-Madison, 3422 Genetics-Biotechnology Center, 425 Henry Mall, Madison, WI 53704, United States. Tel: (608)265-0859; E-mail:
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5
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El Barnossi A, Moussaid F, Iraqi Housseini A. Tangerine, banana and pomegranate peels valorisation for sustainable environment: A review. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 29:e00574. [PMID: 33376681 PMCID: PMC7758358 DOI: 10.1016/j.btre.2020.e00574] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/01/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022]
Abstract
Over the last decade the world has been generating a high quantity of tangerine peel waste (TPW), pomegranate peel waste (PPW) and banana peel waste (BPW). These peels have several economic benefits but there is mismanagement or inappropriate valorisation that could present risks to environment and public health. In the current review, we discussed the use of TPW, PPW and BPW directly for animal feed, soil fertilization, specific compost production and bio-adsorbent. We also discussed the valorisation of these peels for manufacturing the value-added products including enzymes, essential oil and other products that can be used in human food, in medical and cosmetic industry. Additionally, recent studies concerning the valorisation of these peels by biorefinery for bioethanol, biogas and biohydrogen production have been discussed. In the same context some other recent studies about valorisation of microorganisms isolated from these peels for medical, agronomic and industrial interests have been also discussed.
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Affiliation(s)
- Azeddin El Barnossi
- Laboratory of Biotechnology, Environment, Agri-Food and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohammed Ben Abdellah University, Fez, Morocco
| | - Fatimazhrae Moussaid
- Laboratory of Biotechnology, Environment, Agri-Food and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohammed Ben Abdellah University, Fez, Morocco
| | - Abdelilah Iraqi Housseini
- Laboratory of Biotechnology, Environment, Agri-Food and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohammed Ben Abdellah University, Fez, Morocco
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6
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Liang Z, Zhang P, Fang Z. Modern technologies for extraction of aroma compounds from fruit peels: a review. Crit Rev Food Sci Nutr 2020; 62:1284-1307. [PMID: 33124893 DOI: 10.1080/10408398.2020.1840333] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Fruit peel is an agricultural by-product and potential source to extract natural aroma compounds with low cost. In the past few decades, the extraction of plant aroma volatiles experienced a transition from traditional to modern technologies. This review summarizes the main aroma compounds in different fruit peels, evaluates modern extraction techniques applicable for these aroma compounds in terms of mechanism, procedure, merits and demerits, and practice. Additionally, the applications of fruit peel aroma extract in food, pharmaceutical and cosmetic industries are also discussed. This review provides comprehensive information for extraction and application of aroma compounds from fruit peels, which could facilitate the valorization of the agricultural by-products and reduce environmental impacts.
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Affiliation(s)
- Zijian Liang
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Pangzhen Zhang
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Zhongxiang Fang
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
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7
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Wilkinson IVL, Terstappen GC, Russell AJ. Combining experimental strategies for successful target deconvolution. Drug Discov Today 2020; 25:S1359-6446(20)30373-1. [PMID: 32971235 DOI: 10.1016/j.drudis.2020.09.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/10/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023]
Abstract
Investment in phenotypic drug discovery has led to increased demand for rapid and robust target deconvolution to aid successful drug development. Although methods for target identification and mechanism of action (MoA) discovery are flourishing, they typically lead to lists of putative targets. Validating which target(s) are involved in the therapeutic mechanism of a compound poses a significant challenge, requiring direct binding, target engagement, and functional studies in relevant physiological contexts. A combination of orthogonal approaches can allow target identification beyond the proteome as well as aid prioritisation for resource-intensive target validation studies.
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Affiliation(s)
- Isabel V L Wilkinson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Georg C Terstappen
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3PQ, UK
| | - Angela J Russell
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK; Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3PQ, UK.
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8
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Xue A, Robbins N, Cowen LE. Advances in fungal chemical genomics for the discovery of new antifungal agents. Ann N Y Acad Sci 2020; 1496:5-22. [PMID: 32860238 DOI: 10.1111/nyas.14484] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/09/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022]
Abstract
Invasive fungal infections have escalated from a rare curiosity to a major cause of human mortality around the globe. This is in part due to a scarcity in the number of antifungal drugs available to combat mycotic disease, making the discovery of novel bioactive compounds and determining their mode of action of utmost importance. The development and application of chemical genomic assays using the model yeast Saccharomyces cerevisiae has provided powerful methods to identify the mechanism of action of diverse molecules in a living cell. Furthermore, complementary assays are continually being developed in fungal pathogens, most notably Candida albicans and Cryptococcus neoformans, to elucidate compound mechanism of action directly in the pathogen of interest. Collectively, the suite of chemical genetic assays that have been developed in multiple fungal species enables the identification of candidate drug target genes, as well as genes involved in buffering drug target pathways, and genes involved in general cellular responses to small molecules. In this review, we examine current yeast chemical genomic assays and highlight how such resources provide powerful tools that can be utilized to bolster the antifungal pipeline.
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Affiliation(s)
- Alice Xue
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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9
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Benslimane Y, Bertomeu T, Coulombe-Huntington J, McQuaid M, Sánchez-Osuna M, Papadopoli D, Avizonis D, Russo MDST, Huard C, Topisirovic I, Wurtele H, Tyers M, Harrington L. Genome-Wide Screens Reveal that Resveratrol Induces Replicative Stress in Human Cells. Mol Cell 2020; 79:846-856.e8. [PMID: 32755594 DOI: 10.1016/j.molcel.2020.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 05/12/2020] [Accepted: 07/07/2020] [Indexed: 12/26/2022]
Abstract
Resveratrol is a natural product associated with wide-ranging effects in animal and cellular models, including lifespan extension. To identify the genetic target of resveratrol in human cells, we conducted genome-wide CRISPR-Cas9 screens to pinpoint genes that confer sensitivity or resistance to resveratrol. An extensive network of DNA damage response and replicative stress genes exhibited genetic interactions with resveratrol and its analog pterostilbene. These genetic profiles showed similarity to the response to hydroxyurea, an inhibitor of ribonucleotide reductase that causes replicative stress. Resveratrol, pterostilbene, and hydroxyurea caused similar depletion of nucleotide pools, inhibition of replication fork progression, and induction of replicative stress. The ability of resveratrol to inhibit cell proliferation and S phase transit was independent of the histone deacetylase sirtuin 1, which has been implicated in lifespan extension by resveratrol. These results establish that a primary impact of resveratrol on human cell proliferation is the induction of low-level replicative stress.
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Affiliation(s)
- Yahya Benslimane
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada
| | - Thierry Bertomeu
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada
| | - Jasmin Coulombe-Huntington
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada
| | - Mary McQuaid
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montréal, QC H1T 2M4, Canada
| | - María Sánchez-Osuna
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada
| | - David Papadopoli
- Gerald Bronfman Department of Oncology, Departments of Biochemistry and Experimental Medicine and Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC H3T 1E2, Canada
| | - Daina Avizonis
- Goodman Cancer Research Center, Metabolomics Core Facility, 1160 Pine Avenue West, Room 418, Montréal, QC H3A 1A3, Canada
| | - Mariana De Sa Tavares Russo
- Goodman Cancer Research Center, Metabolomics Core Facility, 1160 Pine Avenue West, Room 418, Montréal, QC H3A 1A3, Canada
| | - Caroline Huard
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada
| | - Ivan Topisirovic
- Gerald Bronfman Department of Oncology, Departments of Biochemistry and Experimental Medicine and Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC H3T 1E2, Canada
| | - Hugo Wurtele
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montréal, QC H1T 2M4, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada
| | - Lea Harrington
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada.
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Imipridone Anticancer Compounds Ectopically Activate the ClpP Protease and Represent a New Scaffold for Antibiotic Development. Genetics 2020; 214:1103-1120. [PMID: 32094149 PMCID: PMC7153937 DOI: 10.1534/genetics.119.302851] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/06/2020] [Indexed: 11/18/2022] Open
Abstract
The imipridones ONC201 and ONC212 selectively kill cancer cells and have been ascribed multiple mechanisms-of-action. Genome-wide CRISPR knockout screens revealed that loss of the mitochondrial proteases CLPP and MIPEP confer strong resistance to both compounds... Systematic genetic interaction profiles can reveal the mechanisms-of-action of bioactive compounds. The imipridone ONC201, which is currently in cancer clinical trials, has been ascribed a variety of different targets. To investigate the genetic dependencies of imipridone action, we screened a genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) knockout library in the presence of either ONC201 or its more potent analog ONC212. Loss of the mitochondrial matrix protease CLPP or the mitochondrial intermediate peptidase MIPEP conferred strong resistance to both compounds. Biochemical and surrogate genetic assays showed that impridones directly activate CLPP and that MIPEP is necessary for proteolytic maturation of CLPP into a catalytically competent form. Quantitative proteomic analysis of cells treated with ONC212 revealed degradation of many mitochondrial as well as nonmitochondrial proteins. Prompted by the conservation of ClpP from bacteria to humans, we found that the imipridones also activate ClpP from Escherichia coli, Bacillus subtilis, and Staphylococcus aureus in biochemical and genetic assays. ONC212 and acyldepsipeptide-4 (ADEP4), a known activator of bacterial ClpP, caused similar proteome-wide degradation profiles in S. aureus. ONC212 suppressed the proliferation of a number of Gram-positive (S. aureus, B. subtilis, and Enterococcus faecium) and Gram-negative species (E. coli and Neisseria gonorrhoeae). Moreover, ONC212 enhanced the ability of rifampin to eradicate antibiotic-tolerant S. aureus persister cells. These results reveal the genetic dependencies of imipridone action in human cells and identify the imipridone scaffold as a new entry point for antibiotic development.
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Screening the Saccharomyces cerevisiae Nonessential Gene Deletion Library Reveals Diverse Mechanisms of Action for Antifungal Plant Defensins. Antimicrob Agents Chemother 2019; 63:AAC.01097-19. [PMID: 31451498 DOI: 10.1128/aac.01097-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/14/2019] [Indexed: 12/28/2022] Open
Abstract
Plant defensins are a large family of proteins, most of which have antifungal activity against a broad spectrum of fungi. However, little is known about how they exert their activity. The mechanisms of action of only a few members of the family have been investigated and, in most cases, there are still a number of unknowns. To gain a better understanding of the antifungal mechanisms of a set of four defensins, NaD1, DmAMP1, NbD6, and SBI6, we screened a pooled collection of the nonessential gene deletion set of Saccharomyces cerevisiae Strains with increased or decreased ability to survive defensin treatment were identified based on the relative abundance of the strain-specific barcode as determined by MiSeq next-generation sequencing. Analysis of the functions of genes that are deleted in strains with differential growth in the presence of defensin provides insight into the mechanism of action. The screen identified a novel role for the vacuole in the mechanisms of action for defensins NbD6 and SBI6. The effect of these defensins on vacuoles was further confirmed by using confocal microscopy in both S. cerevisiae and the cereal pathogen Fusarium graminearum These results demonstrate the utility of this screening method to identify novel mechanisms of action for plant defensins.
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Decyl Gallate as a Possible Inhibitor of N-Glycosylation Process in Paracoccidioides lutzii. Antimicrob Agents Chemother 2019; 63:AAC.01909-18. [PMID: 31451502 DOI: 10.1128/aac.01909-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 07/28/2019] [Indexed: 01/29/2023] Open
Abstract
The available antifungal therapeutic arsenal is limited. The search for alternative drugs with fewer side effects and new targets remains a major challenge. Decyl gallate (G14) is a derivative of gallic acid with a range of biological activities and broad-spectrum antifungal activity. Previously, our group demonstrated the promising anti-Paracoccidioides activity of G14. In this work, to evaluate the antifungal characteristics of G14 for Paracoccidioides lutzii, a chemical-genetic interaction analysis was conducted on a Saccharomyces cerevisiae model. N-glycosylation and/or the unfolded protein response pathway was identified as a high-confidence process for drug target prediction. The overactivation of unfolded protein response (UPR) signaling was confirmed using this model with IRE1/ATF6/PERK genes tagged with green fluorescent protein (GFP). In P. lutzii, this prediction was confirmed by the low activity of glycosylated enzymes [α-(1,3)-glucanase, N-acetyl-β-d-glucosaminidase (NAGase), and α-(1,4)-amylase], by hyperexpression of genes involved with the UPR and glycosylated enzymes, and by the reduction in the amounts of glycosylated proteins and chitin. All of these components are involved in fungal cell wall integrity and are dependent on the N-glycosylation process. This loss of integrity was confirmed by the reduction in mitochondrial activity, impaired budding, enhancement of wall permeability, and a decrease in viability. These events led to a reduction of the ability of fungi to adhere on human lung epithelial cells (A549) in vitro Therefore, G14 may have an important role in balancing the inflammatory reaction caused by fungal infection, without interfering with the microbicidal activity of nitric oxide. This work provides new information on the activity of G14, a potential anti-Paracoccidioides compound.
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Zhou FL, Li SC, Zhu Y, Guo WJ, Shao LJ, Nelson J, Simpkins S, Yang DH, Liu Q, Yashiroda Y, Xu JB, Fan YY, Yue JM, Yoshida M, Xia T, Myers CL, Boone C, Wang MW. Integrating yeast chemical genomics and mammalian cell pathway analysis. Acta Pharmacol Sin 2019; 40:1245-1255. [PMID: 31138898 PMCID: PMC6786357 DOI: 10.1038/s41401-019-0231-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/14/2019] [Indexed: 12/27/2022] Open
Abstract
Chemical genomics has been applied extensively to evaluate small molecules that modulate biological processes in Saccharomyces cerevisiae. Here, we use yeast as a surrogate system for studying compounds that are active against metazoan targets. Large-scale chemical-genetic profiling of thousands of synthetic and natural compounds from the Chinese National Compound Library identified those with high-confidence bioprocess target predictions. To discover compounds that have the potential to function like therapeutic agents with known targets, we also analyzed a reference library of approved drugs. Previously uncharacterized compounds with chemical-genetic profiles resembling existing drugs that modulate autophagy and Wnt/β-catenin signal transduction were further examined in mammalian cells, and new modulators with specific modes of action were validated. This analysis exploits yeast as a general platform for predicting compound bioactivity in mammalian cells.
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Affiliation(s)
- Fu-Lai Zhou
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sheena C Li
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, 3510198, Japan
| | - Yue Zhu
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wan-Jing Guo
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Jun Shao
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Justin Nelson
- Bioinformatics and Computational Biology Program, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455, USA
| | - Scott Simpkins
- Bioinformatics and Computational Biology Program, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455, USA
| | - De-Hua Yang
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, 201203, China
| | - Qing Liu
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, 201203, China
| | - Yoko Yashiroda
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, 3510198, Japan
| | - Jin-Biao Xu
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yao-Yue Fan
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jian-Min Yue
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, 3510198, Japan
- Department of Biology, The University of Tokyo, Bunkyo-ku, Tokyo, 1138657, Japan
- Collaborative Research for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 1138657, Japan
| | - Tian Xia
- Department of Electronics and Information Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Chad L Myers
- Bioinformatics and Computational Biology Program, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455, USA.
| | - Charles Boone
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, 3510198, Japan.
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Ontario, M5S 3E1, Canada.
| | - Ming-Wei Wang
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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14
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From Yeast to Humans: Leveraging New Approaches in Yeast to Accelerate Discovery of Therapeutic Targets for Synucleinopathies. Methods Mol Biol 2019; 2049:419-444. [PMID: 31602625 DOI: 10.1007/978-1-4939-9736-7_24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Neurodegenerative diseases (ND) represent a growing, global health crisis, one that lacks any disease-modifying therapeutic strategy. This critical need for new therapies must be met with an exhaustive approach to exploit all tools available. A yeast (Saccharomyces cerevisiae) model of α-synuclein toxicity-the protein causally linked to Parkinson's disease and other synucleinopathies-offers a powerful approach that takes advantage of the unique offerings of this system: tractable genetics, robust high-throughput screening strategies, unparalleled data repositories, powerful computational tools, and extensive evolutionary conservation of fundamental biological pathways. These attributes have enabled genetic and small molecule screens that have revealed toxic phenotypes and drug targets that translate directly to patient-derived iPSC neurons. Extending these insights, recent advances in genetic network analyses have generated the first "humanized" α-synuclein network, which has identified druggable proteins and led to validation of the toxic phenotypes in patient-derived cells. Unbiased phenotypic small molecule screens can identify compounds targeting critical proteins within α-synuclein networks. While identification of direct drug targets for phenotypic screen hits represents a bottleneck, high-throughput chemical genetic methods provide a means to uncover cellular targets and pathways for large numbers of compounds in parallel. Taken together, the yeast α-synuclein model and associated tools can reveal insights into underlying cellular pathologies, lead molecules and their cognate targets, and strategies to translate mechanisms of toxicity and cytoprotection into complex neuronal systems.
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15
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Maestri E, Pavlicevic M, Montorsi M, Marmiroli N. Meta-Analysis for Correlating Structure of Bioactive Peptides in Foods of Animal Origin with Regard to Effect and Stability. Compr Rev Food Sci Food Saf 2018; 18:3-30. [PMID: 33337011 DOI: 10.1111/1541-4337.12402] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 09/28/2018] [Accepted: 09/29/2018] [Indexed: 01/09/2023]
Abstract
Amino acid (AA) sequences of 807 bioactive peptides from foods of animal origin were examined in order to correlate peptide structure with activity (antihypertensive, antioxidative, immunomodulatory, antimicrobial, hypolipidemic, antithrombotic, and opioid) and stability in vivo. Food sources, such as milk, meat, eggs, and marine products, show different frequencies of bioactive peptides exhibiting specific effects. There is a correlation of peptide structure and effect, depending on type and position of AA. Opioid peptides contain a high percentage of aromatic AA residues, while antimicrobial peptides show an excess of positively charged AAs. AA residue position is significant, with those in the first and penultimate positions having the biggest effects on peptide activity. Peptides that have activity in vivo contain a high percentage (67%) of proline residues, but the positions of proline in the sequence depend on the length of the peptide. We also discuss the influence of processing on activity of these peptides, as well as methods for predicting release from the source protein and activity of peptides.
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Affiliation(s)
- Elena Maestri
- Dept. of Chemistry, Life Sciences and Environmental Sustainability, Univ. of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy.,Interdepartmental Centre for Food Safety, Technologies and Innovation for Agri-food (SITEIA.PARMA), Univ. of Parma, Parco Area delle Scienze, 43124, Parma, Italy
| | - Milica Pavlicevic
- Inst. for Food Technology and Biochemistry, Faculty of Agriculture, Univ. of Belgrade, Belgrade, Serbia
| | - Michela Montorsi
- Dept. of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open Univ., Via F. Daverio 7, 20122, Milan, Italy.,Consorzio Italbiotec, Via Fantoli, 16/15, 20138, Milano, Italy.,Inst. of Bioimaging and Molecular Physiology, National Council of Research (CNR), Via Fratelli Cervi 93, 20090, Segrate, Italy
| | - Nelson Marmiroli
- Dept. of Chemistry, Life Sciences and Environmental Sustainability, Univ. of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy.,Interdepartmental Centre for Food Safety, Technologies and Innovation for Agri-food (SITEIA.PARMA), Univ. of Parma, Parco Area delle Scienze, 43124, Parma, Italy.,Consorzio Italbiotec, Via Fantoli, 16/15, 20138, Milano, Italy
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16
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How Surrogate and Chemical Genetics in Model Organisms Can Suggest Therapies for Human Genetic Diseases. Genetics 2018; 208:833-851. [PMID: 29487144 PMCID: PMC5844338 DOI: 10.1534/genetics.117.300124] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/26/2017] [Indexed: 12/12/2022] Open
Abstract
Genetic diseases are both inherited and acquired. Many genetic diseases fall under the paradigm of orphan diseases, a disease found in < 1 in 2000 persons. With rapid and cost-effective genome sequencing becoming the norm, many causal mutations for genetic diseases are being rapidly determined. In this regard, model organisms are playing an important role in validating if specific mutations identified in patients drive the observed phenotype. An emerging challenge for model organism researchers is the application of genetic and chemical genetic platforms to discover drug targets and drugs/drug-like molecules for potential treatment options for patients with genetic disease. This review provides an overview of how model organisms have contributed to our understanding of genetic disease, with a focus on the roles of yeast and zebrafish in gene discovery and the identification of compounds that could potentially treat human genetic diseases.
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17
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Chen Y, Wang J, Yang N, Wen Z, Sun X, Chai Y, Ma Z. Wheat microbiome bacteria can reduce virulence of a plant pathogenic fungus by altering histone acetylation. Nat Commun 2018; 9:3429. [PMID: 30143616 PMCID: PMC6109063 DOI: 10.1038/s41467-018-05683-7] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 07/16/2018] [Indexed: 02/07/2023] Open
Abstract
Interactions between bacteria and fungi have great environmental, medical, and agricultural importance, but the molecular mechanisms are largely unknown. Here, we study the interactions between the bacterium Pseudomonas piscium, from the wheat head microbiome, and the plant pathogenic fungus Fusarium graminearum. We show that a compound secreted by the bacteria (phenazine-1-carboxamide) directly affects the activity of fungal protein FgGcn5, a histone acetyltransferase of the SAGA complex. This leads to deregulation of histone acetylation at H2BK11, H3K14, H3K18, and H3K27 in F. graminearum, as well as suppression of fungal growth, virulence, and mycotoxin biosynthesis. Therefore, an antagonistic bacterium can inhibit growth and virulence of a plant pathogenic fungus by manipulating fungal histone modification.
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Affiliation(s)
- Yun Chen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Jing Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Nan Yang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ziyue Wen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xuepeng Sun
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yunrong Chai
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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18
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Abstract
A long-standing challenge in drug development is the identification of the mechanisms of action of small molecules with therapeutic potential. A number of methods have been developed to address this challenge, each with inherent strengths and limitations. We here provide a brief review of these methods with a focus on chemical-genetic methods that are based on systematically profiling the effects of genetic perturbations on drug sensitivity. In particular, application of these methods to mammalian systems has been facilitated by the recent advent of CRISPR-based approaches, which enable one to readily repress, induce, or delete a given gene and determine the resulting effects on drug sensitivity.
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Affiliation(s)
- Marco Jost
- Department
of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute,
Center for RNA Systems Biology, University of California, San Francisco, San
Francisco, California 94158, United States
- Department
of Microbiology and Immunology, University of California, San Francisco, San
Francisco, California 94158, United States
| | - Jonathan S. Weissman
- Department
of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute,
Center for RNA Systems Biology, University of California, San Francisco, San
Francisco, California 94158, United States
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19
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Abstract
Spatial analysis of functional enrichment (SAFE) is a systematic quantitative approach for annotating large biological networks. SAFE detects network regions that are statistically overrepresented for functional groups or quantitative phenotypes of interest, and provides an intuitive visual representation of their relative positioning within the network. In doing so, SAFE determines which functions cocluster in a network, which parts of the network they are associated with and how they are potentially related to one another.Here, I provide a detailed stepwise description of how to perform a SAFE analysis. As an example, I use SAFE to annotate the genome-scale genetic interaction similarity network from Saccharomyces cerevisiae with Gene Ontology (GO) biological process terms. In addition, I show how integrating GO with chemical genomic data in SAFE can recapitulate known modes of action of chemical compounds and potentially identify novel drug mechanisms.
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20
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Jost M, Chen Y, Gilbert LA, Horlbeck MA, Krenning L, Menchon G, Rai A, Cho MY, Stern JJ, Prota AE, Kampmann M, Akhmanova A, Steinmetz MO, Tanenbaum ME, Weissman JS. Combined CRISPRi/a-Based Chemical Genetic Screens Reveal that Rigosertib Is a Microtubule-Destabilizing Agent. Mol Cell 2017; 68:210-223.e6. [PMID: 28985505 PMCID: PMC5640507 DOI: 10.1016/j.molcel.2017.09.012] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/19/2017] [Accepted: 09/07/2017] [Indexed: 02/08/2023]
Abstract
Chemical libraries paired with phenotypic screens can now readily identify compounds with therapeutic potential. A central limitation to exploiting these compounds, however, has been in identifying their relevant cellular targets. Here, we present a two-tiered CRISPR-mediated chemical-genetic strategy for target identification: combined genome-wide knockdown and overexpression screening as well as focused, comparative chemical-genetic profiling. Application of these strategies to rigosertib, a drug in phase 3 clinical trials for high-risk myelodysplastic syndrome whose molecular target had remained controversial, pointed singularly to microtubules as rigosertib's target. We showed that rigosertib indeed directly binds to and destabilizes microtubules using cell biological, in vitro, and structural approaches. Finally, expression of tubulin with a structure-guided mutation in the rigosertib-binding pocket conferred resistance to rigosertib, establishing that rigosertib kills cancer cells by destabilizing microtubules. These results demonstrate the power of our chemical-genetic screening strategies for pinpointing the physiologically relevant targets of chemical agents.
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Affiliation(s)
- Marco Jost
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuwen Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Luke A Gilbert
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lenno Krenning
- Hubrecht Institute - KNAW and University Medical Center Utrecht, 3584CT Utrecht, the Netherlands
| | - Grégory Menchon
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Ankit Rai
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3548CH Utrecht, the Netherlands
| | - Min Y Cho
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jacob J Stern
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrea E Prota
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Martin Kampmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Anna Akhmanova
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3548CH Utrecht, the Netherlands
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland; Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Marvin E Tanenbaum
- Hubrecht Institute - KNAW and University Medical Center Utrecht, 3584CT Utrecht, the Netherlands.
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
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21
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Guan M, Zhang X. Functional genomic assessment of 2, 2-bis (bromomethyl)-1, 3-propanediol induced cytotoxicity in a single-gene knockout library of E. coli. CHEMOSPHERE 2017; 185:582-588. [PMID: 28719877 DOI: 10.1016/j.chemosphere.2017.07.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/05/2017] [Accepted: 07/08/2017] [Indexed: 06/07/2023]
Abstract
Functional gene fingerprinting of chemicals could be used to understand the direct gene-chemical interaction in the process of toxification from a genome-wide scale. 2, 2-bis (bromomethyl)-1, 3-propanediol (BMP) is a brominated flame retardant with widespread production but with very limited toxicological data. Here the cytotoxicity of BMP was assessed by Escherichia coli (E. coli) functional genome-wide knockout mutants screening and the underlying molecular mechanism was investigated. The median inhibition concentration (IC50) of BMP was 1.608 ± 0.078 mg/ml after 24 h exposure. 119 initial, including 66 sensitive and 53 resistant single gene mutants, were identified by a full library screening of BMP at the concentration of IC50. The resistant genes were significantly enriched in nucleobase-containing compound biosynthetic process (GO: 0034654) by gene ontology (GO) biological process analyses, which suggested that the pathway of DNA repair is a critical cellular process in the survival of cells exposed to BMP. Meanwhile, function annotation of all BMP responsive genes suggested the mechanism of BMP was associated with DNA damage, oxidative stress and cellular transmembrane transport process. Many genes were exclusively responsive to BMP comparing with other chemicals that has been assessed by E. coli mutant screening approach, which indicated that BMP has a distinct mode of toxic action. Overall, the functional genomic screening approach presented here provides a great tool to assess the cellular toxicological mechanism of environmental chemicals.
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Affiliation(s)
- Miao Guan
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China; Research Center for Environmental Toxicology & Safety of Chemicals, Nanjing University, PR China; Jiangsu Key Laboratory of Environmental Safety and Health Risk of Chemicals, Nanjing, 210023, PR China.
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22
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Wyche TP, Ramos Alvarenga RF, Piotrowski JS, Duster MN, Warrack SR, Cornilescu G, De Wolfe TJ, Hou Y, Braun DR, Ellis GA, Simpkins SW, Nelson J, Myers CL, Steele J, Mori H, Safdar N, Markley JL, Rajski SR, Bugni TS. Chemical Genomics, Structure Elucidation, and in Vivo Studies of the Marine-Derived Anticlostridial Ecteinamycin. ACS Chem Biol 2017; 12:2287-2295. [PMID: 28708379 PMCID: PMC5697710 DOI: 10.1021/acschembio.7b00388] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A polyether antibiotic, ecteinamycin (1), was isolated from a marine Actinomadura sp., cultivated from the ascidian Ecteinascidia turbinata. 13C enrichment, high resolution NMR spectroscopy, and molecular modeling enabled elucidation of the structure of 1, which was validated on the basis of comparisons with its recently reported crystal structure. Importantly, ecteinamycin demonstrated potent activity against the toxigenic strain of Clostridium difficile NAP1/B1/027 (MIC = 59 ng/μL), as well as other toxigenic and nontoxigenic C. difficile isolates both in vitro and in vivo. Additionally, chemical genomics studies using Escherichia coli barcoded deletion mutants led to the identification of sensitive mutants such as trkA and kdpD involved in potassium cation transport and homeostasis supporting a mechanistic proposal that ecteinamycin acts as an ionophore antibiotic. This is the first antibacterial agent whose mechanism of action has been studied using E. coli chemical genomics. On the basis of these data, we propose ecteinamycin as an ionophore antibiotic that causes C. difficile detoxification and cell death via potassium transport dysregulation.
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Affiliation(s)
- Thomas P. Wyche
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - René F. Ramos Alvarenga
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | | | - Megan N. Duster
- Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Simone R. Warrack
- Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Travis J. De Wolfe
- Department of Food Science, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Yanpeng Hou
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Doug R. Braun
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Gregory A. Ellis
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Scott W. Simpkins
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Justin Nelson
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Chad L. Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | - James Steele
- Department of Food Science, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Hirotada Mori
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Nasia Safdar
- Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - John L. Markley
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Scott R. Rajski
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Tim S. Bugni
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
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23
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A New Natural Product Analog of Blasticidin S Reveals Cellular Uptake Facilitated by the NorA Multidrug Transporter. Antimicrob Agents Chemother 2017; 61:AAC.02635-16. [PMID: 28373194 DOI: 10.1128/aac.02635-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/29/2017] [Indexed: 01/27/2023] Open
Abstract
The permeation of antibiotics through bacterial membranes to their target site is a crucial determinant of drug activity but in many cases remains poorly understood. During screening efforts to discover new broad-spectrum antibiotic compounds from marine sponge samples, we identified a new analog of the peptidyl nucleoside antibiotic blasticidin S that exhibited up to 16-fold-improved potency against a range of laboratory and clinical bacterial strains which we named P10. Whole-genome sequencing of laboratory-evolved strains of Staphylococcus aureus resistant to blasticidin S and P10, combined with genome-wide assessment of the fitness of barcoded Escherichia coli knockout strains in the presence of the antibiotics, revealed that restriction of cellular access was a key feature in the development of resistance to this class of drug. In particular, the gene encoding the well-characterized multidrug efflux pump NorA was found to be mutated in 69% of all S. aureus isolates resistant to blasticidin S or P10. Unexpectedly, resistance was associated with inactivation of norA, suggesting that the NorA transporter facilitates cellular entry of peptidyl nucleosides in addition to its known role in the efflux of diverse compounds, including fluoroquinolone antibiotics.
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24
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Sardi M, Rovinskiy N, Zhang Y, Gasch AP. Leveraging Genetic-Background Effects in Saccharomyces cerevisiae To Improve Lignocellulosic Hydrolysate Tolerance. Appl Environ Microbiol 2016; 82:5838-49. [PMID: 27451446 PMCID: PMC5038035 DOI: 10.1128/aem.01603-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/14/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED A major obstacle to sustainable lignocellulosic biofuel production is microbe inhibition by the combinatorial stresses in pretreated plant hydrolysate. Chemical biomass pretreatment releases a suite of toxins that interact with other stressors, including high osmolarity and temperature, which together can have poorly understood synergistic effects on cells. Improving tolerance in industrial strains has been hindered, in part because the mechanisms of tolerance reported in the literature often fail to recapitulate in other strain backgrounds. Here, we explored and then exploited variations in stress tolerance, toxin-induced transcriptomic responses, and fitness effects of gene overexpression in different Saccharomyces cerevisiae (yeast) strains to identify genes and processes linked to tolerance of hydrolysate stressors. Using six different S. cerevisiae strains that together maximized phenotypic and genetic diversity, first we explored transcriptomic differences between resistant and sensitive strains to identify common and strain-specific responses. This comparative analysis implicated primary cellular targets of hydrolysate toxins, secondary effects of defective defense strategies, and mechanisms of tolerance. Dissecting the responses to individual hydrolysate components across strains pointed to synergistic interactions between osmolarity, pH, hydrolysate toxins, and nutrient composition. By characterizing the effects of high-copy gene overexpression in three different strains, we revealed the breadth of the background-specific effects of gene fitness contributions in synthetic hydrolysate. Our approach identified new genes for engineering improved stress tolerance in diverse strains while illuminating the effects of genetic background on molecular mechanisms. IMPORTANCE Recent studies on natural variation within Saccharomyces cerevisiae have uncovered substantial phenotypic diversity. Here, we took advantage of this diversity, using it as a tool to infer the effects of combinatorial stress found in lignocellulosic hydrolysate. By comparing sensitive and tolerant strains, we implicated primary cellular targets of hydrolysate toxins and elucidated the physiological states of cells when exposed to this stress. We also explored the strain-specific effects of gene overexpression to further identify strain-specific responses to hydrolysate stresses and to identify genes that improve hydrolysate tolerance independent of strain background. This study underscores the importance of studying multiple strains to understand the effects of hydrolysate stress and provides a method to find genes that improve tolerance across strain backgrounds.
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Affiliation(s)
- Maria Sardi
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA Microbiology Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nikolay Rovinskiy
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Yaoping Zhang
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Audrey P Gasch
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Coorey NVC, Matthews JH, Bellows DS, Atkinson PH. Pleiotropic drug-resistance attenuated genomic library improves elucidation of drug mechanisms. MOLECULAR BIOSYSTEMS 2016; 11:3129-36. [PMID: 26381459 DOI: 10.1039/c5mb00406c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Identifying Saccharomyces cerevisiae genome-wide gene deletion mutants that confer hypersensitivity to a xenobiotic aids the elucidation of its mechanism of action (MoA). However, the biological activities of many xenobiotics are masked by the pleiotropic drug resistance (PDR) network which effluxes xenobiotics that are PDR substrates. The PDR network in S. cerevisiae is almost entirely under the control of two functionally homologous transcription factors Pdr1p and Pdr3p. Herein we report the construction of a PDR-attenuated haploid non-essential DMA (PA-DMA), lacking PDR1 and PDR3, which permits the MoA elucidation of xenobiotics that are PDR substrates at low concentrations. The functionality of four key cellular processes commonly activated in response to xenobiotic stress: oxidative stress response, general stress response, unfolded stress response and calcium signalling pathways were assessed in the absence of PDR1 and PDR3 genes and were found to unaltered, therefore, these key chemogenomic signatures are not lost when using the PA-DMA. Efficacy of the PA-DMA was demonstrated using cycloheximide and latrunculin A at low nanomolar concentrations to attain chemical genetic profiles that were more specific to their known main mechanisms. We also found a two-fold increase in the number of compounds that are bioactive in the pdr1Δpdr3Δ compared to the wild type strain in screening the commercially available LOPAC(1280) library. The PA-DMA should be particularly applicable to mechanism determination of xenobiotics that have limited availability, such as natural products.
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Affiliation(s)
- Namal V C Coorey
- Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Kelburn, Wellington, 6011, New Zealand.
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26
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Baryshnikova A. Systematic Functional Annotation and Visualization of Biological Networks. Cell Syst 2016; 2:412-21. [DOI: 10.1016/j.cels.2016.04.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 02/09/2016] [Accepted: 04/18/2016] [Indexed: 10/21/2022]
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Sarks C, Higbee A, Piotrowski J, Xue S, Coon JJ, Sato TK, Jin M, Balan V, Dale BE. Quantifying pretreatment degradation compounds in solution and accumulated by cells during solids and yeast recycling in the Rapid Bioconversion with Integrated recycling Technology process using AFEX™ corn stover. BIORESOURCE TECHNOLOGY 2016; 205:24-33. [PMID: 26802184 DOI: 10.1016/j.biortech.2016.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 01/03/2016] [Accepted: 01/05/2016] [Indexed: 05/09/2023]
Abstract
Effects of degradation products (low molecular weight compounds produced during pretreatment) on the microbes used in the RaBIT (Rapid Bioconversion with Integrated recycling Technology) process that reduces enzyme usage up to 40% by efficient enzyme recycling were studied. Chemical genomic profiling was performed, showing no yeast response differences in hydrolysates produced during RaBIT enzymatic hydrolysis. Concentrations of degradation products in solution were quantified after different enzymatic hydrolysis cycles and fermentation cycles. Intracellular degradation product concentrations were also measured following fermentation. Degradation product concentrations in hydrolysate did not change between RaBIT enzymatic hydrolysis cycles; the cell population retained its ability to oxidize/reduce (detoxify) aldehydes over five RaBIT fermentation cycles; and degradation products accumulated within or on the cells as RaBIT fermentation cycles increased. Synthetic hydrolysate was used to confirm that pretreatment degradation products are the sole cause of decreased xylose consumption during RaBIT fermentations.
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Affiliation(s)
- Cory Sarks
- Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, 3815 Technology Boulevard, Lansing, MI 48910, United States; DOE Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, United States.
| | - Alan Higbee
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53704, United States.
| | - Jeff Piotrowski
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53704, United States.
| | - Saisi Xue
- Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, 3815 Technology Boulevard, Lansing, MI 48910, United States; DOE Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, United States.
| | - Joshua J Coon
- Departments of Chemistry and Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53704, United States.
| | - Trey K Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53704, United States.
| | - Mingjie Jin
- Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, 3815 Technology Boulevard, Lansing, MI 48910, United States; DOE Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, United States.
| | - Venkatesh Balan
- Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, 3815 Technology Boulevard, Lansing, MI 48910, United States; DOE Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, United States.
| | - Bruce E Dale
- Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, 3815 Technology Boulevard, Lansing, MI 48910, United States; DOE Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, United States.
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Functional genomics to uncover drug mechanism of action. Nat Chem Biol 2015; 11:942-8. [PMID: 26575241 DOI: 10.1038/nchembio.1963] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 10/15/2015] [Indexed: 02/06/2023]
Abstract
The upswing in US Food and Drug Administration and European Medicines Agency drug approvals in 2014 may have marked an end to the dry spell that has troubled the pharmaceutical industry over the past decade. Regardless, the attrition rate of drugs in late clinical phases remains high, and a lack of target validation has been highlighted as an explanation. This has led to a resurgence in appreciation of phenotypic drug screens, as these may be more likely to yield compounds with relevant modes of action. However, cell-based screening approaches do not directly reveal cellular targets, and hence target deconvolution and a detailed understanding of drug action are needed for efficient lead optimization and biomarker development. Here, recently developed functional genomics technologies that address this need are reviewed. The approaches pioneered in model organisms, particularly in yeast, and more recently adapted to mammalian systems are discussed. Finally, areas of particular interest and directions for future tool development are highlighted.
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The Monoterpene Carvacrol Generates Endoplasmic Reticulum Stress in the Pathogenic Fungus Candida albicans. Antimicrob Agents Chemother 2015; 59:4584-92. [PMID: 26014932 DOI: 10.1128/aac.00551-15] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/06/2015] [Indexed: 12/15/2022] Open
Abstract
The monoterpene carvacrol, the major component of oregano and thyme oils, is known to exert potent antifungal activity against the pathogenic yeast Candida albicans. This monoterpene has been the subject of a considerable number of investigations that uncovered extensive pharmacological properties, including antifungal and antibacterial effects. However, its mechanism of action remains elusive. Here, we used integrative chemogenomic approaches, including genome-scale chemical-genetic and transcriptional profiling, to uncover the mechanism of action of carvacrol associated with its antifungal property. Our results clearly demonstrated that fungal cells require the unfolded protein response (UPR) signaling pathway to resist carvacrol. The mutants most sensitive to carvacrol in our genome-wide competitive fitness assay in the yeast Saccharomyces cerevisiae expressed mutations of the transcription factor Hac1 and the endonuclease Ire1, which is required for Hac1 activation by removing a nonconventional intron from the 3' region of HAC1 mRNA. Confocal fluorescence live-cell imaging revealed that carvacrol affects the morphology and the integrity of the endoplasmic reticulum (ER). Transcriptional profiling of pathogenic yeast C. albicans cells treated with carvacrol demonstrated a bona fide UPR transcriptional signature. Ire1 activity detected by the splicing of HAC1 mRNA in C. albicans was activated by carvacrol. Furthermore, carvacrol was found to potentiate antifungal activity of the echinocandin antifungal caspofungin and UPR inducers dithiothreitol and tunicamycin against C. albicans. This comprehensive chemogenomic investigation demonstrated that carvacrol exerts its antifungal activity by altering ER integrity, leading to ER stress and the activation of the UPR to restore protein-folding homeostasis.
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Ugrankar R, Berglund E, Akdemir F, Tran C, Kim MS, Noh J, Schneider R, Ebert B, Graff JM. Drosophila glucome screening identifies Ck1alpha as a regulator of mammalian glucose metabolism. Nat Commun 2015; 6:7102. [PMID: 25994086 PMCID: PMC4455130 DOI: 10.1038/ncomms8102] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 04/07/2015] [Indexed: 01/18/2023] Open
Abstract
Circulating carbohydrates are an essential energy source, perturbations in which are pathognomonic of various diseases, diabetes being the most prevalent. Yet many of the genes underlying diabetes and its characteristic hyperglycaemia remain elusive. Here we use physiological and genetic interrogations in D. melanogaster to uncover the ‘glucome', the complete set of genes involved in glucose regulation in flies. Partial genomic screens of ∼1,000 genes yield ∼160 hyperglycaemia ‘flyabetes' candidates that we classify using fat body- and muscle-specific knockdown and biochemical assays. The results highlight the minor glucose fraction as a physiological indicator of metabolism in Drosophila. The hits uncovered in our screen may have conserved functions in mammalian glucose homeostasis, as heterozygous and homozygous mutants of Ck1alpha in the murine adipose lineage, develop diabetes. Our findings demonstrate that glucose has a role in fly biology and that genetic screenings carried out in flies may increase our understanding of mammalian pathophysiology. Diabetes is associated with aberrations in glucose metabolism. Here the authors perform a genomic screen in fruit flies to identify new regulators of fly glucose metabolism, and show that mice lacking the murine homologue of one of their hits, the protein kinase CK1alpha, in the adipose lineage develop diabetes.
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Affiliation(s)
- Rupali Ugrankar
- Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Eric Berglund
- 1] Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA [2] Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Fatih Akdemir
- Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Christopher Tran
- 1] Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA [2] University of Texas, Dallas, Texas 75080, USA
| | - Min Soo Kim
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jungsik Noh
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Rebekka Schneider
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Benjamin Ebert
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jonathan M Graff
- 1] Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA [2] Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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Piotrowski JS, Okada H, Lu F, Li SC, Hinchman L, Ranjan A, Smith DL, Higbee AJ, Ulbrich A, Coon JJ, Deshpande R, Bukhman YV, McIlwain S, Ong IM, Myers CL, Boone C, Landick R, Ralph J, Kabbage M, Ohya Y. Plant-derived antifungal agent poacic acid targets β-1,3-glucan. Proc Natl Acad Sci U S A 2015; 112:E1490-7. [PMID: 25775513 PMCID: PMC4378397 DOI: 10.1073/pnas.1410400112] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A rise in resistance to current antifungals necessitates strategies to identify alternative sources of effective fungicides. We report the discovery of poacic acid, a potent antifungal compound found in lignocellulosic hydrolysates of grasses. Chemical genomics using Saccharomyces cerevisiae showed that loss of cell wall synthesis and maintenance genes conferred increased sensitivity to poacic acid. Morphological analysis revealed that cells treated with poacic acid behaved similarly to cells treated with other cell wall-targeting drugs and mutants with deletions in genes involved in processes related to cell wall biogenesis. Poacic acid causes rapid cell lysis and is synergistic with caspofungin and fluconazole. The cellular target was identified; poacic acid localized to the cell wall and inhibited β-1,3-glucan synthesis in vivo and in vitro, apparently by directly binding β-1,3-glucan. Through its activity on the glucan layer, poacic acid inhibits growth of the fungi Sclerotinia sclerotiorum and Alternaria solani as well as the oomycete Phytophthora sojae. A single application of poacic acid to leaves infected with the broad-range fungal pathogen S. sclerotiorum substantially reduced lesion development. The discovery of poacic acid as a natural antifungal agent targeting β-1,3-glucan highlights the potential side use of products generated in the processing of renewable biomass toward biofuels as a source of valuable bioactive compounds and further clarifies the nature and mechanism of fermentation inhibitors found in lignocellulosic hydrolysates.
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Affiliation(s)
- Jeff S Piotrowski
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703;
| | - Hiroki Okada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan 277-8561
| | - Fachuang Lu
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703
| | - Sheena C Li
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan 351-0198
| | - Li Hinchman
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703
| | | | | | - Alan J Higbee
- Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Arne Ulbrich
- Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Joshua J Coon
- Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Raamesh Deshpande
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455; and
| | - Yury V Bukhman
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703
| | - Sean McIlwain
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703
| | - Irene M Ong
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455; and
| | - Charles Boone
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan 351-0198; Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1
| | - Robert Landick
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703
| | - John Ralph
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703
| | | | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan 277-8561;
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Harvey AL, Edrada-Ebel R, Quinn RJ. The re-emergence of natural products for drug discovery in the genomics era. Nat Rev Drug Discov 2015; 14:111-29. [PMID: 25614221 DOI: 10.1038/nrd4510] [Citation(s) in RCA: 1508] [Impact Index Per Article: 167.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Natural products have been a rich source of compounds for drug discovery. However, their use has diminished in the past two decades, in part because of technical barriers to screening natural products in high-throughput assays against molecular targets. Here, we review strategies for natural product screening that harness the recent technical advances that have reduced these barriers. We also assess the use of genomic and metabolomic approaches to augment traditional methods of studying natural products, and highlight recent examples of natural products in antimicrobial drug discovery and as inhibitors of protein-protein interactions. The growing appreciation of functional assays and phenotypic screens may further contribute to a revival of interest in natural products for drug discovery.
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Affiliation(s)
- Alan L Harvey
- 1] Research and Innovation Support, Dublin City University, Dublin 9, Ireland. [2] Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow G4 0NR, UK
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow G4 0NR, UK
| | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia
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Piotrowski JS, Simpkins SW, Li SC, Deshpande R, McIlwain SJ, Ong IM, Myers CL, Boone C, Andersen RJ. Chemical genomic profiling via barcode sequencing to predict compound mode of action. Methods Mol Biol 2015; 1263:299-318. [PMID: 25618354 DOI: 10.1007/978-1-4939-2269-7_23] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chemical genomics is an unbiased, whole-cell approach to characterizing novel compounds to determine mode of action and cellular target. Our version of this technique is built upon barcoded deletion mutants of Saccharomyces cerevisiae and has been adapted to a high-throughput methodology using next-generation sequencing. Here we describe the steps to generate a chemical genomic profile from a compound of interest, and how to use this information to predict molecular mechanism and targets of bioactive compounds.
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Affiliation(s)
- Jeff S Piotrowski
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WEI4152, 1552 University Ave., Madison, WI, 53726, USA,
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Wyche TP, Piotrowski JS, Hou Y, Braun D, Deshpande R, McIlwain S, Ong IM, Myers CL, Guzei IA, Westler WM, Andes DR, Bugni TS. Forazoline A: marine-derived polyketide with antifungal in vivo efficacy. Angew Chem Int Ed Engl 2014; 53:11583-6. [PMID: 25197007 PMCID: PMC4215405 DOI: 10.1002/anie.201405990] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Indexed: 11/10/2022]
Abstract
Forazoline A, a novel antifungal polyketide with in vivo efficacy against Candida albicans, was discovered using LCMS-based metabolomics to investigate marine-invertebrate-associated bacteria. Forazoline A had a highly unusual and unprecedented skeleton. Acquisition of (13)C-(13)C gCOSY and (13)C-(15)N HMQC NMR data provided the direct carbon-carbon and carbon-nitrogen connectivity, respectively. This approach represents the first example of determining direct (13)C-(15)N connectivity for a natural product. Using yeast chemical genomics, we propose that forazoline A operated through a new mechanism of action with a phenotypic outcome of disrupting membrane integrity.
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Affiliation(s)
- Thomas P. Wyche
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI 53705 (USA)
| | - Jeff S. Piotrowski
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726 (USA)
| | - Yanpeng Hou
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI 53705 (USA)
| | - Doug Braun
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI 53705 (USA)
| | - Raamesh Deshpande
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455 (USA)
| | - Sean McIlwain
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726 (USA)
| | - Irene M. Ong
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726 (USA)
| | - Chad L. Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455 (USA)
| | - Ilia A. Guzei
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 (USA)
| | - William M. Westler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 (USA)
| | - David R. Andes
- School of Medicine, University of Wisconsin-Madison, Madison, WI 53705 (USA)
| | - Tim S. Bugni
- Pharmaceutical Sciences Division, University of Wisconsin-Madison Madison, WI 53705 (USA)
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Wyche TP, Piotrowski JS, Hou Y, Braun D, Deshpande R, McIlwain S, Ong IM, Myers CL, Guzei IA, Westler WM, Andes DR, Bugni TS. Forazoline A: Marine-Derived Polyketide with Antifungal In Vivo Efficacy. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405990] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Bertrand S, Bohni N, Schnee S, Schumpp O, Gindro K, Wolfender JL. Metabolite induction via microorganism co-culture: a potential way to enhance chemical diversity for drug discovery. Biotechnol Adv 2014; 32:1180-204. [PMID: 24651031 DOI: 10.1016/j.biotechadv.2014.03.001] [Citation(s) in RCA: 297] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/28/2014] [Accepted: 03/03/2014] [Indexed: 02/08/2023]
Abstract
Microorganisms have a long track record as important sources of novel bioactive natural products, particularly in the field of drug discovery. While microbes have been shown to biosynthesize a wide array of molecules, recent advances in genome sequencing have revealed that such organisms have the potential to yield even more structurally diverse secondary metabolites. Thus, many microbial gene clusters may be silent under standard laboratory growth conditions. In the last ten years, several methods have been developed to aid in the activation of these cryptic biosynthetic pathways. In addition to the techniques that demand prior knowledge of the genome sequences of the studied microorganisms, several genome sequence-independent tools have been developed. One of these approaches is microorganism co-culture, involving the cultivation of two or more microorganisms in the same confined environment. Microorganism co-culture is inspired by the natural microbe communities that are omnipresent in nature. Within these communities, microbes interact through signaling or defense molecules. Such compounds, produced dynamically, are of potential interest as new leads for drug discovery. Microorganism co-culture can be achieved in either solid or liquid media and has recently been used increasingly extensively to study natural interactions and discover new bioactive metabolites. Because of the complexity of microbial extracts, advanced analytical methods (e.g., mass spectrometry methods and metabolomics) are key for the successful detection and identification of co-culture-induced metabolites. This review focuses on co-culture studies that aim to increase the diversity of metabolites obtained from microbes. The various strategies are summarized with a special emphasis on the multiple methods of performing co-culture experiments. The analytical approaches for studying these interaction phenomena are discussed, and the chemical diversity and biological activity observed among the induced metabolites are described.
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Affiliation(s)
- Samuel Bertrand
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland; Groupe Mer, Molécules, Santé-EA 2160, Faculté des Sciences pharmaceutiques et biologiques, Université de Nantes, 9 rue Bias, BP 53508, F-44035 Nantes Cedex 01, France
| | - Nadine Bohni
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland
| | - Sylvain Schnee
- Mycology and Biotechnology group, Institute for Plant Production Sciences IPS, Agroscope, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Olivier Schumpp
- Mycology and Biotechnology group, Institute for Plant Production Sciences IPS, Agroscope, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Katia Gindro
- Mycology and Biotechnology group, Institute for Plant Production Sciences IPS, Agroscope, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland.
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Piotrowski JS, Zhang Y, Bates DM, Keating DH, Sato TK, Ong IM, Landick R. Death by a thousand cuts: the challenges and diverse landscape of lignocellulosic hydrolysate inhibitors. Front Microbiol 2014; 5:90. [PMID: 24672514 PMCID: PMC3954026 DOI: 10.3389/fmicb.2014.00090] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 02/18/2014] [Indexed: 11/13/2022] Open
Abstract
Lignocellulosic hydrolysate (LCH) inhibitors are a large class of bioactive molecules that arise from pretreatment, hydrolysis, and fermentation of plant biomass. These diverse compounds reduce lignocellulosic biofuel yields by inhibiting cellular processes and diverting energy into cellular responses. LCH inhibitors present one of the most significant challenges to efficient biofuel production by microbes. Development of new strains that lessen the effects of LCH inhibitors is an economically favorable strategy relative to expensive detoxification methods that also can reduce sugar content in deconstructed biomass. Systems biology analyses and metabolic modeling combined with directed evolution and synthetic biology are successful strategies for biocatalyst development, and methods that leverage state-of-the-art tools are needed to overcome inhibitors more completely. This perspective considers the energetic costs of LCH inhibitors and technologies that can be used to overcome their drain on conversion efficiency. We suggest academic and commercial research groups could benefit by sharing data on LCH inhibitors and implementing "translational biofuel research."
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Affiliation(s)
- Jeff S Piotrowski
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
| | - Yaoping Zhang
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
| | - Donna M Bates
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
| | - David H Keating
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
| | - Trey K Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
| | - Irene M Ong
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
| | - Robert Landick
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
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38
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Christadore LM, Pham L, Kolaczyk ED, Schaus SE. Improvement of experimental testing and network training conditions with genome-wide microarrays for more accurate predictions of drug gene targets. BMC SYSTEMS BIOLOGY 2014; 8:7. [PMID: 24444313 PMCID: PMC3911882 DOI: 10.1186/1752-0509-8-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/21/2013] [Indexed: 11/10/2022]
Abstract
Background Genome-wide microarrays have been useful for predicting chemical-genetic interactions at the gene level. However, interpreting genome-wide microarray results can be overwhelming due to the vast output of gene expression data combined with off-target transcriptional responses many times induced by a drug treatment. This study demonstrates how experimental and computational methods can interact with each other, to arrive at more accurate predictions of drug-induced perturbations. We present a two-stage strategy that links microarray experimental testing and network training conditions to predict gene perturbations for a drug with a known mechanism of action in a well-studied organism. Results S. cerevisiae cells were treated with the antifungal, fluconazole, and expression profiling was conducted under different biological conditions using Affymetrix genome-wide microarrays. Transcripts were filtered with a formal network-based method, sparse simultaneous equation models and Lasso regression (SSEM-Lasso), under different network training conditions. Gene expression results were evaluated using both gene set and single gene target analyses, and the drug’s transcriptional effects were narrowed first by pathway and then by individual genes. Variables included: (i) Testing conditions – exposure time and concentration and (ii) Network training conditions – training compendium modifications. Two analyses of SSEM-Lasso output – gene set and single gene – were conducted to gain a better understanding of how SSEM-Lasso predicts perturbation targets. Conclusions This study demonstrates that genome-wide microarrays can be optimized using a two-stage strategy for a more in-depth understanding of how a cell manifests biological reactions to a drug treatment at the transcription level. Additionally, a more detailed understanding of how the statistical model, SSEM-Lasso, propagates perturbations through a network of gene regulatory interactions is achieved.
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Affiliation(s)
| | | | | | - Scott E Schaus
- Department of Chemistry, Boston University, Boston, MA, USA.
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39
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Fung SY, Sofiyev V, Schneiderman J, Hirschfeld AF, Victor RE, Woods K, Piotrowski JS, Deshpande R, Li SC, de Voogd NJ, Myers CL, Boone C, Andersen RJ, Turvey SE. Unbiased screening of marine sponge extracts for anti-inflammatory agents combined with chemical genomics identifies girolline as an inhibitor of protein synthesis. ACS Chem Biol 2014; 9:247-57. [PMID: 24117378 DOI: 10.1021/cb400740c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Toll-like receptors (TLRs) play a critical role in innate immunity, but activation of TLR signaling pathways is also associated with many harmful inflammatory diseases. Identification of novel anti-inflammatory molecules targeting TLR signaling pathways is central to the development of new treatment approaches for acute and chronic inflammation. We performed high-throughput screening from crude marine sponge extracts on TLR5 signaling and identified girolline. We demonstrated that girolline inhibits signaling through both MyD88-dependent and -independent TLRs (i.e., TLR2, 3, 4, 5, and 7) and reduces cytokine (IL-6 and IL-8) production in human peripheral blood mononuclear cells and macrophages. Using a chemical genomics approach, we identified Elongation Factor 2 as the molecular target of girolline, which inhibits protein synthesis at the elongation step. Together these data identify the sponge natural product girolline as a potential anti-inflammatory agent acting through inhibition of protein synthesis.
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Affiliation(s)
- Shan-Yu Fung
- Department of Pediatrics, British Columbia Children’s Hospital and Child & Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Vladimir Sofiyev
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Julia Schneiderman
- Department of Pediatrics, British Columbia Children’s Hospital and Child & Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Aaron F. Hirschfeld
- Department of Pediatrics, British Columbia Children’s Hospital and Child & Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Rachel E. Victor
- Department of Pediatrics, British Columbia Children’s Hospital and Child & Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Kate Woods
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Jeff S. Piotrowski
- Great
Lakes Bioenergy Research Center, University of Wisconsin−Madison, Madison, Wisconsin 53726, United States
| | - Raamesh Deshpande
- Department
of Computer Science and Engineering, University of Minnesota−Twin Cities, Mineapolis, Minnesota 55455, United States
| | - Sheena C. Li
- Department
of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Nicole J. de Voogd
- Netherlands
Centre for Biodiversity Naturalis, P.O.
Box 9517, 2300 RA, Leiden, The Netherlands
| | - Chad L. Myers
- Department
of Computer Science and Engineering, University of Minnesota−Twin Cities, Mineapolis, Minnesota 55455, United States
| | - Charlie Boone
- Department
of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Raymond J. Andersen
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Stuart E. Turvey
- Department of Pediatrics, British Columbia Children’s Hospital and Child & Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
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40
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Gomes AR, Freitas AC, Rocha-Santos TAP, Duarte AC. Bioactive compounds derived from echinoderms. RSC Adv 2014. [DOI: 10.1039/c4ra03352c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This is the first review paper devoted exclusively to natural compounds isolated from echinoderms with special emphasis on bioactive compounds.
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Affiliation(s)
| | - Ana C. Freitas
- ISEIT/Viseu
- Instituto Piaget
- Viseu, Portugal
- Department of Chemistry and CESAM
- University of Aveiro
| | | | - Armando C. Duarte
- Department of Chemistry and CESAM
- University of Aveiro
- 3810-193 Aveiro, Portugal
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41
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Genomic phenotyping by barcode sequencing broadly distinguishes between alkylating agents, oxidizing agents, and non-genotoxic agents, and reveals a role for aromatic amino acids in cellular recovery after quinone exposure. PLoS One 2013; 8:e73736. [PMID: 24040048 PMCID: PMC3767620 DOI: 10.1371/journal.pone.0073736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 07/21/2013] [Indexed: 12/22/2022] Open
Abstract
Toxicity screening of compounds provides a means to identify compounds harmful for human health and the environment. Here, we further develop the technique of genomic phenotyping to improve throughput while maintaining specificity. We exposed cells to eight different compounds that rely on different modes of action: four genotoxic alkylating (methyl methanesulfonate (MMS), N-Methyl-N-nitrosourea (MNU), N,N′-bis(2-chloroethyl)-N-nitroso-urea (BCNU), N-ethylnitrosourea (ENU)), two oxidizing (2-methylnaphthalene-1,4-dione (menadione, MEN), benzene-1,4-diol (hydroquinone, HYQ)), and two non-genotoxic (methyl carbamate (MC) and dimethyl sulfoxide (DMSO)) compounds. A library of S. cerevisiae 4,852 deletion strains, each identifiable by a unique genetic ‘barcode’, were grown in competition; at different time points the ratio between the strains was assessed by quantitative high throughput ‘barcode’ sequencing. The method was validated by comparison to previous genomic phenotyping studies and 90% of the strains identified as MMS-sensitive here were also identified as MMS-sensitive in a much lower throughput solid agar screen. The data provide profiles of proteins and pathways needed for recovery after both genotoxic and non-genotoxic compounds. In addition, a novel role for aromatic amino acids in the recovery after treatment with oxidizing agents was suggested. The role of aromatic acids was further validated; the quinone subgroup of oxidizing agents were extremely toxic in cells where tryptophan biosynthesis was compromised.
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42
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Heiskanen MA, Aittokallio T. Predicting drug-target interactions through integrative analysis of chemogenetic assays in yeast. MOLECULAR BIOSYSTEMS 2013; 9:768-79. [PMID: 23420501 DOI: 10.1039/c3mb25591c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Chemical-genomic and genetic interaction profiling approaches are widely used to study mechanisms of drug action and resistance. However, there exist a number of scoring algorithms customized to different experimental assays, the relative performance of which remains poorly understood, especially with respect to different types of chemogenetic assays. Using yeast Saccharomyces cerevisiae as a test bed, we carried out a systematic evaluation among the main drug target analysis approaches in terms of predicting global drug-target interaction networks. We found drastic differences in their performance across different chemical-genomic assay types, such as those based on heterozygous and homozygous diploid or haploid deletion mutant libraries. Moreover, a relatively small overlap in the predicted targets was observed between those approaches that use either chemical-genomic screening alone or combined with genetic interaction profiling. A rank-based integration of the complementary scoring approaches led to improved overall performance, demonstrating that genetic interaction profiling provides added information on drug target prediction. Optimal performance was achieved when focusing specifically on the negative tail of the genetic interactions, suggesting that combining synthetic lethal interactions with chemical-genetic interactions provides highest information on drug-target interactions. A network view of rapamycin-interacting genes, pathways and complexes was used as an example to demonstrate the benefits of such integrated and optimized analysis of chemogenetic assays in yeast.
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Affiliation(s)
- Marja A Heiskanen
- Biomathematics Research Group, Department of Mathematics, University of Turku, FI-20014, Finland
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43
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Florent JC. [Small compounds libraries: a research tool for chemical biology]. Biol Aujourdhui 2013; 207:39-54. [PMID: 23694724 DOI: 10.1051/jbio/2013006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Indexed: 06/02/2023]
Abstract
Obtaining and screening collections of small molecules remain a challenge for biologists. Recent advances in analytical techniques and instrumentation now make screening possible in academia. The history of the creation of such public or commercial collections and their accessibility is related. It shows that there is interest for an academic laboratory involved in medicinal chemistry, chemogenomics or "chemical biology" to organize its own collection and make it available through existing networks such as the French National chimiothèque or the European partner network "European Infrastructure of open screening platforms for Chemical Biology" EU-OpenScreen under construction.
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Affiliation(s)
- Jean-Claude Florent
- Laboratoire de Conception, Synthèse et Vectorisation de Biomolécules (CSVB), UMR 176 CNRS-Institut Curie, Institut Curie Centre de Recherche, 75248 Paris Cedex, France.
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Anantharaman V, Iyer LM, Aravind L. Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing. MOLECULAR BIOSYSTEMS 2013; 8:3142-65. [PMID: 23044854 DOI: 10.1039/c2mb25239b] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The mode of action of the bacterial ter cluster and TelA genes, implicated in natural resistance to tellurite and other xenobiotic toxic compounds, pore-forming colicins and several bacteriophages, has remained enigmatic for almost two decades. Using comparative genomics, sequence-profile searches and structural analysis we present evidence that the ter gene products and their functional partners constitute previously underappreciated, chemical stress response and anti-viral defense systems of bacteria. Based on contextual information from conserved gene neighborhoods and domain architectures, we show that the ter gene products and TelA lie at the center of membrane-linked metal recognition complexes with regulatory ramifications encompassing phosphorylation-dependent signal transduction, RNA-dependent regulation, biosynthesis of nucleoside-like metabolites and DNA processing. Our analysis suggests that the multiple metal-binding and non-binding TerD paralogs and TerC are likely to constitute a membrane-associated complex, which might also include TerB and TerY, and feature several, distinct metal-binding sites. Versions of the TerB domain might also bind small molecule ligands and link the TerD paralog-TerC complex to biosynthetic modules comprising phosphoribosyltransferases (PRTases), ATP grasp amidoligases, TIM-barrel carbon-carbon lyases, and HAD phosphoesterases, which are predicted to synthesize novel nucleoside-like molecules. One of the PRTases is also likely to interact with RNA by means of its Pelota/Ribosomal protein L7AE-like domain. The von Willebrand factor A domain protein, TerY, is predicted to be part of a distinct phosphorylation switch, coupling a protein kinase and a PP2C phosphatase. We show, based on the evidence from numerous conserved gene neighborhoods and domain architectures, that both the TerB and TelA domains have been linked to diverse lipid-interaction domains, such as two novel PH-like and the Coq4 domains, in different bacteria, and are likely to comprise membrane-associated sensory complexes that might additionally contain periplasmic binding-protein-II and OmpA domains. We also show that the TerD and TerB domains and the TerY-associated phosphorylation system are functionally linked to many distinct DNA-processing complexes, which feature proteins with SWI2/SNF2 and RecQ-like helicases, multiple AAA+ ATPases, McrC-N-terminal domain proteins, several restriction endonuclease fold DNases, DNA-binding domains and a type-VII/Esx-like system, which is at the center of a predicted DNA transfer apparatus. These DNA-processing modules and associated genes are predicted to be involved in restriction or suicidal action in response to phages and possibly repairing xenobiotic-induced DNA damage. In some eukaryotes, certain components of the ter system appear to be recruited to function in conjunction with the ubiquitin system and calcium-signaling pathways.
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Affiliation(s)
- Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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45
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Gosline SJC, Spencer SJ, Ursu O, Fraenkel E. SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets. Integr Biol (Camb) 2013; 4:1415-27. [PMID: 23060147 DOI: 10.1039/c2ib20072d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The rapid development of high throughput biotechnologies has led to an onslaught of data describing genetic perturbations and changes in mRNA and protein levels in the cell. Because each assay provides a one-dimensional snapshot of active signaling pathways, it has become desirable to perform multiple assays (e.g. mRNA expression and phospho-proteomics) to measure a single condition. However, as experiments expand to accommodate various cellular conditions, proper analysis and interpretation of these data have become more challenging. Here we introduce a novel approach called SAMNet, for Simultaneous Analysis of Multiple Networks, that is able to interpret diverse assays over multiple perturbations. The algorithm uses a constrained optimization approach to integrate mRNA expression data with upstream genes, selecting edges in the protein-protein interaction network that best explain the changes across all perturbations. The result is a putative set of protein interactions that succinctly summarizes the results from all experiments, highlighting the network elements unique to each perturbation. We evaluated SAMNet in both yeast and human datasets. The yeast dataset measured the cellular response to seven different transition metals, and the human dataset measured cellular changes in four different lung cancer models of Epithelial-Mesenchymal Transition (EMT), a crucial process in tumor metastasis. SAMNet was able to identify canonical yeast metal-processing genes unique to each commodity in the yeast dataset, as well as human genes such as β-catenin and TCF7L2/TCF4 that are required for EMT signaling but escaped detection in the mRNA and phospho-proteomic data. Moreover, SAMNet also highlighted drugs likely to modulate EMT, identifying a series of less canonical genes known to be affected by the BCR-ABL inhibitor imatinib (Gleevec), suggesting a possible influence of this drug on EMT.
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Affiliation(s)
- Sara J C Gosline
- Dept. of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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46
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Mishev K, Dejonghe W, Russinova E. Small Molecules for Dissecting Endomembrane Trafficking: A Cross-Systems View. ACTA ACUST UNITED AC 2013; 20:475-86. [DOI: 10.1016/j.chembiol.2013.03.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/19/2013] [Accepted: 03/20/2013] [Indexed: 01/31/2023]
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47
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Brochado AR, Typas A. High-throughput approaches to understanding gene function and mapping network architecture in bacteria. Curr Opin Microbiol 2013; 16:199-206. [DOI: 10.1016/j.mib.2013.01.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 01/09/2013] [Accepted: 01/11/2013] [Indexed: 11/24/2022]
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48
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Chemical tagging of a drug target using 5-sulfonyl tetrazole. Bioorg Med Chem Lett 2013; 23:1608-11. [DOI: 10.1016/j.bmcl.2013.01.092] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Revised: 01/19/2013] [Accepted: 01/22/2013] [Indexed: 12/16/2022]
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49
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Cisar JS, Cravatt B. Fully functionalized small-molecule probes for integrated phenotypic screening and target identification. J Am Chem Soc 2012; 134:10385-8. [PMID: 22667687 PMCID: PMC3426452 DOI: 10.1021/ja304213w] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Phenotypic screening offers a powerful approach to identify small molecules that perturb complex biological processes in cells and organisms. The tendency of small molecules, however, to interact with multiple protein targets, often with moderate to weak affinities, along with the lack of straightforward technologies to characterize these interactions in living systems, has hindered efforts to understand the mechanistic basis for pharmacological activity. Here we address this challenge by creating a fully functionalized small-molecule library whose membership is endowed with: (1) one or more diversity elements to promote interactions with different protein targets in cells, (2) a photoreactive group for UV light-induced covalent cross-linking to interacting proteins, and (3) an alkyne handle for reporter tag conjugation to visualize and identify cross-linked proteins. A library member was found to inhibit cancer cell proliferation selectively under nutrient-limiting (low glucose) conditions. Quantitative chemoproteomics identified MT-ND1, an integral membrane subunit of the ∼1 MDa NADH:ubiquinone oxidoreductase (complex 1) involved in oxidative phosphorylation, as a specific target of the active probe. We further demonstrated that the active probe inhibits complex 1 activity in vitro (IC(50) = 720 nM), an effect that is known to induce cell death in low-glucose conditions. Based on this proof of principle study, we anticipate that the generation and integration of fully functionalized compound libraries into phenotypic screening programs should facilitate the discovery of bioactive probes that are amenable to accelerated target identification and mechanistic characterization using advanced chemoproteomic technologies.
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Affiliation(s)
- Justin S. Cisar
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Benjamin Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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50
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Venancio TM, Bellieny-Rabelo D, Aravind L. Evolutionary and Biochemical Aspects of Chemical Stress Resistance in Saccharomyces cerevisiae. Front Genet 2012; 3:47. [PMID: 22479268 PMCID: PMC3315702 DOI: 10.3389/fgene.2012.00047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 03/15/2012] [Indexed: 01/03/2023] Open
Abstract
Large-scale chemical genetics screens (chemogenomics) in yeast have been widely used to find drug targets, understand the mechanism-of-action of compounds, and unravel the biochemistry of drug resistance. Chemogenomics is based on the comparison of growth of gene deletants in the presence and absence of a chemical substance. Such studies showed that more than 90% of the yeast genes are required for growth in the presence of at least one chemical. Analysis of these data, using computational approaches, has revealed non-trivial features of the natural chemical tolerance systems. As a result two non-overlapping sets of genes are seen to respectively impart robustness and evolvability in the context of natural chemical resistance. The former is composed of multidrug-resistance genes, whereas the latter comprises genes sharing chemical genetic profiles with many others. Recent publications showing the potential applications chemogenomics in studying the pharmacological basis of various drugs are discussed, as well as the expansion of chemogenomics to other organisms. Finally, integration of chemogenomics with sensitive sequence analysis and ubiquitination/phosphorylation data led to the discovery of a new conserved domain and important post-translational modification pathways involved in stress resistance.
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Affiliation(s)
- Thiago Motta Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro Campos dos Goytacazes, Brazil
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