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Ma D, Wang G, Zhu J, Mu W, Dou D, Liu F. Green Leaf Volatile Trans-2-Hexenal Inhibits the Growth of Fusarium graminearum by Inducing Membrane Damage, ROS Accumulation, and Cell Dysfunction. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5646-5657. [PMID: 35481379 DOI: 10.1021/acs.jafc.2c00942] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fusarium graminearum, the main agent of Fusarium head blight (FHB), can cause serious yield loss and secrete mycotoxins to contaminate grain. Here, the biological activity of trans-2-hexenal (T2H) against F. graminearum was determined and its mode of action (MOA) was investigated. Furthermore, surface plasmon resonance with liquid chromatography-tandem mass spectrometry (SPR-LC-MS/MS), bioinformatic analysis, and gene knockout technique were combined to identify the binding proteins of T2H in F. graminearum cells. T2H exhibited satisfactory inhibitory activity against F. graminearum in vitro. Good lipophilicity greatly enhanced the affinity of T2H to F. graminearum mycelia and further caused membrane damage. The FgTRR (thioredoxin reductase) gene negatively regulates the sensitivity of F. graminearum to T2H by reducing the generation of reactive oxygen species (ROS) induced by T2H. Two mutant strains with FgSLX1 (structure-specific endonuclease subunit) and FgCOPB (coatomer subunit β) genes knockout showed decreased sensitivity to T2H, suggesting that these two genes may be involved in the antimicrobial activity of T2H. Taken together, T2H can inhibit F. graminearum growth by multiple MOAs and can be used as a biofumigant to control the occurrence of FHB in the field.
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Affiliation(s)
- Dicheng Ma
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Guoxian Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Jiamei Zhu
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Wei Mu
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Daolong Dou
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Feng Liu
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
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2
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Uelisson da Silva T, Tomaz da Silva E, de Carvalho Pougy K, Henrique da Silva Lima C, de Paula Machado S. Molecular modeling of indazole-3-carboxylic acid and its metal complexes (Zn, Ni, Co, Fe and Mn) as NO synthase inhibitors: DFT calculations, docking studies and molecular dynamics simulations. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2021.109120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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3
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Fillería SG, Nardo AE, Paulino M, Tironi V. Peptides derived from the gastrointestinal digestion of amaranth 11S globulin: Structure and antioxidant functionality. FOOD CHEMISTRY. MOLECULAR SCIENCES 2021; 3:100053. [PMID: 35415655 PMCID: PMC8991498 DOI: 10.1016/j.fochms.2021.100053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 10/11/2021] [Accepted: 11/15/2021] [Indexed: 12/28/2022]
Abstract
The relationship between structural and physicochemical properties and antioxidant activity of peptides from amaranth 11S-globulin was studied. Peptides AWEEREQGSR, TEVWDSNEQ, IYIEQGNGITGM and YLAGKPQQEH had the greatest in vitro activity (ORAC, HORAC). GDRFQDQHQ, HVIKPPSRA and KFNRPETT were the most active ones against Cu+2/H2O2-induced-LDL oxidation. In a cellular system (H2O2-induced-Caco2-TC7), TEVWDSNEQ, IYIEQGNGITGM, GDRFQDQHQ, LAGKPQQEHSGEHQ and KFNRPETT were the most effective in decreasing ROS, while the effects on SOD, GPx, and GSH were variable. To understand the structure-antioxidant activity relationships, the content of aromatic and acidic amino acids, the degree of hydrophobicity and the charge distribution on the accessible surface of peptides structures obtained by molecular dynamics were analysed. The low correlation between in vitro, ex vivo and cellular activities could be explained by the influence of physicochemical and structural properties on the interaction with complex systems (LDL/cells), peptide modifications and/or mechanisms other than direct ROS inhibition in the cells.
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Affiliation(s)
- Susan García Fillería
- Laboratorio de Investigación, Desarrollo e innovación en Proteínas Alimentarias (LIDiPA), Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA-CCT La Plata-CONICET, CICPBA, Facultad de Ciencias Exactas, Universidad Nacional de La Plata), La Plata, Argentina
| | - Agustina Estefania Nardo
- Laboratorio de Investigación, Desarrollo e innovación en Proteínas Alimentarias (LIDiPA), Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA-CCT La Plata-CONICET, CICPBA, Facultad de Ciencias Exactas, Universidad Nacional de La Plata), La Plata, Argentina
| | - Margot Paulino
- Centro de Bioinformática Estructural (CeBioInfo), Departamento de Experimentación y Teoría de la Estructura de la Materia y sus Aplicaciones, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Valeria Tironi
- Laboratorio de Investigación, Desarrollo e innovación en Proteínas Alimentarias (LIDiPA), Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA-CCT La Plata-CONICET, CICPBA, Facultad de Ciencias Exactas, Universidad Nacional de La Plata), La Plata, Argentina.,Centro de Bioinformática Estructural (CeBioInfo), Departamento de Experimentación y Teoría de la Estructura de la Materia y sus Aplicaciones, Facultad de Química, Universidad de la República, Montevideo, Uruguay
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4
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Van den Kerkhof M, Sterckx YGJ, Leprohon P, Maes L, Caljon G. Experimental Strategies to Explore Drug Action and Resistance in Kinetoplastid Parasites. Microorganisms 2020; 8:E950. [PMID: 32599761 PMCID: PMC7356981 DOI: 10.3390/microorganisms8060950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 06/22/2020] [Indexed: 12/17/2022] Open
Abstract
Kinetoplastids are the causative agents of leishmaniasis, human African trypanosomiasis, and American trypanosomiasis. They are responsible for high mortality and morbidity in (sub)tropical regions. Adequate treatment options are limited and have several drawbacks, such as toxicity, need for parenteral administration, and occurrence of treatment failure and drug resistance. Therefore, there is an urgency for the development of new drugs. Phenotypic screening already allowed the identification of promising new chemical entities with anti-kinetoplastid activity potential, but knowledge on their mode-of-action (MoA) is lacking due to the generally applied whole-cell based approach. However, identification of the drug target is essential to steer further drug discovery and development. Multiple complementary techniques have indeed been used for MoA elucidation. In this review, the different 'omics' approaches employed to define the MoA or mode-of-resistance of current reference drugs and some new anti-kinetoplastid compounds are discussed.
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Affiliation(s)
- Magali Van den Kerkhof
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry (LMB), University of Antwerp, 2610 Wilrijk, Belgium;
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du Centre Hospitalier Universitaire de Québec, Université Laval, Québec, QC G1V 0A6, Canada;
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
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5
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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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6
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Schneider P, Schneider G. De-orphaning the marine natural product (±)-marinopyrrole A by computational target prediction and biochemical validation. Chem Commun (Camb) 2017; 53:2272-2274. [DOI: 10.1039/c6cc09693j] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A machine-learning method led to the discovery of the macromolecular targets of the natural anticancer compound marinopyrrol A.
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Affiliation(s)
- P. Schneider
- Department of Chemistry and Applied Biosciences
- Swiss Federal Institute of Technology (ETH)
- Zurich
- Switzerland
- inSili.com LLC
| | - G. Schneider
- Department of Chemistry and Applied Biosciences
- Swiss Federal Institute of Technology (ETH)
- Zurich
- Switzerland
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7
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Competitive Growth Enhances Conditional Growth Mutant Sensitivity to Antibiotics and Exposes a Two-Component System as an Emerging Antibacterial Target in Burkholderia cenocepacia. Antimicrob Agents Chemother 2016; 61:AAC.00790-16. [PMID: 27799222 DOI: 10.1128/aac.00790-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 10/26/2016] [Indexed: 01/08/2023] Open
Abstract
Chemogenetic approaches to profile an antibiotic mode of action are based on detecting differential sensitivities of engineered bacterial strains in which the antibacterial target (usually encoded by an essential gene) or an associated process is regulated. We previously developed an essential-gene knockdown mutant library in the multidrug-resistant Burkholderia cenocepacia by transposon delivery of a rhamnose-inducible promoter. In this work, we used Illumina sequencing of multiplex-PCR-amplified transposon junctions to track individual mutants during pooled growth in the presence of antibiotics. We found that competition from nontarget mutants magnified the hypersensitivity of a clone underexpressing gyrB to novobiocin by 8-fold compared with hypersensitivity measured during clonal growth. Additional profiling of various antibiotics against a pilot library representing most categories of essential genes revealed a two-component system with unknown function, which, upon depletion of the response regulator, sensitized B. cenocepacia to novobiocin, ciprofloxacin, tetracycline, chloramphenicol, kanamycin, meropenem, and carbonyl cyanide 3-chlorophenylhydrazone, but not to colistin, hydrogen peroxide, and dimethyl sulfoxide. We named the gene cluster esaSR for enhanced sensitivity to antibiotics sensor and response regulator. Mutational analysis and efflux activity assays revealed that while esaS is not essential and is involved in antibiotic-induced efflux, esaR is an essential gene and regulates efflux independently of antibiotic-mediated induction. Furthermore, microscopic analysis of cells stained with propidium iodide provided evidence that depletion of EsaR has a profound effect on the integrity of cell membranes. In summary, we unraveled a previously uncharacterized two-component system that can be targeted to reduce antibiotic resistance in B. cenocepacia.
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8
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Schneider G, Schneider P. Macromolecular target prediction by self-organizing feature maps. Expert Opin Drug Discov 2016; 12:271-277. [DOI: 10.1080/17460441.2017.1274727] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Petra Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
- inSili.com LLC, Zurich, Switzerland
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9
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Stubbendieck RM, Straight PD. Escape from Lethal Bacterial Competition through Coupled Activation of Antibiotic Resistance and a Mobilized Subpopulation. PLoS Genet 2015; 11:e1005722. [PMID: 26647299 PMCID: PMC4672918 DOI: 10.1371/journal.pgen.1005722] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/12/2015] [Indexed: 11/18/2022] Open
Abstract
Bacteria have diverse mechanisms for competition that include biosynthesis of extracellular enzymes and antibiotic metabolites, as well as changes in community physiology, such as biofilm formation or motility. Considered collectively, networks of competitive functions for any organism determine success or failure in competition. How bacteria integrate different mechanisms to optimize competitive fitness is not well studied. Here we study a model competitive interaction between two soil bacteria: Bacillus subtilis and Streptomyces sp. Mg1 (S. Mg1). On an agar surface, colonies of B. subtilis suffer cellular lysis and progressive degradation caused by S. Mg1 cultured at a distance. We identify the lytic and degradative activity (LDA) as linearmycins, which are produced by S. Mg1 and are sufficient to cause lysis of B. subtilis. We obtained B. subtilis mutants spontaneously resistant to LDA (LDAR) that have visibly distinctive morphology and spread across the agar surface. Every LDAR mutant identified had a missense mutation in yfiJK, which encodes a previously uncharacterized two-component signaling system. We confirmed that gain-of-function alleles in yfiJK cause a combination of LDAR, changes in colony morphology, and motility. Downstream of yfiJK are the yfiLMN genes, which encode an ATP-binding cassette transporter. We show that yfiLMN genes are necessary for LDA resistance. The developmental phenotypes of LDAR mutants are genetically separable from LDA resistance, suggesting that the two competitive functions are distinct, but regulated by a single two-component system. Our findings suggest that a subpopulation of B. subtilis activate an array of defensive responses to counter lytic stress imposed by competition. Coordinated regulation of development and antibiotic resistance is a streamlined mechanism to promote competitive fitness of bacteria. Antibiotics are one mechanism among many that bacteria use to compete with each other. Bacteria in the environment and in host organisms likely use networks of competitive mechanisms to survive and to shape the composition and function of diverse communities. In this study, we cultured two species of soil bacteria to observe the outcome of competition and to identify competitive functions that dictate the outcome. We show that one organism, Streptomyces sp. Mg1, produces antibiotic linearmycins that cause cellular lysis and degradation of a competing colony of Bacillus subtilis. In turn, the B. subtilis activate a resistance mechanism, either transiently or through mutation of a two-component signaling system. Activation of the signaling system produces a suite of identified responses, which include resistance to linearmycins, altered colony morphology that resembles biofilms, and enhanced motility of B. subtilis. This work identifies a unified, multifaceted survival response that is induced by a subpopulation of bacteria to escape lethal consequences of antibiotic-mediated competition.
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Affiliation(s)
- Reed M. Stubbendieck
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Paul D. Straight
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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10
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Carson C, Raman P, Tullai J, Xu L, Henault M, Thomas E, Yeola S, Lao J, McPate M, Verkuyl JM, Marsh G, Sarber J, Amaral A, Bailey S, Lubicka D, Pham H, Miranda N, Ding J, Tang HM, Ju H, Tranter P, Ji N, Krastel P, Jain RK, Schumacher AM, Loureiro JJ, George E, Berellini G, Ross NT, Bushell SM, Erdemli G, Solomon JM. Englerin A Agonizes the TRPC4/C5 Cation Channels to Inhibit Tumor Cell Line Proliferation. PLoS One 2015; 10:e0127498. [PMID: 26098886 PMCID: PMC4476799 DOI: 10.1371/journal.pone.0127498] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 04/14/2015] [Indexed: 01/19/2023] Open
Abstract
Englerin A is a structurally unique natural product reported to selectively inhibit growth of renal cell carcinoma cell lines. A large scale phenotypic cell profiling experiment (CLiP) of englerin A on ¬over 500 well characterized cancer cell lines showed that englerin A inhibits growth of a subset of tumor cell lines from many lineages, not just renal cell carcinomas. Expression of the TRPC4 cation channel was the cell line feature that best correlated with sensitivity to englerin A, suggesting the hypothesis that TRPC4 is the efficacy target for englerin A. Genetic experiments demonstrate that TRPC4 expression is both necessary and sufficient for englerin A induced growth inhibition. Englerin A induces calcium influx and membrane depolarization in cells expressing high levels of TRPC4 or its close ortholog TRPC5. Electrophysiology experiments confirmed that englerin A is a TRPC4 agonist. Both the englerin A induced current and the englerin A induced growth inhibition can be blocked by the TRPC4/C5 inhibitor ML204. These experiments confirm that activation of TRPC4/C5 channels inhibits tumor cell line proliferation and confirms the TRPC4 target hypothesis generated by the cell line profiling. In selectivity assays englerin A weakly inhibits TRPA1, TRPV3/V4, and TRPM8 which suggests that englerin A may bind a common feature of TRP ion channels. In vivo experiments show that englerin A is lethal in rodents near doses needed to activate the TRPC4 channel. This toxicity suggests that englerin A itself is probably unsuitable for further drug development. However, since englerin A can be synthesized in the laboratory, it may be a useful chemical starting point to identify novel modulators of other TRP family channels.
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Affiliation(s)
- Cheryl Carson
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Pichai Raman
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Jennifer Tullai
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Lei Xu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Martin Henault
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Emily Thomas
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Sarita Yeola
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Jianmin Lao
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Mark McPate
- Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - J. Martin Verkuyl
- Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - George Marsh
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Jason Sarber
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Adam Amaral
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Scott Bailey
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Danuta Lubicka
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Helen Pham
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Nicolette Miranda
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Jian Ding
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Hai-Ming Tang
- Novartis Institutes for Biomedical Research, East Hanover, New Jersey, United States of America
| | - Haisong Ju
- Novartis Institutes for Biomedical Research, East Hanover, New Jersey, United States of America
| | - Pamela Tranter
- Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - Nan Ji
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Philipp Krastel
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Rishi K. Jain
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Andrew M. Schumacher
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Joseph J. Loureiro
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Elizabeth George
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Giuliano Berellini
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Nathan T. Ross
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Simon M. Bushell
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Gül Erdemli
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Jonathan M. Solomon
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
- * E-mail:
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11
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Zhang C, Chen Y, Yin Y, Ji HH, Shim WB, Hou Y, Zhou M, Li XD, Ma Z. A small molecule species specifically inhibits Fusarium myosin I. Environ Microbiol 2015; 17:2735-46. [PMID: 25404531 DOI: 10.1111/1462-2920.12711] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/03/2014] [Accepted: 11/05/2014] [Indexed: 11/28/2022]
Abstract
Fusarium head blight (FHB) caused by Fusarium graminearum is a devastating disease of cereal crops worldwide. Recently, a novel fungicide JS399-19 has been launched into the marketplace to manage FHB. It is compelling that JS399-19 shows highly inhibitory activity towards some Fusarium species, but not to other fungi, indicating that it is an environmentally compatible fungicide. To explore the mode of action of this species-specific compound, we conducted a whole-genome transcript profiling together with genetic and biochemical assays, and discovered that JS399-19 targets the myosin I of F. graminearum (FgMyo1). FgMyo1 is essential for F. graminearum growth. A point mutation S217L or E420K in FgMyo1 is responsible for F. graminearum resistance to JS399-19. In addition, transformation of F. graminearum with the myosin I gene of Magnaporthe grisea, the causal agent of rice blast, also led to JS399-19 resistance. JS399-19 strongly inhibits the ATPase activity of the wild-type FgMyo1, but not the mutated FgMyo1(S217L/E420K) . These results provide us a new insight into the design of species-specific antifungal compounds. Furthermore, our strategy can be applied to identify novel drug targets in various pathogenic organisms.
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Affiliation(s)
- Chengqi Zhang
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yun Chen
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yanni Yin
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Huan-Hong Ji
- National Laboratory of Integrated Management of Insect Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Won-Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843-2132, USA
| | - Yiping Hou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingguo Zhou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiang-Dong Li
- National Laboratory of Integrated Management of Insect Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhonghua Ma
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
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12
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Screening of a Leptospira biflexa mutant library to identify genes involved in ethidium bromide tolerance. Appl Environ Microbiol 2014; 80:6091-103. [PMID: 25063661 DOI: 10.1128/aem.01619-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Leptospira spp. are spirochete bacteria comprising both pathogenic and free-living species. The saprophyte L. biflexa is a model bacterium for studying leptospiral biology due to relative ease of culturing and genetic manipulation. In this study, we constructed a library of 4,996 random transposon mutants in L. biflexa. We screened the library for increased susceptibility to the DNA intercalating agent, ethidium bromide (EtBr), in order to identify genetic determinants that reduce L. biflexa susceptibility to antimicrobial agents. By phenotypic screening, using subinhibitory EtBr concentrations, we identified 29 genes that, when disrupted via transposon insertion, led to increased sensitivity of the bacteria to EtBr. At the functional level, these genes could be categorized by function as follows: regulation and signaling (n=11), transport (n=6), membrane structure (n=5), stress response (n=2), DNA damage repair (n=1), and other processes (n=3), while 1 gene had no predicted function. Genes involved in transport (including efflux pumps) and regulation (two-component systems, anti-sigma factor antagonists, etc.) were overrepresented, demonstrating that these genes are major contributors to EtBr tolerance. This finding suggests that transport genes which would prevent EtBr to enter the cell cytoplasm are critical for EtBr resistance. We identified genes required for the growth of L. biflexa in the presence of sublethal EtBr concentration and characterized their potential as antibiotic resistance determinants. This study will help to delineate mechanisms of adaptation to toxic compounds, as well as potential mechanisms of antibiotic resistance development in pathogenic L. interrogans.
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Bornot A, Blackett C, Engkvist O, Murray C, Bendtsen C. The Role of Historical Bioactivity Data in the Deconvolution of Phenotypic Screens. ACTA ACUST UNITED AC 2014; 19:696-706. [PMID: 24441646 DOI: 10.1177/1087057113518966] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 12/07/2013] [Indexed: 12/20/2022]
Abstract
A substantial challenge in phenotypic drug discovery is the identification of the molecular targets that govern a phenotypic response of interest. Several experimental strategies are available for this, the so-called target deconvolution process. Most of these approaches exploit the affinity between a small-molecule compound and its putative targets or use large-scale genetic manipulations and profiling. Each of these methods has strengths but also limitations such as bias toward high-affinity interactions or risks from genetic compensation. The use of computational methods for target and mechanism of action identification is a complementary approach that can influence each step of a phenotypic screening campaign. Here, we describe how cheminformatics and bioinformatics are embedded in the process from initial selection of a focused compound library from a large set of historical small-molecule screens through the analysis of screening results. We present a deconvolution method based on enrichment analysis and using known bioactivity data of screened compounds to infer putative targets, pathways, and biological processes that are consistent with the observed phenotypic response. As an example, the approach is applied to a cellular screen aiming at identifying inhibitors of tumor necrosis factor-α production in lipopolysaccharide-stimulated THP-1 cells. In summary, we find that the approach can contribute to solving the often very complex target deconvolution task.
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Affiliation(s)
- Aurelie Bornot
- AstraZeneca R&D, Discovery Sciences, Computational Biology, Macclesfield, Cheshire, UK
| | - Carolyn Blackett
- AstraZeneca R&D, Discovery Sciences, HTS, Macclesfield, Cheshire, UK
| | - Ola Engkvist
- AstraZeneca R&D, Discovery Sciences, Chemistry Innovation Centre, Mölndal, Sweden
| | - Clare Murray
- AstraZeneca R&D, New Opportunities, Macclesfield, Cheshire, UK
| | - Claus Bendtsen
- AstraZeneca R&D, Discovery Sciences, Computational Biology, Macclesfield, Cheshire, UK
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Dikicioglu D, Pir P, Oliver SG. Predicting complex phenotype-genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory. Biotechnol J 2013; 8:1017-34. [PMID: 24031036 PMCID: PMC3910164 DOI: 10.1002/biot.201300138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 07/15/2013] [Accepted: 08/07/2013] [Indexed: 11/08/2022]
Abstract
There is an increasing use of systems biology approaches in both "red" and "white" biotechnology in order to enable medical, medicinal, and industrial applications. The intricate links between genotype and phenotype may be explained through the use of the tools developed in systems biology, synthetic biology, and evolutionary engineering. Biomedical and biotechnological research are among the fields that could benefit most from the elucidation of this complex relationship. Researchers have studied fitness extensively to explain the phenotypic impacts of genetic variations. This elaborate network of dependencies and relationships so revealed are further complicated by the influence of environmental effects that present major challenges to our achieving an understanding of the cellular mechanisms leading to healthy or diseased phenotypes or optimized production yields. An improved comprehension of complex genotype-phenotype interactions and their accurate prediction should enable us to more effectively engineer yeast as a cell factory and to use it as a living model of human or pathogen cells in intelligent screens for new drugs. This review presents different methods and approaches undertaken toward improving our understanding and prediction of the growth phenotype of the yeast Saccharomyces cerevisiae as both a model and a production organism.
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Affiliation(s)
- Duygu Dikicioglu
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
| | - Pınar Pir
- Babraham Institute, Babraham Research Campus, CB22 3AT, Cambridge, UK
| | - Stephen G Oliver
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
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Iwaki A, Ohnuki S, Suga Y, Izawa S, Ohya Y. Vanillin inhibits translation and induces messenger ribonucleoprotein (mRNP) granule formation in saccharomyces cerevisiae: application and validation of high-content, image-based profiling. PLoS One 2013; 8:e61748. [PMID: 23637899 PMCID: PMC3634847 DOI: 10.1371/journal.pone.0061748] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 03/13/2013] [Indexed: 11/18/2022] Open
Abstract
Vanillin, generated by acid hydrolysis of lignocellulose, acts as a potent inhibitor of the growth of the yeast Saccharomyces cerevisiae. Here, we investigated the cellular processes affected by vanillin using high-content, image-based profiling. Among 4,718 non-essential yeast deletion mutants, the morphology of those defective in the large ribosomal subunit showed significant similarity to that of vanillin-treated cells. The defects in these mutants were clustered in three domains of the ribosome: the mRNA tunnel entrance, exit and backbone required for small subunit attachment. To confirm that vanillin inhibited ribosomal function, we assessed polysome and messenger ribonucleoprotein granule formation after treatment with vanillin. Analysis of polysome profiles showed disassembly of the polysomes in the presence of vanillin. Processing bodies and stress granules, which are composed of non-translating mRNAs and various proteins, were formed after treatment with vanillin. These results suggest that vanillin represses translation in yeast cells.
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Affiliation(s)
- Aya Iwaki
- The Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Kyoto, Japan
| | - Shinsuke Ohnuki
- The Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Yohei Suga
- The Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Shingo Izawa
- The Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Kyoto, Japan
| | - Yoshikazu Ohya
- The Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
- * E-mail:
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Trippier PC. Synthetic strategies for the biotinylation of bioactive small molecules. ChemMedChem 2013; 8:190-203. [PMID: 23303486 DOI: 10.1002/cmdc.201200498] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 12/07/2012] [Indexed: 01/19/2023]
Abstract
Biotinylation, the functional appendage of a biotin moiety to a bioactive compound (including small molecules and biological macromolecules), represents a common technique for identification of the intracellular binding partners that underlie the foundation of observed biological activity. Introduction of an attachment tether to the framework of a compound of interest must be planned at an early stage of development, and many considerations apply: 1) region of attachment, so as not to impede the pharmacophore; 2) stability of the parent molecular architecture to biotinylation conditions; 3) regioselectivity for the chosen tethering location over other reactive functionalities; 4) toxicity of reagents if biotinylation is to be performed in vitro; and 5) overall ease of synthesis. This review is intended to serve as a guide for the selection of appropriate tethering modalities. Examples of the common techniques used to affix biotin, including amide bond formation, [3+2] cycloadditions through "click" chemistry, Staudinger ligation, and thioether formation will be discussed, along with analysis of the wider applications of synthetic methodology that have been applied toward the biotinylation of small molecules.
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Affiliation(s)
- Paul C Trippier
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, USA.
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