1
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Wang Z, Zhang C, Wu J, Li B, Chrostowska A, Karamanis P, Liu SY. trans-Hydroalkynylation of Internal 1,3-Enynes Enabled by Cooperative Catalysis. J Am Chem Soc 2023; 145:5624-5630. [PMID: 36862947 PMCID: PMC10162690 DOI: 10.1021/jacs.3c00514] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
A cooperative catalyst system involving a Pd(0)/Senphos complex, tris(pentafluorophenyl)borane, copper bromide, and an amine base, is demonstrated to catalyze trans-hydroalkynylation of internal 1,3-enynes. For the first time, a Lewis acid catalyst is shown to promote the reaction involving the emerging outer-sphere oxidative reaction step. The resulting cross-conjugated dieneynes are versatile synthons for organic synthesis, and their characterization reveals distinct photophysical properties depending on the positioning of the donor/acceptor substituents along the conjugation path.
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Affiliation(s)
- Ziyong Wang
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467-3860, United States
| | - Chen Zhang
- Université de Pau et des Pays de l'Adour, E2S UPPA/CNRS, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux IPREM UMR 5254. Hélioparc, 2 Avenue P. Angot, 64053 Pau Cedex 09, France
| | - Jason Wu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467-3860, United States
| | - Bo Li
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467-3860, United States
| | - Anna Chrostowska
- Université de Pau et des Pays de l'Adour, E2S UPPA/CNRS, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux IPREM UMR 5254. Hélioparc, 2 Avenue P. Angot, 64053 Pau Cedex 09, France
| | - Panaghiotis Karamanis
- Université de Pau et des Pays de l'Adour, E2S UPPA/CNRS, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux IPREM UMR 5254. Hélioparc, 2 Avenue P. Angot, 64053 Pau Cedex 09, France
| | - Shih-Yuan Liu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467-3860, United States
- Université de Pau et des Pays de l'Adour, E2S UPPA/CNRS, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux IPREM UMR 5254. Hélioparc, 2 Avenue P. Angot, 64053 Pau Cedex 09, France
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2
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Bacheley L, Llopis Q, Westermeyer A, Guillamot G, Phansavath P, Ratovelomanana-Vidal V. Synthesis of 2-acetal-1,3-enynes by Sonogashira reaction of bromovinyl acetals with alkynes: application to the formal synthesis of a glucagon antagonist. NEW J CHEM 2022. [DOI: 10.1039/d2nj01541b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The preparation of functionalized 1,3-enynes bearing an acetal moiety at the 2-position has been studied through Sonogashira reaction of bromovinyl acetals with various alkyl- and aryl-substituted terminal alkynes.
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Affiliation(s)
- Lucas Bacheley
- PSL University, Chimie ParisTech, Institute of Chemistry for Life & Health Sciences, CNRS UMR8060, CSB2D Team, 11 rue Pierre et Marie Curie, 75005, Paris, France
- SEQENS, 2-8 rue de Rouen, ZI de Limay-Porcheville, 78440, Porcheville, France
| | - Quentin Llopis
- PSL University, Chimie ParisTech, Institute of Chemistry for Life & Health Sciences, CNRS UMR8060, CSB2D Team, 11 rue Pierre et Marie Curie, 75005, Paris, France
- SEQENS, 2-8 rue de Rouen, ZI de Limay-Porcheville, 78440, Porcheville, France
| | - Anne Westermeyer
- PSL University, Chimie ParisTech, Institute of Chemistry for Life & Health Sciences, CNRS UMR8060, CSB2D Team, 11 rue Pierre et Marie Curie, 75005, Paris, France
- SEQENS, 2-8 rue de Rouen, ZI de Limay-Porcheville, 78440, Porcheville, France
| | - Gérard Guillamot
- SEQENS, 2-8 rue de Rouen, ZI de Limay-Porcheville, 78440, Porcheville, France
| | - Phannarath Phansavath
- PSL University, Chimie ParisTech, Institute of Chemistry for Life & Health Sciences, CNRS UMR8060, CSB2D Team, 11 rue Pierre et Marie Curie, 75005, Paris, France
| | - Virginie Ratovelomanana-Vidal
- PSL University, Chimie ParisTech, Institute of Chemistry for Life & Health Sciences, CNRS UMR8060, CSB2D Team, 11 rue Pierre et Marie Curie, 75005, Paris, France
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3
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Bereketoglu C, Nacar G, Sari T, Mertoglu B, Pradhan A. Transcriptomic analysis of nonylphenol effect on Saccharomyces cerevisiae. PeerJ 2021; 9:e10794. [PMID: 33614281 PMCID: PMC7882136 DOI: 10.7717/peerj.10794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/28/2020] [Indexed: 11/29/2022] Open
Abstract
Nonylphenol (NP) is a bioaccumulative environmental estrogen that is widely used as a nonionic surfactant. We have previously examined short-term effects of NP on yeast cells using microarray technology. In the present study, we investigated the adaptive response of Saccharomyces cerevisiae BY4742 cells to NP exposure by analyzing genome-wide transcriptional profiles using RNA-sequencing. We used 2 mg/L NP concentration for 40 days of exposure. Gene expression analysis showed that a total of 948 genes were differentially expressed. Of these, 834 genes were downregulated, while 114 genes were significantly upregulated. GO enrichment analysis revealed that 369 GO terms were significantly affected by NP exposure. Further analysis showed that many of the differentially expressed genes were associated with oxidative phosphorylation, iron and copper acquisition, autophagy, pleiotropic drug resistance and cell cycle progression related processes such as DNA and mismatch repair, chromosome segregation, spindle checkpoint activity, and kinetochore organization. Overall, these results provide considerable information and a comprehensive understanding of the adaptive response to NP exposure at the gene expression level.
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Affiliation(s)
- Ceyhun Bereketoglu
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Iskenderun Technical University, Hatay, Turkey
| | - Gozde Nacar
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Tugba Sari
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Bulent Mertoglu
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Ajay Pradhan
- Biology, The Life Science Center, School of Science and Technology, Örebro University, Örebro, Sweden
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4
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Ueda Y, Tsurugi H, Mashima K. Cobalt‐Catalyzed
E
‐Selective Cross‐Dimerization of Terminal Alkynes: A Mechanism Involving Cobalt(0/II) Redox Cycles. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yohei Ueda
- Department of Chemistry Graduate School of Engineering Science Osaka University, Toyonaka Osaka Japan
| | - Hayato Tsurugi
- Department of Chemistry Graduate School of Engineering Science Osaka University, Toyonaka Osaka Japan
| | - Kazushi Mashima
- Department of Chemistry Graduate School of Engineering Science Osaka University, Toyonaka Osaka Japan
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5
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Ueda Y, Tsurugi H, Mashima K. Cobalt-Catalyzed E-Selective Cross-Dimerization of Terminal Alkynes: A Mechanism Involving Cobalt(0/II) Redox Cycles. Angew Chem Int Ed Engl 2019; 59:1552-1556. [PMID: 31710140 DOI: 10.1002/anie.201913835] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Indexed: 11/08/2022]
Abstract
A highly E-selective cross-dimerization of terminal alkynes with either terminal silylacetylenes, tert-butylacetylene, or 1-trimethylsilyloxy-1,1-diphenyl-2-propyne in the presence of a dichlorocobalt(II) complex bearing a sterically demanding 2,9-bis(2,4,6-triisopropylphenyl)-1,10-phenanthroline, activated with two equivalents of EtMgBr, gives a variety of (E)-1,3-enynes. A well-characterized diolefin/cobalt(0) complex, with divinyltetramethyldisiloxane, acted as a catalytically active species without any activation, clearly indicating that a cobalt(0) species is involved in the catalytic cycle.
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Affiliation(s)
- Yohei Ueda
- Department of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Hayato Tsurugi
- Department of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Kazushi Mashima
- Department of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
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6
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Chen S, Xie SH, Ai CY, Zhang XL. Palladium catalyzed cross-dimerization of terminal acetylenes and acrylates. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.03.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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7
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Pradhan TR, Kim HW, Park JK. Regiodivergent Synthesis of 1,3- and 1,4-Enynes through Kinetically Favored Hydropalladation and Ligand-Enforced Carbopalladation. Angew Chem Int Ed Engl 2018; 57:9930-9935. [DOI: 10.1002/anie.201805408] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Tapas R. Pradhan
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 46241 Korea
| | - Hong Won Kim
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 46241 Korea
| | - Jin Kyoon Park
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 46241 Korea
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8
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Pradhan TR, Kim HW, Park JK. Regiodivergent Synthesis of 1,3- and 1,4-Enynes through Kinetically Favored Hydropalladation and Ligand-Enforced Carbopalladation. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805408] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tapas R. Pradhan
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 46241 Korea
| | - Hong Won Kim
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 46241 Korea
| | - Jin Kyoon Park
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 46241 Korea
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9
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Ye C, Qian B, Li Y, Su M, Li D, Bao H. Iron-Catalyzed Dehydrative Alkylation of Propargyl Alcohol with Alkyl Peroxides To Form Substituted 1,3-Enynes. Org Lett 2018; 20:3202-3205. [PMID: 29786445 DOI: 10.1021/acs.orglett.8b01043] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This paper reports a new method for the generation of substituted 1,3-enynes, whose synthesis by other methods could be a challenge. The dehydrative decarboxylative cascade coupling reaction of propargyl alcohol with alkyl peroxides is enabled by an iron catalyst and alkylating reagents. Primary, secondary, and tertiary alkyl groups can be introduced into 1,3-enynes, affording various substituted 1,3-enynes in moderate to good yields. Mechanistic studies suggest the involvement of a radical-polar crossover pathway.
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Affiliation(s)
- Changqing Ye
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, State Key Laboratory of Structural Chemistry , Fujian Institute of Research on the Structure of Matter, Center for Excellence in Molecular Synthesis, Chinese Academy of Sciences , 155 Yangqiao Road West , Fuzhou , Fujian 350002 , P. R. China.,University of Chinese Academy of Sciences , Beijing , 100049 , P. R. China
| | - Bo Qian
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, State Key Laboratory of Structural Chemistry , Fujian Institute of Research on the Structure of Matter, Center for Excellence in Molecular Synthesis, Chinese Academy of Sciences , 155 Yangqiao Road West , Fuzhou , Fujian 350002 , P. R. China
| | - Yajun Li
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, State Key Laboratory of Structural Chemistry , Fujian Institute of Research on the Structure of Matter, Center for Excellence in Molecular Synthesis, Chinese Academy of Sciences , 155 Yangqiao Road West , Fuzhou , Fujian 350002 , P. R. China
| | - Min Su
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, State Key Laboratory of Structural Chemistry , Fujian Institute of Research on the Structure of Matter, Center for Excellence in Molecular Synthesis, Chinese Academy of Sciences , 155 Yangqiao Road West , Fuzhou , Fujian 350002 , P. R. China.,University of Chinese Academy of Sciences , Beijing , 100049 , P. R. China
| | - Daliang Li
- Biomedical Research Center of South China & College of Life Science , Fujian Normal University , No. 1 Keji Road, Shangjie , Fuzhou , Fujian 350117 , P. R. China
| | - Hongli Bao
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, State Key Laboratory of Structural Chemistry , Fujian Institute of Research on the Structure of Matter, Center for Excellence in Molecular Synthesis, Chinese Academy of Sciences , 155 Yangqiao Road West , Fuzhou , Fujian 350002 , P. R. China.,University of Chinese Academy of Sciences , Beijing , 100049 , P. R. China
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10
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Jin X, Zhu T, Zhang JZH, He X. Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes. Front Chem 2018; 6:150. [PMID: 29868556 PMCID: PMC5952040 DOI: 10.3389/fchem.2018.00150] [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: 01/30/2018] [Accepted: 04/16/2018] [Indexed: 01/13/2023] Open
Abstract
In this study, the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method was applied for NMR chemical shift calculations of protein-ligand complexes. In the AF-QM/MM approach, the protein binding pocket is automatically divided into capped fragments (within ~200 atoms) for density functional theory (DFT) calculations of NMR chemical shifts. Meanwhile, the solvent effect was also included using the Poission-Boltzmann (PB) model, which properly accounts for the electrostatic polarization effect from the solvent for protein-ligand complexes. The NMR chemical shifts of neocarzinostatin (NCS)-chromophore binding complex calculated by AF-QM/MM accurately reproduce the large-sized system results. The 1H chemical shift perturbations (CSP) between apo-NCS and holo-NCS predicted by AF-QM/MM are also in excellent agreement with experimental results. Furthermore, the DFT calculated chemical shifts of the chromophore and residues in the NCS binding pocket can be utilized as molecular probes to identify the correct ligand binding conformation. By combining the CSP of the atoms in the binding pocket with the Glide scoring function, the new scoring function can accurately distinguish the native ligand pose from decoy structures. Therefore, the AF-QM/MM approach provides an accurate and efficient platform for protein-ligand binding structure prediction based on NMR derived information.
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Affiliation(s)
- Xinsheng Jin
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, China
| | - Tong Zhu
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
| | - John Z. H. Zhang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
- Department of Chemistry, New York University, New York, NY, United States
| | - Xiao He
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
- National Engineering Research Centre for Nanotechnology, Shanghai, China
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11
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Henry JL, Posevins D, Yang B, Qiu Y, Bäckvall JE. Highly Selective Olefin-Assisted PdII
-Catalyzed Oxidative Alkynylation of Enallenes. Chemistry 2017; 23:7896-7899. [DOI: 10.1002/chem.201701654] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Jeffrey L. Henry
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University 10691 Stockholm Sweden
| | - Daniels Posevins
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University 10691 Stockholm Sweden
| | - Bin Yang
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University 10691 Stockholm Sweden
| | - Youai Qiu
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University 10691 Stockholm Sweden
| | - Jan-E. Bäckvall
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University 10691 Stockholm Sweden
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12
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Trost BM, Masters JT, Le Vaillant F, Lumb JP. Synthesis of a 1,3-Bridged Macrobicyclic Enyne via Chemoselective Cycloisomerization Using Palladium-Catalyzed Alkyne-Alkyne Coupling. J Org Chem 2016; 81:10023-10028. [PMID: 27648602 DOI: 10.1021/acs.joc.6b01920] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A unique intramolecular Pd-catalyzed alkyne-alkyne coupling is presented. This transformation generates a strained, 1,3-bridged, macrocyclic enyne. The process was readily executed on gram scale, and the structure of the product was elucidated via X-ray crystallographic analysis. A mechanistic rationale for the observed chemoselectivity is provided.
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Affiliation(s)
- Barry M Trost
- Department of Chemistry, Stanford University , Stanford, California 94305-4401, United States
| | - James T Masters
- Department of Chemistry, Stanford University , Stanford, California 94305-4401, United States
| | - Franck Le Vaillant
- Department of Chemistry, Stanford University , Stanford, California 94305-4401, United States
| | - Jean-Philip Lumb
- Department of Chemistry, Stanford University , Stanford, California 94305-4401, United States
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13
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Comparative transcriptome assembly and genome-guided profiling for Brettanomyces bruxellensis LAMAP2480 during p-coumaric acid stress. Sci Rep 2016; 6:34304. [PMID: 27678167 PMCID: PMC5039629 DOI: 10.1038/srep34304] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/07/2016] [Indexed: 11/08/2022] Open
Abstract
Brettanomyces bruxellensis has been described as the main contaminant yeast in wine production, due to its ability to convert the hydroxycinnamic acids naturally present in the grape phenolic derivatives, into volatile phenols. Currently, there are no studies in B. bruxellensis which explains the resistance mechanisms to hydroxycinnamic acids, and in particular to p-coumaric acid which is directly involved in alterations to wine. In this work, we performed a transcriptome analysis of B. bruxellensis LAMAP248rown in the presence and absence of p-coumaric acid during lag phase. Because of reported genetic variability among B. bruxellensis strains, to complement de novo assembly of the transcripts, we used the high-quality genome of B. bruxellensis AWRI1499, as well as the draft genomes of strains CBS2499 and0 g LAMAP2480. The results from the transcriptome analysis allowed us to propose a model in which the entrance of p-coumaric acid to the cell generates a generalized stress condition, in which the expression of proton pump and efflux of toxic compounds are induced. In addition, these mechanisms could be involved in the outflux of nitrogen compounds, such as amino acids, decreasing the overall concentration and triggering the expression of nitrogen metabolism genes.
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14
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Analysis of transcriptional profiles of Saccharomyces cerevisiae exposed to bisphenol A. Curr Genet 2016; 63:253-274. [DOI: 10.1007/s00294-016-0633-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/14/2016] [Accepted: 07/16/2016] [Indexed: 01/06/2023]
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15
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Trost BM, Masters JT. Transition metal-catalyzed couplings of alkynes to 1,3-enynes: modern methods and synthetic applications. Chem Soc Rev 2016; 45:2212-38. [PMID: 27086769 PMCID: PMC4837660 DOI: 10.1039/c5cs00892a] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The metal-catalyzed coupling of alkynes is a powerful method for the preparation of 1,3-enynes, compounds that are of broad interest in organic synthesis. Numerous strategies have been developed for the homo- and cross coupling of alkynes to enynes via transition metal catalysis. In such reactions, a major issue is the control of regio-, stereo-, and, where applicable, chemoselectivity. Herein, we highlight prominent methods for the selective synthesis of these valuable compounds. Further, we illustrate the utility of these processes through specific examples of their application in carbocycle, heterocycle, and natural product syntheses.
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Affiliation(s)
- Barry M Trost
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.
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16
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Jiao J, Wang S, Chen C, Liu Q, Xi C. Directly Oxidative Cross-Coupling between Alkenylzirconocene and Alkynylcopper Reagents. Organometallics 2016. [DOI: 10.1021/acs.organomet.6b00015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiajia Jiao
- Institute
of Chemistry and Chemical Engineering, Hebei Normal University, Shijiazhuang 050091, People’s Republic of China
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Sheng Wang
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Chao Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Qingbin Liu
- Institute
of Chemistry and Chemical Engineering, Hebei Normal University, Shijiazhuang 050091, People’s Republic of China
| | - Chanjuan Xi
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, People’s Republic of China
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17
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Garcia L, Franzoni S, Mussi F, Aumont-Niçaise M, Bertrand H, Desmadril M, Pelosi G, Buschini A, Policar C. Apo-neocarzinostatin: A protein carrier for Cu(II) glycocomplexes and Cu(II) into U937 and HT29 cell lines. J Inorg Biochem 2014; 135:40-4. [DOI: 10.1016/j.jinorgbio.2014.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 12/25/2013] [Accepted: 02/15/2014] [Indexed: 12/15/2022]
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18
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Moody P, Burlina F, Martin SR, Morgan RE, Offer J, Smith ME, Molloy JE, Caddick S. Evaluating the use of Apo-neocarzinostatin as a cell penetrating protein. Protein Eng Des Sel 2013; 26:277-81. [PMID: 23322746 PMCID: PMC3601848 DOI: 10.1093/protein/gzs104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 11/24/2012] [Accepted: 11/27/2012] [Indexed: 11/12/2022] Open
Abstract
Protein-ligand complex neocarzinostatin (NCS) is a small, thermostable protein-ligand complex that is able to deliver its ligand cargo into live mammalian cells where it induces DNA damage. Apo-NCS is able to functionally display complementarity determining regions loops, and has been hypothesised to act as a cell-penetrating protein, which would make it an ideal scaffold for cell targeting, and subsequent intracellular delivery of small-molecule drugs. In order to evaluate apo-NCS as a cell penetrating protein, we have evaluated the efficiency of its internalisation into live HeLa cells using matrix-assisted laser-desorption ionization-time-of-flight mass spectrometry and fluorescence microscopy. Following incubation of cells with apo-NCS, we observed no evidence of internalisation.
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Affiliation(s)
- Paul Moody
- Department of Chemistry, University College London, Gordon Street, London WC1H 0AJ, UK
- Division of Physical Biochemistry, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Fabienne Burlina
- UPMC Univ Paris 06, CNRS, ENS, UMR 7203, Laboratoire des Biomolécules, 4 place Jussieu, 75 005 Paris, France
| | - Stephen R. Martin
- Division of Physical Biochemistry, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Rachel E. Morgan
- Department of Chemistry, University College London, Gordon Street, London WC1H 0AJ, UK
| | - John Offer
- Division of Physical Biochemistry, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Mark E.B. Smith
- Department of Chemistry, University College London, Gordon Street, London WC1H 0AJ, UK
| | - Justin E. Molloy
- Division of Physical Biochemistry, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Stephen Caddick
- Division of Physical Biochemistry, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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19
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Xu HD, Zhang RW, Li X, Huang S, Tang W, Hu WH. Rhodium-catalyzed chemo- and regioselective cross-dimerization of two terminal alkynes. Org Lett 2013; 15:840-3. [PMID: 23356993 DOI: 10.1021/ol303531m] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cross-dimerization of terminal arylacetylenes and terminal propargylic alcohols/amides has been achieved in the presence of a rhodium catalyst. This method features high chemo- and regioselectivities rendering convenient and atom economical access to functionalized enynes.
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Affiliation(s)
- Hua-Dong Xu
- Shanghai Engineering Research Centre of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, 200062, China.
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20
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Burrill DR, Silver PA. Synthetic circuit identifies subpopulations with sustained memory of DNA damage. Genes Dev 2011; 25:434-9. [PMID: 21363961 DOI: 10.1101/gad.1994911] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Differential responses to stimuli can affect how cells succumb to disease. In yeast, DNA damage can create heterogeneous responses. To delineate how a response contributes to a cell's future behavior, we constructed a transcription-based memory circuit that detects DNA repair to isolate subpopulations with heritable damage responses. Strongly responsive cells show multigenerational effects, including growth defects and iron-associated gene expression. Less-responsive cells exhibit increased mutation frequencies but resume wild-type behavior. These two subpopulations remain distinct for multiple generations, indicating a transmissible memory of damage. Collectively, this work demonstrates the efficacy of using synthetic biology to define how environmental exposure contributes to distinct cell fates.
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Affiliation(s)
- Devin R Burrill
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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21
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Hariharan P, Sudhahar CG, Chou SH, Chin DH. Lipid Bilayer-Assisted Release of an Enediyne Antibiotic from Neocarzinostatin Chromoprotein. Biochemistry 2010; 49:7722-32. [DOI: 10.1021/bi100735v] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Parameswaran Hariharan
- Department of Chemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | | | - Shan-Ho Chou
- Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Der-Hang Chin
- Department of Chemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
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22
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Wang B, Merz Jr. KM. Importance of loop dynamics in the neocarzinostatin chromophore binding and release mechanisms. Phys Chem Chem Phys 2010; 12:3443-9. [DOI: 10.1039/b924951f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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23
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Lotito L, Russo A, Bueno S, Chillemi G, Fogli MV, Capranico G. A specific transcriptional response of yeast cells to camptothecin dependent on the Swi4 and Mbp1 factors. Eur J Pharmacol 2008; 603:29-36. [PMID: 19094980 DOI: 10.1016/j.ejphar.2008.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Revised: 12/01/2008] [Accepted: 12/03/2008] [Indexed: 10/21/2022]
Abstract
Topoisomerase I (Top1) is the specific target of the anticancer drug camptothecin (CPT) that interferes with enzyme activity promoting Top1-mediated DNA breaks and inhibition of DNA and RNA synthesis. To define the specific transcriptional response to CPT, we have determined the CPT-altered transcription profiles in yeast by using a relatively low concentration of the drug. CPT could alter global expression profiles only if a catalytically active Top1p was expressed in the cell, demonstrating that drug interference with Top1 was the sole trigger of the response. A total of 95 genes showed a statistically-significant alterations. Gene Ontology term analyses suggested that the cell response was mainly to the inhibition of nucleic acid synthesis and cell cycle progression. Promoter sequence analyses of the 22 up-regulated genes and expression studies in gene-deleted strains showed that the transcription factors, Swi4p and Mbp1p, mediate at least partially the transcriptional response to CPT. The MBP1 gene deletion abrogates a transient cell growth delay caused by CPT whereas the SWI4 gene deletion increases yeast resistance to CPT. Thus, the findings show that yeast cells have a highly selective and sensitive transcriptional response to CPT depending on SWI4 and MBP1 genes suggesting a complex regulation of cell cycle progression by the two factors in the presence of CPT.
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Affiliation(s)
- Luca Lotito
- G Moruzzi Department of Biochemistry, University of Bologna, Bologna, Italy
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24
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Affiliation(s)
- Peter C. Dedon
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, NE47-277, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
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25
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Baker JR, Woolfson DN, Muskett FW, Stoneman RG, Urbaniak MD, Caddick S. Protein–Small Molecule Interactions in Neocarzinostatin, the Prototypical Enediyne Chromoprotein Antibiotic. Chembiochem 2007; 8:704-17. [PMID: 17451164 DOI: 10.1002/cbic.200600534] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The enediyne chromoproteins are a class of potent antitumour antibiotics comprising a 1:1 complex of a protein and a noncovalently bound chromophore. The protein is required to protect and transport the highly labile chromophore, which acts as the cytotoxic component by reacting with DNA leading to strand cleavage. A derivative of the best-studied member of this class, neocarzinostatin (NCS), is currently in use as a chemotherapeutic in Japan. The application of the chromoproteins as therapeutics along with their unique mode of action has prompted widespread interest in this area. Notable developments include the discovery of non-natural ligands for the apoproteins and the observation that multiple binding modes are available for these ligands in the binding site. Mutation studies on the apoproteins have revealed much about their stability and variability, and the application of an in vitro evolution method has conferred new binding specificity for unrelated ligands. These investigations hold great promise for the application of the apoproteins for drug-delivery, transport and stabilisation systems.
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Affiliation(s)
- James R Baker
- University College London, Department of Chemistry, Christopher Ingold Laboratories, 20 Gordon Street, London, WC1H 0AJ, UK
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26
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Gamberi T, Cavalieri D, Magherini F, Mangoni ML, De Filippo C, Borro M, Gentile G, Simmaco M, Modesti A. An integrated analysis of the effects of Esculentin 1-21 on Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:688-700. [PMID: 17521974 DOI: 10.1016/j.bbapap.2007.04.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Revised: 04/03/2007] [Accepted: 04/05/2007] [Indexed: 11/19/2022]
Abstract
The antimicrobial peptide esculentin 1-21 (Esc 1-21) is a shorter synthetic version of the 46-residue peptide occurring in the Rana esculenta skin secretion. Here we propose an integrated proteomic and transcriptomic approach to interpret the biological effects of this peptide on Saccharomyces cerevisiae. We further investigated the response to this peptide by correlating the results of the transcriptome and proteome analysis with phenotypic effects. The results show that S. cerevisiae adapts to Esc 1-21 using the High Osmolarity Glycerol (HOG) pathway involved in osmotic tolerance and cell wall maintenance. Comparative proteomics reveals that Esc 1-21 causes downregulation of enzymes of the lower glycolytic pathway and in genes involved in spindle body formation and remodelling of cell-wall synthesis. Moreover the peptide induces downexpression of protein actin within 45 min and cells pre-treated with peptide show less sensitivity to osmotic stress and increased sensitivity to heat shock stress. The results obtained with the two different methodologies are in agreement at the cellular process levels. A combined approach may help elucidate the main aspects related to the effects of this peptide on the eukaryotic cell. The employment of different technologies may reveal the potential and limitations of each adapted approach in a prospective application for drug screening.
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Affiliation(s)
- Tania Gamberi
- Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, Viale G. Morgagni, 50 I-50134 Firenze, Italy
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27
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Desmyter L, Verstraelen J, Dewaele S, Libert C, Contreras R, Chen C. Nonclassical export pathway: overexpression of NCE102 reduces protein and DNA damage and prolongs lifespan in an SGS1 deficient Saccharomyces cerevisiae. Biogerontology 2007; 8:527-35. [PMID: 17415679 DOI: 10.1007/s10522-007-9095-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Accepted: 03/05/2007] [Indexed: 01/12/2023]
Abstract
In this study, we used our recently developed screening method, Bud-Scar-based Screening (BSS), to screen a yeast cDNA expression library in an SGS1 deletion BY4742 yeast strain. One gene involved in a nonclassical export pathway, NCE102, was found to extend the life span of Deltasgs1 yeast. Deletion of NCE102 in a wild type yeast strain increased its sensitivity to oxidative stress upon diethylmaleate (DEM) treatment but did not shorten its lifespan, indicating that this gene is not essential in determining yeast lifespan. Transformation of NCE102 into either Deltance102 or Deltasgs1 strains could rescue its tolerance to DEM stress, indicating that NCE102 is protective during oxidative stress. Moreover, overexpression of NCE102 in Deltasgs1 strain leads to reduced protein damage. However, overexpression of NCE102 in wild type yeast strain BY4742 neither protected against oxidative stress due to DEM nor extended yeast lifespan compared to its parental wild type strain, indicating that nonclassical export is redundant and DNA repair is fully sufficient in the wild type strain. We therefore demonstrate that a nonclassical export pathway functions as an alternative clearance/detoxification pathway to eliminate damaged material, when the basic repair pathway is not sufficient.
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28
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The DNA-damage signature in Saccharomyces cerevisiae is associated with single-strand breaks in DNA. BMC Genomics 2006; 7:313. [PMID: 17163986 PMCID: PMC1764021 DOI: 10.1186/1471-2164-7-313] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Accepted: 12/12/2006] [Indexed: 11/18/2022] Open
Abstract
Background Upon exposure to agents that damage DNA, Saccharomyces cerevisiae undergo widespread reprogramming of gene expression. Such a vast response may be due not only to damage to DNA but also damage to proteins, RNA, and lipids. Here the transcriptional response of S. cerevisiae specifically induced by DNA damage was discerned by exposing S. cerevisiae to a panel of three "radiomimetic" enediyne antibiotics (calicheamicin γ1I, esperamicin A1 and neocarzinostatin) that bind specifically to DNA and generate varying proportions of single- and double-strand DNA breaks. The genome-wide responses were compared to those induced by the non-selective oxidant γ-radiation. Results Given well-controlled exposures that resulted in similar and minimal cell death (~20–25%) across all conditions, the extent of gene expression modulation was markedly different depending on treatment with the enediynes or γ-radiation. Exposure to γ-radiation resulted in more extensive transcriptional changes classified both by the number of genes modulated and the magnitude of change. Common biological responses were identified between the enediynes and γ-radiation, with the induction of DNA repair and stress response genes, and the repression of ribosomal biogenesis genes. Despite these common responses, a fraction of the response induced by gamma radiation was repressed by the enediynes and vise versa, suggesting that the enediyne response is not entirely "radiomimetic." Regression analysis identified 55 transcripts with gene expression induction associated both with double- or single-strand break formation. The S. cerevisiae "DNA damage signature" genes as defined by Gasch et al. [1] were enriched among regulated transcripts associated with single-strand breaks, while genes involved in cell cycle regulation were associated with double-strand breaks. Conclusion Dissection of the transcriptional response in yeast that is specifically signaled by DNA strand breaks has identified that single-strand breaks provide the signal for activation of transcripts encoding proteins involved in the DNA damage signature in S. cerevisiae, and double-strand breaks signal changes in cell cycle regulation genes.
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29
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Kitanovic A, Wölfl S. Fructose-1,6-bisphosphatase mediates cellular responses to DNA damage and aging in Saccharomyces cerevisiae. Mutat Res 2006; 594:135-47. [PMID: 16199065 DOI: 10.1016/j.mrfmmm.2005.08.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2005] [Revised: 08/13/2005] [Accepted: 08/24/2005] [Indexed: 05/04/2023]
Abstract
Response to DNA damage, lack of nutrients and other stress conditions is an essential property of living systems. The coordinate response includes DNA damage repair, activation of alternate biochemical pathways, adjustment of cellular proliferation and cell cycle progression as well as drastic measures like cellular suicide which prevents proliferation of severely damaged cells. Investigating the transcriptional response of Saccharomyces cerevisiae to low doses of the alkylating agent methylmethane sulfonate (MMS) we observed induction of genes involved in glucose metabolism. RT-PCR analysis showed that the expression of the key enzyme in gluconeogenesis fructose-1,6-bisphosphatase (FBP1) was clearly up-regulated by MMS in glucose-rich medium. Interestingly, deletion of FBP1 led to reduced sensitivity to MMS, but not to other DNA-damaging agents, such as 4-NQO or phleomycin. Reintroduction of FBP1 in the knockout restored the wild-type phenotype while overexpression increased MMS sensitivity of wild-type, shortened life span and increased induction of RNR2 after treatment with MMS. Deletion of FBP1 reduced production of reactive oxygen species (ROS) in response to MMS treatment and in untreated aged cells, and increased the amount of cells able to propagate and to form colonies, but had no influence on the genotoxic effect of MMS. Our results indicate that FBP1 influences the connection between DNA damage, aging and oxidative stress through either direct signalling or an intricate adaptation in energy metabolism.
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Affiliation(s)
- Ana Kitanovic
- Institut für Pharmazie und Molekulare Biotechnologie, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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30
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Singh RK, Krishna M. DNA strand breaks signal the induction of DNA double-strand break repair in Saccharomyces cerevisiae. Radiat Res 2006; 164:781-90. [PMID: 16296884 DOI: 10.1667/rr3460.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Genotoxic stress induces a checkpoint signaling cascade to generate a stress response. Saccharomyces cerevisiae shows an altered radiation response under different type of stress. Although the induction of repair has been implicated in enhanced survival after exposure to the challenging stress, the nature of the signal remains poorly understood. This study demonstrates that low doses of gamma radiation and bleomycin induce RAD52-dependent recombination repair pathway in the wild-type strain D-261. Prior exposure of cells to DNA-damaging agents (gamma radiation or bleomycin) equips them better for the subsequent damage caused by challenging doses. However, exposure to UV light, which does not cause strand breaks, was ineffective. This was confirmed by PFGE studies. This indicates that the strand breaks probably serve as the signal for induction of the recombination repair pathway while pyrimidine dimers do not. The nature of the induced repair was investigated by mutation scoring in special strain D-7, which showed that the induced repair is essentially error free.
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Affiliation(s)
- Rakesh Kumar Singh
- Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India 400085.
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31
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Wu HI, Brown JA, Dorie MJ, Lazzeroni L, Brown JM. Genome-Wide Identification of Genes Conferring Resistance to the Anticancer Agents Cisplatin, Oxaliplatin, and Mitomycin C. Cancer Res 2004; 64:3940-8. [PMID: 15173006 DOI: 10.1158/0008-5472.can-03-3113] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cisplatin is a crucial agent in the treatment of many solid tumors, yet many tumors have either acquired or intrinsic resistance to the drug. We have used the homozygous diploid deletion pool of Saccharomyces cerevisiae, containing 4728 strains with individual deletion of all nonessential genes, to systematically identify genes that when deleted confer sensitivity to the anticancer agents cisplatin, oxaliplatin, and mitomycin C. We found that deletions of genes involved in nucleotide excision repair, recombinational repair, postreplication repair including translesional synthesis, and DNA interstrand cross-link repair resulted in sensitivity to all three of the agents, although with some differences between the platinum drugs and mitomycin C in the spectrum of required translesional polymerases. Putative defective repair of oxidative damage (imp2'Delta strain) also resulted in sensitivity to platinum and oxaliplatin, but not to mitomycin C. Surprisingly in light of their different profiles of clinical activity, cisplatin and oxaliplatin have very similar sensitivity profiles. Finally, we identified three novel genes (PSY1-3, "platinum sensitivity") that, when deleted, demonstrate sensitivity to cisplatin and oxaliplatin, but not to mitomycin C. Our results emphasize the importance of multiple DNA repair pathways responsible for normal cellular resistance to all three of the agents. Also, the similarity of the sensitivity profiles of the platinum agents with that of the known DNA interstrand cross-linking agent mitomycin C, and the importance of the gene PSO2 known to be involved in DNA interstrand cross-link repair strongly suggests that interstrand cross-links are important toxic lesions for cisplatin and oxaliplatin, at least in yeast.
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Affiliation(s)
- H Irene Wu
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California 94305-5152, USA
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32
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Nicaise M, Valerio-Lepiniec M, Minard P, Desmadril M. Affinity transfer by CDR grafting on a nonimmunoglobulin scaffold. Protein Sci 2004; 13:1882-91. [PMID: 15169956 PMCID: PMC2279932 DOI: 10.1110/ps.03540504] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Neocarzinostatin (NCS) is a small "all beta" protein displaying the same overall fold as immunoglobulins. This protein possesses a well-defined hydrophobic core and two loops structurally equivalent to the CDR1 and CDR3 of immunoglobulins. NCS is the most studied member of the enediynechromoprotein family, and is clinically used as an antitumoral agent. NCS has promise as a drug delivery vehicle if new binding specificities could be conferred on its protein scaffold. Previous studies have shown that the binding specificity of the crevasse can be extended to compounds completely unrelated to the natural enediyne chromophore family. We show here that it is possible to introduce new interaction capacities to obtain a protein useful for drug targeting by modifying the immunoglobulin CDR-like loops. We transferred the CDR3 of the VHH chain of camel antilysozyme immunoglobulin to the equivalent site in the corresponding loop of neocarzinostatin. We then evaluated the stability of the resulting structure and its affinity for lysozyme. The engineered NCS-CDR3 presents a structure similar to that of the wild-type NCS, and is stable and efficiently produced. ELISA, ITC, and SPR measurements demonstrated that the new NCS-CDR3 specifically bound lysozyme.
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Affiliation(s)
- Magali Nicaise
- Laboratoire de Modélisation et d'Ingénierie des Protéines, UMR8619, Université de Paris-Sud, Bât 430, F-91405 Orsay Cedex, France
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33
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Woyke T, Berens ME, Hoelzinger DB, Pettit GR, Winkelmann G, Pettit RK. Differential gene expression in auristatin PHE-treated Cryptococcus neoformans. Antimicrob Agents Chemother 2004; 48:561-7. [PMID: 14742210 PMCID: PMC321525 DOI: 10.1128/aac.48.2.561-567.2004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The antifungal pentapeptide auristatin PHE was recently shown to interfere with microtubule dynamics and nuclear and cellular division in the opportunistic pathogen Cryptococcus neoformans. To gain a broader understanding of the cellular response of C. neoformans to auristatin PHE, mRNA differential display (DD) and reverse transcriptase PCR (RT-PCR) were applied. Examination of approximately 60% of the cell transcriptome from cells treated with 1.5 times the MIC (7.89 micro M) of auristatin PHE for 90 min revealed 29 transcript expression differences between control and drug-treated populations. Differential expression of seven of the transcripts was confirmed by RT-PCR, as was drug-dependent modulation of an additional seven transcripts by RT-PCR only. Among genes found to be differentially expressed were those encoding proteins involved in transport, cell cycle regulation, signal transduction, cell stress, DNA repair, nucleotide metabolism, and capsule production. For example, RHO1 and an open reading frame (ORF) encoding a protein with 91% similarity to the Schizophyllum commune 14-3-3 protein, both involved in cell cycle regulation, were down-regulated, as was the gene encoding the multidrug efflux pump Afr1p. An ORF encoding a protein with 57% identity to the heat shock protein HSP104 in Pleurotus sajor-caju was up-regulated. Also, three transcripts of unknown function were responsive to auristatin PHE, which may eventually contribute to the elucidation of the function of their gene products. Further study of these differentially expressed genes and expression of their corresponding proteins are warranted to evaluate how they may be involved in the mechanism of action of auristatin PHE. This information may also contribute to an explanation of the selectivity of auristatin PHE for C. neoformans. This is the first report of drug action using DD in C. neoformans.
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MESH Headings
- Antifungal Agents/pharmacology
- Biological Transport, Active/drug effects
- Biological Transport, Active/genetics
- Cell Cycle/drug effects
- Cell Cycle/genetics
- Cloning, Molecular
- Cryptococcus neoformans/drug effects
- Cryptococcus neoformans/genetics
- Cryptococcus neoformans/metabolism
- Culture Media
- DNA Repair/drug effects
- DNA Repair/genetics
- DNA, Complementary/biosynthesis
- DNA, Complementary/genetics
- Fungal Proteins/biosynthesis
- Fungal Proteins/genetics
- Gene Expression Regulation, Fungal/drug effects
- Microbial Sensitivity Tests
- Oligopeptides/pharmacology
- Purines/biosynthesis
- RNA, Fungal/biosynthesis
- RNA, Fungal/isolation & purification
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Signal Transduction/drug effects
- Signal Transduction/genetics
- Transcription, Genetic/drug effects
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Affiliation(s)
- Tanja Woyke
- Cancer Research Institute, Arizona State University, Tempe, Arizona 85287, USA
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34
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Kang B, Kim DH, Do Y, Chang S. Conjugated enynes as a new type of substrates for olefin metathesis. Org Lett 2003; 5:3041-3. [PMID: 12916976 DOI: 10.1021/ol035014z] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] It has been demonstrated for the first time that conjugated enynes can be employed as a facile substrate in olefin metathesis with the use of a bispyridine-substituted ruthenium benzylidene catalyst. Cross-metathesis of the enynes with alkenes turns out to proceed with preferential formation of (Z)-isomers over (E)-isomers up to >25:1 in moderate to good yields. The intramolecular version of conjugated enynes affords novel butadienyl cycloalkenes, which are a highly useful synthetic building blocks, in acceptable yields.
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Affiliation(s)
- Byungman Kang
- Center for Molecular Design and Synthesis, Department of Chemistry and School of Molecular Science (BK21), Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
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35
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Chen MH, Citovsky V. Systemic movement of a tobamovirus requires host cell pectin methylesterase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 35:771-86. [PMID: 12887589 DOI: 10.1046/j.1365-313x.2003.01847.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Systemic movement of plant viruses through the host vasculature, one of the central events of the infection process, is essential for maximal viral accumulation and development of disease symptoms. The host plant proteins involved in this transport, however, remain unknown. Here, we examined whether or not pectin methylesterase (PME), one of the few cellular proteins known to be involved in local, cell-to-cell movement of tobacco mosaic virus (TMV), is also required for the systemic spread of viral infection through the plant vascular system. In a reverse genetics approach, PME levels were reduced in tobacco plants using antisense suppression. The resulting PME antisense plants displayed a significant degree of PME suppression in their vascular tissues but retained the wild-type pattern of phloem loading and unloading of a fluorescent solute. Systemic transport of TMV in these plants, however, was substantially delayed as compared to the wild-type tobacco, suggesting a role for PME in TMV systemic infection. Our analysis of virus distribution in the PME antisense plants suggested that TMV systemic movement may be a polar process in which the virions enter and exit the vascular system by two different mechanisms, and it is the viral exit out of the vascular system that involves PME.
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Affiliation(s)
- Min-Huei Chen
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA
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36
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Birrell GW, Brown JA, Wu HI, Giaever G, Chu AM, Davis RW, Brown JM. Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents. Proc Natl Acad Sci U S A 2002; 99:8778-83. [PMID: 12077312 PMCID: PMC124375 DOI: 10.1073/pnas.132275199] [Citation(s) in RCA: 195] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2002] [Indexed: 12/20/2022] Open
Abstract
The recent completion of the deletion of all of the nonessential genes in budding yeast has provided a powerful new way of determining those genes that affect the sensitivity of this organism to cytotoxic agents. We have used this system to test the hypothesis that genes whose transcription is increased after DNA damage are important for the survival to that damage. We used a pool of 4,627 diploid strains each with homozygous deletion of a nonessential gene to identify those genes that are important for the survival of yeast to four DNA-damaging agents: ionizing radiation, UV radiation, and exposure to cisplatin or to hydrogen peroxide. In addition we measured the transcriptional response of the wild-type parental strain to the same DNA-damaging agents. We found no relationship between the genes necessary for survival to the DNA-damaging agents and those genes whose transcription is increased after exposure. These data show that few, if any, of the genes involved in repairing the DNA lesions produced in this study, including double-strand breaks, pyrimidine dimers, single-strand breaks, base damage, and DNA cross-links, are induced in response to toxic doses of the agents that produce these lesions. This finding suggests that the enzymes necessary for the repair of these lesions are at sufficient levels within the cell. The data also suggest that the nature of the lesions produced by DNA-damaging agents cannot easily be deduced from gene expression profiling.
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Affiliation(s)
- Geoff W Birrell
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
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37
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Plowright AT, Schaus SE, Myers AG. Transcriptional response pathways in a yeast strain sensitive to saframycin a and a more potent analog: evidence for a common basis of activity. CHEMISTRY & BIOLOGY 2002; 9:607-18. [PMID: 12031667 DOI: 10.1016/s1074-5521(02)00137-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Saframycin A (SafA) is a natural product that inhibits human cancer cell proliferation. Its synthetic analog, QAD, is a more potent inhibitor of these cells. SafA does not affect wild-type yeast, but it does inhibit growth of the strain CCY333 (DeltaPDR1/PDR3/ERG6) (IC50 = 0.9 microM). QAD is also a more effective inhibitor of CCY333 growth (IC50 = 0.4 microM). Transcription profiling of SafA- and QAD-treated CCY333 cultures showed that both drugs generated nearly identical profiles, with altered expression levels (> or =2-fold) of more than 240 genes. Both agents induced the overexpression of genes involved in glycolysis, oxidative stress, and protein degradation and repressed genes encoding histones, biosynthetic enzymes, and the cellular import machinery. Significantly, neither drug affected the expression of known DNA-damage repair genes, as might have been expected if their primary mechanism of action involved the covalent modification of DNA.
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Affiliation(s)
- Alleyn T Plowright
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
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Current awareness on yeast. Yeast 2002; 19:285-92. [PMID: 11816036 DOI: 10.1002/yea.821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In order to keep subscribers up-to-date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly-published material on yeasts. Each bibliography is divided into 10 sections. 1 Books, Reviews & Symposia; 2 General; 3 Biochemistry; 4 Biotechnology; 5 Cell Biology; 6 Gene Expression; 7 Genetics; 8 Physiology; 9 Medical Mycology; 10 Recombinant DNA Technology. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted. (3 weeks journals - search completed 5th. Dec. 2001)
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Bar-Shira A, Rashi-Elkeles S, Zlochover L, Moyal L, Smorodinsky NI, Seger R, Shiloh Y. ATM-dependent activation of the gene encoding MAP kinase phosphatase 5 by radiomimetic DNA damage. Oncogene 2002; 21:849-55. [PMID: 11850813 DOI: 10.1038/sj.onc.1205127] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2001] [Revised: 10/29/2001] [Accepted: 10/31/2001] [Indexed: 12/17/2022]
Abstract
Cellular responses to DNA damage are mediated by an extensive network of signaling pathways. The ATM protein kinase is a master regulator of the response to double-strand breaks (DSBs), the most cytotoxic DNA lesion caused by ionizing radiation. ATM is the protein missing or inactive in patients with the pleiotropic genetic disorder ataxia-telangiectasia (A-T). A major response to DNA damage is altered expression of numerous genes. While studying gene expression in control and A-T cells following treatment with the radiomimetic chemical neocarzinostatin (NCS), we identified an expressed sequence tag that represented a gene that was induced by DSBs in an ATM-dependent manner. The corresponding cDNA encoded a dual specificity phosphatase of the MAP kinase phosphatase family, MKP-5. MKP-5 dephosphorylates and inactivates the stress-activated MAP kinases JNK and p38. The phosphorylation-dephosphorylation cycle of JNK and p38 by NCS was attenuated in A-T cells. Thus, ATM modulates this cycle in response to DSBs. These results further highlight ATM as a link between the DNA damage response and major signaling pathways involved in proliferative and apoptotic processes.
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Affiliation(s)
- Anat Bar-Shira
- The David and Inez Myers Laboratory for Genetic Research, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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