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Ni X, Li S, Yuan Y, Chang R, Liu Q, Liu Z, Li Z, Wang Y. Effect of siaD on Ag-8 to improve resistance to crown gall in grapes and related mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:108869. [PMID: 39142011 DOI: 10.1016/j.plaphy.2024.108869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 08/16/2024]
Abstract
Crown gall caused by Agrobacterium vitis (A. vitis) is one of the crucial issues restricting the to grape industry. In this study, Agrobacterium tumefaciens (Ag-8) was separated from the soil that could prevent the occurrence of grape crown gall. By the mutagenesis of Ag-8 transposon, the siaD gene deletion strain (ΔsiaD) showed significantly lower efficacy in grape and tomato plants for controlling grape crown gall, but the relevant mechanism was not clear. The biofilm formation and motility of ΔsiaD were significantly decreased, and the colonization ability of ΔsiaD in tomato roots was significantly reduced. RNA-seq analysis showed that the expression of nemR significantly reduced in the ΔsiaD and that the expression of nemR showed a high correlation with biofilm and motility. Further studies showed that the nemR gene deletion strain of Ag-8 (ΔnemR) showed significantly reduced motility, biofilm formation and control of grape crown gall compared to Ag-8, and the nemR gene complementary strain of Ag-8 (ΔnemR-comp) recovered to Ag-8 wild-type levels. The inoculation experiments of preventive, curative or simultaneous treatment further showed that the preferential inoculation with Ag-8 reduced the incidence of grape crown gall on tomato plants, and studies showed that the mutation of siaD affected the site competition between Ag-8 and A. vitis, and that the mutation of nemR was consistent with the previous results. This study provides a new strategy for the prevention and control of grape crown gall, which is of great significance to the grape industry to increase production and income.
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Affiliation(s)
- Xuemei Ni
- Tianjin Agricultural University, College of Horticulture and Landscape Architecture, Tianjin, 300394, China
| | - Shiyu Li
- Tianjin Agricultural University, College of Horticulture and Landscape Architecture, Tianjin, 300394, China
| | - Yujin Yuan
- Tianjin Agricultural University, College of Horticulture and Landscape Architecture, Tianjin, 300394, China
| | - Ruokui Chang
- Tianjin Agricultural University, College of Engineering and Technology Architecture, Tianjin, 300394, China
| | - Quanyong Liu
- Tianjin Agricultural University, College of Horticulture and Landscape Architecture, Tianjin, 300394, China
| | - Zhenxing Liu
- Tianjin Agricultural University, College of Horticulture and Landscape Architecture, Tianjin, 300394, China
| | - Zhuoran Li
- Tianjin Agricultural University, College of Horticulture and Landscape Architecture, Tianjin, 300394, China.
| | - Yuanhong Wang
- Tianjin Agricultural University, College of Horticulture and Landscape Architecture, Tianjin, 300394, China.
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2
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Moréra S, Vigouroux A, Aumont-Nicaise M, Ahmar M, Meyer T, El Sahili A, Deicsics G, González-Mula A, Li S, Doré J, Sirigu S, Legrand P, Penot C, André F, Faure D, Soulère L, Queneau Y, Vial L. A highly conserved ligand-binding site for AccA transporters of antibiotic and quorum-sensing regulator in Agrobacterium leads to a different specificity. Biochem J 2024; 481:93-117. [PMID: 38058289 DOI: 10.1042/bcj20230273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/08/2023]
Abstract
Plants genetically modified by the pathogenic Agrobacterium strain C58 synthesize agrocinopines A and B, whereas those modified by the pathogenic strain Bo542 produce agrocinopines C and D. The four agrocinopines (A, B, C and D) serve as nutrients by agrobacteria and signaling molecule for the dissemination of virulence genes. They share the uncommon pyranose-2-phosphate motif, represented by the l-arabinopyranose moiety in agrocinopines A/B and the d-glucopyranose moiety in agrocinopines C/D, also found in the antibiotic agrocin 84. They are imported into agrobacterial cytoplasm via the Acc transport system, including the solute-binding protein AccA coupled to an ABC transporter. We have previously shown that unexpectedly, AccA from strain C58 (AccAC58) recognizes the pyranose-2-phosphate motif present in all four agrocinopines and agrocin 84, meaning that strain C58 is able to import agrocinopines C/D, originating from the competitor strain Bo542. Here, using agrocinopine derivatives and combining crystallography, affinity and stability measurements, modeling, molecular dynamics, in vitro and vivo assays, we show that AccABo542 and AccAC58 behave differently despite 75% sequence identity and a nearly identical ligand binding site. Indeed, strain Bo542 imports only compounds containing the d-glucopyranose-2-phosphate moiety, and with a lower affinity compared with strain C58. This difference in import efficiency makes C58 more competitive than Bo542 in culture media. We can now explain why Agrobacterium/Allorhizobium vitis strain S4 is insensitive to agrocin 84, although its genome contains a conserved Acc transport system. Overall, our work highlights AccA proteins as a case study, for which stability and dynamics drive specificity.
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Affiliation(s)
- Solange Moréra
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Armelle Vigouroux
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Magali Aumont-Nicaise
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Mohammed Ahmar
- Univ Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, CNRS, Université Lyon 1, INSA Lyon, CPE Lyon, ICBMS, UMR 5246; Université Claude Bernard, Bâtiment Lederer, 69622 Villeurbanne Cedex, France
| | - Thibault Meyer
- UMR Ecologie Microbienne, CNRS, INRAE, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, F-69622 Lyon, France
| | - Abbas El Sahili
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Grégory Deicsics
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Almudena González-Mula
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Sizhe Li
- Univ Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, CNRS, Université Lyon 1, INSA Lyon, CPE Lyon, ICBMS, UMR 5246; Université Claude Bernard, Bâtiment Lederer, 69622 Villeurbanne Cedex, France
| | - Jeanne Doré
- UMR Ecologie Microbienne, CNRS, INRAE, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, F-69622 Lyon, France
| | - Serena Sirigu
- Synchrotron SOLEIL, HelioBio Group, 91190 Saint-Aubin, France
| | - Pierre Legrand
- Synchrotron SOLEIL, HelioBio Group, 91190 Saint-Aubin, France
| | - Camille Penot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - François André
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Denis Faure
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Laurent Soulère
- Univ Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, CNRS, Université Lyon 1, INSA Lyon, CPE Lyon, ICBMS, UMR 5246; Université Claude Bernard, Bâtiment Lederer, 69622 Villeurbanne Cedex, France
| | - Yves Queneau
- Univ Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, CNRS, Université Lyon 1, INSA Lyon, CPE Lyon, ICBMS, UMR 5246; Université Claude Bernard, Bâtiment Lederer, 69622 Villeurbanne Cedex, France
| | - Ludovic Vial
- UMR Ecologie Microbienne, CNRS, INRAE, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, F-69622 Lyon, France
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3
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Ishii T, Tsuchida N, Hemelda NM, Saito K, Bao J, Watanabe M, Toyoda A, Matsubara T, Sato M, Toyooka K, Ishihama N, Shirasu K, Matsui H, Toyoda K, Ichinose Y, Hayashi T, Kawaguchi A, Noutoshi Y. Rhizoviticin is an alphaproteobacterial tailocin that mediates biocontrol of grapevine crown gall disease. THE ISME JOURNAL 2024; 18:wrad003. [PMID: 38365227 PMCID: PMC10811719 DOI: 10.1093/ismejo/wrad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 02/18/2024]
Abstract
Tailocins are headless phage tail structures that mediate interbacterial antagonism. Although the prototypical tailocins, R- and F-pyocins, in Pseudomonas aeruginosa, and other predominantly R-type tailocins have been studied, their presence in Alphaproteobacteria remains unexplored. Here, we report the first alphaproteobacterial F-type tailocin, named rhizoviticin, as a determinant of the biocontrol activity of Allorhizobium vitis VAR03-1 against crown gall. Rhizoviticin is encoded by a chimeric prophage genome, one providing transcriptional regulators and the other contributing to tail formation and cell lysis, but lacking head formation genes. The rhizoviticin genome retains a nearly intact early phage region containing an integrase remnant and replication-related genes critical for downstream gene transcription, suggesting an ongoing transition of this locus from a prophage to a tailocin-coding region. Rhizoviticin is responsible for the most antagonistic activity in VAR03-1 culture supernatant against pathogenic A. vitis strain, and rhizoviticin deficiency resulted in a significant reduction in the antitumorigenic activity in planta. We identified the rhizoviticin-coding locus in eight additional A. vitis strains from diverse geographical locations, highlighting a unique survival strategy of certain Rhizobiales bacteria in the rhizosphere. These findings advance our understanding of the evolutionary dynamics of tailocins and provide a scientific foundation for employing rhizoviticin-producing strains in plant disease control.
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Affiliation(s)
- Tomoya Ishii
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Natsuki Tsuchida
- Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan
- Present address: Division of Biological Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Niarsi Merry Hemelda
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Department of Biology, University of Indonesia, Depok 16424, Indonesia
| | - Kirara Saito
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Present address: Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Miyazaki 885-0091, Japan
| | - Jiyuan Bao
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Megumi Watanabe
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takehiro Matsubara
- Okayama University Hospital Biobank, Okayama University Hospital, Okayama 700-8558, Japan
| | - Mayuko Sato
- Mass Spectrometry and Microscopy Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Kiminori Toyooka
- Mass Spectrometry and Microscopy Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Nobuaki Ishihama
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Ken Shirasu
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
- Graduate School of Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Hidenori Matsui
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan
| | - Kazuhiro Toyoda
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan
| | - Yuki Ichinose
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Akira Kawaguchi
- Western Region Agricultural Research Center (WARC), National Agricultural and Food Research Organization (NARO), Fukuyama, Hiroshima 721-8514, Japan
| | - Yoshiteru Noutoshi
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan
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4
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Brown PJB, Chang JH, Fuqua C. Agrobacterium tumefaciens: a Transformative Agent for Fundamental Insights into Host-Microbe Interactions, Genome Biology, Chemical Signaling, and Cell Biology. J Bacteriol 2023; 205:e0000523. [PMID: 36892285 PMCID: PMC10127608 DOI: 10.1128/jb.00005-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
Agrobacterium tumefaciens incites the formation of readily visible macroscopic structures known as crown galls on plant tissues that it infects. Records from biologists as early as the 17th century noted these unusual plant growths and began examining the basis for their formation. These studies eventually led to isolation of the infectious agent, A. tumefaciens, and decades of study revealed the remarkable mechanisms by which A. tumefaciens causes crown gall through stable horizontal genetic transfer to plants. This fundamental discovery generated a barrage of applications in the genetic manipulation of plants that is still under way. As a consequence of the intense study of A. tumefaciens and its role in plant disease, this pathogen was developed as a model for the study of critical processes that are shared by many bacteria, including host perception during pathogenesis, DNA transfer and toxin secretion, bacterial cell-cell communication, plasmid biology, and more recently, asymmetric cell biology and composite genome coordination and evolution. As such, studies of A. tumefaciens have had an outsized impact on diverse areas within microbiology and plant biology that extend far beyond its remarkable agricultural applications. In this review, we attempt to highlight the colorful history of A. tumefaciens as a study system, as well as current areas that are actively demonstrating its value and utility as a model microorganism.
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Affiliation(s)
- Pamela J. B. Brown
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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5
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Hoffmann G, Le Gorrec M, Mestdach E, Cusack S, Salmon L, Jensen MR, Palencia A. Adenosine-Dependent Activation Mechanism of Prodrugs Targeting an Aminoacyl-tRNA Synthetase. J Am Chem Soc 2023; 145:800-810. [PMID: 36599057 PMCID: PMC9853866 DOI: 10.1021/jacs.2c04808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Prodrugs have little or no pharmacological activity and are converted to active drugs in the body by enzymes, metabolic reactions, or through human-controlled actions. However, prodrugs promoting their chemical bioconversion without any of these processes have not been reported before. Here, we present an enzyme-independent prodrug activation mechanism by boron-based compounds (benzoxaboroles) targeting leucyl-tRNA synthetase (LeuRS), including an antibiotic that recently has completed phase II clinical trials to cure tuberculosis. We combine nuclear magnetic resonance spectroscopy and X-ray crystallography with isothermal titration calorimetry to show that these benzoxaboroles do not bind directly to their drug target LeuRS, instead they are prodrugs that activate their bioconversion by forming a highly specific and reversible LeuRS inhibition adduct with ATP, AMP, or the terminal adenosine of the tRNALeu. We demonstrate how the oxaborole group of the prodrugs cyclizes with the adenosine ribose at physiological concentrations to form the active molecule. This bioconversion mechanism explains the remarkably good druglike properties of benzoxaboroles showing efficacy against radically different human pathogens and fully explains the mechanism of action of these compounds. Thus, this adenosine-dependent activation mechanism represents a novel concept in prodrug chemistry that can be applied to improve the solubility, permeability and metabolic stability of challenging drugs.
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Affiliation(s)
- Guillaume Hoffmann
- Institute
for Advanced Biosciences (IAB), Structural Biology of Novel Targets
in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble
Alpes, 38000 Grenoble, France
| | - Madalen Le Gorrec
- Institute
for Advanced Biosciences (IAB), Structural Biology of Novel Targets
in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble
Alpes, 38000 Grenoble, France
| | - Emeline Mestdach
- Centre
de Résonance Magnétique Nucléaire à Très
Hauts Champs, (CRMN), UMR 5082, CNRS, ENS Lyon, UCBL, Université
de Lyon, 69100 Villeurbanne, France
| | - Stephen Cusack
- European
Molecular Biology Laboratory, 38042 Grenoble, France
| | - Loïc Salmon
- Centre
de Résonance Magnétique Nucléaire à Très
Hauts Champs, (CRMN), UMR 5082, CNRS, ENS Lyon, UCBL, Université
de Lyon, 69100 Villeurbanne, France
| | | | - Andrés Palencia
- Institute
for Advanced Biosciences (IAB), Structural Biology of Novel Targets
in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble
Alpes, 38000 Grenoble, France,
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6
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Mechi H, Sanhoury M, Laribi F, Dhia MTB. Synthesis and characterization of new bis(fluoroalkyl) phosphoramidates bearing sulfoximine groups. J Sulphur Chem 2021. [DOI: 10.1080/17415993.2021.1931213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Hanen Mechi
- Laboratory of Structural Organic Chemistry: Synthesis and Physico-chemical Studies, Department of Chemistry. Faculty of Sciences of Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - M.A.K. Sanhoury
- Laboratory of Structural Organic Chemistry: Synthesis and Physico-chemical Studies, Department of Chemistry. Faculty of Sciences of Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Department of Chemistry. Faculty of Sciences and Techniques, Materials Chemistry Research Unit, UNA, Nouakchott, Mauritania
| | - F. Laribi
- Laboratory of Structural Organic Chemistry: Synthesis and Physico-chemical Studies, Department of Chemistry. Faculty of Sciences of Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - M. T. Ben Dhia
- Laboratory of Structural Organic Chemistry: Synthesis and Physico-chemical Studies, Department of Chemistry. Faculty of Sciences of Tunis, University of Tunis El-Manar, Tunis, Tunisia
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7
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Abstract
Organophosphorus compounds play a vital role as nucleic acids, nucleotide coenzymes, metabolic intermediates and are involved in many biochemical processes. They are part of DNA, RNA, ATP and a number of important biological elements of living organisms. Synthetic compounds of this class have found practical application as agrochemicals, pharmaceuticals, bioregulators, and othrs. In recent years, a large number of phosphorus compounds containing P-O, P-N, P-C bonds have been isolated from natural sources. Many of them have shown interesting biological properties and have become the objects of intensive scientific research. Most of these compounds contain asymmetric centers, the absolute configurations of which have a significant effect on the biological properties of the products of their transformations. This area of research on natural phosphorus compounds is still little-studied, that prompted us to analyze and discuss it in our review. Moreover natural organophosphorus compounds represent interesting models for the development of new biologically active compounds, and a number of promising drugs and agrochemicals have already been obtained on their basis. The review also discusses the history of the development of ideas about the role of organophosphorus compounds and stereochemistry in the origin of life on Earth, starting from the prebiotic period, that allows us in a new way to consider this most important problem of fundamental science.
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8
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Travin DY, Severinov K, Dubiley S. Natural Trojan horse inhibitors of aminoacyl-tRNA synthetases. RSC Chem Biol 2021; 2:468-485. [PMID: 34382000 PMCID: PMC8323819 DOI: 10.1039/d0cb00208a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/10/2021] [Indexed: 12/18/2022] Open
Abstract
For most antimicrobial compounds with intracellular targets, getting inside the cell is the major obstacle limiting their activity. To pass this barrier some antibiotics mimic the compounds of specific interest for the microbe (siderophores, peptides, carbohydrates, etc.) and hijack the transport systems involved in their active uptake followed by the release of a toxic warhead inside the cell. In this review, we summarize the information about the structures, biosynthesis, and transport of natural inhibitors of aminoacyl-tRNA synthetases (albomycin, microcin C-related compounds, and agrocin 84) that rely on such "Trojan horse" strategy to enter the cell. In addition, we provide new data on the composition and distribution of biosynthetic gene clusters reminiscent of those coding for known Trojan horse aminoacyl-tRNA synthetases inhibitors. The products of these clusters are likely new antimicrobials that warrant further investigation.
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Affiliation(s)
- Dmitrii Y Travin
- Center of Life Sciences, Skolkovo Institute of Science and Technology Moscow Russia
- Institute of Gene Biology, Russian Academy of Sciences Moscow Russia
| | - Konstantin Severinov
- Center of Life Sciences, Skolkovo Institute of Science and Technology Moscow Russia
- Institute of Gene Biology, Russian Academy of Sciences Moscow Russia
- Waksman Institute for Microbiology, Rutgers, Piscataway New Jersey USA
| | - Svetlana Dubiley
- Center of Life Sciences, Skolkovo Institute of Science and Technology Moscow Russia
- Institute of Gene Biology, Russian Academy of Sciences Moscow Russia
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9
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Shaik MS, Nadiveedhi MR, Gundluru M, Sarva S, Allagadda R, Chippada AR, Chamarthi N, Cirandur SR. Green synthesis of phosphoramidates and evaluation of their α-amylase activity by in silico and in vitro studies. SYNTHETIC COMMUN 2021. [DOI: 10.1080/00397911.2021.1876239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
| | | | - Mohan Gundluru
- Department of Chemistry, Sri Venkateswara University, Tirupati, AP, India
- DST–PURSE Centre, Sri Venkateswara University, Tirupati, AP, India
| | - Santhisudha Sarva
- Department of Chemistry, Sri Venkateswara University, Tirupati, AP, India
| | | | - Appa Rao Chippada
- Department of Biochemistry, Sri Venkateswara University, Tirupati, AP, India
| | - Nagaraju Chamarthi
- Department of Chemistry, Sri Venkateswara University, Tirupati, AP, India
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10
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Bouchareb F, Berredjem M, Bouzina A, Guerfi M. Ultrasound-promoted, rapid and green synthesis of phosphonamide derivatives under catalyst and solvent-free conditions. PHOSPHORUS SULFUR 2020. [DOI: 10.1080/10426507.2020.1854254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Fouzia Bouchareb
- Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Faculty of Sciences, Department of Chemistry, Badji-Mokhtar – Annaba University, Annaba, Algeria
- Department of Chemistry, Faculty of Sciences and Technology, Chadli Bendjedid – EL Tarf University, El Tarf, Algeria
| | - Malika Berredjem
- Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Faculty of Sciences, Department of Chemistry, Badji-Mokhtar – Annaba University, Annaba, Algeria
| | - Abdeslem Bouzina
- Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Faculty of Sciences, Department of Chemistry, Badji-Mokhtar – Annaba University, Annaba, Algeria
| | - Meriem Guerfi
- Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Faculty of Sciences, Department of Chemistry, Badji-Mokhtar – Annaba University, Annaba, Algeria
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11
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Noutoshi Y, Toyoda A, Ishii T, Saito K, Watanabe M, Kawaguchi A. Complete Genome Sequence Data of Nonpathogenic Strain Rhizobium vitis VAR03-1, a Biological Control Agent for Grapevine Crown Gall Disease. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1451-1453. [PMID: 33026970 DOI: 10.1094/mpmi-07-20-0181-a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Crown gall disease in grapevine is caused by pathogenic strains of Rhizobium vitis with a tumor-inducing (Ti) plasmids. A nonpathogenic strain, VAR03-1 of R. vitis, has been isolated from the grapevine root of nursery stock and it was shown to act as a biological control agent to crown gall disease. Its disease-suppressive effect was observed even when it was coinoculated with the pathogen in a 1:1 ratio. Here, we present the complete genome data of R. vitis VAR03-1, assembled by sequencing reads obtained by both PacBio and Illumina technologies with annotation. This genome sequence could contribute to investigations of the molecular basis underlying the biocontrol activity as well as the root-colonization ability of this bacterial strain.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Yoshiteru Noutoshi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tomoya Ishii
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Kirara Saito
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Megumi Watanabe
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Akira Kawaguchi
- Western Region Agricultural Research Center, National Agricultural and Food Research Organization (NARO), Fukuyama, Hiroshima, Japan
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12
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Esters of Glucose-2-Phosphate: Occurrence and Chemistry. Molecules 2020; 25:molecules25122829. [PMID: 32575421 PMCID: PMC7356202 DOI: 10.3390/molecules25122829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 01/10/2023] Open
Abstract
Phosphodiesters of glucose-2-phosphate (G2P) are found only in few natural compounds such as agrocinopine D and agrocin 84. Agrocinopine D is a G2P phosphodiester produced by plants infected by Agrobacterium fabrum C58 and recognized by the bacterial periplasmic binding protein AccA for being transported into the bacteria before cleavage by the phosphodiesterase AccF, releasing G2P, which promotes virulence by binding the repressor protein AccR. The G2P amide agrocin 84 is a natural antibiotic produced by the non-pathogenic Agrobacterium radiobacter K84 strain used as a biocontrol agent by competing with Agrobacterium fabrum C58. G2P esters are also found in irregular glycogen structures. The rare glucopyranosyl-2-phophoryl moiety found in agrocin 84 is the key structural signature enabling its action as a natural antibiotic. Likewise, G2P and G2P esters can also dupe the Agrobacterium agrocinopine catabolism cascade. Such observations illustrate the importance of G2P esters on which we have recently focused our interest. After a brief review of the reported phosphorylation coupling methods and the choice of carbohydrate building blocks used in G2P chemistry, a flexible access to glucose-2-phosphate esters using the phosphoramidite route is proposed.
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Sivala MR, Chintha V, Potla KM, Chinnam S, Chamarthi NR. In silico docking studies and synthesis of new phosphoramidate derivatives of 6-fluoro-3-(piperidin-4-yl)benzo[d]isoxazole as potential antimicrobial agents. J Recept Signal Transduct Res 2020; 40:486-492. [DOI: 10.1080/10799893.2020.1752719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
| | - Venkataramaiah Chintha
- Division of Molecular Biology, Department of Zoology, Sri Venkateswara University, Tirupati, India
- Department of Zoology, Sri Venkateswara Vedic University, Tirupati, India
| | - Krishna Murthy Potla
- Department of Chemistry, Bapatla Engineering College (Autonomous), Acharya Nagarjuna University Post Graduate Research Centre, Bapatla, India
| | - Sampath Chinnam
- Department of Chemistry, B.M.S. College of Engineering, Bengaluru, India
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Zhang P, Ma S. Recent development of leucyl-tRNA synthetase inhibitors as antimicrobial agents. MEDCHEMCOMM 2019; 10:1329-1341. [PMID: 31534653 PMCID: PMC6727470 DOI: 10.1039/c9md00139e] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/26/2019] [Indexed: 12/14/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) widely exist in organisms and mediate protein synthesis. Inhibiting these synthetases can lead to the termination of protein synthesis and subsequently achieve antibacterial and antiparasitic purposes. Moreover, the structures of aaRSs found in eukaryotes have considerable structural differences compared to those in prokaryotes, based on which it is possible to develop highly selective inhibitors. Leucyl-tRNA synthetase (LeuRS) with unique synthesis and editing sites is one of 20 kinds of aaRSs. Many inhibitors targeting LeuRS have been designed and synthesized, some of which have entered clinical use. For example, the benzoxaborole compound AN2690 has been approved by the FDA for the treatment of onychomycosis. AN3365 is suspended in the phase II clinical trial due to the rapid development of AN3365 resistance, but it may be used in combination with other antibiotics. The aaRSs, especially LeuRS, are being considered as targets of new potential anti-infective drugs for the treatment of not only bacterial or fungal infections but also infections by trypanosomes and malaria parasites. This review mainly describes the development of LeuRS inhibitors, focusing on their mechanisms of action, structure-activity relationships (SARs), and in vitro and in vivo activities.
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Affiliation(s)
- Panpan Zhang
- Department of Medicinal Chemistry , Key Laboratory of Chemical Biology , Ministry of Education , School of Pharmaceutical Sciences , Shandong University , 44, West Culture Road , Jinan 250012 , P. R. China . E mail:
| | - Shutao Ma
- Department of Medicinal Chemistry , Key Laboratory of Chemical Biology , Ministry of Education , School of Pharmaceutical Sciences , Shandong University , 44, West Culture Road , Jinan 250012 , P. R. China . E mail:
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Li Q, Sun X, Yang X, Wu M, Sun S, Chen X. Transition-metal-free amination phosphoryl azide for the synthesis of phosphoramidates. RSC Adv 2019; 9:16040-16043. [PMID: 35521381 PMCID: PMC9064390 DOI: 10.1039/c9ra03389k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 01/06/2023] Open
Abstract
A facile and efficient approach to phosphoramidates was developed via amination of phosphoryl azides. A variety of phosphoramidates were obtained in one step with good to excellent yields under a mild reaction system. The process uses easily available amines as a N source and offers a new opportunity for P–N bond formation. A facile and efficient approach to phosphoramidates was developed via amination of phosphoryl azides.![]()
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Affiliation(s)
- Qing Li
- Non-power Nuclear Technology Collaborative Innovation Center, School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology Xianning 437100 China +86-715-8338007
| | | | - Xiaoqin Yang
- Non-power Nuclear Technology Collaborative Innovation Center, School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology Xianning 437100 China +86-715-8338007
| | - Minghu Wu
- Non-power Nuclear Technology Collaborative Innovation Center, School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology Xianning 437100 China +86-715-8338007
| | - Shaofa Sun
- Non-power Nuclear Technology Collaborative Innovation Center, School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology Xianning 437100 China +86-715-8338007
| | - Xiuling Chen
- Non-power Nuclear Technology Collaborative Innovation Center, School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology Xianning 437100 China +86-715-8338007
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Li SZ, Vigouroux A, Ahmar M, El Sahili A, Soulère L, Sago L, Cornu D, Moréra S, Queneau Y. Synthesis of a non-natural glucose-2-phosphate ester able to dupe the acc system of Agrobacterium fabrum. Org Biomol Chem 2019; 17:1090-1096. [PMID: 30632589 DOI: 10.1039/c8ob03086c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The first non-natural derivative of the rare d-glucose-2-phosphate (G2P), namely glucose-2-(O-lactic acid phosphate) (G2LP), has been synthesized. When used as sole carbon source, G2LP enables bacterial growth of the plant pathogenic strain Agrobacterium fabrum C58 (formerly referred to as Agrobacterium tumefaciens). X-ray crystallography and affinity measurements investigations reveal that G2LP binds the periplasmic binding protein (PBP) AccA similarly to the natural compounds and with the same affinity. Moreover, enzymatic assays show that it is able to serve as substrate of the phosphodiesterase AccF. The properties found for G2LP demonstrate that the very unusual glucose-2-phosphoryl residue, present in G2LP, can be used as structural feature for designing non-natural systems fully compatible with the Acc cascade of A. fabrum.
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Affiliation(s)
- Si-Zhe Li
- Univ Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, CNRS, Université Lyon 1, INSA Lyon, CPE Lyon, ICBMS, UMR 5246, Université Claude Bernard, Bâtiment Lederer, 1 Rue Victor Grignard, 69622 Villeurbanne Cedex, France.
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Chen X, Xiao Z, Chu H, Wang B, Peng AY. Reinvestigation of the iodine-mediated phosphoramidation reaction of amines and P(OR) 3 and its synthetic applications. Org Biomol Chem 2019; 16:6783-6790. [PMID: 30198043 DOI: 10.1039/c8ob01840e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A systematic study on the iodine-mediated phosphoramidation reaction of amines and trialkyl phosphites was conducted, which not only disclosed the factors affecting the reaction but also revealed that it could proceed smoothly in CH2Cl2 at room temperature in open air. Using this method, various phosphoramidates with different aliphatic amines and aromatic amines were synthesized in good to excellent yields. Our present investigation shows that this underused method is actually a mild, practical and general way to synthesize phosphoramidates and will have wide applications.
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Affiliation(s)
- Xunwei Chen
- School of Chemistry, Sun Yat-sen University, 135 Xingangxi Lu, Guangzhou, 510275, China.
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Petkowski JJ, Bains W, Seager S. Natural Products Containing 'Rare' Organophosphorus Functional Groups. Molecules 2019; 24:E866. [PMID: 30823503 PMCID: PMC6429109 DOI: 10.3390/molecules24050866] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/13/2019] [Accepted: 02/22/2019] [Indexed: 12/25/2022] Open
Abstract
Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.
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Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
| | - William Bains
- Rufus Scientific, 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK.
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
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Nayab Rasool SK, Subramanyam C, Janakiramudu DB, Supraja P, Usha R, Raju CN. Convenient one-pot synthesis and biological evaluation of phosphoramidates and phosphonates containing heterocycles. PHOSPHORUS SULFUR 2018. [DOI: 10.1080/10426507.2018.1452229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- SK. Nayab Rasool
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - Ch. Subramanyam
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - D. B. Janakiramudu
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - P. Supraja
- Department of Biotechnology, Sri Padmavathi Mahila Visvavidyalayam, Tirupati, Andhra Pradesh, India
| | - R. Usha
- Department of Biotechnology, Sri Padmavathi Mahila Visvavidyalayam, Tirupati, Andhra Pradesh, India
| | - C. Naga Raju
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
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20
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Nayab Rasool SK, Babu PH, Janaki Ramudu DB, Jyothi Kumar MV, Appa Rao C, Raju CN. Synthesis and bioactivity evaluation of new phenyl N,N′-phenylphosphorodiamidates. PHOSPHORUS SULFUR 2018. [DOI: 10.1080/10426507.2017.1370468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- SK. Nayab Rasool
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - P. Hari Babu
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - D. B. Janaki Ramudu
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - M. V. Jyothi Kumar
- Department of Biotechnology, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - Ch. Appa Rao
- Department of Bio-Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - C. Naga Raju
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
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Pan C, Wang Y, Wu C, Yu JT. Iridium-catalyzed C–H phosphoramidation of N-aryl-7-azaindoles with phosphoryl azides. Org Biomol Chem 2018; 16:3711-3715. [DOI: 10.1039/c8ob00776d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An iridium-catalyzed C–H phosphoramidation of N-aryl-7-azaindoles with phosphoryl azides was developed, affording a series of 7-azaindole phenylphosphoramidates.
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Affiliation(s)
- Changduo Pan
- School of Chemical & Environmental Engineering
- Jiangsu University of Technology
- Changzhou 213001
- P. R. China
| | - Yun Wang
- School of Chemical & Environmental Engineering
- Jiangsu University of Technology
- Changzhou 213001
- P. R. China
| | - Chao Wu
- School of Chemical & Environmental Engineering
- Jiangsu University of Technology
- Changzhou 213001
- P. R. China
| | - Jin-Tao Yu
- School of Petrochemical Engineering
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology
- Changzhou University
- Changzhou 213164
- P. R. China
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22
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Structural characterization of antibiotic self-immunity tRNA synthetase in plant tumour biocontrol agent. Nat Commun 2016; 7:12928. [PMID: 27713402 PMCID: PMC5059758 DOI: 10.1038/ncomms12928] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 08/16/2016] [Indexed: 01/08/2023] Open
Abstract
Antibiotic-producing microbes evolved self-resistance mechanisms to avoid suicide. The biocontrol Agrobacterium radiobacter K84 secretes the Trojan Horse antibiotic agrocin 84 that is selectively transported into the plant pathogen A. tumefaciens and processed into the toxin TM84. We previously showed that TM84 employs a unique tRNA-dependent mechanism to inhibit leucyl-tRNA synthetase (LeuRS), while the TM84-producer prevents self-poisoning by expressing a resistant LeuRS AgnB2. We now identify a mechanism by which the antibiotic-producing microbe resists its own toxin. Using a combination of structural, biochemical and biophysical approaches, we show that AgnB2 evolved structural changes so as to resist the antibiotic by eliminating the tRNA-dependence of TM84 binding. Mutagenesis of key resistance determinants results in mutants adopting an antibiotic-sensitive phenotype. This study illuminates the evolution of resistance in self-immunity genes and provides mechanistic insights into a fascinating tRNA-dependent antibiotic with applications for the development of anti-infectives and the prevention of biocontrol emasculation.
The bacterium Agrobacterium radiobacter K84 secretes an antibiotic that is transported into the plant pathogen A. tumefaciens and processed into the toxin TM84. Here, the authors identify a mechanism whereby the antibiotic-producing microbe resists its own toxin.
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23
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Li Y, Liang F. With DBU-activated N-bromophthalimide as potential N-sources to achieve P–N cross-coupling of P(O)–H compounds. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.05.076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Dar BA. Catalyst free, one pot synthesis of phosphoramidates under environment friendly conditions. J IND ENG CHEM 2016. [DOI: 10.1016/j.jiec.2016.01.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Elshahawi SI, Shaaban KA, Kharel MK, Thorson JS. A comprehensive review of glycosylated bacterial natural products. Chem Soc Rev 2015; 44:7591-697. [PMID: 25735878 PMCID: PMC4560691 DOI: 10.1039/c4cs00426d] [Citation(s) in RCA: 299] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A systematic analysis of all naturally-occurring glycosylated bacterial secondary metabolites reported in the scientific literature up through early 2013 is presented. This comprehensive analysis of 15 940 bacterial natural products revealed 3426 glycosides containing 344 distinct appended carbohydrates and highlights a range of unique opportunities for future biosynthetic study and glycodiversification efforts.
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Affiliation(s)
- Sherif I Elshahawi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Khaled A Shaaban
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Madan K Kharel
- School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, Maryland, USA
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
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El Sahili A, Li SZ, Lang J, Virus C, Planamente S, Ahmar M, Guimaraes BG, Aumont-Nicaise M, Vigouroux A, Soulère L, Reader J, Queneau Y, Faure D, Moréra S. A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens. PLoS Pathog 2015; 11:e1005071. [PMID: 26244338 PMCID: PMC4526662 DOI: 10.1371/journal.ppat.1005071] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/06/2015] [Indexed: 11/18/2022] Open
Abstract
Periplasmic binding proteins (PBPs) in association with ABC transporters select and import a wide variety of ligands into bacterial cytoplasm. They can also take up toxic molecules, as observed in the case of the phytopathogen Agrobacterium tumefaciens strain C58. This organism contains a PBP called AccA that mediates the import of the antibiotic agrocin 84, as well as the opine agrocinopine A that acts as both a nutrient and a signalling molecule for the dissemination of virulence genes through quorum-sensing. Here, we characterized the binding mode of AccA using purified agrocin 84 and synthetic agrocinopine A by X-ray crystallography at very high resolution and performed affinity measurements. Structural and affinity analyses revealed that AccA recognizes an uncommon and specific motif, a pyranose-2-phosphate moiety which is present in both imported molecules via the L-arabinopyranose moiety in agrocinopine A and the D-glucopyranose moiety in agrocin 84. We hypothesized that AccA is a gateway allowing the import of any compound possessing a pyranose-2-phosphate motif at one end. This was structurally and functionally confirmed by experiments using four synthetic compounds: agrocinopine 3'-O-benzoate, L-arabinose-2-isopropylphosphate, L-arabinose-2-phosphate and D-glucose-2-phosphate. By combining affinity measurements and in vivo assays, we demonstrated that both L-arabinose-2-phosphate and D-glucose-2-phosphate, which are the AccF mediated degradation products of agrocinopine A and agrocin 84 respectively, interact with the master transcriptional regulator AccR and activate the quorum-sensing signal synthesis and Ti plasmid transfer in A. tumefaciens C58. Our findings shed light on the role of agrocinopine and antibiotic agrocin 84 on quorum-sensing regulation in A. tumefaciens and reveal how the PBP AccA acts as vehicle for the importation of both molecules by means of a key-recognition motif. It also opens future possibilities for the rational design of antibiotic and anti-virulence compounds against A. tumefaciens or other pathogens possessing similar PBPs.
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Affiliation(s)
- Abbas El Sahili
- Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
| | - Si-Zhe Li
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, ICBMS, Université de Lyon, INSA Lyon, UMR 5246, CNRS, Université Lyon 1, INSA Lyon, CPE-Lyon, Bât J. Verne, Villeurbanne, France
| | - Julien Lang
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
| | - Cornelia Virus
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sara Planamente
- Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
| | - Mohammed Ahmar
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, ICBMS, Université de Lyon, INSA Lyon, UMR 5246, CNRS, Université Lyon 1, INSA Lyon, CPE-Lyon, Bât J. Verne, Villeurbanne, France
| | | | - Magali Aumont-Nicaise
- Institute for Integrative Biology of the Cell (I2BC), Protein-Protein Interaction Platform, CNRS CEA University Paris-Sud, Orsay, France
| | - Armelle Vigouroux
- Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
| | - Laurent Soulère
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, ICBMS, Université de Lyon, INSA Lyon, UMR 5246, CNRS, Université Lyon 1, INSA Lyon, CPE-Lyon, Bât J. Verne, Villeurbanne, France
| | - John Reader
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yves Queneau
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, ICBMS, Université de Lyon, INSA Lyon, UMR 5246, CNRS, Université Lyon 1, INSA Lyon, CPE-Lyon, Bât J. Verne, Villeurbanne, France
- * E-mail: (YQ); (DF); (SM)
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
- * E-mail: (YQ); (DF); (SM)
| | - Solange Moréra
- Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
- * E-mail: (YQ); (DF); (SM)
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Mousa WK, Raizada MN. Biodiversity of genes encoding anti-microbial traits within plant associated microbes. FRONTIERS IN PLANT SCIENCE 2015; 6:231. [PMID: 25914708 PMCID: PMC4392301 DOI: 10.3389/fpls.2015.00231] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/23/2015] [Indexed: 05/10/2023]
Abstract
The plant is an attractive versatile home for diverse associated microbes. A subset of these microbes produces a diversity of anti-microbial natural products including polyketides, non-ribosomal peptides, terpenoids, heterocylic nitrogenous compounds, volatile compounds, bacteriocins, and lytic enzymes. In recent years, detailed molecular analysis has led to a better understanding of the underlying genetic mechanisms. New genomic and bioinformatic tools have permitted comparisons of orthologous genes between species, leading to predictions of the associated evolutionary mechanisms responsible for diversification at the genetic and corresponding biochemical levels. The purpose of this review is to describe the biodiversity of biosynthetic genes of plant-associated bacteria and fungi that encode selected examples of antimicrobial natural products. For each compound, the target pathogen and biochemical mode of action are described, in order to draw attention to the complexity of these phenomena. We review recent information of the underlying molecular diversity and draw lessons through comparative genomic analysis of the orthologous coding sequences (CDS). We conclude by discussing emerging themes and gaps, discuss the metabolic pathways in the context of the phylogeny and ecology of their microbial hosts, and discuss potential evolutionary mechanisms that led to the diversification of biosynthetic gene clusters.
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Affiliation(s)
- Walaa K. Mousa
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura UniversityMansoura, Egypt
| | - Manish N. Raizada
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
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Abstract
Transfer RNAs (tRNAs) are central players in the protein translation machinery and as such are prominent targets for a large number of natural and synthetic antibiotics. This review focuses on the role of tRNAs in bacterial antibiosis. We will discuss examples of antibiotics that target multiple stages in tRNA biology from tRNA biogenesis and modification, mature tRNAs, aminoacylation of tRNA as well as prevention of proper tRNA function by small molecules binding to the ribosome. Finally, the role of deacylated tRNAs in the bacterial “stringent response” mechanism that can lead to bacteria displaying antibiotic persistence phenotypes will be discussed.
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Agrobacterium uses a unique ligand-binding mode for trapping opines and acquiring a competitive advantage in the niche construction on plant host. PLoS Pathog 2014; 10:e1004444. [PMID: 25299655 PMCID: PMC4192606 DOI: 10.1371/journal.ppat.1004444] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 09/02/2014] [Indexed: 11/20/2022] Open
Abstract
By modifying the nuclear genome of its host, the plant pathogen Agrobacterium tumefaciens induces the development of plant tumours in which it proliferates. The transformed plant tissues accumulate uncommon low molecular weight compounds called opines that are growth substrates for A. tumefaciens. In the pathogen-induced niche (the plant tumour), a selective advantage conferred by opine assimilation has been hypothesized, but not experimentally demonstrated. Here, using genetics and structural biology, we deciphered how the pathogen is able to bind opines and use them to efficiently compete in the plant tumour. We report high resolution X-ray structures of the periplasmic binding protein (PBP) NocT unliganded and liganded with the opine nopaline (a condensation product of arginine and α-ketoglurate) and its lactam derivative pyronopaline. NocT exhibited an affinity for pyronopaline (KD of 0.6 µM) greater than that for nopaline (KD of 3.7 µM). Although the binding-mode of the arginine part of nopaline/pyronopaline in NocT resembled that of arginine in other PBPs, affinity measurement by two different techniques showed that NocT did not bind arginine. In contrast, NocT presented specific residues such as M117 to stabilize the bound opines. NocT relatives that exhibit the nopaline/pyronopaline-binding mode were only found in genomes of the genus Agrobacterium. Transcriptomics and reverse genetics revealed that A. tumefaciens uses the same pathway for assimilating nopaline and pyronopaline. Fitness measurements showed that NocT is required for a competitive colonization of the plant tumour by A. tumefaciens. Moreover, even though the Ti-plasmid conjugal transfer was not regulated by nopaline, the competitive advantage gained by the nopaline-assimilating Ti-plasmid donors led to a preferential horizontal propagation of this Ti-plasmid amongst the agrobacteria colonizing the plant-tumour niche. This work provided structural and genetic evidences to support the niche construction paradigm in bacterial pathogens. An ecological niche is defined, in a given environment, by the availability of nutritive resources, which can be specifically assimilated by certain living organisms to promote their proliferation. The bacterial pathogen Agrobacterium tumefaciens is able to engineer an ecological niche in the infected host via the transformation of the plant genome and diversion of the plant metabolism towards production of the opine nutrients. In this work, we quantified the selective advantage conferred to a member of the phytopathogenic species A. tumefaciens which is able to assimilate the opine nopaline. This opine is a condensate of arginine and α-ketoglurate that is produced both under linear and cyclic forms in the plant tumour environment. We further determined at the molecular and atomistic levels how A. tumefaciens is able to sense the nopaline molecules, and which metabolic pathways are activated in response. Overall, this work deciphered some key molecular events in the niche construction of the pathogen A. tumefaciens that is unique among living organisms and used to develop bioengineering tools.
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Kim H, Park J, Kim JG, Chang S. Synthesis of Phosphoramidates: A Facile Approach Based on the C–N Bond Formation via Ir-Catalyzed Direct C–H Amidation. Org Lett 2014; 16:5466-9. [DOI: 10.1021/ol502722j] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hyunwoo Kim
- Department
of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
- Center
for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 305-701, Korea
| | - Juhyeon Park
- Department
of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
- Center
for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 305-701, Korea
| | - Jeung Gon Kim
- Department
of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
- Center
for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 305-701, Korea
| | - Sukbok Chang
- Department
of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
- Center
for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 305-701, Korea
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Pan C, Jin N, Zhang H, Han J, Zhu C. Iridium-Catalyzed Phosphoramidation of Arene C–H Bonds with Phosphoryl Azide. J Org Chem 2014; 79:9427-32. [DOI: 10.1021/jo5018052] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Changduo Pan
- State
Key Laboratory of Coordination Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
- Wenzhou Institute of Industry & Science, Wenzhou 325000, P. R. China
| | - Ning Jin
- State
Key Laboratory of Coordination Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
| | - Honglin Zhang
- State
Key Laboratory of Coordination Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
| | - Jie Han
- State
Key Laboratory of Coordination Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
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Dar BA, Dangroo NA, Gupta A, Wali A, Khuroo MA, Vishwakarma RA, Singh B. Iodine catalyzed solvent-free cross-dehydrogenative coupling of arylamines and H-phosphonates for the synthesis of N-arylphosphoramidates under atmospheric conditions. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.01.064] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Dewan V, Reader J, Forsyth KM. Role of aminoacyl-tRNA synthetases in infectious diseases and targets for therapeutic development. Top Curr Chem (Cham) 2013; 344:293-329. [PMID: 23666077 DOI: 10.1007/128_2013_425] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aminoacyl-tRNA synthetases (AARSs) play a pivotal role in protein synthesis and cell viability. These 22 "housekeeping" enzymes (1 for each standard amino acid plus pyrrolysine and o-phosphoserine) are specifically involved in recognizing and aminoacylating their cognate tRNAs in the cellular pool with the correct amino acid prior to delivery of the charged tRNA to the protein synthesis machinery. Besides serving this canonical function, higher eukaryotic AARSs, some of which are organized in the cytoplasm as a multisynthetase complex of nine enzymes plus additional cellular factors, have also been implicated in a variety of non-canonical roles. AARSs are involved in the regulation of transcription, translation, and various signaling pathways, thereby ensuring cell survival. Based in part on their versatility, AARSs have been recruited by viruses to perform essential functions. For example, host synthetases are packaged into some retroviruses and are required for their replication. Other viruses mimic tRNA-like structures in their genomes, and these motifs are aminoacylated by the host synthetase as part of the viral replication cycle. More recently, it has been shown that certain large DNA viruses infecting animals and other diverse unicellular eukaryotes encode tRNAs, AARSs, and additional components of the protein-synthesis machinery. This chapter will review our current understanding of the role of host AARSs and tRNA-like structures in viruses and discuss their potential as anti-viral drug targets. The identification and development of compounds that target bacterial AARSs, thereby serving as novel antibiotics, will also be discussed. Particular attention will be given to recent work on a number of tRNA-dependent AARS inhibitors and to advances in a new class of natural "pro-drug" antibiotics called Trojan Horse inhibitors. Finally, we will explore how bacteria that naturally produce AARS-targeting antibiotics must protect themselves against cell suicide using naturally antibiotic resistant AARSs, and how horizontal gene transfer of these AARS genes to pathogens may threaten the future use of this class of antibiotics.
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Affiliation(s)
- Varun Dewan
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, Center for RNA Biology, and Center for Retroviral Research, The Ohio State University, Columbus, OH, 43210, USA
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35
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Fraser J, Wilson LJ, Blundell RK, Hayes CJ. Phosphoramidate synthesis via copper-catalysed aerobic oxidative coupling of amines and H-phosphonates. Chem Commun (Camb) 2013; 49:8919-21. [DOI: 10.1039/c3cc45680c] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Nocek B, Tikhonov A, Babnigg G, Gu M, Zhou M, Makarova KS, Vondenhoff G, Van Aerschot A, Kwon K, Anderson WF, Severinov K, Joachimiak A. Structural and functional characterization of microcin C resistance peptidase MccF from Bacillus anthracis. J Mol Biol 2012; 420:366-83. [PMID: 22516613 DOI: 10.1016/j.jmb.2012.04.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 04/06/2012] [Accepted: 04/10/2012] [Indexed: 11/16/2022]
Abstract
Microcin C (McC) is heptapeptide adenylate antibiotic produced by Escherichia coli strains carrying the mccABCDEF gene cluster encoding enzymes, in addition to the heptapeptide structural gene mccA, necessary for McC biosynthesis and self-immunity of the producing cell. The heptapeptide facilitates McC transport into susceptible cells, where it is processed releasing a non-hydrolyzable aminoacyl adenylate that inhibits an essential aminoacyl-tRNA synthetase. The self-immunity gene mccF encodes a specialized serine peptidase that cleaves an amide bond connecting the peptidyl or aminoacyl moieties of, respectively, intact and processed McC with the nucleotidyl moiety. Most mccF orthologs from organisms other than E. coli are not linked to the McC biosynthesis gene cluster. Here, we show that a protein product of one such gene, MccF from Bacillus anthracis (BaMccF), is able to cleave intact and processed McC, and we present a series of structures of this protein. Structural analysis of apo-BaMccF and its adenosine monophosphate complex reveals specific features of MccF-like peptidases that allow them to interact with substrates containing nucleotidyl moieties. Sequence analyses and phylogenetic reconstructions suggest that several distinct subfamilies form the MccF clade of the large S66 family of bacterial serine peptidases. We show that various representatives of the MccF clade can specifically detoxify non-hydrolyzable aminoacyl adenylates differing in their aminoacyl moieties. We hypothesize that bacterial mccF genes serve as a source of bacterial antibiotic resistance.
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Affiliation(s)
- Boguslaw Nocek
- Center for Structural Genomics of Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892-6612, USA
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37
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Agarwal V, Nair SK. Aminoacyl tRNA synthetases as targets for antibiotic development. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20032e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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38
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Tikhonov A, Kazakov T, Semenova E, Serebryakova M, Vondenhoff G, Van Aerschot A, Reader JS, Govorun VM, Severinov K. The mechanism of microcin C resistance provided by the MccF peptidase. J Biol Chem 2010; 285:37944-52. [PMID: 20876530 DOI: 10.1074/jbc.m110.179135] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The heptapeptide-nucleotide microcin C (McC) is a potent inhibitor of enteric bacteria growth. Inside a sensitive cell, McC is processed by aminopeptidases, which release a nonhydrolyzable aspartyl-adenylate, a strong inhibitor of aspartyl-tRNA synthetase. The mccABCDE operon is sufficient for McC production and resistance of the producing cell to McC. An additional gene, mccF, which is adjacent to but not part of the mccABCDE operon, also provides resistance to exogenous McC. MccF is similar to Escherichia coli LdcA, an L,D-carboxypeptidase whose substrate is monomeric murotetrapeptide L-Ala-D-Glu-meso-A(2)pm-D-Ala or its UDP-activated murein precursor. The mechanism by which MccF provides McC resistance remained unknown. Here, we show that MccF detoxifies both intact and processed McC by cleaving an amide bond between the C-terminal aspartate and the nucleotide moiety. MccF also cleaves the same bond in nonhydrolyzable aminoacyl sulfamoyl adenosines containing aspartyl, glutamyl, and, to a lesser extent, seryl aminoacyl moieties but is ineffective against other aminoacyl adenylates.
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Affiliation(s)
- Anton Tikhonov
- Institutes of Molecular Genetics and Gene Biology, Russian Academy of Sciences, Moscow, Russia
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39
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Opine-based Agrobacterium competitiveness: dual expression control of the agrocinopine catabolism (acc) operon by agrocinopines and phosphate levels. J Bacteriol 2008; 190:3700-11. [PMID: 18344359 DOI: 10.1128/jb.00067-08] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Agrobacterium tumefaciens strain C58 can transform plant cells to produce and secrete the sugar-phosphate conjugate opines agrocinopines A and B. The bacterium then moves in response to the opines and utilizes them as exclusive sources of carbon, energy, and phosphate via the functions encoded by the acc operon. These privileged opine-involved activities contribute to the formation of agrobacterial niches in the environment. We found that the expression of the acc operon is induced by agrocinopines and also by limitation of phosphate. The main promoter is present in front of the first gene, accR, which codes for a repressor. This operon structure enables efficient repression when opine levels are low. The promoter contains two putative operators, one overlapping the -10 sequence and the other in the further upstream from it; two partly overlapped putative pho boxes between the two operators; and two consecutive transcription start sites. DNA fragments containing either of the operators bound purified repressor AccR in the absence of agrocinopines but not in the presence of the opines, demonstrating the on-off switch of the promoter. Induction of the acc operon can occur under low-phosphate conditions in the absence of agrocinopines and further increases when the opines also are present. Such opine-phosphate dual regulatory system of the operon may ensure maximum utilization of agrocinopines when available and thereby increase the chances of agrobacterial survival in the highly competitive environment with limited general food sources.
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40
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Chen F, Guo YB, Wang JH, Li JY, Wang HM. Biological Control of Grape Crown Gall by Rahnella aquatilis HX2. PLANT DISEASE 2007; 91:957-963. [PMID: 30780428 DOI: 10.1094/pdis-91-8-0957] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Crown gall induced by Agrobacterium vitis is a worldwide plant disease in grape-growing regions. Rahnella aquatilis HX2, a new isolate from vineyard soil in Beijing, showed a significant inhibition effect on the development of crown galls in grapevines. In field trials, immersion of the basal ends of grape cuttings with HX2 cell suspension inhibited or completely prevented crown gall formation caused by A. vitis K308 in the roots of the plants from the cuttings. The 3-year average disease incidence in grape plants treated with HX2 was 30.8% compared to 93.5% in plants without HX2. The culture supernatant of HX2 exhibited a stronger inhibition effect on disease development than did the cell suspension. HX2 could be found in the grape rhizosphere, grown under field conditions, for up to 90 days after inoculation. There was no significant difference in the mean population sizes of root microflora between plants treated and not treated with HX2. The inhibition effect of HX2 on crown gall in sunflower, caused by different agrobacterial strains, varied between 30.7 and 100%, depending on strains. Our results showed that Rahnella aquatilis HX2 may be used as a biological control agent for crown gall disease of grapes.
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Affiliation(s)
- F Chen
- Department of Plant Pathology, China Agricultural University, Beijing 100094, PR. China
| | - Y B Guo
- Department of Plant Pathology, China Agricultural University, Beijing 100094, PR. China
| | - J H Wang
- Department of Plant Pathology, China Agricultural University, Beijing 100094, PR. China
| | - J Y Li
- Department of Plant Pathology, China Agricultural University, Beijing 100094, PR. China
| | - H M Wang
- Department of Plant Pathology, China Agricultural University, Beijing 100094, PR. China
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41
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Kim JG, Park BK, Kim SU, Choi D, Nahm BH, Moon JS, Reader JS, Farrand SK, Hwang I. Bases of biocontrol: sequence predicts synthesis and mode of action of agrocin 84, the Trojan horse antibiotic that controls crown gall. Proc Natl Acad Sci U S A 2006; 103:8846-51. [PMID: 16731618 PMCID: PMC1482666 DOI: 10.1073/pnas.0602965103] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Agrobacterium radiobacter K84, used worldwide to biocontrol crown gall disease caused by Agrobacterium tumefaciens, produces an antiagrobacterial compound called agrocin 84. We report the nucleotide sequence of pAgK84, a 44.42-kb plasmid coding for production of this disubstituted adenine nucleotide antibiotic. pAgK84 encodes 36 ORFs, 17 of which (agn) code for synthesis of or immunity to agrocin 84. Two genes, agnB2 and agnA, encode aminoacyl tRNA synthetase homologues. We have shown that the toxic moiety of agrocin 84 inhibits cellular leucyl-tRNA synthetases and AgnB2, which confers immunity to the antibiotic, is a resistant form of this enzyme. AgnA, a truncated homologue of asparaginyl tRNA synthetase could catalyze the phosphoramidate bond between a precursor of the methyl pentanamide side group and the nucleotide. We propose previously undescribed chemistry, catalyzed by AgnB1, to generate the precursor necessary for this phosphoramidate linkage. AgnC7 is related to ribonucleotide reductases and could generate the 3'-deoxyarabinose moiety of the nucleoside. Bioinformatics suggest that agnC3, agnC4, and agnC6 contribute to maturation of the methyl pentanamide, whereas agnC2 may produce the glucofuranose side group bound to the adenine ring. AgnG is related to bacterial exporters. An agnG mutant accumulated agrocin 84 intracellularly but did not export the antibiotic. pAgK84 is transmissible and encodes genes for conjugative DNA processing but lacks a type IV secretion system, suggesting that pAgK84 transfers by mobilization. By sequence analysis, the deletion engineered into pAgK1026 removed the oriT and essential tra genes, confirming the enhanced environmental safety of this modified form of pAgK84.
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Affiliation(s)
- Jung-Gun Kim
- *School of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921, Korea
| | | | | | - Doil Choi
- Plant Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-333, Korea
| | - Baek Hie Nahm
- Division of Biological Science and Bioinformatics, Myongji University, Yongin 449-728, Korea
| | - Jae Sun Moon
- Plant Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-333, Korea
| | - John S. Reader
- Department of Medicine, University of North Carolina, Chapel Hill, NC 27599; and
| | - Stephen K. Farrand
- Department of Microbiology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- **To whom correspondence may be addressed. E-mail:
or
| | - Ingyu Hwang
- *School of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921, Korea
- **To whom correspondence may be addressed. E-mail:
or
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42
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Deacon JW, Berry LA. Biocontrol of soil-borne plant pathogens: Concepts and their application. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/ps.2780370417] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Humann J, Andrews S, Ream W. VirE1-Mediated Resistance to Crown Gall in Transgenic Arabidopsis thaliana. PHYTOPATHOLOGY 2006; 96:105-110. [PMID: 18944210 DOI: 10.1094/phyto-96-0105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Crown gall disease, caused by Agrobacterium tumefaciens, remains a serious agricultural problem despite current biocontrol methods. Agrobacterium tumefaciens transfers single-stranded DNA (T-strands) into plant cells along with several virulence proteins, including a single-stranded DNA-binding protein (VirE2). In plant cells, T-strands are protected from nucleases and targeted to the nucleus by VirE2, which is essential for efficient transmission (transfer and integration) of T-strands. VirE1 is the secretory chaperone for VirE2; it prevents VirE2 from forming aggregates and from binding the T-strands in bacterial cells. Therefore, we hypothesized that sufficient quantities of VirE1 expressed in plant cells might block T-DNA transmission by preventing VirE2 from binding T-strands. Here we show that root explants from Arabidopsis thaliana plants that expressed virE1 formed 3.5-fold fewer tumors than roots from plants without virE1. Also, this resistance was specific for VirE2-mediated Agrobacterium transformation. Plants that have been genetically altered to resist crown gall may prove more effective than biological control.
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44
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Reader JS, Ordoukhanian PT, Kim JG, de Crécy-Lagard V, Hwang I, Farrand S, Schimmel P. Major biocontrol of plant tumors targets tRNA synthetase. Science 2005; 309:1533. [PMID: 16141066 DOI: 10.1126/science.1116841] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Crops can be devastated by pathogenic strains of Agrobacterium tumefaciens that cause crown gall tumors. This devastation can be prevented by the nonpathogenic biocontrol agent A. radiobacter K84, which prevents disease by production of the "Trojan horse" toxin agrocin 84, which is specifically imported into tumorgenic A. tumefaciens strains to cause cell death. We demonstrate that this biocontrol agent targets A. tumefaciens leucyl-tRNA synthetase (LeuRS), an essential enzyme for cell viability, while the agent itself survives by having a second, self-protective copy of the synthetase. In principle, this strategy from nature could be applied to other crop diseases by direct intervention.
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Affiliation(s)
- John S Reader
- Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA 92037, USA
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45
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Baraniak J, Kaczmarek R, Wasilewska E, Korczyński D, Stec WJ. New approach to preparation of N-acylphosphoramido(thio)(seleno)ates. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.04.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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46
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Moriguchi T, Asai N, Okada K, Seio K, Sasaki T, Sekine M. First synthesis and anticancer activity of phosmidosine and its related compounds. J Org Chem 2002; 67:3290-300. [PMID: 12003538 DOI: 10.1021/jo016176g] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper describes the first synthesis of phosmidosine and phosmidosine B, i.e., nucleotide antibiotics composed of 8-oxoadenosine and L-proline which are connected via a unique N-acyl phosphoramidate linkage. Phosmidosine has a yet-undetermined chiral center at the phosphorus atom of the N-acyl phosphoramidate linkage. Phosmidosine B is a demethylated phosmidosine derivative with no chirality on the phosphorus. Phosmidosine B was successfully synthesized by the reaction of an N-acetyl-8-oxoadenosine 5'-O-phosphoramidite derivative with an N-protected prolinamide in the presence of 5-(3,5-dinitrophenyl)-1H-tetrazole. The successful synthesis of phosmidosine was achieved by use of a tert-butoxycarbonyl (Boc) group, which was found to be selectively introduced into the 7-NH function of 8-oxoadenosine and to serve as a pseudo-protecting group due to its steric effect in such manner that the unmasked 6-amino group was not phosphitylated. Final coupling reaction of the 8-oxoadenosine 5'-phosphoramidite derivative with N-tritylprolinamide followed by full deprotection gave a mixture of phosmidosine and its diastereoisomer. The (13)C NMR spectra of the diastereomers suggest that the slow-eluted diastereomer 1b is the naturally occurring phosmidosine. The growth inhibitory activity of phosmidosine 1b, its diastereomer 1a, and phosmidosine B in various tumor cell lines was evaluated by the MTT assay. As the result, phosmidosine B showed high anticancer activities and both the diastereomers 1a and 1b of phosmidosine isolated were found to have similar but approximately 10 times higher anticancer activities than phosmidosine B. Moreover, it turned out that these phosmidosine derivatives showed characteristic inhibitory activities against cancer cells independent of their p53 phenotypes. These results suggest that phosmidosine and its related compounds would be promising as a new type of anticancer agents having a wide range of inhibitory activities against tumor cells.
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Affiliation(s)
- Tomohisa Moriguchi
- Faculty of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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47
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Effect of molecular sieves in the liquid-phase synthesis of nucleotides via the phosphoramidite method. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(01)00880-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Heu S, Oh J, Kang Y, Ryu S, Cho SK, Cho Y, Cho M. gly gene cloning and expression and purification of glycinecin A, a bacteriocin produced by Xanthomonas campestris pv. glycines 8ra. Appl Environ Microbiol 2001; 67:4105-10. [PMID: 11526012 PMCID: PMC93136 DOI: 10.1128/aem.67.9.4105-4110.2001] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glycinecin A, a bacteriocin produced by Xanthomonas campestris pv. glycines, inhibits the growth of X. campestris pv. vesicatoria. We have cloned and expressed the genes encoding glycinecin A in Escherichia coli. Recombinant glycinecin A was purified from cell extracts by ammonium sulfate precipitation followed by chromatography on Q-Sepharose, Mono Q (ion exchange), and size exclusion columns. Purified glycinecin A is composed of two polypeptides, is active over a wide pH range (6 to 9), and is stable at temperatures up to 60 degrees C. Glycinecin A is a heterodimer consisting of 39- and 14-kDa subunits, as revealed through size exclusion chromatography and cross-linking analysis. Two genes, glyA and glyB, encoding the 39- and 14-kDa subunits, respectively, were identified based on the N-terminal sequences of the subunits. From the nucleotide sequences of glyA and glyB, we conclude that both genes are translated as bacteriocin precursors that include N-terminal leader sequences. When expressed in E. coli, recombinant glycinecin A was found primarily in cell extracts. In contrast, most glycinecin A from Xanthomonas was found in the culture media. E. coli transformed with either glyA or glyB separately did not show the bacteriocin activity.
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Affiliation(s)
- S Heu
- Department of Agricultural Biology, College of Agriculture and Life Sciences, Seoul National University, Suwon 441-744, Korea
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Moriguchi T, Yanagi T, Kunimori M, Wada T, Sekine M. Synthesis and properties of aminoacylamido-AMP: chemical optimization for the construction of an N-acyl phosphoramidate linkage. J Org Chem 2000; 65:8229-38. [PMID: 11101378 DOI: 10.1021/jo0008338] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper describes the design and synthesis of a new type of aminoacyl-adenylate analogue (aa-AMPN) having an N-acyl phosphoramidate linkage where the oxygen atom of the mixed anhydride bond of aminoacyl-adenylate (aa-AMP) is replaced by an amino group. This new type of aa-AMP analogue is expected to be useful as material for studies on the recognition mechanism of the aminoacylation of tRNA and other biochemical reactions. The condensation of phosphoramidite derivatives of carboxamides with nucleoside derivatives failed, because the activated phosphoramidite derivatives reacted with not only the hydroxyl groups but also another reactive species. An alternative approach was examined by the reaction of 5'-O-phosphoramidite adenosine derivatives with carboxamide derivatives. The TBTr and TSE groups were chosen for protection of the amino group of amino acid amides and the phosphate group, respectively. Detailed studies revealed that the use of 5-(3,5-dinitrophenyl)-1H-tetrazole as an activating catalyst of phosphoramidites resulted in rapid condensation within 10 min to give fully protected aa-AMPN derivatives. No side reaction occurred. Deprotection of these products via a two-step procedure gave aa-AMPN derivatives in good yields. It also turned out that aa-AMPNs thus obtained are stable under both acidic and basic conditions, such as 0.1 M HCl (pH 1.0) and 0.1 M NaOH (pH 13.0).
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Affiliation(s)
- T Moriguchi
- Faculty of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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Abstract
Kinetics of a self-capping RNA, Iso6, have been investigated to constrain the catalytic mechanism. The role of phosphates has been examined by varying the number of phosphates on the nucleophilic attacking group or on the RNA. While the number of phosphates in the nucleophile affects capping kinetics, only KM but not kcat is altered. The KM values for GMP, GDP, GTP and ppppG are 200, 11, 13 and 31 microM, respectively. A reaction product, pyrophosphate, is also found to strongly inhibit RNA activities through a competitive exchange mechanism with an apparent Ki of 200 nM. Uniquely strong binding of pyrophosphate supports the idea that capping originated by utilization of the initial pyrophosphate leaving group site for capping nucleophiles. In contrast to the nucleophile phosphate, change of 5' RNA terminus from triphosphate to tetraphosphate enhances the overall rate and kcat by 40%, with little effect on KM. Thus, only the leaving group appears to affect the rate of the chemical transformation. We propose two possible mechanisms that explain this apparent rate-limiting chemical step, either dissociation of pyrophosphate to form a metaphosphate monoester intermediate or formation of a circular phosphoramidate intermediate, using an internal RNA nitrogenous group. A single essential Ca ion is required for all activities.
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Affiliation(s)
- F Huang
- Department of Molecular Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, CO, 80309-0347, USA
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