1
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Barone GD, Zhou Y, Wang H, Xu S, Ma Z, Cernava T, Chen Y. Implications of bacteria‒bacteria interactions within the plant microbiota for plant health and productivity. J Zhejiang Univ Sci B 2024:1-16. [PMID: 38773879 DOI: 10.1631/jzus.b2300914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/26/2024] [Indexed: 05/24/2024]
Abstract
Crop production currently relies on the widespread use of agrochemicals to ensure food security. This practice is considered unsustainable, yet has no viable alternative at present. The plant microbiota can fulfil various functions for its host, some of which could be the basis for developing sustainable protection and fertilization strategies for plants without relying on chemicals. To harness such functions, a detailed understanding of plant‒microbe and microbe‒microbe interactions is necessary. Among interactions within the plant microbiota, those between bacteria are the most common ones; they are not only of ecological importance but also essential for maintaining the health and productivity of the host plants. This review focuses on recent literature in this field and highlights various consequences of bacteria‒bacteria interactions under different agricultural settings. In addition, the molecular and genetic backgrounds of bacteria that facilitate such interactions are emphasized. Representative examples of commonly found bacterial metabolites with bioactive properties, as well as their modes of action, are given. Integrating our understanding of various binary interactions into complex models that encompass the entire microbiota will benefit future developments in agriculture and beyond, which could be further facilitated by artificial intelligence-based technologies.
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Affiliation(s)
| | - Yaqi Zhou
- State Key Laboratory of Rice Biology and Breeding; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects; Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects; Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hongkai Wang
- State Key Laboratory of Rice Biology and Breeding; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects; Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects; Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Sunde Xu
- State Key Laboratory of Rice Biology and Breeding; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects; Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects; Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology and Breeding; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects; Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects; Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Tomislav Cernava
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ Southampton, UK.
| | - Yun Chen
- State Key Laboratory of Rice Biology and Breeding; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects; Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects; Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
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2
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Degen G, Ahmed ST, Stow PR, Butler A, Andresen Eguiluz RC. pH-Tolerant Wet Adhesion of Catechol Analogs. ACS APPLIED MATERIALS & INTERFACES 2024; 16:22689-22695. [PMID: 38622496 PMCID: PMC11071048 DOI: 10.1021/acsami.4c01740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/17/2024]
Abstract
The need for improved wet adhesives has driven research on mussel-inspired materials incorporating dihydroxyphenylalanine (DOPA) and related analogs of the parent catechol, but their susceptibility to oxidation limits practical application of these functionalities. Here, we investigate the molecular-level adhesion of the catechol analogs dihydroxybenzamide (DHB) and hydroxypyridinone (HOPO) as a function of pH. We find that the molecular structure of the catechol analogs influences their susceptibility to oxidation in alkaline conditions, with HOPO emerging as a particularly promising candidate for pH-tolerant adhesives for diverse environmental conditions.
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Affiliation(s)
- George
D. Degen
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Syeda Tajin Ahmed
- Department
of Materials Science and Engineering, University
of California, Merced, California 95344, United States
| | - Parker R. Stow
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Alison Butler
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Roberto C. Andresen Eguiluz
- Department
of Materials Science and Engineering, University
of California, Merced, California 95344, United States
- Health
Sciences Research Institute, University
of California, Merced, California 95344, United States
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3
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Rehm K, Vollenweider V, Gu S, Friman VP, Kümmerli R, Wei Z, Bigler L. Chryseochelins-structural characterization of novel citrate-based siderophores produced by plant protecting Chryseobacterium spp. Metallomics 2023; 15:7040575. [PMID: 36792066 PMCID: PMC9989332 DOI: 10.1093/mtomcs/mfad008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/29/2023] [Indexed: 02/17/2023]
Abstract
Bacteria secrete siderophores whose function is to acquire iron. In recent years, the siderophores of several Chryseobacterium species were shown to promote the health and growth of various plants such as tomato or rice. However, the chemical nature of Chryseobacterium siderophores remained unexplored despite great interest. In this work, we present the purification and structure elucidation by nuclear magnetic resonance (NMR) spectroscopy and tandem mass spectrometry (MS/MS) of chryseochelin A, a novel citrate-based siderophore secreted by three Chryseobacterium strains involved in plant protection. It contains the unusual building blocks 3-hydroxycadaverine and fumaric acid. Furthermore, the unstable structural isomer chryseochelin B and its stable derivative containing fatty acid chains, named chryseochelin C, were identified by mass spectrometric methods. The latter two incorporate an unusual ester connectivity to the citrate moiety showing similarities to achromobactin from the plant pathogen Dickeya dadantii. Finally, we show that chryseochelin A acts in a concentration-dependent manner against the plant-pathogenic Ralstonia solanacearum strain by reducing its access to iron. Thus, our study provides valuable knowledge about the siderophores of Chryseobacterium strains, which have great potential in various applications.
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Affiliation(s)
- Karoline Rehm
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Vera Vollenweider
- University of Zurich, Department of Quantitative Biomedicine, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Shaohua Gu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Ville-Petri Friman
- University of York, Department of Biology, Wentworth Way, York YO10 5DD, UK
| | - Rolf Kümmerli
- University of Zurich, Department of Quantitative Biomedicine, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, PR China
| | - Laurent Bigler
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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4
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Tao Y, Ge Y, Yang J, Song W, Jin D, Lin H, Zheng H, Lu S, Luo W, Huang Y, Zhuang Z, Xu J. A novel phytopathogen Erwinia sorbitola sp. nov., isolated from the feces of ruddy shelducks. Front Cell Infect Microbiol 2023; 13:1109634. [PMID: 36875519 PMCID: PMC9978198 DOI: 10.3389/fcimb.2023.1109634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/02/2023] [Indexed: 02/18/2023] Open
Abstract
The species in the genus Erwinia are Gram-stain-negative, facultatively anaerobic, motile, and rod-shaped. Most species in the genus Erwinia are phytopathogens. Also, Erwinia persicina was involved in several human infections. Based on the reverse microbial etiology principles, it is worth analyzing the pathogenicity of species in this genus. In this study, we isolated and sequenced two species of Erwinia. Phylogenetic, phenotypic, biochemical, and chemotaxonomic analyses were performed to identify its taxonomy position. The virulence tests on plant leaves and pear fruits were used to identify the plant pathogenicity of two species of Erwinia. Bioinformatic methods predicted the possible pathogenic determinants based on the genome sequence. Meanwhile, adhesion, invasion, and cytotoxicity assays on RAW 264.7 cells were applied to identify animal pathogenicity. We isolated two Gram-stain-negative, facultatively anaerobic, motile, and rod-shaped strains from the feces of ruddy shelducks in the Tibet Plateau of China, designated J780T and J316. Distinct phylogenetic, genomic, phenotypic, biochemical, and chemotaxonomic characters of J780T and J316 identified they were novel species and belonged to the genus Erwinia, for which the name Erwinia sorbitola sp. nov. was proposed, the type strain was J780T (= CGMCC 1.17334T = GDMCC 1.1666T = JCM 33839T). Virulence tests showed blight and rot on the leaves and pear fruits confirmed Erwinia sorbitola sp. nov. was a phytopathogen. Predicted gene clusters of motility, biofilm formation, exopolysaccharides, stress survival, siderophores, and Type VI secretion system might be the causes of pathogenicity. In addition, predicted polysaccharide biosynthesis gene clusters on the genome sequence, and the high capacity for adhesion, invasion, and cytotoxicity to animal cells confirmed it has pathogenicity on animals. In conclusion, we isolated and identified a novel phytopathogen Erwinia sorbitola sp. nov. in ruddy shelducks. A predefined pathogen is beneficial for preventing from suffering potential economic losses caused by this new pathogen.
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Affiliation(s)
- Yuanmeihui Tao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Yajun Ge
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Weitao Song
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Hong Lin
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Wenbo Luo
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Zhenhong Zhuang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Zhenhong Zhuang, ; Jianguo Xu,
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
- Research Institute of Public Health, Nankai University, Tianjin, China
- *Correspondence: Zhenhong Zhuang, ; Jianguo Xu,
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5
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Butler A, Jelowicki AM, Ogasawara HA, Reitz ZL, Stow PR, Thomsen E. Mining elements of siderophore chirality encoded in microbial genomes. FEBS Lett 2023; 597:134-140. [PMID: 36370136 DOI: 10.1002/1873-3468.14539] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
The vast majority of bacteria require iron to grow. A significant iron acquisition strategy is the production of siderophores, which are secondary microbial metabolites synthesized to sequester iron(III). Siderophore structures encompass a variety of forms, of which highly modified peptidic siderophores are of interest herein. State-of-the-art genome mining tools, such as antiSMASH (antibiotics & Secondary Metabolite Analysis SHell), hold the potential to predict and discover new peptidic siderophores, including a combinatoric suite of triscatechol siderophores framed on a triserine-ester backbone of the general class, (DHB-l/d CAA-l Ser)3 (CAA, cationic amino acid). Siderophores with l/d Arg, l/d Lys and l Orn, but not d Orn, were predicted in bacterial genomes. Fortuitously the d Orn siderophore was identified, yet its lack of prediction highlights the limitation of current genome mining tools. The full combinatoric suite of these siderophores, which form chiral iron(III) complexes, reveals stereospecific coordination chemistry encoded in microbial genomes. The chirality embedded in this suite of Fe(III)-siderophores raises the question of whether the relevant siderophore-mediated iron acquisition pathways are stereospecific and selective for ferric siderophore complexes of a defined configuration.
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Affiliation(s)
- Alison Butler
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Aneta M Jelowicki
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Haley A Ogasawara
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Zachary L Reitz
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Parker R Stow
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Emil Thomsen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
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6
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Timofeeva AM, Galyamova MR, Sedykh SE. Bacterial Siderophores: Classification, Biosynthesis, Perspectives of Use in Agriculture. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223065. [PMID: 36432794 PMCID: PMC9694258 DOI: 10.3390/plants11223065] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 06/07/2023]
Abstract
Siderophores are synthesized and secreted by many bacteria, yeasts, fungi, and plants for Fe (III) chelation. A variety of plant-growth-promoting bacteria (PGPB) colonize the rhizosphere and contribute to iron assimilation by plants. These microorganisms possess mechanisms to produce Fe ions under iron-deficient conditions. Under appropriate conditions, they synthesize and release siderophores, thereby increasing and regulating iron bioavailability. This review focuses on various bacterial strains that positively affect plant growth and development through synthesizing siderophores. Here we discuss the diverse chemical nature of siderophores produced by plant root bacteria; the life cycle of siderophores, from their biosynthesis to the Fe-siderophore complex degradation; three mechanisms of siderophore biosynthesis in bacteria; the methods for analyzing siderophores and the siderophore-producing activity of bacteria and the methods for screening the siderophore-producing activity of bacterial colonies. Further analysis of biochemical, molecular-biological, and physiological features of siderophore synthesis by bacteria and their use by plants will allow one to create effective microbiological preparations for improving soil fertility and increasing plant biomass, which is highly relevant for sustainable agriculture.
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Affiliation(s)
- Anna M. Timofeeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia
| | - Maria R. Galyamova
- Center for Entrepreneurial Initiatives, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Sergey E. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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7
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Khilyas IV, Markelova MI, Valeeva LR, Gritseva AS, Sorokina AV, Shafigullina LT, Tukhbatova RI, Shagimardanova EI, Berkutova ES, Sharipova MR, Lochnit G, Cohen MF. Genomic and metabolomic profiling of endolithic Rhodococcus fascians strain S11 isolated from an arid serpentine environment. Arch Microbiol 2022; 204:336. [PMID: 35587838 DOI: 10.1007/s00203-022-02955-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/29/2022]
Abstract
Genomic and metabolomic studies of endolithic bacteria are essential for understanding their adaptations to extreme conditions of the rock environment and their contributions to mineralization and weathering processes. The endoliths of arid serpentine rocks are exposed to different environmental stresses, including desiccation and re-hydration, temperature fluctuations, oligotrophy, and high concentrations of heavy metals. Bacteria of the genus Rhodococcus commonly inhabit endolithic environments. Here, we describe genomic and metabolomic analyses of the non-pathogenic wild-type Rhodococcus fascians strain S11, isolated from weathered serpentine rock at the arid Khalilovsky massif, Russia. We found that strain S11 lacks the virulence plasmid that functions in the phytopathogenecity of some R. fascians strains. Phenotypic profiling revealed a high pH tolerance, phytase activity and siderophore production. A widely untargeted metabolome analysis performed using an Orbitrap LC-MS/MS method demonstrated the presence of chrysobactin-type siderophores in the culture medium of strain S11. The natural variation of secondary metabolites produced by strain S11 might provide a practical basis for revealing antibacterial, fungicide or insecticidal activities. Finally, plant infection and plant growth stimulation studies showed no observable effect of exposure strain S11 bacteria on the aerial and root parts of Arabidopsis thaliana plants. Based on our findings, R. fascians strain S11 might be promising tool for investigations of organo-mineral interactions, heavy metal bioremediation, and mechanisms of bacterial mediated weathering of plant-free serpentine rock to soil.
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Affiliation(s)
- Irina V Khilyas
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation.
| | - Maria I Markelova
- Laboratory of Omics Technologies, Institute Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Lia R Valeeva
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Anastasia S Gritseva
- Department of Genetics, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Alyona V Sorokina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Lilia T Shafigullina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Rezeda I Tukhbatova
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region), Federal University, Kazan, Russian Federation
| | - Elena I Shagimardanova
- Laboratory of Extreme Biology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Ekaterina S Berkutova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Margarita R Sharipova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Guenter Lochnit
- Faculty of Medicine Protein Analytics, Institute of Biochemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Michael F Cohen
- Department of Biology, Sonoma State University, Rohnert Park, CA, USA
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8
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Thomsen E, Reitz ZL, Stow PR, Dulaney K, Butler A. Ruckerbactin Produced by Yersinia ruckeri YRB Is a Diastereomer of the Siderophore Trivanchrobactin Produced by Vibrio campbellii DS40M4. JOURNAL OF NATURAL PRODUCTS 2022; 85:264-269. [PMID: 34942075 DOI: 10.1021/acs.jnatprod.1c01047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The Gram-negative bacterium Yersinia ruckeri is the causative agent for enteric red mouth disease in salmonids. The genome of Y. ruckeri YRB contains a biosynthetic gene cluster encoding the biosynthesis of catechol siderophores that are diastereomeric with the known vanchrobactin class of siderophores, (DHBDArgLSer)(1-3). Ruckerbactin (1), produced by Y. ruckeri YRB, was found to be the linear tris-l-serine ester composed of l-arginine and 2,3-dihydroxybenzoic acid, (DHBLArgLSer)3. The biscatechol, (DHBLArgLSer)2 (2), and monocatechol, DHBLArgLSer (3), compounds were also isolated and characterized. The macrolactone of ruckerbactin was not detected. The presence of LArg in ruckerbactin makes it the diastereomer of trivanchrobactin with DArg. The electronic circular dichroism spectra of Fe(III)-ruckerbactin and Fe(III)-trivanchrobactin reveal the opposite enantiomeric configurations at the Fe(III) sites. Fe(III)-ruckerbactin adopts the Δ configuration, and Fe(III)-trivanchrobactin adopts the Λ configuration. Y. ruckeri YRB was also found to produce the antimicrobial agent holomycin (4).
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Affiliation(s)
- Emil Thomsen
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Zachary L Reitz
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Parker R Stow
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Kalana Dulaney
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Alison Butler
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, United States
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9
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Stow PR, Reitz ZL, Johnstone TC, Butler A. Genomics-driven discovery of chiral triscatechol siderophores with enantiomeric Fe(iii) coordination. Chem Sci 2021; 12:12485-12493. [PMID: 34603680 PMCID: PMC8480324 DOI: 10.1039/d1sc03541j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/18/2021] [Indexed: 11/21/2022] Open
Abstract
Ferric complexes of triscatechol siderophores may assume one of two enantiomeric configurations at the iron site. Chirality is known to be important in the iron uptake process, however an understanding of the molecular features directing stereospecific coordination remains ambiguous. Synthesis of the full suite of (DHBL/DLysL/DSer)3 macrolactone diastereomers, which includes the siderophore cyclic trichrysobactin (CTC), enables the effects that the chirality of Lys and Ser residues exert on the configuration of the Fe(iii) complex to be defined. Computationally optimized geometries indicate that the Λ/Δ configurational preferences are set by steric interactions between the Lys sidechains and the peptide backbone. The ability of each (DHBL/DLysL/DSer)3 diastereomer to form a stable Fe(iii) complex prompted a genomic search for biosynthetic gene clusters (BGCs) encoding the synthesis of these diastereomers in microbes. The genome of the plant pathogen Dickeya chrysanthemi EC16 was sequenced and the genes responsible for the biosynthesis of CTC were identified. A related but distinct BGC was identified in the genome of the opportunistic pathogen Yersinia frederiksenii ATCC 33641; isolation of the siderophore from Y. frederiksenii ATCC 33641, named frederiksenibactin (FSB), revealed the triscatechol oligoester, linear-(DHBLLysLSer)3. Circular dichroism (CD) spectroscopy establishes that Fe(iii)-CTC and Fe(iii)-FSB are formed in opposite enantiomeric configuration, consistent with the results of the ferric complexes of the cyclic (DHBL/DLysL/DSer)3 diastereomers.
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Affiliation(s)
- Parker R Stow
- Department of Chemistry and Biochemistry, University of California Santa Barbara CA 93106-9510 USA
| | - Zachary L Reitz
- Department of Chemistry and Biochemistry, University of California Santa Barbara CA 93106-9510 USA
| | - Timothy C Johnstone
- Department of Chemistry and Biochemistry, University of California Santa Cruz CA 95064 USA
| | - Alison Butler
- Department of Chemistry and Biochemistry, University of California Santa Barbara CA 93106-9510 USA
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10
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Reitz ZL, Butler A. Precursor-directed biosynthesis of catechol compounds in Acinetobacter bouvetii DSM 14964. Chem Commun (Camb) 2020; 56:12222-12225. [PMID: 32926028 DOI: 10.1039/d0cc04171h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Genome mining for VibH homologs reveals several species of Acinetobacter with a gene cluster that putatively encodes the biosynthesis of catechol siderophores with an amine core. A. bouvetii DSM 14964 produces three novel biscatechol siderophores: propanochelin (1), butanochelin (2), and pentanochelin (3). This strain has a relaxed specificity for the amine substrate, allowing for the biosynthesis of a variety of non-natural siderophore analogs by precursor directed biosynthesis. Of potential synthetic utility, A. bouvetii DSM 14964 condenses 2,3-dihydroxybenzoic acid (2,3-DHB) to allylamine and propargylamine, producing catecholic compounds which bind iron(iii) and may be further modified via thiol-ene or azide-alkyne click chemistry.
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Affiliation(s)
- Zachary L Reitz
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA.
| | - Alison Butler
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA.
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11
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dos Santos RM, Diaz PAE, Lobo LLB, Rigobelo EC. Use of Plant Growth-Promoting Rhizobacteria in Maize and Sugarcane: Characteristics and Applications. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.00136] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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12
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The position of lysine controls the catechol-mediated surface adhesion and cohesion in underwater mussel adhesion. J Colloid Interface Sci 2020; 563:168-176. [DOI: 10.1016/j.jcis.2019.12.082] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 12/20/2022]
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13
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Degen GD, Stow PR, Lewis RB, Andresen Eguiluz RC, Valois E, Kristiansen K, Butler A, Israelachvili JN. Impact of Molecular Architecture and Adsorption Density on Adhesion of Mussel-Inspired Surface Primers with Catechol-Cation Synergy. J Am Chem Soc 2019; 141:18673-18681. [DOI: 10.1021/jacs.9b04337] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Ferreira CMH, Soares HMVM, Soares EV. Promising bacterial genera for agricultural practices: An insight on plant growth-promoting properties and microbial safety aspects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 682:779-799. [PMID: 31146074 DOI: 10.1016/j.scitotenv.2019.04.225] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 05/20/2023]
Abstract
In order to address the ever-increasing problem of the world's population food needs, the optimization of farming crops yield, the combat of iron deficiency in plants (chlorosis) and the elimination/reduction of crop pathogens are of key challenges to solve. Traditional ways of solving these problems are either unpractical on a large scale (e.g. use of manure) or are not environmental friendly (e.g. application of iron-synthetic fertilizers or indiscriminate use of pesticides). Therefore, the search for greener substitutes, such as the application of siderophores of bacterial source or the use of plant-growth promoting bacteria (PGPB), is presented as a very promising alternative to enhance yield of crops and performance. However, the use of microorganisms is not a risk-free solution and the potential biohazards associated with the utilization of bacteria in agriculture should be considered. The present work gives a current overview of the main mechanisms associated with the use of bacteria in the promotion of plant growth. The potentiality of several bacterial genera (Azotobacter, Azospirillum, Bacillus, Pantoea, Pseudomonas and Rhizobium) regarding to siderophore production capacity and other plant growth-promoting properties are presented. In addition, the field performance of these bacteria genera as well as the biosafety aspects related with their use for agricultural proposes are reviewed and discussed.
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Affiliation(s)
- Carlos M H Ferreira
- REQUIMTE/LAQV, Departamento de Engenharia Química, Faculdade de Engenharia, Universidade do Porto, rua Dr. Roberto Frias, 4200-465 Porto, Portugal; Bioengineering Laboratory, Chemical Engineering Department, ISEP-School of Engineering of Polytechnic Institute of Porto, rua Dr António Bernardino de Almeida, 431, 4249-015 Porto, Portugal; CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Helena M V M Soares
- REQUIMTE/LAQV, Departamento de Engenharia Química, Faculdade de Engenharia, Universidade do Porto, rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
| | - Eduardo V Soares
- Bioengineering Laboratory, Chemical Engineering Department, ISEP-School of Engineering of Polytechnic Institute of Porto, rua Dr António Bernardino de Almeida, 431, 4249-015 Porto, Portugal; CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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Duprey A, Taib N, Leonard S, Garin T, Flandrois JP, Nasser W, Brochier-Armanet C, Reverchon S. The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity. Environ Microbiol 2019; 21:2809-2835. [PMID: 30969462 DOI: 10.1111/1462-2920.14627] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 12/13/2022]
Abstract
Dickeya is a genus of phytopathogenic enterobacterales causing soft rot in a variety of plants (e.g. potato, chicory, maize). Among the species affiliated to this genus, Dickeya aquatica, described in 2014, remained particularly mysterious because it had no known host. Furthermore, while D. aquatica was proposed to represent a deep-branching species among Dickeya genus, its precise phylogenetic position remained elusive. Here, we report the complete genome sequence of the D. aquatica type strain 174/2. We demonstrate the affinity of D. aquatica strain 174/2 for acidic fruits such as tomato and cucumber and show that exposure of this bacterium to acidic pH induces twitching motility. An in-depth phylogenomic analysis of all available Dickeya proteomes pinpoints D. aquatica as the second deepest branching lineage within this genus and reclassifies two lineages that likely correspond to new genomospecies (gs.): Dickeya gs. poaceaephila (Dickeya sp NCPPB 569) and Dickeya gs. undicola (Dickeya sp 2B12), together with a new putative genus, tentatively named Prodigiosinella. Finally, from comparative analyses of Dickeya proteomes, we infer the complex evolutionary history of this genus, paving the way to study the adaptive patterns and processes of Dickeya to different environmental niches and hosts. In particular, we hypothesize that the lack of xylanases and xylose degradation pathways in D. aquatica could reflect adaptation to aquatic charophyte hosts which, in contrast to land plants, do not contain xyloglucans.
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Affiliation(s)
- Alexandre Duprey
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
| | - Najwa Taib
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Simon Leonard
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
| | - Tiffany Garin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Jean-Pierre Flandrois
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - William Nasser
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
| | - Céline Brochier-Armanet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Sylvie Reverchon
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
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Pan H, Tian X, Shao M, Xie Y, Huang H, Hu J, Ju J. Genome mining and metabolic profiling illuminate the chemistry driving diverse biological activities of Bacillus siamensis SCSIO 05746. Appl Microbiol Biotechnol 2019; 103:4153-4165. [DOI: 10.1007/s00253-019-09759-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 03/07/2019] [Accepted: 03/10/2019] [Indexed: 10/27/2022]
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17
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Baldeweg F, Hoffmeister D, Nett M. A genomics perspective on natural product biosynthesis in plant pathogenic bacteria. Nat Prod Rep 2019; 36:307-325. [DOI: 10.1039/c8np00025e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This review summarizes findings from genomics-inspired natural product research in plant pathogenic bacteria and discusses emerging trends in this field.
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Affiliation(s)
- Florian Baldeweg
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute
- Friedrich-Schiller-University Jena
- 07745 Jena
- Germany
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute
- Friedrich-Schiller-University Jena
- 07745 Jena
- Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering
- TU Dortmund University
- 44227 Dortmund
- Germany
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18
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McRose DL, Seyedsayamdost MR, Morel FMM. Multiple siderophores: bug or feature? J Biol Inorg Chem 2018; 23:983-993. [PMID: 30264174 DOI: 10.1007/s00775-018-1617-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/04/2018] [Indexed: 12/31/2022]
Abstract
It is common for bacteria to produce chemically diverse sets of small Fe-binding molecules called siderophores. Studies of siderophore bioinorganic chemistry have firmly established the role of these molecules in Fe uptake and provided great insight into Fe complexation. However, we still do not fully understand why microbes make so many siderophores. In many cases, the release of small structural variants or siderophore fragments has been ignored, or considered as an inefficiency of siderophore biosynthesis. Yet, in natural settings, microbes live in complex consortia and it has become increasingly clear that the secondary metabolite repertoires of microbes reflect this dynamic environment. Multiple siderophore production may, therefore, provide a window into microbial life in the wild. This minireview focuses on three biochemical routes by which multiple siderophores can be released by the same organism-multiple biosynthetic gene clusters, fragment release, and precursor-directed biosynthesis-and highlights emergent themes related to each. We also emphasize the plurality of reasons for multiple siderophore production, which include enhanced iron uptake via synergistic siderophore use, microbial warfare and cooperation, and non-classical functions such as the use of siderophores to take up metals other than Fe.
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Affiliation(s)
- Darcy L McRose
- Department of Geosciences, Princeton University, Princeton, USA.
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, USA.,Department of Molecular Biology, Princeton University, Princeton, USA
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Reitz ZL, Sandy M, Butler A. Biosynthetic considerations of triscatechol siderophores framed on serine and threonine macrolactone scaffolds. Metallomics 2018; 9:824-839. [PMID: 28594012 DOI: 10.1039/c7mt00111h] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Bacteria often produce siderophores to facilitate iron uptake. One of the most studied siderophores is enterobactin, the macrolactone trimer of 2,3-dihydroxybenzoyl-l-serine, produced by E. coli and many other enteric bacteria. Other siderophores are variants of enterobactin, with structural modifications including expansion of the tri-serine core to a tetra-serine macrolactone, substitution of l-serine with l-threonine, insertion of amino acids (i.e., Gly, l-Ala, d-Lys, d- and l-Arg, l-Orn), catechol glucosylation, and linearization of the tri-serine macrolactone core. In this review we summarize the current understanding of the biosyntheses of these enterobactin variants, placing them in contrast with the well-established biosynthesis of enterobactin.
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Affiliation(s)
- Zachary L Reitz
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA.
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20
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Li J, Liu S, Jiang Z, Sun C. Catechol amide iron chelators produced by a mangrove-derived Bacillus subtilis. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Zhang K, Zhang F, Song Y, Fan JB, Wang S. Recent Progress of Mussel-Inspired Underwater Adhesives. CHINESE J CHEM 2017. [DOI: 10.1002/cjoc.201600778] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ke Zhang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, CAS Center for Excellence in Nanoscience, Technical Institute of Physics and Chemistry; Chinese Academy of Sciences; Beijing 100190 China
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou Henan 450001 China
| | - Feilong Zhang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, CAS Center for Excellence in Nanoscience, Technical Institute of Physics and Chemistry; Chinese Academy of Sciences; Beijing 100190 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Yongyang Song
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, CAS Center for Excellence in Nanoscience, Technical Institute of Physics and Chemistry; Chinese Academy of Sciences; Beijing 100190 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Jun-Bing Fan
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, CAS Center for Excellence in Nanoscience, Technical Institute of Physics and Chemistry; Chinese Academy of Sciences; Beijing 100190 China
| | - Shutao Wang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, CAS Center for Excellence in Nanoscience, Technical Institute of Physics and Chemistry; Chinese Academy of Sciences; Beijing 100190 China
- University of Chinese Academy of Sciences; Beijing 100049 China
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22
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Siderophores and mussel foot proteins: the role of catechol, cations, and metal coordination in surface adhesion. J Biol Inorg Chem 2017; 22:739-749. [DOI: 10.1007/s00775-017-1451-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/22/2017] [Indexed: 12/27/2022]
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23
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Rapp MV, Maier GP, Dobbs HA, Higdon NJ, Waite JH, Butler A, Israelachvili JN. Defining the Catechol–Cation Synergy for Enhanced Wet Adhesion to Mineral Surfaces. J Am Chem Soc 2016; 138:9013-6. [DOI: 10.1021/jacs.6b03453] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Michael V. Rapp
- Department
of Chemical Engineering, ‡Department of Chemistry and Biochemistry, §Molecular, Cellular,
and Developmental Biology, and ∥Materials Department, University of California, Santa
Barbara, California 93106, United States
| | - Greg P. Maier
- Department
of Chemical Engineering, ‡Department of Chemistry and Biochemistry, §Molecular, Cellular,
and Developmental Biology, and ∥Materials Department, University of California, Santa
Barbara, California 93106, United States
| | - Howard A. Dobbs
- Department
of Chemical Engineering, ‡Department of Chemistry and Biochemistry, §Molecular, Cellular,
and Developmental Biology, and ∥Materials Department, University of California, Santa
Barbara, California 93106, United States
| | - Nicholas J. Higdon
- Department
of Chemical Engineering, ‡Department of Chemistry and Biochemistry, §Molecular, Cellular,
and Developmental Biology, and ∥Materials Department, University of California, Santa
Barbara, California 93106, United States
| | - J. Herbert Waite
- Department
of Chemical Engineering, ‡Department of Chemistry and Biochemistry, §Molecular, Cellular,
and Developmental Biology, and ∥Materials Department, University of California, Santa
Barbara, California 93106, United States
| | - Alison Butler
- Department
of Chemical Engineering, ‡Department of Chemistry and Biochemistry, §Molecular, Cellular,
and Developmental Biology, and ∥Materials Department, University of California, Santa
Barbara, California 93106, United States
| | - Jacob N. Israelachvili
- Department
of Chemical Engineering, ‡Department of Chemistry and Biochemistry, §Molecular, Cellular,
and Developmental Biology, and ∥Materials Department, University of California, Santa
Barbara, California 93106, United States
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24
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Zou F, Tang X, Huang Y, Wan S, Lu F, Chen ZN, Wu A, Zhang H. Fluorescence of a triple-stranded helicate iron(iii) complex from a novel bis-β-diketone ligand: synthesis, structure and spectroscopic studies. CrystEngComm 2016. [DOI: 10.1039/c6ce01231k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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25
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Fazary AE, Ju YH, Al-Shihri AS, Alfaifi MY, Alshehri MA. Biodegradable siderophores: survey on their production, chelating and complexing properties. REV INORG CHEM 2016. [DOI: 10.1515/revic-2016-0002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe academic and industrial research on the interactions of complexing agents with the environment has received more attention for more than half a century ago and has always been concerned with the applications of chelating agents in the environment. In contrast, in recent years, an increasing scholarly interest has been demonstrated in the chemical and biological degradation of chelating agents. This is reflected by the increasing number of chelating agents-related publications between 1950 and middle of 2016. Consequently, the discovery of new green biodegradable chelating agents is of great importance and has an impact in the non-biodegradable chelating agent’s replacement with their green chemistry analogs. To acquire iron, many bacteria growing aerobically, including marine species, produce siderophores, which are low-molecular-weight compounds produced to facilitate acquisition of iron. To date and to the best of our knowledge, this is a concise and complete review article of the current and previous relevant studies conducted in the field of production, purification of siderophore compounds and their metal complexes, and their roles in biology and medicine.
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Maier GP, Rapp MV, Waite JH, Israelachvili JN, Butler A. BIOLOGICAL ADHESIVES. Adaptive synergy between catechol and lysine promotes wet adhesion by surface salt displacement. Science 2015; 349:628-32. [PMID: 26250681 DOI: 10.1126/science.aab0556] [Citation(s) in RCA: 396] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In physiological fluids and seawater, adhesion of synthetic polymers to solid surfaces is severely limited by high salt, pH, and hydration, yet these conditions have not deterred the evolution of effective adhesion by mussels. Mussel foot proteins provide insights about adhesive adaptations: Notably, the abundance and proximity of catecholic Dopa (3,4-dihydroxyphenylalanine) and lysine residues hint at a synergistic interplay in adhesion. Certain siderophores—bacterial iron chelators—consist of paired catechol and lysine functionalities, thereby providing a convenient experimental platform to explore molecular synergies in bioadhesion. These siderophores and synthetic analogs exhibit robust adhesion energies (E(ad) ≥-15 millijoules per square meter) to mica in saline pH 3.5 to 7.5 and resist oxidation. The adjacent catechol-lysine placement provides a "one-two punch," whereby lysine evicts hydrated cations from the mineral surface, allowing catechol binding to underlying oxides.
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Affiliation(s)
- Greg P Maier
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
| | - Michael V Rapp
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - J Herbert Waite
- Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.
| | - Jacob N Israelachvili
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA. Materials Department, University of California, Santa Barbara, CA 93106, USA.
| | - Alison Butler
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA.
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27
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Latham JA, Chen D, Allen KN, Dunaway-Mariano D. Divergence of substrate specificity and function in the Escherichia coli hotdog-fold thioesterase paralogs YdiI and YbdB. Biochemistry 2014; 53:4775-87. [PMID: 24992697 PMCID: PMC4116150 DOI: 10.1021/bi500333m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The work described in this paper, and its companion paper (Wu, R., Latham, J. A., Chen, D., Farelli, J., Zhao, H., Matthews, K. Allen, K. N., and Dunaway-Mariano, D. (2014) Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB. Biochemistry, DOI: 10.1021/bi500334v), focuses on the evolution of a pair of paralogous hotdog-fold superfamily thioesterases of E. coli, YbdB and YdiI, which share a high level of sequence identity but perform different biological functions (viz., proofreader of 2,3-dihydroxybenzoyl-holoEntB in the enterobactin biosynthetic pathway and catalyst of the 1,4-dihydoxynapthoyl-CoA hydrolysis step in the menaquinone biosynthetic pathway, respectively). In vitro substrate activity screening of a library of thioester metabolites showed that YbdB displays high activity with benzoyl-holoEntB and benzoyl-CoA substrates, marginal activity with acyl-CoA thioesters, and no activity with 1,4-dihydoxynapthoyl-CoA. YdiI, on the other hand, showed a high level of activity with its physiological substrate, significant activity toward a wide range of acyl-CoA thioesters, and minimal activity toward benzoyl-holoEntB. These results were interpreted as evidence for substrate promiscuity that facilitates YbdB and YdiI evolvability, and divergence in substrate preference, which correlates with their assumed biological function. YdiI support of the menaquinone biosynthetic pathway was confirmed by demonstrating reduced anaerobic growth of the E. coli ydiI-knockout mutant (vs wild-type E. coli) on glucose in the presence of the electron acceptor fumarate. Bioinformatic analysis revealed that a small biological range exists for YbdB orthologs (i.e., limited to Enterobacteriales) relative to that of YdiI orthologs. The divergence in YbdB and YdiI substrate specificity detailed in this paper set the stage for their structural analyses reported in the companion paper.
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Affiliation(s)
- John A Latham
- Department of Chemistry & Chemical Biology, University of New Mexico , Albuquerque, New Mexico 87131, United States
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Han AW, Sandy M, Fishman B, Trindade-Silva AE, Soares CAG, Distel DL, Butler A, Haygood MG. Turnerbactin, a novel triscatecholate siderophore from the shipworm endosymbiont Teredinibacter turnerae T7901. PLoS One 2013; 8:e76151. [PMID: 24146831 PMCID: PMC3795760 DOI: 10.1371/journal.pone.0076151] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 08/19/2013] [Indexed: 12/29/2022] Open
Abstract
Shipworms are marine bivalve mollusks (Family Teredinidae) that use wood for shelter and food. They harbor a group of closely related, yet phylogenetically distinct, bacterial endosymbionts in bacteriocytes located in the gills. This endosymbiotic community is believed to support the host's nutrition in multiple ways, through the production of cellulolytic enzymes and the fixation of nitrogen. The genome of the shipworm endosymbiont Teredinibacter turnerae T7901 was recently sequenced and in addition to the potential for cellulolytic enzymes and diazotrophy, the genome also revealed a rich potential for secondary metabolites. With nine distinct biosynthetic gene clusters, nearly 7% of the genome is dedicated to secondary metabolites. Bioinformatic analyses predict that one of the gene clusters is responsible for the production of a catecholate siderophore. Here we describe this gene cluster in detail and present the siderophore product from this cluster. Genes similar to the entCEBA genes of enterobactin biosynthesis involved in the production and activation of dihydroxybenzoic acid (DHB) are present in this cluster, as well as a two-module non-ribosomal peptide synthetase (NRPS). A novel triscatecholate siderophore, turnerbactin, was isolated from the supernatant of iron-limited T. turnerae T7901 cultures. Turnerbactin is a trimer of N-(2,3-DHB)-L-Orn-L-Ser with the three monomeric units linked by Ser ester linkages. A monomer, dimer, dehydrated dimer, and dehydrated trimer of 2,3-DHB-L-Orn-L-Ser were also found in the supernatant. A link between the gene cluster and siderophore product was made by constructing a NRPS mutant, TtAH03. Siderophores could not be detected in cultures of TtAH03 by HPLC analysis and Fe-binding activity of culture supernatant was significantly reduced. Regulation of the pathway by iron is supported by identification of putative Fur box sequences and observation of increased Fe-binding activity under iron restriction. Evidence of a turnerbactin fragment was found in shipworm extracts, suggesting the production of turnerbactin in the symbiosis.
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Affiliation(s)
- Andrew W. Han
- Institute of Environmental Health, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Moriah Sandy
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Brian Fishman
- Institute of Environmental Health, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Amaro E. Trindade-Silva
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Ilha do Fundão, CCS, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Carlos A. G. Soares
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Ilha do Fundão, CCS, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Daniel L. Distel
- Ocean Genome Legacy, Inc., Ipswich, Massachusetts, United States of America
| | - Alison Butler
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Margo G. Haygood
- Institute of Environmental Health, Oregon Health & Science University, Beaverton, Oregon, United States of America
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Franza T, Expert D. Role of iron homeostasis in the virulence of phytopathogenic bacteria: an 'à la carte' menu. MOLECULAR PLANT PATHOLOGY 2013; 14:429-38. [PMID: 23171271 PMCID: PMC6638640 DOI: 10.1111/mpp.12007] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The interaction between pathogenic microbes and their hosts is determined by survival strategies on both sides. As a result of its redox properties, iron is vital for the growth and proliferation of nearly all organisms, including pathogenic bacteria. In bacteria-vertebrate interactions, competition for this essential metal is critical for the outcome of the infection. The role of iron in the virulence of plant pathogenic bacteria has only been explored in a few pathosystems in the past. However, in the last 5 years, intensive research has provided new insights into the mechanisms of iron homeostasis in phytopathogenic bacteria that are involved in virulence. This review, which includes important plant pathosystems, discusses the recent advances in the understanding of iron transport and homeostasis during plant pathogenesis. By summarizing the recent progress, we wish to provide an updated view clarifying the various roles played by this metal in the virulence of bacterial phytopathogens as a nutritional and regulatory element. The complex intertwining of iron metabolism and oxidative stress during infection is emphasized.
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Affiliation(s)
- Thierry Franza
- Laboratoire des Interactions Plantes Pathogènes UMR 217, AgroParisTech/INRA/UMPC, 16 rue Claude Bernard 75005, Paris, France.
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30
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Miethke M. Molecular strategies of microbial iron assimilation: from high-affinity complexes to cofactor assembly systems. Metallomics 2013. [DOI: 10.1039/c2mt20193c] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Charkowski A, Blanco C, Condemine G, Expert D, Franza T, Hayes C, Hugouvieux-Cotte-Pattat N, López Solanilla E, Low D, Moleleki L, Pirhonen M, Pitman A, Perna N, Reverchon S, Rodríguez Palenzuela P, San Francisco M, Toth I, Tsuyumu S, van der Waals J, van der Wolf J, Van Gijsegem F, Yang CH, Yedidia I. The role of secretion systems and small molecules in soft-rot Enterobacteriaceae pathogenicity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:425-49. [PMID: 22702350 DOI: 10.1146/annurev-phyto-081211-173013] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Soft-rot Enterobacteriaceae (SRE), which belong to the genera Pectobacterium and Dickeya, consist mainly of broad host-range pathogens that cause wilt, rot, and blackleg diseases on a wide range of plants. They are found in plants, insects, soil, and water in agricultural regions worldwide. SRE encode all six known protein secretion systems present in gram-negative bacteria, and these systems are involved in attacking host plants and competing bacteria. They also produce and detect multiple types of small molecules to coordinate pathogenesis, modify the plant environment, attack competing microbes, and perhaps to attract insect vectors. This review integrates new information about the role protein secretion and detection and production of ions and small molecules play in soft-rot pathogenicity.
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Affiliation(s)
- Amy Charkowski
- Department of Plant Pathology, University of Wisconsin, Madison, Wisconsin 53706, USA.
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