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Xie B, Wei X, Wan C, Zhao W, Song R, Xin S, Song K. Exploring the Biological Pathways of Siderophores and Their Multidisciplinary Applications: A Comprehensive Review. Molecules 2024; 29:2318. [PMID: 38792179 PMCID: PMC11123847 DOI: 10.3390/molecules29102318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Siderophores are a class of small molecules renowned for their high iron binding capacity, essential for all life forms requiring iron. This article provides a detailed review of the diverse classifications, and biosynthetic pathways of siderophores, with a particular emphasis on siderophores synthesized via nonribosomal peptide synthetase (NRPS) and non-NRPS pathways. We further explore the secretion mechanisms of siderophores in microbes and plants, and their role in regulating bioavailable iron levels. Beyond biological functions, the applications of siderophores in medicine, agriculture, and environmental sciences are extensively discussed. These applications include biological pest control, disease treatment, ecological pollution remediation, and heavy metal ion removal. Through a comprehensive analysis of the chemical properties and biological activities of siderophores, this paper demonstrates their wide prospects in scientific research and practical applications, while also highlighting current research gaps and potential future directions.
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Affiliation(s)
| | | | | | | | | | - Shuquan Xin
- School of Life Science, Changchun Normal University, Changchun 130032, China; (B.X.); (X.W.); (C.W.); (W.Z.); (R.S.)
| | - Kai Song
- School of Life Science, Changchun Normal University, Changchun 130032, China; (B.X.); (X.W.); (C.W.); (W.Z.); (R.S.)
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Tanabe T, Mitome H, Miyamoto K, Akira K, Tsujibo H, Tomoo K, Nagaoka K, Funahashi T. Analysis of the vibrioferrin biosynthetic pathway of Vibrio parahaemolyticus. Biometals 2024; 37:507-517. [PMID: 38133869 DOI: 10.1007/s10534-023-00566-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/19/2023] [Indexed: 12/23/2023]
Abstract
Siderophores are small-molecule iron chelators produced by many microorganisms that capture and uptake iron from the natural environment and host. Their biosynthesis in microorganisms is generally performed using non-ribosomal peptide synthetase (NRPS) or NRPS-independent siderophore (NIS) enzymes. Vibrio parahaemolyticus secretes its cognate siderophore vibrioferrin under iron-starvation conditions. Vibrioferrin is a dehydrated condensate composed of α-ketoglutarate, L-alanine, aminoethanol, and citrate, and pvsA (the gene encoding the ATP-grasp enzyme), pvsB (the gene encoding the NIS enzyme), pvsD (the gene encoding the NIS enzyme), and pvsE (the gene encoding decarboxylase) are engaged in its biosynthesis. Here, we elucidated the biosynthetic pathway of vibrioferrin through in vitro enzymatic reactions using recombinant PvsA, PvsB, PvsD, and PvsE proteins. We also found that PvsD condenses L-serine and citrate to generate O-citrylserine, and that PvsE decarboxylates O-citrylserine to form O-citrylaminoethanol. In addition, we showed that O-citrylaminoethanol is converted to alanyl-O-citrylaminoethanol by amidification with L-Ala by PvsA and that alanyl-O-citrylaminoethanol is then converted to vibrioferrin by amidification with α-ketoglutarate by PvsB.
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Affiliation(s)
- Tomotaka Tanabe
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan.
| | - Hidemichi Mitome
- Laboratory of Pharmaceutical Analytical Chemistry, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Katsushiro Miyamoto
- Department of Microbiology and Infection Control, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Kazuki Akira
- Laboratory of Pharmaceutical Analytical Chemistry, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Hiroshi Tsujibo
- Department of Microbiology and Infection Control, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Koji Tomoo
- Department of Physical Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Kenjiro Nagaoka
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Tatsuya Funahashi
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
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Zamanzadeh-Nasrabadi SM, Mohammadiapanah F, Sarikhan S, Shariati V, Saghafi K, Hosseini-Mazinani M. Comprehensive genome analysis of Pseudomonas sp. SWRIQ11, a new plant growth-promoting bacterium that alleviates salinity stress in olive. 3 Biotech 2023; 13:347. [PMID: 37750167 PMCID: PMC10517913 DOI: 10.1007/s13205-023-03755-0] [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: 12/20/2022] [Accepted: 08/20/2023] [Indexed: 09/27/2023] Open
Abstract
The study presents the genome analysis of a new Pseudomonas sp. (SWRIQ11), which can alleviate salinity stress effects on growth of olive seedlings in greenhouse study. The strain SWRIQ11 can tolerate salinity up to 6%, produce siderophores, indole acetic acid (IAA), aminocyclopropane-1-carboxylate (ACC) deaminase, and has the phosphate-solubilizing capability. The SWRIQ11 genome contained an assembly size of 6,196,390 bp with a GC content of 60.1%. According to derived indices based on whole-genome sequences for species delineation, including tetra nucleotide usage patterns (TETRA), genome-to-genome distance (GGDC), and average nucleotide identity (ANI), Pseudomonas sp. SWRIQ11 can be considered a novel species candidate. The phylogenetic analysis revealed SWRIQ11 clusters with Pseudomonas tehranensis SWRI196 in the same clade. The SWRIQ11 genome was rich in genes related to stress sensing, signaling, and response, chaperones, motility, attachments, colonization, and enzymes for degrading plant-derived carbohydrates. Furthermore, the genes for production of exopolysaccharides, osmoprotectants, phytohormones, and ACC deaminase, ion homeostasis, nutrient acquisition, and antioxidant defenses were identified in the SWRIQ11 genome. The results of genome analysis (identification of more than 825 CDSs related to plant growth-promoting and stress-alleviating traits in the SWRIQ11 genome which is more than 15% of its total CDSs) are in accordance with laboratory and greenhouse experiments assigning the Pseudomonas sp. SWRIQ11 as a halotolerant plant growth-promoting bacterium (PGPB). This research highlights the potential safe application of this new PGPB species in agriculture as a potent biofertilizer.
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Affiliation(s)
- Seyyedeh Maryam Zamanzadeh-Nasrabadi
- Pharmaceutial Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455 Iran
| | - Fatemeh Mohammadiapanah
- Pharmaceutial Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455 Iran
| | - Sajjad Sarikhan
- Molecular Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Vahid Shariati
- Agricultural Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Kobra Saghafi
- Soil and Water Research Institute (SWRI), Karaj, Iran
| | - Mehdi Hosseini-Mazinani
- Agricultural Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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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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Girard L, Lood C, De Mot R, van Noort V, Baudart J. Genomic diversity and metabolic potential of marine Pseudomonadaceae. Front Microbiol 2023; 14:1071039. [PMID: 37168120 PMCID: PMC10165715 DOI: 10.3389/fmicb.2023.1071039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/21/2023] [Indexed: 05/13/2023] Open
Abstract
Recent changes in the taxonomy of the Pseudomonadaceae family have led to the delineation of three new genera (Atopomonas, Halopseudomonas and Stutzerimonas). However, the genus Pseudomonas remains the most densely populated and displays a broad genetic diversity. Pseudomonas are able to produce a wide variety of secondary metabolites which drives important ecological functions and have a great impact in sustaining their lifestyles. While soilborne Pseudomonas are constantly examined, we currently lack studies aiming to explore the genetic diversity and metabolic potential of marine Pseudomonas spp. In this study, 23 Pseudomonas strains were co-isolated with Vibrio strains from three marine microalgal cultures and rpoD-based phylogeny allowed their assignment to the Pseudomonas oleovorans group (Pseudomonas chengduensis, Pseudomonas toyotomiensis and one new species). We combined whole genome sequencing on three selected strains with an inventory of marine Pseudomonas genomes to assess their phylogenetic assignations and explore their metabolic potential. Our results revealed that most strains are incorrectly assigned at the species level and half of them do not belong to the genus Pseudomonas but instead to the genera Halopseudomonas or Stutzerimonas. We highlight the presence of 26 new species (Halopseudomonas (n = 5), Stutzerimonas (n = 7) and Pseudomonas (n = 14)) and describe one new species, Pseudomonas chaetocerotis sp. nov. (type strain 536T = LMG 31766T = DSM 111343T). We used genome mining to identify numerous BGCs coding for the production of diverse known metabolites (i.e., osmoprotectants, photoprotectants, quorum sensing molecules, siderophores, cyclic lipopeptides) but also unknown metabolites (e.g., ARE, hybrid ARE-DAR, siderophores, orphan NRPS gene clusters) awaiting chemical characterization. Finally, this study underlines that marine environments host a huge diversity of Pseudomonadaceae that can drive the discovery of new secondary metabolites.
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Affiliation(s)
- Léa Girard
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Léa Girard,
| | - Cédric Lood
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - Julia Baudart
- Laboratoire de Biodiversité et Biotechnologie Microbiennes, Sorbonne Université, CNRS, Observatoire Océanologique, Banyuls-sur-Mer, France
- *Correspondence: Julia Baudart,
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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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Iron acquisition strategies in pseudomonads: mechanisms, ecology, and evolution. Biometals 2022:10.1007/s10534-022-00480-8. [PMID: 36508064 PMCID: PMC10393863 DOI: 10.1007/s10534-022-00480-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
AbstractIron is important for bacterial growth and survival, as it is a common co-factor in essential enzymes. Although iron is very abundant in the earth crust, its bioavailability is low in most habitats because ferric iron is largely insoluble under aerobic conditions and at neutral pH. Consequently, bacteria have evolved a plethora of mechanisms to solubilize and acquire iron from environmental and host stocks. In this review, I focus on Pseudomonas spp. and first present the main iron uptake mechanisms of this taxa, which involve the direct uptake of ferrous iron via importers, the production of iron-chelating siderophores, the exploitation of siderophores produced by other microbial species, and the use of iron-chelating compounds produced by plants and animals. In the second part of this review, I elaborate on how these mechanisms affect interactions between bacteria in microbial communities, and between bacteria and their hosts. This is important because Pseudomonas spp. live in diverse communities and certain iron-uptake strategies might have evolved not only to acquire this essential nutrient, but also to gain relative advantages over competitors in the race for iron. Thus, an integrative understanding of the mechanisms of iron acquisition and the eco-evolutionary dynamics they drive at the community level might prove most useful to understand why Pseudomonas spp., in particular, and many other bacterial species, in general, have evolved such diverse iron uptake repertoires.
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Roskova Z, Skarohlid R, McGachy L. Siderophores: an alternative bioremediation strategy? THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 819:153144. [PMID: 35038542 DOI: 10.1016/j.scitotenv.2022.153144] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 05/15/2023]
Abstract
Siderophores are small molecular weight iron scavengers that are mainly produced by bacteria, fungi, and plants. Recently, they have attracted increasing attention because of their potential role in environmental bioremediation. Although siderophores are generally considered to exhibit high specificity for iron, they have also been reported to bind to various metal and metalloid ions. This unique ability allows siderophores to solubilise and mobilise heavy metals and metalloids from soil, thereby facilitating their bioremediation. In addition, because of their redox nature, they can mediate the production of reactive oxygen species (ROS), and thus promote the biodegradation of organic contaminants. The aim of this review is to summarise the existing knowledge on the developed strategies of siderophore-assisted bioremediation of metals, metalloids, and organic contaminants. Additionally, this review also includes the biosynthesis and classification of microbial and plant siderophores.
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Affiliation(s)
- Zuzana Roskova
- Department of Environmental Chemistry, University of Chemistry and Technology Prague, Technická 5, 16628 Prague, Czech Republic
| | - Radek Skarohlid
- Department of Environmental Chemistry, University of Chemistry and Technology Prague, Technická 5, 16628 Prague, Czech Republic
| | - Lenka McGachy
- Department of Environmental Chemistry, University of Chemistry and Technology Prague, Technická 5, 16628 Prague, Czech Republic.
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Pacheco-Moreno A, Stefanato FL, Ford JJ, Trippel C, Uszkoreit S, Ferrafiat L, Grenga L, Dickens R, Kelly N, Kingdon AD, Ambrosetti L, Nepogodiev SA, Findlay KC, Cheema J, Trick M, Chandra G, Tomalin G, Malone JG, Truman AW. Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition. eLife 2021; 10:71900. [PMID: 34792466 PMCID: PMC8719888 DOI: 10.7554/elife.71900] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022] Open
Abstract
Agricultural soil harbors a diverse microbiome that can form beneficial relationships with plants, including the inhibition of plant pathogens. Pseudomonas spp. are one of the most abundant bacterial genera in the soil and rhizosphere and play important roles in promoting plant health. However, the genetic determinants of this beneficial activity are only partially understood. Here, we genetically and phenotypically characterize the Pseudomonas fluorescens population in a commercial potato field, where we identify strong correlations between specialized metabolite biosynthesis and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans. Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialized metabolites associated with S. scabies inhibition, which was supported by in planta biocontrol experiments. We show that a single potato field contains a hugely diverse and dynamic population of Pseudomonas bacteria, whose capacity to produce specialized metabolites is shaped both by plant colonization and defined environmental inputs. Potato scab and blight are two major diseases which can cause heavy crop losses. They are caused, respectively, by the bacterium Streptomyces scabies and an oomycete (a fungus-like organism) known as Phytophthora infestans. Fighting these disease-causing microorganisms can involve crop management techniques – for example, ensuring that a field is well irrigated helps to keep S. scabies at bay. Harnessing biological control agents can also offer ways to control disease while respecting the environment. Biocontrol bacteria, such as Pseudomonas, can produce compounds that keep S. scabies and P. infestans in check. However, the identity of these molecules and how irrigation can influence Pseudomonas population remains unknown. To examine these questions, Pacheco-Moreno et al. sampled and isolated hundreds of Pseudomonas strains from a commercial potato field, closely examining the genomes of 69 of these. Comparing the genetic information of strains based on whether they could control the growth of S. scabies revealed that compounds known as cyclic lipopeptides are key to controlling the growth of S. scabies and P. infestans. Whether the field was irrigated also had a large impact on the strains forming the Pseudomonas population. Working out how Pseudomonas bacteria block disease could speed up the search for biological control agents. The approach developed by Pacheco-Moreno et al. could help to predict which strains might be most effective based on their genetic features. Similar experiments could also work for other combinations of plants and diseases.
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Affiliation(s)
- Alba Pacheco-Moreno
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Jonathan J Ford
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Christine Trippel
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Simon Uszkoreit
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Laura Ferrafiat
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Lucia Grenga
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Ruth Dickens
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Nathan Kelly
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Alexander Dh Kingdon
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Liana Ambrosetti
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Sergey A Nepogodiev
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Kim C Findlay
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Jitender Cheema
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Martin Trick
- Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Jacob G Malone
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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Liu Y, Zhou Y, Qiao J, Yu W, Pan X, Zhang T, Liu Y, Lu SE. Phenazine-1-carboxylic Acid Produced by Pseudomonas chlororaphis YL-1 Is Effective against Acidovorax citrulli. Microorganisms 2021; 9:microorganisms9102012. [PMID: 34683333 PMCID: PMC8541086 DOI: 10.3390/microorganisms9102012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 11/16/2022] Open
Abstract
The bacterial pathogen Acidovorax citrulli causes the destructive fruit blotch (BFB) on cucurbit plants. Pseudomonas chlororaphis YL-1 is a bacterial strain isolated from Mississippi soil and its genome harbors some antimicrobial-related gene clusters, such as phenazine, pyrrolnitrin, and pyoverdine. Here, we evaluated the antimicrobial activity of strain YL-1 as compared with its deficient mutants of antimicrobial-related genes, which were obtained using a sacB-based site-specific mutagenesis strategy. We found that only phenazine-deficient mutants ΔphzE and ΔphzF almost lost the inhibitory effects against A. citrulli in LB plates compared with the wild-type strain YL-1, and that the main antibacterial compound produced by strain YL-1 in LB medium was phenazine-1-carboxylic acid (PCA) based on the liquid chromatography-mass spectrometry (LC-MS) analysis. Gene expression analyses revealed that PCA enhanced the accumulation of reactive oxygen species (ROS) and increased the activity of catalase (CAT) in A. citrulli. The inhibition effect of PCA against A. citrulli was lowered by adding exogenous CAT. PCA significantly upregulated the transcript level of katB from 6 to 10 h, which encodes CAT that helps to protect the bacteria against oxidative stress. Collectively, the findings of this research suggest PCA is one of the key antimicrobial metabolites of bacterial strain YL-1, a promising biocontrol agent for disease management of BFB of cucurbit plants.
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Affiliation(s)
- Youzhou Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (Y.Z.); (J.Q.); (X.P.)
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS 39759, USA
| | - Yaqiu Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (Y.Z.); (J.Q.); (X.P.)
| | - Junqing Qiao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (Y.Z.); (J.Q.); (X.P.)
| | - Wenjie Yu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (W.Y.); (T.Z.)
| | - Xiayan Pan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (Y.Z.); (J.Q.); (X.P.)
| | - Tingting Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (W.Y.); (T.Z.)
| | - Yongfeng Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (Y.Z.); (J.Q.); (X.P.)
- Correspondence: (Y.L.); (S.-E.L.)
| | - Shi-En Lu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS 39759, USA
- Correspondence: (Y.L.); (S.-E.L.)
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11
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Li B, Deng X, Kim SH, Buhrow L, Tomchick DR, Phillips MA, Michael AJ. Alternative pathways utilize or circumvent putrescine for biosynthesis of putrescine-containing rhizoferrin. J Biol Chem 2020; 296:100146. [PMID: 33277357 PMCID: PMC7857480 DOI: 10.1074/jbc.ra120.016738] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 11/23/2022] Open
Abstract
The siderophore rhizoferrin (N1,N4-dicitrylputrescine) is produced in fungi and bacteria to scavenge iron. Putrescine-producing bacterium Ralstonia pickettii synthesizes rhizoferrin and encodes a single nonribosomal peptide synthetase-independent siderophore (NIS) synthetase. From biosynthetic logic, we hypothesized that this single enzyme is sufficient for rhizoferrin biosynthesis. We confirmed this by expression of R. pickettii NIS synthetase in Escherichia coli, resulting in rhizoferrin production. This was further confirmed in vitro using the recombinant NIS synthetase, synthesizing rhizoferrin from putrescine and citrate. Heterologous expression of homologous lbtA from Legionella pneumophila, required for rhizoferrin biosynthesis in that species, produced siderophore activity in E. coli. Rhizoferrin is also synthesized by Francisella tularensis and Francisella novicida, but unlike R. pickettii or L. pneumophila, Francisella species lack putrescine biosynthetic pathways because of genomic decay. Francisella encodes a NIS synthetase FslA/FigA and an ornithine decarboxylase homolog FslC/FigC, required for rhizoferrin biosynthesis. Ornithine decarboxylase produces putrescine from ornithine, but we show here in vitro that FigA synthesizes N-citrylornithine, and FigC is an N-citrylornithine decarboxylase that together synthesize rhizoferrin without using putrescine. We co-expressed F. novicida figA and figC in E. coli and produced rhizoferrin. A 2.1 Å X-ray crystal structure of the FigC N-citrylornithine decarboxylase reveals how the larger substrate is accommodated and how active site residues have changed to recognize N-citrylornithine. FigC belongs to a new subfamily of alanine racemase-fold PLP-dependent decarboxylases that are not involved in polyamine biosynthesis. These data reveal a natural product biosynthetic workaround that evolved to bypass a missing precursor and re-establish it in the final structure.
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Affiliation(s)
- Bin Li
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Xiaoyi Deng
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Sok Ho Kim
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Leann Buhrow
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Diana R Tomchick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Margaret A Phillips
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Anthony J Michael
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA.
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12
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Kügler S, Cooper RE, Boessneck J, Küsel K, Wichard T. Rhizobactin B is the preferred siderophore by a novel Pseudomonas isolate to obtain iron from dissolved organic matter in peatlands. Biometals 2020; 33:415-433. [PMID: 33026607 PMCID: PMC7676072 DOI: 10.1007/s10534-020-00258-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 09/30/2020] [Indexed: 01/12/2023]
Abstract
Bacteria often release diverse iron-chelating compounds called siderophores to scavenge iron from the environment for many essential biological processes. In peatlands, where the biogeochemical cycle of iron and dissolved organic matter (DOM) are coupled, bacterial iron acquisition can be challenging even at high total iron concentrations. We found that the bacterium Pseudomonas sp. FEN, isolated from an Fe-rich peatland in the Northern Bavarian Fichtelgebirge (Germany), released an unprecedented siderophore for its genus. High-resolution mass spectrometry (HR-MS) using metal isotope-coded profiling (MICP), MS/MS experiments, and nuclear magnetic resonance spectroscopy (NMR) identified the amino polycarboxylic acid rhizobactin and a novel derivative at even higher amounts, which was named rhizobactin B. Interestingly, pyoverdine-like siderophores, typical for this genus, were not detected. With peat water extract (PWE), studies revealed that rhizobactin B could acquire Fe complexed by DOM, potentially through a TonB-dependent transporter, implying a higher Fe binding constant of rhizobactin B than DOM. The further uptake of Fe-rhizobactin B by Pseudomonas sp. FEN suggested its role as a siderophore. Rhizobactin B can complex several other metals, including Al, Cu, Mo, and Zn. The study demonstrates that the utilization of rhizobactin B can increase the Fe availability for Pseudomonas sp. FEN through ligand exchange with Fe-DOM, which has implications for the biogeochemical cycling of Fe in this peatland.
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Affiliation(s)
- Stefan Kügler
- Institute for Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, 07743, Jena, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Rebecca E Cooper
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Johanna Boessneck
- Institute for Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, 07743, Jena, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
- The German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, 07743, Jena, Germany.
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13
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Zboralski A, Filion M. Genetic factors involved in rhizosphere colonization by phytobeneficial Pseudomonas spp. Comput Struct Biotechnol J 2020; 18:3539-3554. [PMID: 33304453 PMCID: PMC7711191 DOI: 10.1016/j.csbj.2020.11.025] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/13/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) actively colonize the soil portion under the influence of plant roots, called the rhizosphere. Many plant-beneficial Pseudomonas spp. have been characterized as PGPR. They are ubiquitous rod-shaped motile Gram-negative bacteria displaying a high metabolic versatility. Their capacity to protect plants from pathogens and improve plant growth closely depends on their rhizosphere colonization abilities. Various molecular and cellular mechanisms are involved in this complex process, such as chemotaxis, biofilm formation, secondary metabolites biosynthesis, metabolic versatility, and evasion of plant immunity. The burst in Pseudomonas spp. genome sequencing in recent years has been crucial to better understand how they colonize the rhizosphere. In this review, we discuss the recent advances regarding these mechanisms and the underlying bacterial genetic factors required for successful rhizosphere colonization.
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Affiliation(s)
- Antoine Zboralski
- Department of Biology, Université de Moncton, Moncton, NB E1A 3E9, Canada
| | - Martin Filion
- Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
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14
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Storey N, Rabiey M, Neuman BW, Jackson RW, Mulley G. Genomic Characterisation of Mushroom Pathogenic Pseudomonads and Their Interaction with Bacteriophages. Viruses 2020; 12:E1286. [PMID: 33182769 PMCID: PMC7696170 DOI: 10.3390/v12111286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 01/16/2023] Open
Abstract
Bacterial diseases of the edible white button mushroom Agaricus bisporus caused by Pseudomonas species cause a reduction in crop yield, resulting in considerable economic loss. We examined bacterial pathogens of mushrooms and bacteriophages that target them to understand the disease and opportunities for control. The Pseudomonastolaasii genome encoded a single type III protein secretion system (T3SS), but contained the largest number of non-ribosomal peptide synthase (NRPS) genes, multimodular enzymes that can play a role in pathogenicity, including a putative tolaasin-producing gene cluster, a toxin causing blotch disease symptom. However, Pseudomonasagarici encoded the lowest number of NRPS and three putative T3SS while non-pathogenic Pseudomonas sp. NS1 had intermediate numbers. Potential bacteriophage resistance mechanisms were identified in all three strains, but only P. agarici NCPPB 2472 was observed to have a single Type I-F CRISPR/Cas system predicted to be involved in phage resistance. Three novel bacteriophages, NV1, ϕNV3, and NV6, were isolated from environmental samples. Bacteriophage NV1 and ϕNV3 had a narrow host range for specific mushroom pathogens, whereas phage NV6 was able to infect both mushroom pathogens. ϕNV3 and NV6 genomes were almost identical and differentiated within their T7-like tail fiber protein, indicating this is likely the major host specificity determinant. Our findings provide the foundations for future comparative analyses to study mushroom disease and phage resistance.
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Affiliation(s)
- Nathaniel Storey
- School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK; (N.S.); (R.W.J.); (G.M.)
| | - Mojgan Rabiey
- School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK; (N.S.); (R.W.J.); (G.M.)
- School of Biosciences and Birmingham Institute of Forest Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Benjamin W. Neuman
- Biology Department, College of Arts, Sciences and Education, TAMUT, Texarkana, TX 75503, USA;
| | - Robert W. Jackson
- School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK; (N.S.); (R.W.J.); (G.M.)
- School of Biosciences and Birmingham Institute of Forest Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Geraldine Mulley
- School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK; (N.S.); (R.W.J.); (G.M.)
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15
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Sheldon JR, Skaar EP. Acinetobacter baumannii can use multiple siderophores for iron acquisition, but only acinetobactin is required for virulence. PLoS Pathog 2020; 16:e1008995. [PMID: 33075115 PMCID: PMC7595644 DOI: 10.1371/journal.ppat.1008995] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 10/29/2020] [Accepted: 09/18/2020] [Indexed: 12/22/2022] Open
Abstract
Acinetobacter baumannii is an emerging pathogen that poses a global health threat due to a lack of therapeutic options for treating drug-resistant strains. In addition to acquiring resistance to last-resort antibiotics, the success of A. baumannii is partially due to its ability to effectively compete with the host for essential metals. Iron is fundamental in shaping host-pathogen interactions, where the host restricts availability of this nutrient in an effort to curtail bacterial proliferation. To circumvent restriction, pathogens possess numerous mechanisms to obtain iron, including through the use of iron-scavenging siderophores. A. baumannii elaborates up to ten distinct siderophores, encoded from three different loci: acinetobactin and pre-acinetobactin (collectively, acinetobactin), baumannoferrins A and B, and fimsbactins A-F. The expression of multiple siderophores is common amongst bacterial pathogens and often linked to virulence, yet the collective contribution of these siderophores to A. baumannii survival and pathogenesis has not been investigated. Here we begin dissecting functional redundancy in the siderophore-based iron acquisition pathways of A. baumannii. Excess iron inhibits overall siderophore production by the bacterium, and the siderophore-associated loci are uniformly upregulated during iron restriction in vitro and in vivo. Further, disrupting all of the siderophore biosynthetic pathways is necessary to drastically reduce total siderophore production by A. baumannii, together suggesting a high degree of functional redundancy between the metabolites. By contrast, inactivation of acinetobactin biosynthesis alone impairs growth on human serum, transferrin, and lactoferrin, and severely attenuates survival of A. baumannii in a murine bacteremia model. These results suggest that whilst A. baumannii synthesizes multiple iron chelators, acinetobactin is critical to supporting growth of the pathogen on host iron sources. Given the acinetobactin locus is highly conserved and required for virulence of A. baumannii, designing therapeutics targeting the biosynthesis and/or transport of this siderophore may represent an effective means of combating this pathogen.
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Affiliation(s)
- Jessica R. Sheldon
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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16
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Hofmann M, Martin del Campo JS, Sobrado P, Tischler D. Biosynthesis of desferrioxamine siderophores initiated by decarboxylases: A functional investigation of two lysine/ornithine-decarboxylases from Gordonia rubripertincta CWB2 and Pimelobacter simplex 3E. Arch Biochem Biophys 2020; 689:108429. [DOI: 10.1016/j.abb.2020.108429] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/14/2022]
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17
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Draft Genome Sequence of Lipopeptide-Producing Strain Pseudomonas fluorescens DSM 11579 and Comparative Genomics with Pseudomonas sp. Strain SH-C52, a Closely Related Lipopeptide-Producing Strain. Microbiol Resour Announc 2020; 9:9/21/e00304-20. [PMID: 32439665 PMCID: PMC7242667 DOI: 10.1128/mra.00304-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas fluorescens DSM 11579 is known to be a producer of the lipopeptides brabantamide and thanamycin. Its draft genome gives insight into the complete secondary metabolite production capacity of the strain and builds the basis for a comparative study with Pseudomonas sp. strain SH-C52, a lipopeptide-producing strain involved in natural disease-suppressive soils. Pseudomonas fluorescens DSM 11579 is known to be a producer of the lipopeptides brabantamide and thanamycin. Its draft genome gives insight into the complete secondary metabolite production capacity of the strain and builds the basis for a comparative study with Pseudomonas sp. strain SH-C52, a lipopeptide-producing strain involved in natural disease-suppressive soils.
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18
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Schalk IJ, Rigouin C, Godet J. An overview of siderophore biosynthesis among fluorescent Pseudomonads and new insights into their complex cellular organization. Environ Microbiol 2020; 22:1447-1466. [PMID: 32011068 DOI: 10.1111/1462-2920.14937] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/25/2020] [Accepted: 01/28/2020] [Indexed: 01/02/2023]
Abstract
Siderophores are iron-chelating molecules produced by bacteria to access iron, a key nutrient. These compounds have highly diverse chemical structures, with various chelating groups. They are released by bacteria into their environment to scavenge iron and bring it back into the cells. The biosynthesis of siderophores requires complex enzymatic processes and expression of the enzymes involved is very finely regulated by iron availability and diverse transcriptional regulators. Recent data have also highlighted the organization of the enzymes involved in siderophore biosynthesis into siderosomes, multi-enzymatic complexes involved in siderophore synthesis. An understanding of siderophore biosynthesis is of great importance, as these compounds have many potential biotechnological applications because of their metal-chelating properties and their key role in bacterial growth and virulence. This review focuses on the biosynthesis of siderophores produced by fluorescent Pseudomonads, bacteria capable of colonizing a large variety of ecological niches. They are characterized by the production of chromopeptide siderophores, called pyoverdines, which give the typical green colour characteristic of fluorescent pseudomonad cultures. Secondary siderophores are also produced by these strains and can have highly diverse structures (such as pyochelins, pseudomonine, yersiniabactin, corrugatin, achromobactin and quinolobactin).
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Affiliation(s)
- Isabelle J Schalk
- CNRS, UMR7242, ESBS, Illkirch, Strasbourg, France.,Université de Strasbourg, UMR7242, ESBS, Illkirch, Strasbourg, France
| | - Coraline Rigouin
- CNRS, UMR7242, ESBS, Illkirch, Strasbourg, France.,Université de Strasbourg, UMR7242, ESBS, Illkirch, Strasbourg, France
| | - Julien Godet
- Université de Strasbourg, Laboratoire de BioImagerie et Pathologies, UMR CNRS, 7021, Illkirch, France
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19
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Draft Genome Sequence of Pseudomonas chlororaphis subsp. aurantiaca ARS-38, a Bacterial Strain with Plant Growth Promotion Potential, Isolated from the Rhizosphere of Cotton in Pakistan. Microbiol Resour Announc 2020; 9:9/3/e01398-19. [PMID: 31948966 PMCID: PMC6965584 DOI: 10.1128/mra.01398-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Strain ARS-38 is a potential plant growth-promoting rhizobacterium that exhibits antifungal properties. Here, we report a 6.6-Mb draft genome, which gives insight into the complete secondary metabolite production capacity and reveals genes putatively responsible for its antifungal activity, as well as genes which contribute to plant growth promotion. Strain ARS-38 is a potential plant growth-promoting rhizobacterium that exhibits antifungal properties. Here, we report a 6.6-Mb draft genome, which gives insight into the complete secondary metabolite production capacity and reveals genes putatively responsible for its antifungal activity, as well as genes which contribute to plant growth promotion.
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20
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Prabha R, Singh DP, Gupta S, Gupta VK, El-Enshasy HA, Verma MK. Rhizosphere Metagenomics of Paspalum scrobiculatum L. (Kodo Millet) Reveals Rhizobiome Multifunctionalities. Microorganisms 2019; 7:microorganisms7120608. [PMID: 31771141 PMCID: PMC6956225 DOI: 10.3390/microorganisms7120608] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
Multifunctionalities linked with the microbial communities associated with the millet crop rhizosphere has remained unexplored. In this study, we are analyzing microbial communities inhabiting rhizosphere of kodo millet and their associated functions and its impact over plant growth and survival. Metagenomics of Paspalum scrobiculatum L.(kodo millet) rhizopshere revealed taxonomic communities with functional capabilities linked to support growth and development of the plants under nutrient-deprived, semi-arid and dry biotic conditions. Among 65 taxonomically diverse phyla identified in the rhizobiome, Actinobacteria were the most abundant followed by the Proteobacteria. Functions identified for different genes/proteins led to revelations that multifunctional rhizobiome performs several metabolic functions including carbon fixation, nitrogen, phosphorus, sulfur, iron and aromatic compound metabolism, stress response, secondary metabolite synthesis and virulence, disease, and defense. Abundance of genes linked with N, P, S, Fe and aromatic compound metabolism and phytohormone synthesis—along with other prominent functions—clearly justifies growth, development, and survival of the plants under nutrient deprived dry environment conditions. The dominance of actinobacteria, the known antibiotic producing communities shows that the kodo rhizobiome possesses metabolic capabilities to defend themselves against biotic stresses. The study opens avenues to revisit multi-functionalities of the crop rhizosphere for establishing link between taxonomic abundance and targeted functions that help plant growth and development in stressed and nutrient deprived soil conditions. It further helps in understanding the role of rhizosphere microbiome in adaptation and survival of plants in harsh abiotic conditions.
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Affiliation(s)
- Ratna Prabha
- Chhattisgarh Swami Vivekananda Technical University, Bhilai, Chhattisgarh 491107, India; (R.P.); (M.K.V.)
| | - Dhananjaya P. Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research, Kushmaur, Maunath Bhanjan 275101, UP, India
- Correspondence:
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock 18057, Germany;
| | - Vijai Kumar Gupta
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, Tallinn University of Technology, 12618 Tallinn, Estonia;
| | - Hesham A. El-Enshasy
- Institute of Bioproduct Development, Universiti Teknologi Malaysia, Skudai 81310, Johor Bahru, Johor, Malaysia;
| | - Mukesh K. Verma
- Chhattisgarh Swami Vivekananda Technical University, Bhilai, Chhattisgarh 491107, India; (R.P.); (M.K.V.)
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21
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Tang J, Ju Y, Gu Q, Xu J, Zhou H. Structural Insights into Substrate Recognition and Activity Regulation of the Key Decarboxylase SbnH in Staphyloferrin B Biosynthesis. J Mol Biol 2019; 431:4868-4881. [PMID: 31634470 DOI: 10.1016/j.jmb.2019.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 12/21/2022]
Abstract
Staphyloferrin B is a hydroxycarboxylate siderophore that is crucial for the invasion and virulence of Staphylococcus aureus in mammalian hosts where free iron ions are scarce. The assembly of staphyloferrin B involves four enzymatic steps, in which SbnH, a pyridoxal 5'-phosphate (PLP)-dependent decarboxylase, catalyzes the second step. Here, we report the X-ray crystal structures of S. aureus SbnH (SaSbnH) in complex with PLP, citrate, and the decarboxylation product citryl-diaminoethane (citryl-Dae). The overall structure of SaSbnH resembles those of the previously reported PLP-dependent amino acid decarboxylases, but the active site of SaSbnH showed unique structural features. Structural and mutagenesis analysis revealed that the citryl moiety of the substrate citryl-l-2,3-diaminopropionic acid (citryl-l-Dap) inserts into a narrow groove at the dimer interface of SaSbnH and forms hydrogen bonding interactions with both subunits. In the active site, a conserved lysine residue forms an aldimine linkage with the cofactor PLP, and a phenylalanine residue is essential for accommodating the l-configuration Dap of the substrate. Interestingly, the freestanding citrate molecule was found to bind to SaSbnH in a conformation inverse to that of the citryl group of citryl-Dae and efficiently inhibit SaSbnH. As an intermediate in the tricarboxylic acid (TCA) cycle, citrate is highly abundant in bacterial cells until iron depletion; thus, its inhibition of SaSbnH may serve as an iron-dependent regulatory mechanism in staphyloferrin B biosynthesis.
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Affiliation(s)
- Jieyu Tang
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yingchen Ju
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Huihao Zhou
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
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22
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Carmichael JR, Zhou H, Butler A. A suite of asymmetric citrate siderophores isolated from a marine Shewanella species. J Inorg Biochem 2019; 198:110736. [DOI: 10.1016/j.jinorgbio.2019.110736] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 10/26/2022]
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Affiliation(s)
- Mark R. Petchey
- York Structural Biology Laboratory, Department of Chemistry University of York Heslington, York YO10 5DD U.K
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry University of York Heslington, York YO10 5DD U.K
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Maglangit F, Tong MH, Jaspars M, Kyeremeh K, Deng H. Legonoxamines A-B, two new hydroxamate siderophores from the soil bacterium, Streptomyces sp. MA37. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2018.11.063] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Carroll CS, Moore MM. Ironing out siderophore biosynthesis: a review of non-ribosomal peptide synthetase (NRPS)-independent siderophore synthetases. Crit Rev Biochem Mol Biol 2018; 53:356-381. [DOI: 10.1080/10409238.2018.1476449] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
| | - Margo M. Moore
- Department of Biological Sciences, Simon Fraser University, Burnaby, Canada
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26
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Shahid I, Malik KA, Mehnaz S. A decade of understanding secondary metabolism in Pseudomonas spp. for sustainable agriculture and pharmaceutical applications. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s42398-018-0006-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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27
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Genome Sequence of Pseudomonas chlororaphis Lzh-T5, a Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity. GENOME ANNOUNCEMENTS 2018; 6:6/18/e00328-18. [PMID: 29724833 PMCID: PMC5940960 DOI: 10.1128/genomea.00328-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pseudomonas chlororaphis Lzh-T5 is a plant growth-promoting rhizobacterium (PGPR) with antimicrobial activity isolated from tomato rhizosphere in the city of Dezhou, Shandong Province, China. Here, the draft genome sequence of P. chlororaphis Lzh-T5 is reported, and several functional genes related to antifungal antibiotics and siderophore biosynthesis have been found in the genome.
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Dias GM, Bidault A, Le Chevalier P, Choquet G, Der Sarkissian C, Orlando L, Medigue C, Barbe V, Mangenot S, Thompson CC, Thompson FL, Jacq A, Pichereau V, Paillard C. Vibrio tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs. Front Microbiol 2018; 9:227. [PMID: 29515533 PMCID: PMC5825899 DOI: 10.3389/fmicb.2018.00227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The Brown Ring Disease (BRD) caused high mortality rates since 1986 in the Manila clam Venerupis philippinarum introduced and cultured in Western Europe from the 1970s. The causative agent of BRD is a Gram-Negative bacterium, Vibrio tapetis, which is also pathogenic to fish. Here we report the first assembly of the complete genome of V. tapetis CECT4600T, together with the genome sequences of 16 additional strains isolated across a broad host and geographic range. Our extensive genome dataset allowed us to describe the pathogen pan- and core genomes and to identify putative virulence factors. The V. tapetis core genome consists of 3,352 genes, including multiple potential virulence factors represented by haemolysins, transcriptional regulators, Type I restriction modification system, GGDEF domain proteins, several conjugative plasmids, and a Type IV secretion system. Future research on the coevolutionary arms race between V. tapetis virulence factors and host resistance mechanisms will improve our understanding of how pathogenicity develops in this emerging pathogen.
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Affiliation(s)
- Graciela M. Dias
- Laboratoire des Sciences de l'Environnement Marin, Université de Bretagne Occidentale, UMR 6539 UBO/Centre National de la Recherche Scientifique/IRD/Ifremer, Institut Universitaire Européen de la Mer, Plouzané, France
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adeline Bidault
- Laboratoire des Sciences de l'Environnement Marin, Université de Bretagne Occidentale, UMR 6539 UBO/Centre National de la Recherche Scientifique/IRD/Ifremer, Institut Universitaire Européen de la Mer, Plouzané, France
| | - Patrick Le Chevalier
- Laboratoire de Biotechnologie et Chimie Marine, Université de Bretagne Occidentale, Quimper, France
| | - Gwenaëlle Choquet
- Laboratoire des Sciences de l'Environnement Marin, Université de Bretagne Occidentale, UMR 6539 UBO/Centre National de la Recherche Scientifique/IRD/Ifremer, Institut Universitaire Européen de la Mer, Plouzané, France
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Centre National de la Recherche Scientifique UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Claudine Medigue
- CEA, Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université d'Evry, Centre National de la Recherche Scientifique-UMR 8030, Evry, France
| | - Valerie Barbe
- CEA, Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université d'Evry, Centre National de la Recherche Scientifique-UMR 8030, Evry, France
| | - Sophie Mangenot
- CEA, Institut de biologie François-Jacob, Genoscope, Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, Evry, France
| | - Cristiane C. Thompson
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabiano L. Thompson
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Annick Jacq
- Institute for Integrative Biology of the Cell, CEA, Centre National de la Recherche Scientifique, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Vianney Pichereau
- Laboratoire des Sciences de l'Environnement Marin, Université de Bretagne Occidentale, UMR 6539 UBO/Centre National de la Recherche Scientifique/IRD/Ifremer, Institut Universitaire Européen de la Mer, Plouzané, France
| | - Christine Paillard
- Laboratoire des Sciences de l'Environnement Marin, Université de Bretagne Occidentale, UMR 6539 UBO/Centre National de la Recherche Scientifique/IRD/Ifremer, Institut Universitaire Européen de la Mer, Plouzané, France
- *Correspondence: Christine Paillard
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Carroll CS, Grieve CL, Murugathasan I, Bennet AJ, Czekster CM, Liu H, Naismith J, Moore MM. The rhizoferrin biosynthetic gene in the fungal pathogen Rhizopus delemar is a novel member of the NIS gene family. Int J Biochem Cell Biol 2017; 89:136-146. [DOI: 10.1016/j.biocel.2017.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 05/30/2017] [Accepted: 06/03/2017] [Indexed: 11/29/2022]
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Sonnenschein EC, Stierhof M, Goralczyk S, Vabre FM, Pellissier L, Hanssen KØ, de la Cruz M, Díaz C, de Witte P, Copmans D, Andersen JH, Hansen E, Kristoffersen V, Tormo JR, Ebel R, Milne BF, Deng H, Gram L, Jaspars M, Tabudravu JN. Pseudochelin A, a siderophore of Pseudoalteromonas piscicida S2040. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.03.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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31
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Das S, Bora SS, Yadav RNS, Barooah M. A metagenomic approach to decipher the indigenous microbial communities of arsenic contaminated groundwater of Assam. GENOMICS DATA 2017; 12:89-96. [PMID: 28409115 PMCID: PMC5379903 DOI: 10.1016/j.gdata.2017.03.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 03/22/2017] [Accepted: 03/26/2017] [Indexed: 02/01/2023]
Abstract
Metagenomic approach was used to understand the structural and functional diversity present in arsenic contaminated groundwater of the Ganges Brahmaputra Delta aquifer system. A metagene dataset (coded as TTGW1) of 89,171 sequences (totaling 125,449,864 base pairs) with an average length of 1406 bps was annotated. About 74,478 sequences containing 101,948 predicted protein coding regions passed the quality control. Taxonomical classification revealed abundance of bacteria that accounted for 98.3% of the microbial population of the metagenome. Eukaryota had an abundance of 1.1% followed by archea that showed 0.4% abundance. In phylum based classification, Proteobacteria was dominant (62.6%) followed by Bacteroidetes (11.7%), Planctomycetes (7.7%), Verrucomicrobia (5.6%), Actinobacteria (3.7%) and Firmicutes (1.9%). The Clusters of Orthologous Groups (COGs) analysis indicated that the protein regulating the metabolic functions constituted a high percentage (18,199 reads; 39.3%) of the whole metagenome followed by the proteins regulating the cellular processes (22.3%). About 0.07% sequences of the whole metagenome were related to genes coding for arsenic resistant mechanisms. Nearly 50% sequences of these coded for the arsenate reductase enzyme (EC. 1.20.4.1), the dominant enzyme of ars operon. Proteins associated with iron acquisition and metabolism were coded by 2% of the metagenome as revealed through SEED analysis. Our study reveals the microbial diversity and provides an insight into the functional aspect of the genes that might play crucial role in arsenic geocycle in contaminated ground water of Assam.
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Affiliation(s)
- Saurav Das
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India.,Centre for Studies in Biotechnology, Dibrugarh University, Dibrugarh, Assam, India
| | - Sudipta Sankar Bora
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - R N S Yadav
- Centre for Studies in Biotechnology, Dibrugarh University, Dibrugarh, Assam, India
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
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Tanabe T. Regulation of the Expression of Iron-acquisition System Genes in Pathogenic Vibrio Species. YAKUGAKU ZASSHI 2016; 136:1525-1532. [PMID: 27803484 DOI: 10.1248/yakushi.16-00192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genus Vibrio includes >70 species, of which roughly a dozen cause vibriosis such as gastroenteritis, wound infections, and septicemia. Most bacteria, including Vibrio species, require iron for survival and growth. However, the bioavailability of iron is extremely low because it is usually present as an insoluble ferric complex in an aerobic environment or is bound to iron-binding proteins in mammalian hosts. Therefore many bacteria have developed iron acquisition systems, including biosynthesis and secretion of low-molecular-mass iron-chelating compounds called siderophores, and uptake of iron-bound siderophores into bacterial cells through specific active transport systems. Vibrio parahaemolyticus, a major pathogenic Vibrio species, contains multiple iron-acquisition systems mediated by its own siderophore vibrioferrin and several xenosiderophores produced by other microorganisms. In this review, I have focused on the transcriptional and posttranscriptional regulation of genes encoding iron acquisition systems in V. parahaemolyticus. All genes involved in its iron acquisition systems are repressed by Fur, which acts as a ferrous-dependent transcriptional repressor. Furthermore, the stability of polycistronic mRNA involved in vibrioferrin biosynthesis is positively regulated by a small RNA, RyhB, which is repressed by Fur. Expression of PeuA receptor required for utilization of a xenosiderophore, enterobactin, occurs under iron-limiting conditions at alkaline pH. PeuA expression is induced by a two-component regulatory system, PeuRS, which enhances expression of an alternative peuA transcript without an intrinsic translation-inhibitory structure in response to changes in alkaline pH.
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Affiliation(s)
- Tomotaka Tanabe
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University
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An overview of siderophores for iron acquisition in microorganisms living in the extreme. Biometals 2016; 29:551-71. [PMID: 27457587 DOI: 10.1007/s10534-016-9949-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/08/2016] [Indexed: 12/11/2022]
Abstract
Siderophores are iron-chelating molecules produced by microbes when intracellular iron concentrations are low. Low iron triggers a cascade of gene activation, allowing the cell to survive due to the synthesis of important proteins involved in siderophore synthesis and transport. Generally, siderophores are classified by their functional groups as catecholates, hydroxamates and hydroxycarboxylates. Although other chemical structural modifications and functional groups can be found. The functional groups participate in the iron-chelating process when the ferri-siderophore complex is formed. Classified as acidophiles, alkaliphiles, halophiles, thermophiles, psychrophiles, piezophiles, extremophiles have particular iron requirements depending on the environmental conditions in where they grow. Most of the work done in siderophore production by extremophiles is based in siderophore concentration and/or genomic studies determining the presence of siderophore synthesis and transport genes. Siderophores produced by extremophiles are not well known and more work needs to be done to elucidate chemical structures and their role in microorganism survival and metal cycling in extreme environments.
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Fazary AE, Al-Shihri AS, Alfaifi MY, Saleh KA, Alshehri MA, Elbehairi SEI, Ju YH. Microbial production of four biodegradable siderophores under submerged fermentation. Int J Biol Macromol 2016; 88:527-41. [DOI: 10.1016/j.ijbiomac.2016.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 03/03/2016] [Accepted: 03/07/2016] [Indexed: 11/29/2022]
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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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Quibod IL, Grande G, Oreiro EG, Borja FN, Dossa GS, Mauleon R, Cruz CV, Oliva R. Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot. PLoS One 2015; 10:e0139256. [PMID: 26422147 PMCID: PMC4589537 DOI: 10.1371/journal.pone.0139256] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/09/2015] [Indexed: 12/26/2022] Open
Abstract
Sheath rot complex and seed discoloration in rice involve a number of pathogenic bacteria that cannot be associated with distinctive symptoms. These pathogens can easily travel on asymptomatic seeds and therefore represent a threat to rice cropping systems. Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world. The appearance of a similar Pseudomonas population, which here we named P. fuscovaginae-like, represents a perfect opportunity to understand common genomic features that can explain the infection mechanism in rice. We showed that the novel population is indeed closely related to P. fuscovaginae. A comparative genomics approach on eight rice-infecting Pseudomonas revealed heterogeneous genomes and a high number of strain-specific genes. The genomes of P. fuscovaginae-like harbor four secretion systems (Type I, II, III, and VI) and other important pathogenicity machinery that could probably facilitate rice colonization. We identified 123 core secreted proteins, most of which have strong signatures of positive selection suggesting functional adaptation. Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism. The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.
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Affiliation(s)
- Ian Lorenzo Quibod
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Genelou Grande
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Eula Gems Oreiro
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Frances Nikki Borja
- T.T. Chang- Genetic Resources Center, International Rice Research Institute, Los Baños, Philippines
| | - Gerbert Sylvestre Dossa
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
- Department of Phytomedicine, Leibniz Universität Hannover, Hannover, Germany
| | - Ramil Mauleon
- T.T. Chang- Genetic Resources Center, International Rice Research Institute, Los Baños, Philippines
| | - Casiana Vera Cruz
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Ricardo Oliva
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
- * E-mail:
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Martínez-García PM, Rodríguez-Palenzuela P, Arrebola E, Carrión VJ, Gutiérrez-Barranquero JA, Pérez-García A, Ramos C, Cazorla FM, de Vicente A. Bioinformatics Analysis of the Complete Genome Sequence of the Mango Tree Pathogen Pseudomonas syringae pv. syringae UMAF0158 Reveals Traits Relevant to Virulence and Epiphytic Lifestyle. PLoS One 2015; 10:e0136101. [PMID: 26313942 PMCID: PMC4551802 DOI: 10.1371/journal.pone.0136101] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/29/2015] [Indexed: 01/11/2023] Open
Abstract
The genome sequence of more than 100 Pseudomonas syringae strains has been sequenced to date; however only few of them have been fully assembled, including P. syringae pv. syringae B728a. Different strains of pv. syringae cause different diseases and have different host specificities; so, UMAF0158 is a P. syringae pv. syringae strain related to B728a but instead of being a bean pathogen it causes apical necrosis of mango trees, and the two strains belong to different phylotypes of pv.syringae and clades of P. syringae. In this study we report the complete sequence and annotation of P. syringae pv. syringae UMAF0158 chromosome and plasmid pPSS158. A comparative analysis with the available sequenced genomes of other 25 P. syringae strains, both closed (the reference genomes DC3000, 1448A and B728a) and draft genomes was performed. The 5.8 Mb UMAF0158 chromosome has 59.3% GC content and comprises 5017 predicted protein-coding genes. Bioinformatics analysis revealed the presence of genes potentially implicated in the virulence and epiphytic fitness of this strain. We identified several genetic features, which are absent in B728a, that may explain the ability of UMAF0158 to colonize and infect mango trees: the mangotoxin biosynthetic operon mbo, a gene cluster for cellulose production, two different type III and two type VI secretion systems, and a particular T3SS effector repertoire. A mutant strain defective in the rhizobial-like T3SS Rhc showed no differences compared to wild-type during its interaction with host and non-host plants and worms. Here we report the first complete sequence of the chromosome of a pv. syringae strain pathogenic to a woody plant host. Our data also shed light on the genetic factors that possibly determine the pathogenic and epiphytic lifestyle of UMAF0158. This work provides the basis for further analysis on specific mechanisms that enable this strain to infect woody plants and for the functional analysis of host specificity in the P. syringae complex.
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Affiliation(s)
- Pedro Manuel Martínez-García
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, Parque Científico y Tecnológico de la Universidad Politécnica de Madrid. Pozuelo de Alarcón, Madrid, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Área de Genética, Facultad de Ciencias, Málaga, Spain
| | - Pablo Rodríguez-Palenzuela
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, Parque Científico y Tecnológico de la Universidad Politécnica de Madrid. Pozuelo de Alarcón, Madrid, Spain
| | - Eva Arrebola
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Estación Experimental La Mayora, Algarrobo-Costa, Málaga, Spain
| | - Víctor J. Carrión
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Facultad de Ciencias, Málaga, Spain
| | - José Antonio Gutiérrez-Barranquero
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Facultad de Ciencias, Málaga, Spain
| | - Alejandro Pérez-García
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Facultad de Ciencias, Málaga, Spain
| | - Cayo Ramos
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Área de Genética, Facultad de Ciencias, Málaga, Spain
| | - Francisco M. Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Facultad de Ciencias, Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Facultad de Ciencias, Málaga, Spain
- * E-mail:
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38
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Trantas EA, Licciardello G, Almeida NF, Witek K, Strano CP, Duxbury Z, Ververidis F, Goumas DE, Jones JDG, Guttman DS, Catara V, Sarris PF. Comparative genomic analysis of multiple strains of two unusual plant pathogens: Pseudomonas corrugata and Pseudomonas mediterranea. Front Microbiol 2015; 6:811. [PMID: 26300874 PMCID: PMC4528175 DOI: 10.3389/fmicb.2015.00811] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/22/2015] [Indexed: 11/13/2022] Open
Abstract
The non-fluorescent pseudomonads, Pseudomonas corrugata (Pcor) and P. mediterranea (Pmed), are closely related species that cause pith necrosis, a disease of tomato that causes severe crop losses. However, they also show strong antagonistic effects against economically important pathogens, demonstrating their potential for utilization as biological control agents. In addition, their metabolic versatility makes them attractive for the production of commercial biomolecules and bioremediation. An extensive comparative genomics study is required to dissect the mechanisms that Pcor and Pmed employ to cause disease, prevent disease caused by other pathogens, and to mine their genomes for genes that encode proteins involved in commercially important chemical pathways. Here, we present the draft genomes of nine Pcor and Pmed strains from different geographical locations. This analysis covered significant genetic heterogeneity and allowed in-depth genomic comparison. All examined strains were able to trigger symptoms in tomato plants but not all induced a hypersensitive-like response in Nicotiana benthamiana. Genome-mining revealed the absence of type III secretion system and known type III effector-encoding genes from all examined Pcor and Pmed strains. The lack of a type III secretion system appears to be unique among the plant pathogenic pseudomonads. Several gene clusters coding for type VI secretion system were detected in all genomes. Genome-mining also revealed the presence of gene clusters for biosynthesis of siderophores, polyketides, non-ribosomal peptides, and hydrogen cyanide. A highly conserved quorum sensing system was detected in all strains, although species specific differences were observed. Our study provides the basis for in-depth investigations regarding the molecular mechanisms underlying virulence strategies in the battle between plants and microbes.
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Affiliation(s)
- Emmanouil A Trantas
- Plant Biochemistry and Biotechnology Laboratory, Department of Agriculture, School of Agriculture and Food Technology, Technological Educational Institute of Crete Heraklion, Greece
| | | | - Nalvo F Almeida
- School of Computing, Federal University of Mato Grosso do Sul Campo Grande, Brazil
| | - Kamil Witek
- The Sainsbury Laboratory, John Innes Centre Norwich, UK
| | - Cinzia P Strano
- Department of Agriculture, Food and Environment, University of Catania Catania, Italy
| | - Zane Duxbury
- The Sainsbury Laboratory, John Innes Centre Norwich, UK
| | - Filippos Ververidis
- Plant Biochemistry and Biotechnology Laboratory, Department of Agriculture, School of Agriculture and Food Technology, Technological Educational Institute of Crete Heraklion, Greece
| | - Dimitrios E Goumas
- Plant Biochemistry and Biotechnology Laboratory, Department of Agriculture, School of Agriculture and Food Technology, Technological Educational Institute of Crete Heraklion, Greece ; Plant Pathology and Bacteriology Laboratory, Department of Agriculture, School of Agriculture and Food Technology, Technological Educational Institute of Crete Heraklion, Greece
| | | | - David S Guttman
- Centre for the Analysis of Genome Evolution & Function, University of Toronto Toronto, ON, Canada
| | - Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania Catania, Italy
| | - Panagiotis F Sarris
- Plant Biochemistry and Biotechnology Laboratory, Department of Agriculture, School of Agriculture and Food Technology, Technological Educational Institute of Crete Heraklion, Greece ; The Sainsbury Laboratory, John Innes Centre Norwich, UK
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Penwell WF, DeGrace N, Tentarelli S, Gauthier L, Gilbert CM, Arivett BA, Miller AA, Durand-Reville TF, Joubran C, Actis LA. Discovery and Characterization of New Hydroxamate Siderophores, Baumannoferrin A and B, produced by Acinetobacter baumannii. Chembiochem 2015; 16:1896-1904. [PMID: 26235845 DOI: 10.1002/cbic.201500147] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Indexed: 12/14/2022]
Abstract
Acinetobacter baumannii AYE does not produce acinetobactin but grows under iron limitation. Accordingly, analyses of AYE iron-restricted culture supernatants resulted in the isolation of two fractions, which contained only hydroxamates and showed siderophore activity. Structural analyses identified baumannoferrin A and baumannoferrin B, which differ only by a double bond. These siderophores are composed of citrate, 1,3-diaminopropane, 2,4-diaminobutyrate, decenoic acid, and α-ketoglutarate. Analysis of the AYE genome showed the presence of a 12-gene cluster coding for proteins similar to those involved in the production and utilization of the hydroxamate siderophores acinetoferrin and achromobactin. As A. baumannii AYE does not produce acinetobactin and harbors only one gene cluster encoding the production and utilization of a siderophore, this strain's growth under iron limitation depends on baumannoferrin, a novel hydroxamate that could play a role in its virulence.
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Affiliation(s)
- William F Penwell
- Infection Innovative Medicines, AstraZeneca Research and Development, 35 Gatehouse Drive, Waltham, MA 02451 (USA).,Department of Microbiology, Miami University, 500 East High Street, Oxford, OH 45056-1602 (USA)
| | - Nancy DeGrace
- Infection Innovative Medicines, AstraZeneca Research and Development, 35 Gatehouse Drive, Waltham, MA 02451 (USA)
| | - Sharon Tentarelli
- Infection Innovative Medicines, AstraZeneca Research and Development, 35 Gatehouse Drive, Waltham, MA 02451 (USA)
| | - Lise Gauthier
- Waters Corporation, 34 Maple Street, Milford, MA 01757-3604 (USA)
| | - Catherine M Gilbert
- Infection Innovative Medicines, AstraZeneca Research and Development, 35 Gatehouse Drive, Waltham, MA 02451 (USA)
| | - Brock A Arivett
- Department of Microbiology, Miami University, 500 East High Street, Oxford, OH 45056-1602 (USA)
| | - Alita A Miller
- Infection Innovative Medicines, AstraZeneca Research and Development, 35 Gatehouse Drive, Waltham, MA 02451 (USA)
| | - Thomas F Durand-Reville
- Infection Innovative Medicines, AstraZeneca Research and Development, 35 Gatehouse Drive, Waltham, MA 02451 (USA)
| | - Camil Joubran
- Infection Innovative Medicines, AstraZeneca Research and Development, 35 Gatehouse Drive, Waltham, MA 02451 (USA)
| | - Luis A Actis
- Department of Microbiology, Miami University, 500 East High Street, Oxford, OH 45056-1602 (USA)
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Van Der Voort M, Meijer HJG, Schmidt Y, Watrous J, Dekkers E, Mendes R, Dorrestein PC, Gross H, Raaijmakers JM. Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds. Front Microbiol 2015. [PMID: 26217324 PMCID: PMC4493835 DOI: 10.3389/fmicb.2015.00693] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The plant microbiome represents an enormous untapped resource for discovering novel genes and bioactive compounds. Previously, we isolated Pseudomonas sp. SH-C52 from the rhizosphere of sugar beet plants grown in a soil suppressive to the fungal pathogen Rhizoctonia solani and showed that its antifungal activity is, in part, attributed to the production of the chlorinated 9-amino-acid lipopeptide thanamycin (Mendes et al., 2011). To get more insight into its biosynthetic repertoire, the genome of Pseudomonas sp. SH-C52 was sequenced and subjected to in silico, mutational and functional analyses. The sequencing revealed a genome size of 6.3 Mb and 5579 predicted ORFs. Phylogenetic analysis placed strain SH-C52 within the Pseudomonas corrugata clade. In silico analysis for secondary metabolites revealed a total of six non-ribosomal peptide synthetase (NRPS) gene clusters, including the two previously described NRPS clusters for thanamycin and the 2-amino acid antibacterial lipopeptide brabantamide. Here we show that thanamycin also has activity against an array of other fungi and that brabantamide A exhibits anti-oomycete activity and affects phospholipases of the late blight pathogen Phytophthora infestans. Most notably, mass spectrometry led to the discovery of a third lipopeptide, designated thanapeptin, with a 22-amino-acid peptide moiety. Seven structural variants of thanapeptin were found with varying degrees of activity against P. infestans. Of the remaining four NRPS clusters, one was predicted to encode for yet another and unknown lipopeptide with a predicted peptide moiety of 8-amino acids. Collectively, these results show an enormous metabolic potential for Pseudomonas sp. SH-C52, with at least three structurally diverse lipopeptides, each with a different antimicrobial activity spectrum.
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Affiliation(s)
| | - Harold J G Meijer
- Laboratory of Phytopathology, Wageningen University Wageningen, Netherlands
| | - Yvonne Schmidt
- Institute for Pharmaceutical Biology, University of Bonn Bonn, Germany
| | - Jeramie Watrous
- Departments of Pharmacology and Chemistry and Biochemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego San Diego, CA, USA
| | - Ester Dekkers
- Laboratory of Phytopathology, Wageningen University Wageningen, Netherlands
| | - Rodrigo Mendes
- Laboratory of Phytopathology, Wageningen University Wageningen, Netherlands ; Brazilian Agricultural Research Corporation, Embrapa Environment Jaguariuna, Brazil
| | - Pieter C Dorrestein
- Departments of Pharmacology and Chemistry and Biochemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego San Diego, CA, USA
| | - Harald Gross
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen Tübingen, Germany
| | - Jos M Raaijmakers
- Laboratory of Phytopathology, Wageningen University Wageningen, Netherlands ; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
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Calderón CE, Ramos C, de Vicente A, Cazorla FM. Comparative Genomic Analysis of Pseudomonas chlororaphis PCL1606 Reveals New Insight into Antifungal Compounds Involved in Biocontrol. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:249-260. [PMID: 25679537 DOI: 10.1094/mpmi-10-14-0326-fi] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Pseudomonas chlororaphis PCL1606 is a rhizobacterium that has biocontrol activity against many soilborne phytopathogenic fungi. The whole genome sequence of this strain was obtained using the Illumina Hiseq 2000 sequencing platform and was assembled using SOAP denovo software. The resulting 6.66-Mb complete sequence of the PCL1606 genome was further analyzed. A comparative genomic analysis using 10 plant-associated strains within the fluorescent Pseudomonas group, including the complete genome of P. chlororaphis PCL1606, revealed a diverse spectrum of traits involved in multitrophic interactions with plants and microbes as well as biological control. Phylogenetic analysis of these strains using eight housekeeping genes clearly placed strain PCL1606 into the P. chlororaphis group. The genome sequence of P. chlororaphis PCL1606 revealed the presence of sequences that were homologous to biosynthetic genes for the antifungal compounds 2-hexyl, 5-propyl resorcinol (HPR), hydrogen cyanide, and pyrrolnitrin; this is the first report of pyrrolnitrin encoding genes in this P. chlororaphis strain. Single-, double-, and triple-insertional mutants in the biosynthetic genes of each antifungal compound were used to test their roles in the production of these antifungal compounds and in antagonism and biocontrol of two fungal pathogens. The results confirmed the function of HPR in the antagonistic phenotype and in the biocontrol activity of P. chlororaphis PCL1606.
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Transcriptional analysis of the global regulatory networks active in Pseudomonas syringae during leaf colonization. mBio 2014; 5:e01683-14. [PMID: 25182327 PMCID: PMC4173789 DOI: 10.1128/mbio.01683-14] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The plant pathogen Pseudomonas syringae pv. syringae B728a grows and survives on leaf surfaces and in the leaf apoplast of its host, bean (Phaseolus vulgaris). To understand the contribution of distinct regulators to B728a fitness and pathogenicity, we performed a transcriptome analysis of strain B728a and nine regulatory mutants recovered from the surfaces and interior of leaves and exposed to environmental stresses in culture. The quorum-sensing regulators AhlR and AefR influenced few genes in planta or in vitro. In contrast, GacS and a downstream regulator, SalA, formed a large regulatory network that included a branch that regulated diverse traits and was independent of plant-specific environmental signals and a plant signal-dependent branch that positively regulated secondary metabolite genes and negatively regulated the type III secretion system. SalA functioned as a central regulator of iron status based on its reciprocal regulation of pyoverdine and achromobactin genes and also sulfur uptake, suggesting a role in the iron-sulfur balance. RetS functioned almost exclusively to repress secondary metabolite genes when the cells were not on leaves. Among the sigma factors examined, AlgU influenced many more genes than RpoS, and most AlgU-regulated genes depended on RpoN. RpoN differentially impacted many AlgU- and GacS-activated genes in cells recovered from apoplastic versus epiphytic sites, suggesting differences in environmental signals or bacterial stress status in these two habitats. Collectively, our findings illustrate a central role for GacS, SalA, RpoN, and AlgU in global regulation in B728a in planta and a high level of plasticity in these regulators’ responses to distinct environmental signals. Leaves harbor abundant microorganisms, all of which must withstand challenges such as active plant defenses and a highly dynamic environment. Some of these microbes can influence plant health. Despite knowledge of individual regulators that affect the fitness or pathogenicity of foliar pathogens, our understanding of the relative importance of various global regulators to leaf colonization is limited. Pseudomonas syringae strain B728a is a plant pathogen and a good colonist of both the surfaces and interior of leaves. This study used global transcript profiles of strain B728a to investigate the complex regulatory network of putative quorum-sensing regulators, two-component regulators, and sigma factors in cells colonizing the leaf surface and leaf interior under stressful in vitro conditions. The results highlighted the value of evaluating these networks in planta due to the impact of leaf-specific environmental signals and suggested signal differences that may enable cells to differentiate surface versus interior leaf habitats.
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Ye L, Matthijs S, Bodilis J, Hildebrand F, Raes J, Cornelis P. Analysis of the draft genome of Pseudomonas fluorescens ATCC17400 indicates a capacity to take up iron from a wide range of sources, including different exogenous pyoverdines. Biometals 2014; 27:633-44. [PMID: 24756978 DOI: 10.1007/s10534-014-9734-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 04/03/2014] [Indexed: 12/16/2022]
Abstract
All fluorescent pseudomonads (Pseudomonas aeruginosa, P. putida, P. fluorescens, P. syringae and others) are known to produce the high-affinity peptidic yellow-green fluorescent siderophore pyoverdine. These siderophores have peptide chains that are quite diverse and more than 50 pyoverdine structures have been elucidated. In the majority of the cases, a Pseudomonas species is also able to produce a second siderophore of lower affinity for iron. Pseudomonas fluorescens ATCC 17400 has been shown to produce a unique second siderophore, (thio)quinolobactin, which has an antimicrobial activity against the phytopathogenic Oomycete Pythium debaryanum. We show that this strain has the capacity to utilize 16 different pyoverdines, suggesting the presence of several ferripyoverdine receptors. Analysis of the draft genome of P. fluorescens ATCC 17400 confirmed the presence of 55 TonB-dependent receptors, the largest so far for Pseudomonas, among which 15 are predicted to be ferripyoverdine receptors (Fpv). Phylogenetic analysis revealed the presence of two different clades containing ferripyoverdine receptors, with sequences similar to the P. aeruginosa type II FpvA forming a separate cluster. Among the other receptors we confirmed the presence of the QbsI (thio)quinolobactin receptor, an ferri-achromobactin and an ornicorrugatin receptor, several catecholate and four putative heme receptors. Twenty five of the receptors genes were found to be associated with genes encoding extracytoplasmic sigma factors (ECF σ) and transmembrane anti-σ sensors.
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Affiliation(s)
- Lumeng Ye
- Department of Bioengineering Sciences, Research Group Microbiology, VIB Structural Biology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
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Complete Genome Sequence of the Sugar Cane Endophyte Pseudomonas aurantiaca PB-St2, a Disease-Suppressive Bacterium with Antifungal Activity toward the Plant Pathogen Colletotrichum falcatum. GENOME ANNOUNCEMENTS 2014; 2:2/1/e01108-13. [PMID: 24459254 PMCID: PMC3900886 DOI: 10.1128/genomea.01108-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The endophytic bacterium Pseudomonas aurantiaca PB-St2 exhibits antifungal activity and represents a biocontrol agent to suppress red rot disease of sugar cane. Here, we report the completely sequenced 6.6-Mb genome of P. aurantiaca PB-St2. The sequence contains a repertoire of biosynthetic genes for secondary metabolites that putatively contribute to its antagonistic activity and its plant-microbe interactions.
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45
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Fones H, Preston GM. The impact of transition metals on bacterial plant disease. FEMS Microbiol Rev 2013; 37:495-519. [DOI: 10.1111/1574-6976.12004] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Revised: 09/05/2012] [Accepted: 09/14/2012] [Indexed: 12/24/2022] Open
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Taguchi F, Ichinose Y. Virulence factor regulator (Vfr) controls virulence-associated phenotypes in Pseudomonas syringae pv. tabaci 6605 by a quorum sensing-independent mechanism. MOLECULAR PLANT PATHOLOGY 2013; 14:279-92. [PMID: 23145783 PMCID: PMC6638821 DOI: 10.1111/mpp.12003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Virulence factor regulator (Vfr) is a member of the cyclic 3',5'-adenosine monophosphate (cAMP) receptor proteins that regulate the expression of many important virulence genes in Pseudomonas aeruginosa. The role of Vfr in pathogenicity has not been elucidated fully in phytopathogenic bacteria. To investigate the function of Vfr in Pseudomonas syringae pv. tabaci 6605, the vfr gene was disrupted. The virulence of the vfr mutant towards host tobacco plants was attenuated significantly, and the intracellular cAMP level was decreased. The vfr mutant reduced the expression of flagella-, pili- and type III secretion system-related genes and the defence response in nonhost Arabidopsis leaves. Furthermore, the expression levels of achromobactin-related genes and the iron uptake ability were decreased, suggesting that Vfr regulates positively these virulence-related genes. In contrast, the vfr mutant showed higher tolerance to antimicrobial compounds as a result of the enhanced expression of the resistance-nodulation-division family members, the mexA, mexB and oprM genes. We further demonstrated that the mutant strains of vfr and cyaA, an adenylate cyclase gene responsible for cAMP synthesis, showed a similar phenotype, suggesting that Vfr regulates virulence factors in a cAMP-dependent manner. Because there was no significant difference in the production of acylhomoserine lactone (AHL) quorum sensing molecules in the wild-type, vfr and cyaA mutant strains, Vfr might control important virulence factors by an AHL-independent mechanism in an early stage of infection by this bacterium.
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Affiliation(s)
- Fumiko Taguchi
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, Japan
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47
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Characterization of the achromobactin iron acquisition operon in Sodalis glossinidius. Appl Environ Microbiol 2013; 79:2872-81. [PMID: 23435882 DOI: 10.1128/aem.03959-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Sodalis glossinidius is a facultative, extra- and intracellular symbiont found in most tissues of the tsetse fly (Glossinia sp.). Sodalis has a putative achromobactin siderophore iron acquisition system on the pSG1 plasmid. Reverse transcription (RT)-PCR analysis revealed that the achromobactin operon is transcribed as a single polycistronic molecule and is expressed when Sodalis is within the tsetse fly. Expression of the achromobactin operon was repressed under iron-replete conditions; in a mutant that lacks the iron-responsive transcriptional repressor protein Fur, expression was aberrantly derepressed under these iron-replete conditions, indicating that the Fur protein repressed achromobactin gene expression when iron was plentiful. A putative Fur binding site within the Sodalis achromobactin promoter bound Fur in Escherichia coli Fur titration assays. Wild-type Sodalis produced detectable siderophore in vitro, but a mutation in the putative achromobactin biosynthesis gene acsD eliminated detectable siderophore production in Sodalis. Reduced growth of the siderophore synthesis mutant was reconstituted by addition of exogenous achromobactin, suggesting the strain retains a functional siderophore transport system; however, reduced growth of a Sodalis ferric-siderophore outer membrane receptor mutant with a mutation in acr was not reconstituted by exogenous siderophore due to its defective transporter. The Sodalis siderophore synthesis mutant showed reduced growth in tsetse that lacked endogenous symbionts (aposymbiotic) when the flies were inoculated with Sodalis intrathoracically, but not when inoculated per os. Our findings suggest that Sodalis siderophores play a role in iron acquisition in certain tsetse fly tissues and provide evidence for the regulation of iron acquisition mechanisms in insect symbionts.
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Tohyama S, Tomura A, Ikeda N, Hatano M, Odanaka J, Kubota Y, Umekita M, Igarashi M, Sawa R, Morino T. Discovery and Characterization of NK13650s, Naturally Occurring p300-Selective Histone Acetyltransferase Inhibitors. J Org Chem 2012; 77:9044-52. [DOI: 10.1021/jo301534b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Shigehiro Tohyama
- Institute of Microbial Chemistry, Tokyo, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo
141-0021, Japan
| | - Arihiro Tomura
- Pharmaceuticals Research Laboratories, Research & Development Group, Nippon Kayaku, 3-31-12 Shimo, Kita-ku, Tokyo 115-8588, Japan
| | - Noriko Ikeda
- Institute of Microbial Chemistry, Tokyo, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo
141-0021, Japan
| | - Masaki Hatano
- Institute of Microbial Chemistry, Tokyo, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo
141-0021, Japan
| | - Junko Odanaka
- Pharmaceuticals Research Laboratories, Research & Development Group, Nippon Kayaku, 3-31-12 Shimo, Kita-ku, Tokyo 115-8588, Japan
| | - Yumiko Kubota
- Institute of Microbial Chemistry, Tokyo, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo
141-0021, Japan
| | - Maya Umekita
- Institute of Microbial Chemistry, Tokyo, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo
141-0021, Japan
| | - Masayuki Igarashi
- Institute of Microbial Chemistry, Tokyo, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo
141-0021, Japan
| | - Ryuichi Sawa
- Institute of Microbial Chemistry, Tokyo, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo
141-0021, Japan
| | - Tomio Morino
- Pharmaceuticals Research Laboratories, Research & Development Group, Nippon Kayaku, 3-31-12 Shimo, Kita-ku, Tokyo 115-8588, Japan
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Burrell M, Hanfrey CC, Kinch LN, Elliott KA, Michael AJ. Evolution of a novel lysine decarboxylase in siderophore biosynthesis. Mol Microbiol 2012; 86:485-99. [PMID: 22906379 DOI: 10.1111/j.1365-2958.2012.08208.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2012] [Indexed: 12/30/2022]
Abstract
Structural backbones of iron-scavenging siderophore molecules include polyamines 1,3-diaminopropane and 1,5-diaminopentane (cadaverine). For the cadaverine-based desferroxiamine E siderophore in Streptomyces coelicolor, the corresponding biosynthetic gene cluster contains an ORF encoded by desA that was suspected of producing the cadaverine (decarboxylated lysine) backbone. However, desA encodes an l-2,4-diaminobutyrate decarboxylase (DABA DC) homologue and not any known form of lysine decarboxylase (LDC). The only known function of DABA DC is, together with l-2,4-aminobutyrate aminotransferase (DABA AT), to synthesize 1,3-diaminopropane. We show here that S. coelicolor desA encodes a novel LDC and we hypothesized that DABA DC homologues present in siderophore biosynthetic clusters in the absence of DABA AT ORFs would be novel LDCs. We confirmed this by correctly predicting the LDC activity of a DABA DC homologue from a Yersinia pestis siderophore biosynthetic pathway. The corollary was confirmed for a DABA DC homologue, adjacent to a DABA AT ORF in a siderophore pathway in the cyanobacterium Anabaena variabilis, which was shown to be a bona fide DABA DC. These findings enable prediction of whether a siderophore pathway will utilize 1,3-diaminopropane or cadaverine, and suggest that the majority of bacteria use DABA AT and DABA DC for siderophore, rather than norspermidine/polyamine biosynthesis.
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Loper JE, Hassan KA, Mavrodi DV, Davis EW, Lim CK, Shaffer BT, Elbourne LDH, Stockwell VO, Hartney SL, Breakwell K, Henkels MD, Tetu SG, Rangel LI, Kidarsa TA, Wilson NL, van de Mortel JE, Song C, Blumhagen R, Radune D, Hostetler JB, Brinkac LM, Durkin AS, Kluepfel DA, Wechter WP, Anderson AJ, Kim YC, Pierson LS, Pierson EA, Lindow SE, Kobayashi DY, Raaijmakers JM, Weller DM, Thomashow LS, Allen AE, Paulsen IT. Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Genet 2012; 8:e1002784. [PMID: 22792073 PMCID: PMC3390384 DOI: 10.1371/journal.pgen.1002784] [Citation(s) in RCA: 398] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 05/10/2012] [Indexed: 12/11/2022] Open
Abstract
We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45–52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire. We sequenced the genomes of seven strains of the Pseudomonas fluorescens group that colonize plant surfaces and function as biological control agents, protecting plants from disease. In this study, we demonstrated the genomic diversity of the group by comparing these strains to each other and to three other strains that were sequenced previously. Only about half of the genes in each strain are present in all of the other strains, and each strain has hundreds of unique genes that are not present in the other genomes. We mapped the genes that contribute to biological control in each genome and found that most of the biological control genes are in the variable regions of the genome, which are not shared by all of the other strains. This finding is consistent with our knowledge of the distinctive biology of each strain. Finally, we looked for new genes that are likely to confer antimicrobial traits needed to suppress plant pathogens, but have not been identified previously. In each genome, we discovered many of these new genes, which provide avenues for future discovery of new traits with the potential to manage plant diseases in agriculture or natural ecosystems.
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Affiliation(s)
- Joyce E Loper
- Agricultural Research Service, US Department of Agriculture, Corvallis, Oregon, United States of America.
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