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Wang D, Naqvi STA, Lei F, Zhang Z, Yu H, Ma LZ. Glycosyl hydrolase from Pseudomonas fluorescens inhibits the biofilm formation of Pseudomonads. Biofilm 2023; 6:100155. [PMID: 37928620 PMCID: PMC10622837 DOI: 10.1016/j.bioflm.2023.100155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 11/07/2023] Open
Abstract
Biofilms are complex microbial communities embedded in extracellular matrix. Pathogens within the biofilm become more resistant to the antibiotics than planktonic counterparts. Novel strategies are required to encounter biofilms. Exopolysaccharides are one of the major components of biofilm matrix and play a vital role in biofilm architecture. In previous studies, a glycosyl hydrolase, PslGPA, from Pseudomonas aeruginosa was found to be able to inhibit biofilm formation by disintegrating exopolysaccharide in biofilms. Here, we investigate the potential spectrum of PslG homologous protein with anti-biofilm activity. One glycosyl hydrolase from Pseudomonas fluorescens, PslGPF, exhibits anti-biofilm activities and the key catalytic residues of PslGPF are conserved with those of PslGPA. PslGPF at concentrations as low as 50 nM efficiently inhibits the biofilm formation of P. aeruginosa and disassemble its preformed biofilm. Furthermore, PslGPF exhibits anti-biofilm activity on a series of Pseudomonads, including P. fluorescens, Pseudomonas stutzeri and Pseudomonas syringae pv. phaseolicola. PslGPF stays active under various temperatures. Our findings suggest that P. fluorescens glycosyl hydrolase PslGPF has potential to be a broad spectrum inhibitor on biofilm formation of a wide range of Pseudomonads.
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Affiliation(s)
- Di Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Syed Tatheer Alam Naqvi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Fanglin Lei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- Yunnan University, Kunming, 650500, PR China
| | - Zhenyu Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Luyan Z. Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
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Grosse C, Brandt N, Van Antwerpen P, Wintjens R, Matthijs S. Two new siderophores produced by Pseudomonas sp. NCIMB 10586: The anti-oomycete non-ribosomal peptide synthetase-dependent mupirochelin and the NRPS-independent triabactin. Front Microbiol 2023; 14:1143861. [PMID: 37032897 PMCID: PMC10080011 DOI: 10.3389/fmicb.2023.1143861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/02/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction Globisporangium ultimum is an oomycetal pathogen causing damping-off on over 300 different plant hosts. Currently, as for many phytopathogens, its control relies in the use of chemicals with negative impact on health and ecosystems. Therefore, many biocontrol strategies are under investigation to reduce the use of fungicides. Results In this study, the soil bacterium Pseudomonas sp. NCIMB 10586 demonstrates a strong iron-repressed in vitro antagonism against G. ultimum MUCL 38045. This antagonism does not depend on the secretion of the broad-range antibiotic mupirocin or of the siderophore pyoverdine by the bacterial strain. The inhibitor molecule was identified as a novel non-ribosomal peptide synthetase (NRPS) siderophore named mupirochelin. Its putative structure bears similarities to other siderophores and bioactive compounds. The transcription of its gene cluster is affected by the biosynthesis of pyoverdine, the major known siderophore of the strain. Besides mupirochelin, we observed the production of a third and novel NRPS-independent siderophore (NIS), here termed triabactin. The iron-responsive transcriptional repression of the two newly identified siderophore gene clusters corroborates their role as iron scavengers. However, their respective contributions to the strain fitness are dissimilar. Bacterial growth in iron-deprived conditions is greatly supported by pyoverdine production and, to a lesser extent, by triabactin. On the contrary, mupirochelin does not contribute to the strain fitness under the studied conditions. Conclusion Altogether, we have demonstrated here that besides pyoverdine, Pseudomonas sp. NCIMB 10586 produces two newly identified siderophores, namely mupirochelin, a weak siderophore with strong antagonism activity against G. ultimum, and the potent siderophore triabactin.
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Affiliation(s)
- Camille Grosse
- Unité de Recherche NaturaMonas, Institut de Recherche LABIRIS, Brussels, Belgium
| | - Nathalie Brandt
- Unité de Recherche NaturaMonas, Institut de Recherche LABIRIS, Brussels, Belgium
| | - Pierre Van Antwerpen
- RD3 – Pharmacognosy, Bioanalysis and Drug Discovery and Analytical Platform of the Faculty of Pharmacy, Université Libre de Bruxelles, Brussels, Belgium
| | - René Wintjens
- Unité Microbiologie, Chimie Bioorganique et Macromoléculaire, Department of Research in Drug Development (RD3), Faculty of Pharmacy, Université Libre de Bruxelles, Brussels, Belgium
| | - Sandra Matthijs
- Unité de Recherche NaturaMonas, Institut de Recherche LABIRIS, Brussels, Belgium
- *Correspondence: Sandra Matthijs,
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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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Valenzuela‐Heredia D, Henríquez‐Castillo C, Donoso R, Lavín P, Ringel MT, Brüser T, Campos JL. An unusual overrepresentation of genetic factors related to iron homeostasis in the genome of the fluorescent Pseudomonas sp. ABC1. Microb Biotechnol 2021; 14:1060-1072. [PMID: 33492712 PMCID: PMC8085936 DOI: 10.1111/1751-7915.13753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/29/2020] [Accepted: 01/02/2021] [Indexed: 12/25/2022] Open
Abstract
Members of the genus Pseudomonas inhabit diverse environments, such as soil, water, plants and humans. The variability of habitats is reflected in the diversity of the structure and composition of their genomes. This cosmopolitan bacterial genus includes species of biotechnological, medical and environmental importance. In this study, we report on the most relevant genomic characteristics of Pseudomonas sp. strain ABC1, a siderophore-producing fluorescent strain recently isolated from soil. Phylogenomic analyses revealed that this strain corresponds to a novel species forming a sister clade of the recently proposed Pseudomonas kirkiae. The genomic information reveals an overrepresented repertoire of mechanisms to hoard iron when compared to related strains, including a high representation of fecI-fecR family genes related to iron regulation and acquisition. The genome of the Pseudomonas sp. ABC1 contains the genes for non-ribosomal peptide synthetases (NRPSs) of a novel putative Azotobacter-related pyoverdine-type siderophore, a yersiniabactin-type siderophore and an antimicrobial betalactone; the last two are found only in a limited number of Pseudomonas genomes. Strain ABC1 can produce siderophores in a low-cost medium, and the supernatants from cultures of this strain promote plant growth, highlighting their biotechnological potential as a sustainable industrial microorganism.
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Affiliation(s)
| | - Carlos Henríquez‐Castillo
- Laboratorio de Fisiología y Genética Marina (FIGEMA)Centro de Estudios Avanzados de Zonas Áridas (CEAZA)CoquimboChile
- Facultad de Ciencias del MarUniversidad Católica del NorteCoquimboChile
| | - Raúl Donoso
- Programa Institucional de Fomento a la InvestigaciónDesarrollo, e Innovación (PIDi)Universidad Tecnológica MetropolitanaSantiagoChile
| | - Paris Lavín
- Facultad de Ciencias del Mar y Recursos BiológicosDepartamento de BiotecnologíaLaboratorio de Complejidad Microbiana y Ecología FuncionalInstituto AntofagastaUniversidad de AntofagastaAntofagastaChile
- Network for Extreme Environments Research (NEXER)Universidad de AntofagastaUniversidad de La Frontera y Universidad de MagallanesPunta ArenasChile
| | | | - Thomas Brüser
- Institute of MicrobiologyLeibniz University HannoverHannoverGermany
| | - José Luis Campos
- Facultad de Ingeniería y CienciasUniversidad Adolfo IbáñezViña del MarChile
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Bruce JB, Cooper GA, Chabas H, West SA, Griffin AS. Cheating and resistance to cheating in natural populations of the bacteriumPseudomonas fluorescens. Evolution 2017; 71:2484-2495. [DOI: 10.1111/evo.13328] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 07/14/2017] [Accepted: 08/08/2017] [Indexed: 12/11/2022]
Affiliation(s)
- John B. Bruce
- Department of Zoology; University of Oxford; Oxford UK
| | - Guy A. Cooper
- Department of Zoology; University of Oxford; Oxford UK
| | - Hélène Chabas
- CEFE UMR 5175, CNRS-Université de Montpellier; Université Paul-Valéry Montpellier; Montpellier Cedex 5 France
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Magro M, Fasolato L, Bonaiuto E, Andreani NA, Baratella D, Corraducci V, Miotto G, Cardazzo B, Vianello F. Enlightening mineral iron sensing in Pseudomonas fluorescens by surface active maghemite nanoparticles: Involvement of the OprF porin. Biochim Biophys Acta Gen Subj 2016; 1860:2202-10. [DOI: 10.1016/j.bbagen.2016.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/18/2016] [Accepted: 05/03/2016] [Indexed: 01/05/2023]
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Pyoverdine and histicorrugatin-mediated iron acquisition in Pseudomonas thivervalensis. Biometals 2016; 29:467-85. [DOI: 10.1007/s10534-016-9929-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/19/2016] [Indexed: 12/17/2022]
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Ye L, Hildebrand F, Dingemans J, Ballet S, Laus G, Matthijs S, Berendsen R, Cornelis P. Draft genome sequence analysis of a Pseudomonas putida W15Oct28 strain with antagonistic activity to Gram-positive and Pseudomonas sp. pathogens. PLoS One 2014; 9:e110038. [PMID: 25369289 PMCID: PMC4219678 DOI: 10.1371/journal.pone.0110038] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/09/2014] [Indexed: 12/22/2022] Open
Abstract
Pseudomonas putida is a member of the fluorescent pseudomonads known to produce the yellow-green fluorescent pyoverdine siderophore. P. putida W15Oct28, isolated from a stream in Brussels, was found to produce compound(s) with antimicrobial activity against the opportunistic pathogens Staphylococcus aureus, Pseudomonas aeruginosa, and the plant pathogen Pseudomonas syringae, an unusual characteristic for P. putida. The active compound production only occurred in media with low iron content and without organic nitrogen sources. Transposon mutants which lost their antimicrobial activity had the majority of insertions in genes involved in the biosynthesis of pyoverdine, although purified pyoverdine was not responsible for the antagonism. Separation of compounds present in culture supernatants revealed the presence of two fractions containing highly hydrophobic molecules active against P. aeruginosa. Analysis of the draft genome confirmed the presence of putisolvin biosynthesis genes and the corresponding lipopeptides were found to contribute to the antimicrobial activity. One cluster of ten genes was detected, comprising a NAD-dependent epimerase, an acetylornithine aminotransferase, an acyl CoA dehydrogenase, a short chain dehydrogenase, a fatty acid desaturase and three genes for a RND efflux pump. P. putida W15Oct28 genome also contains 56 genes encoding TonB-dependent receptors, conferring a high capacity to utilize pyoverdines from other pseudomonads. One unique feature of W15Oct28 is also the presence of different secretion systems including a full set of genes for type IV secretion, and several genes for type VI secretion and their VgrG effectors.
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Affiliation(s)
- Lumeng Ye
- Department of Bioengineering Sciences, Research group Microbiology, Vrije Universiteit Brussel and VIB Structural Biology Brussels, Brussels, Belgium
| | - Falk Hildebrand
- Department of Bioengineering Sciences, Research group Microbiology, Vrije Universiteit Brussel and VIB Structural Biology Brussels, Brussels, Belgium
| | - Jozef Dingemans
- Department of Bioengineering Sciences, Research group Microbiology, Vrije Universiteit Brussel and VIB Structural Biology Brussels, Brussels, Belgium
| | - Steven Ballet
- Chemistry Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - George Laus
- Chemistry Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Sandra Matthijs
- Institut de Recherches Microbiologiques - Wiame, Campus du CERIA, Brussels, Belgium
| | - Roeland Berendsen
- Plant-Microbe Interactions, Utrecht University, Utrecht, The Netherlands
| | - Pierre Cornelis
- Department of Bioengineering Sciences, Research group Microbiology, Vrije Universiteit Brussel and VIB Structural Biology Brussels, Brussels, Belgium
- * E-mail:
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Hildebrand F, Tadeo R, Voigt AY, Bork P, Raes J. LotuS: an efficient and user-friendly OTU processing pipeline. MICROBIOME 2014; 2:30. [PMID: 27367037 PMCID: PMC4179863 DOI: 10.1186/2049-2618-2-30] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 08/23/2014] [Indexed: 05/05/2023]
Abstract
BACKGROUND 16S ribosomal DNA (rDNA) amplicon sequencing is frequently used to analyse the structure of bacterial communities from oceans to the human microbiota. However, computational power is still a major bottleneck in the analysis of continuously enlarging metagenomic data sets. Analysis is further complicated by the technical complexity of current bioinformatics tools. RESULTS Here we present the less operational taxonomic units scripts (LotuS), a fast and user-friendly open-source tool to calculate denoised, chimera-checked, operational taxonomic units (OTUs). These are the basis to generate taxonomic abundance tables and phylogenetic trees from multiplexed, next-generation sequencing data (454, illumina MiSeq and HiSeq). LotuS is outstanding in its execution speed, as it can process 16S rDNA data up to two orders of magnitude faster than other existing pipelines. This is partly due to an included stand-alone fast simultaneous demultiplexer and quality filter C++ program, simple demultiplexer (sdm), which comes packaged with LotuS. Additionally, we sequenced two MiSeq runs with the intent to validate future pipelines by sequencing 40 technical replicates; these are made available in this work. CONCLUSION We show that LotuS analyses microbial 16S data with comparable or even better results than existing pipelines, requiring a fraction of the execution time and providing state-of-the-art denoising and phylogenetic reconstruction. LotuS is available through the following URL: http://psbweb05.psb.ugent.be/lotus .
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Affiliation(s)
- Falk Hildebrand
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Pleinlaan 2, Brussels 1050, Belgium
- Department of Bioscience Engineering, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
- Structural & Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Raul Tadeo
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Pleinlaan 2, Brussels 1050, Belgium
- Department of Bioscience Engineering, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
- Department of Microbiology and Immunology, REGA institute, KU Leuven, Herestraat 49, Leuven 3000, Belgium
- VIB Center for the Biology of Disease, Herestraat 49, Leuven 3000, Belgium
| | - Anita Yvonne Voigt
- Structural & Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg 69117, Germany
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peer Bork
- Structural & Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg 69117, Germany
- Max Delbrück Centre for Molecular Medicine, Robert-Rössle-Str. 10, Berlin 13125, Germany
| | - Jeroen Raes
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Pleinlaan 2, Brussels 1050, Belgium
- Department of Bioscience Engineering, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
- Department of Microbiology and Immunology, REGA institute, KU Leuven, Herestraat 49, Leuven 3000, Belgium
- VIB Center for the Biology of Disease, Herestraat 49, Leuven 3000, Belgium
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