<i>In Silico</i> Characterization and Phylogenetic Distribution of Extracellular Matrix Components in the Model Rhizobacteria <i>Pseudomonas fluorescens</i> F113 and Other Pseudomonads
Biofilms are complex structures that are crucial during host–bacteria interaction and colonization. Bacteria within biofilms are surrounded by an extracellular matrix (ECM) typically composed of proteins, polysaccharides, lipids, and DNA. Pseudomonads contain a variety of ECM components, some of whi...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-11-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/8/11/1740 |
| _version_ | 1797548705777188864 |
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| author | Esther Blanco-Romero Daniel Garrido-Sanz Rafael Rivilla Miguel Redondo-Nieto Marta Martín |
| author_facet | Esther Blanco-Romero Daniel Garrido-Sanz Rafael Rivilla Miguel Redondo-Nieto Marta Martín |
| author_sort | Esther Blanco-Romero |
| collection | DOAJ |
| description | Biofilms are complex structures that are crucial during host–bacteria interaction and colonization. Bacteria within biofilms are surrounded by an extracellular matrix (ECM) typically composed of proteins, polysaccharides, lipids, and DNA. Pseudomonads contain a variety of ECM components, some of which have been extensively characterized. However, neither the ECM composition of plant-associated pseudomonads nor their phylogenetic distribution within the genus has been so thoroughly studied. In this work, we use in silico methods to describe the ECM composition of <i>Pseudomonas fluorescens</i> F113, a plant growth-promoting rhizobacteria and model for rhizosphere colonization. These components include the polysaccharides alginate, poly-N-acetyl-glucosamine (PNAG) and levan; the adhesins LapA, MapA and PsmE; and the functional amyloids in <i>Pseudomonas</i>. Interestingly, we identified novel components: the <i>Pseudomonas</i> acidic polysaccharide (Pap), whose presence is limited within the genus; and a novel type of Flp/Tad pilus, partially different from the one described in <i>P. aeruginosa</i>. Furthermore, we explored the phylogenetic distribution of the most relevant ECM components in nearly 600 complete <i>Pseudomonas</i> genomes. Our analyses show that <i>Pseudomonas</i> populations contain a diverse set of gene/gene clusters potentially involved in the formation of their ECMs, showing certain commensal versus pathogen lifestyle specialization. |
| first_indexed | 2024-03-10T15:03:26Z |
| format | Article |
| id | doaj.art-cd13aa3d0e03432fbe06bd523203c207 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T15:03:26Z |
| publishDate | 2020-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-cd13aa3d0e03432fbe06bd523203c2072023-11-20T19:59:50ZengMDPI AGMicroorganisms2076-26072020-11-01811174010.3390/microorganisms8111740<i>In Silico</i> Characterization and Phylogenetic Distribution of Extracellular Matrix Components in the Model Rhizobacteria <i>Pseudomonas fluorescens</i> F113 and Other PseudomonadsEsther Blanco-Romero0Daniel Garrido-Sanz1Rafael Rivilla2Miguel Redondo-Nieto3Marta Martín4Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin 2, 28049 Madrid, SpainDepartamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin 2, 28049 Madrid, SpainDepartamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin 2, 28049 Madrid, SpainDepartamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin 2, 28049 Madrid, SpainDepartamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin 2, 28049 Madrid, SpainBiofilms are complex structures that are crucial during host–bacteria interaction and colonization. Bacteria within biofilms are surrounded by an extracellular matrix (ECM) typically composed of proteins, polysaccharides, lipids, and DNA. Pseudomonads contain a variety of ECM components, some of which have been extensively characterized. However, neither the ECM composition of plant-associated pseudomonads nor their phylogenetic distribution within the genus has been so thoroughly studied. In this work, we use in silico methods to describe the ECM composition of <i>Pseudomonas fluorescens</i> F113, a plant growth-promoting rhizobacteria and model for rhizosphere colonization. These components include the polysaccharides alginate, poly-N-acetyl-glucosamine (PNAG) and levan; the adhesins LapA, MapA and PsmE; and the functional amyloids in <i>Pseudomonas</i>. Interestingly, we identified novel components: the <i>Pseudomonas</i> acidic polysaccharide (Pap), whose presence is limited within the genus; and a novel type of Flp/Tad pilus, partially different from the one described in <i>P. aeruginosa</i>. Furthermore, we explored the phylogenetic distribution of the most relevant ECM components in nearly 600 complete <i>Pseudomonas</i> genomes. Our analyses show that <i>Pseudomonas</i> populations contain a diverse set of gene/gene clusters potentially involved in the formation of their ECMs, showing certain commensal versus pathogen lifestyle specialization.https://www.mdpi.com/2076-2607/8/11/1740extracellular matrix<i>Pseudomonas</i><i>Pseudomonas fluorescens</i> F113phylogeneticbiofilm<i>Pseudomonas</i> acidic polysaccharide |
| spellingShingle | Esther Blanco-Romero Daniel Garrido-Sanz Rafael Rivilla Miguel Redondo-Nieto Marta Martín <i>In Silico</i> Characterization and Phylogenetic Distribution of Extracellular Matrix Components in the Model Rhizobacteria <i>Pseudomonas fluorescens</i> F113 and Other Pseudomonads Microorganisms extracellular matrix <i>Pseudomonas</i> <i>Pseudomonas fluorescens</i> F113 phylogenetic biofilm <i>Pseudomonas</i> acidic polysaccharide |
| title | <i>In Silico</i> Characterization and Phylogenetic Distribution of Extracellular Matrix Components in the Model Rhizobacteria <i>Pseudomonas fluorescens</i> F113 and Other Pseudomonads |
| title_full | <i>In Silico</i> Characterization and Phylogenetic Distribution of Extracellular Matrix Components in the Model Rhizobacteria <i>Pseudomonas fluorescens</i> F113 and Other Pseudomonads |
| title_fullStr | <i>In Silico</i> Characterization and Phylogenetic Distribution of Extracellular Matrix Components in the Model Rhizobacteria <i>Pseudomonas fluorescens</i> F113 and Other Pseudomonads |
| title_full_unstemmed | <i>In Silico</i> Characterization and Phylogenetic Distribution of Extracellular Matrix Components in the Model Rhizobacteria <i>Pseudomonas fluorescens</i> F113 and Other Pseudomonads |
| title_short | <i>In Silico</i> Characterization and Phylogenetic Distribution of Extracellular Matrix Components in the Model Rhizobacteria <i>Pseudomonas fluorescens</i> F113 and Other Pseudomonads |
| title_sort | i in silico i characterization and phylogenetic distribution of extracellular matrix components in the model rhizobacteria i pseudomonas fluorescens i f113 and other pseudomonads |
| topic | extracellular matrix <i>Pseudomonas</i> <i>Pseudomonas fluorescens</i> F113 phylogenetic biofilm <i>Pseudomonas</i> acidic polysaccharide |
| url | https://www.mdpi.com/2076-2607/8/11/1740 |
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