Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5

Abstract

Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. We identified various features that contribute to its commensal lifestyle on plants, including broad catabolic and transport capabilities for utilizing plant-derived compounds, the apparent ability to use a diversity of iron siderophores, detoxification systems to protect from oxidative stress, and the lack of a type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5.

Figure 1. Circular representation of the P. fluorescens Pf-5 overall genome structure.

The outer scale designates coordinates in base pairs (bp). The first circle shows predicted coding regions on the plus strand color-coded by role categories: violet, amino acid biosynthesis; light blue, biosynthesis of cofactors, prosthetic groups and carriers; light green, cell envelope; red, cellular processes; brown, central intermediary metabolism; yellow, DNA metabolism; light gray, energy metabolism; magenta, fatty acid and phospholipid metabolism; pink, protein synthesis and fate; orange, purines, pyrimidines, nucleosides and nucleotides; olive, regulatory functions and signal transduction; dark green, transcription; teal, transport and binding proteins; gray, unknown function; salmon, other categories; blue, hypothetical proteins. The second circle shows predicted coding regions on the minus strand color-coded by role categories. The third circle shows the set of 656 P. fluorescens Pf-5 genes that are not conserved in any of the other three Pseudomonas genomes whose sequences have been published (see Fig. 2). The fourth circle shows nine regions encoding secondary metabolism gene clusters coded by color as follows: green, decapeptide biosynthesis; blue, pyoluteorin biosynthesis; gold, polyketide biosynthesis; yellow, pyochelin biosynthesis; gray, pyrrolnitrin biosynthesis; orange, pyoverdine biosynthesis; olive, nonribosomal peptide synthesis; cyan, 2,4-diacetylphloroglucinol synthesis. The fifth circle shows REP repeat elements. The sixth circle shows transposases in black, the predicted PFGI-1 mobile island in olive, and putative phage regions as follows: green, prophage 1; blue, prophage 2; gold, prophage 3; yellow, prophage 4; gray, prophage 5; orange, prophage 6; cyan, prophage 7. The seventh circle shows trinucleotide composition in black. The eighth circle shows percentage G+C in relation to the mean G+C in a 2,000-bp window. The ninth circle shows rRNA genes in blue and the tenth circle shows tRNA genes in green and sRNA genes in red.

Figure 2. Venn diagram showing the number of P. fluorescens Pf-5 predicted proteins with significant homology (P < 10⁻⁵) with the predicted proteins from the sequenced P. aeruginosa PAO1, P. putida KT2440 and P. syringae DC3000 genomes.

The number outside the circles (656) represents the number of P. fluorescens Pf-5 proteins that do not have significant homologs in any of the Pseudomonas species examined.

Figure 3. Secondary metabolite gene clusters in P. fluorescens Pf-5.

(a) Representation of each biosynthetic cluster discovered on the genome of P. fluorescens Pf-5. Red, structural genes (NRPS/PKS); yellow, regulatory genes; green, transporter/resistance genes; orange, accessory genes; and blue, hypothetical genes. (b) Chemical structure of the product of the biosynthetic gene clusters for compounds known to be produced by P. fluorescens Pf-5. (1) pyoverdine; (2) pyoluteorin; (3) pyochelin; (4) pyrrolnitrin; (5) 2,4-diacetylphloroglucinol; and (6) hydrogen cyanide. (c) Predicted structure of a novel cyclic lipopeptide. Glx, (R1= −NH²) or glutamic acid (R1= −OH). Precise chemical predictions are not available for pathways 8 and 9.