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. 2022 Dec 21;10(6):e0145622.
doi: 10.1128/spectrum.01456-22. Epub 2022 Oct 26.

The Diversity of Lipopeptides in the Pseudomonas syringae Complex Parallels Phylogeny and Sheds Light on Structural Diversification during Evolutionary History

Affiliations

The Diversity of Lipopeptides in the Pseudomonas syringae Complex Parallels Phylogeny and Sheds Light on Structural Diversification during Evolutionary History

Alexandre Bricout et al. Microbiol Spectr. .

Abstract

Pseudomonas spp. colonize diverse aquatic and terrestrial habitats and produce a wide variety of secondary metabolites, including lipopeptides. However, previous studies have often examined a limited number of lipopeptide-producing strains. In this study, we performed a systematic analysis of lipopeptide production across a wide data set of strains of the Pseudomonas syringae complex (724) by using a combined bioinformatics, mass spectrometry, and phylogenetics approach. The large P. syringae complex, which is composed of 13 phylogroups, is known to produce factins (including syringafactin-like lipopeptides), mycins (including syringomycin-like lipopeptides), and peptins (such as syringopeptins). We found that 80.8% of P. syringae strains produced lipopeptides and that factins were the most frequently produced (by 96% of the producing strains). P. syringae strains were either factin monoproducers or factin, mycin, and peptin coproducers or lipopeptide nonproducers in relation to their phylogenetic group. Our analyses led to the discovery of 42 new lipopeptides, bringing the number of lipopeptides identified in the P. syringae complex to 75. We also highlighted that factins have high structural resemblance and are widely distributed among the P. syringae complex, while mycins and peptins are highly structurally diverse and patchily distributed. IMPORTANCE This study provides an insight into the P. syringae metabolome that emphasizes the high diversity of lipopeptides produced within the P. syringae complex. The production profiles of strains are closely related to their phylogenetic classification, indicating that structural diversification of lipopeptides parallels the phylogeny of this bacterial complex, thereby further illustrating the inherent importance of lipopeptides in the ecology of this group of bacteria throughout its evolutionary history. Furthermore, this overview of P. syringae lipopeptides led us to propose a refined classification that could be extended to the lipopeptides produced by other bacterial groups.

Keywords: Pseudomonas syringae; classification; factins; lipopeptide BGC; lipopeptides; mycins; peptins; secondary metabolites.

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Conflict of interest statement

The authors declare a conflict of interest. P. Jacques declares potential competing interests as a co-founder of Lipofabrik and Lipofabrik Belgium and a member of the scientific advisory board of both companies. All other authors declare no potential competing interests.

Figures

FIG 1
FIG 1
Combination of different approaches leading to new lipopeptide discovery. As an example, the workflow is applied to cichofactin produced by P. cichorii CFBP4407. Monomers with undefined isomery are represented by dotted circles. l-Monomers are in white; d-monomers are in gray.
FIG 2
FIG 2
Distribution of lipopeptide families over the 585 producing strains from the P. syringae collection. The blue circle represents factin-producing strains, the red circle represents mycin-producing strains, and the yellow circle represents peptin-producing strains. The number of strains and the percentage over the 585 producing strains in the collection are mentioned in each corresponding area.
FIG 3
FIG 3
Relationship between the source of isolation and the lipopeptide (LP) production profile of P. syringae strains. The percent distribution of LP-producing strains among the 724 strains of the P. syringae collection is shown.
FIG 4
FIG 4
Predicted structures of new factins compared to the previously described factins produced by the P. syringae complex. l-Monomers are in white, d-monomers are in gray. The star above the monomer position number indicates conserved monomers.
FIG 5
FIG 5
Predicted structures of new mycins compared to the previously described mycins produced by the P. syringae complex. l-Monomers are in white, d-monomers are in gray, and achiral monomers are in blue. The star above the monomer position number indicates conserved monomers.
FIG 6
FIG 6
Predicted structures of new peptins compared to the previously described peptins produced by the P. syringae complex. l-Monomers are in white, d-monomers are in gray, and achiral monomers are in blue. The star above the monomer position number indicates conserved monomers.
FIG 7
FIG 7
Phylogenetic distribution of lipopeptide subfamilies produced by 724 strains of the P. syringae complex. The phylogenetic tree was constructed by Berge et al. (8) and was reproduced according to the terms of the Creative Commons Attribution License. The tree was constructed on the concatenated sequences of four housekeeping genes of 216 P. syringae strains: cts (encoding citrate synthase), gapA (glyceraldehyde-3-phosphate dehydrogenase A), rpoD (RNA polymerase sigma70 factor), and gyrB (gyrase B). Lipopeptide subfamilies are represented with colored squares or pentagons. The number of producing strains is indicated inside each symbol.

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