Figure 4. WebLogo signatures for E- and C-domains.

<p>C6,C7 and E6, E7 (signatures 6 and 7 for condensation and epimerisation domains, respectively) are highlighted by the dotted lines. The Weblogos (WL) numbered WL1, WL2 and WL3 are mentioned in blue and the corresponding new signatures are surrounded by black squares.</p

Florine : a workflow dedicated to structure prediction of nonribosomal peptides.

<p>Squared boxes are for data (results of bioinformatic processes) and ovals for data processing. Diamond-shaped boxes indicate questions with yes or no answer, bioinformatic tools and databases are mentioned in blue.</p

Architecture of the bacitracin synthetase.

<p><b>A</b>: Modular organization of the proteins constituting the complete bacitracin synthetase. The names of the proteins are mentioned above the arrows. The monomer activated by each module (M1 to M12) is indicated in the square under the corresponding module, the squares are white for L-monomers and grey for D-monomers. <b>B</b>: Domain architecture of BacC protein : schematic representation inspired from various NRPS analysis tools, A: adenylation domain, C: condensation domain, T: thiolation domain, E: epimerization domain, Te: thioesterase domain. <b>C</b>: Results from InterProScan analysis of BacC protein, the separation between modules has been added and is represented by blue lines.</p

Comparison of D-monomer occurrence within ribosomal and nonribosomal peptides.

<p>The data are extracted from Norine database. <b>A</b>: Distribution of D-monomers in curated NRPs (Nb : number), <b>B</b>: Comparison of structures, activities and size distribution between all peptides and those containing at least 1 D-monomer. For the structures, only the 3 major percentages are indicated (cyclic, partial cyclic and linear). Only percentages related to the main activities studied in the paper are indicated (antibiotic, surfactant and siderophore).</p

Clusters of NRPS genes identified in the genome of <i>Ps. Syringae</i> pv. <i>tomato</i> DC3000.

<p>For each gene, the RefSeq identifier of the corresponding protein is given, as well as the modular organization of this protein.</p><p>A: adenylation domain, C: condensation domain, E: epimerization domain, T: thiolation domain, Te: thioesterase domain, Cy : cyclization domain, PKS : domain(s) belonging to the PolyKetide Synthesis.</p><p>The different types of C- and E-domains are mentioned as identified by the weblogo signatures.</p

Biosynthesis of pyoverdin 19310 by <i>Ps. syringae</i> pv. <i>tomato</i> DC3000 : from the genomic cluster to the product.

<p><b>A</b>: Organization of the synthetase in catalytic domains. The gene tags are above and protein id are below the arrows, A : adenylation domain, C : condensation domain, T : thiolation domain, E : epimerization domain, Te : thioesterase domain. <b>B</b>: Monomeric representation of probable peptides, when several monomers can occupy one position, they are indicated in brackets, the abbreviation of the monomers are those found in the Norine database. <b>C</b>: Successive screen prints of the process leading to the identification of pyoverdin 19310 using Norine.</p

Main features of the tools used in this study to analyse NRPS.

*<p>All types of domains means that the tool outputs all the known domains for the enzymes they cover. “A domains” is for adenylation domains; “KS” for ketosynthase and “C” for condensation domains.</p>**<p>SMILES (<i>simplified molecular-input line-entry system</i>) format is a string representation of chemical structures.</p>***<p>NaPDoS works better with one domain at a time.</p

Image_3_Rhamnolipids and fengycins, very promising amphiphilic antifungal compounds from bacteria secretomes, act on Sclerotiniaceae fungi through different mechanisms.TIF

Rhamnolipids (RLs) and fengycins (FGs) are amphiphilic lipid compounds from bacteria secretomes proposed to replace synthetic pesticides for crop protection. They both display plant defense triggering properties and direct antimicrobial activities. In particular, they have well reported antifungal effects against phytopathogenic fungi. RLs and FGs are considered to act through a direct interaction with membrane lipids and a destabilization of microorganism plasma membrane, thereby limiting the risk of resistance emergence. The main objective of this work was to gain insights in the antimycelial mode of action of these metabolites to promote them as environment and human health friendly biocontrol solutions. Their biocidal effects were studied on two Sclerotiniaceae fungi responsible for diseases in numerous plant species worldwide. We show here that different strains of Botrytis cinerea and Sclerotinia sclerotiorum have opposite sensitivities to RLs and FGs on plate experiments. Overall, B. cinerea is more sensitive to FGs while S. sclerotiorum is more sensitive to RLs. Electron microscopy observations demonstrated that RLs induce mycelial destructuring by asperities emergence and hyphal fusions whereas FGs promote swelling and formation of vesicle-like structures due to vacuole fusions and autophagy. Permeability studies, phosphatidylserine externalization and reactive oxygen species production assessments showed a programmed cell death triggering by RLs at medium concentrations (until 50 μg mL−1) and necrosis characteristics at higher concentration. Programmed cell death was always observed on hyphae treated with FGs. Quantifications of mycelial ergosterol content indicated that a higher ergosterol rate in S. sclerotiorum correlates with increasing sensitivity to RLs. Oppositely, a lower ergosterol rate in B. cinerea correlates with increasing sensitivity to FGs, which was confirmed by ergosterol biosynthesis inhibition with tebuconazole. This gain of knowledge will help to better understand the mode of action of RLs and FGs to fight specific plant fungal diseases.</p