Table 1.
Main features of the tools used in this study to analyse NRPS.
Figure 1.
Comparison of D-monomer occurrence within ribosomal and nonribosomal peptides.
The data are extracted from Norine database. A: Distribution of D-monomers in curated NRPs (Nb : number), 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).
Figure 2.
Architecture of the bacitracin synthetase.
A: 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: 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. C: Results from InterProScan analysis of BacC protein, the separation between modules has been added and is represented by blue lines.
Figure 3.
Up-Seq and Down-Seq regions in condensation and epimerization domains.
aa : aminoacids.
Figure 4.
Figure 4. WebLogo signatures for E- and C-domains.
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.
Figure 5.
Florine : a workflow dedicated to structure prediction of nonribosomal peptides.
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.
Table 2.
Clusters of NRPS genes identified in the genome of Ps. Syringae pv. tomato DC3000.
Figure 6.
Biosynthesis of pyoverdin 19310 by Ps. syringae pv. tomato DC3000 : from the genomic cluster to the product.
A: 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: 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. C: Successive screen prints of the process leading to the identification of pyoverdin 19310 using Norine.