Burkholderia genome mining for nonribosomal peptide synthetases reveals a great potential for novel siderophores and lipopeptides synthesis

Abstract

Burkholderia is an important genus encompassing a variety of species, including pathogenic strains as well as strains that promote plant growth. We have carried out a global strategy, which combined two complementary approaches. The first one is genome guided with deep analysis of genome sequences and the second one is assay guided with experiments to support the predictions obtained in silico. This efficient screening for new secondary metabolites, performed on 48 gapless genomes of Burkholderia species, revealed a total of 161 clusters containing nonribosomal peptide synthetases (NRPSs), with the potential to synthesize at least 11 novel products. Most of them are siderophores or lipopeptides, two classes of products with potential application in biocontrol. The strategy led to the identification, for the first time, of the cluster for cepaciachelin biosynthesis in the genome of Burkholderia ambifaria AMMD and a cluster corresponding to a new malleobactin‐like siderophore, called phymabactin, was identified in Burkholderia phymatum STM815 genome. In both cases, the siderophore was produced when the strain was grown in iron‐limited conditions. Elsewhere, the cluster for the antifungal burkholdin was detected in the genome of B. ambifaria AMMD and also Burkholderia sp. KJ006. Burkholderia pseudomallei strains harbor the genetic potential to produce a novel lipopeptide called burkhomycin, containing a peptidyl moiety of 12 monomers. A mixture of lipopeptides produced by Burkholderia rhizoxinica lowered the surface tension of the supernatant from 70 to 27 mN·m−1. The production of nonribosomal secondary metabolites seems related to the three phylogenetic groups obtained from 16S rRNA sequences. Moreover, the genome‐mining approach gave new insights into the nonribosomal synthesis exemplified by the identification of dual C/E domains in lipopeptide NRPSs, up to now essentially found in Pseudomonas strains.

Iron Acquisition Mechanisms and Their Role in the Virulence of Burkholderia Species

“… g Member species of the Bcc are as listed in Depoorter et al ( 2016 ) with the addition of B. paludis (Ong et al, 2016 ) and a potential new member Bcc ATCC 31433 (Loveridge et al, 2017 ) . h B. ambifaria PHP7 (LMG 11351) and the type strain AMMD (LMG 19182) have been shown to produce cepaciachelin, whereas strains MC40-6, MEX-5 and IOP40-10 do not possess the required genes (this study; Barelmann et al, 1996 ; Esmaeel et al, 2016 ) . i Although, several B. multivorans strains encode the capacity to produce cepaciachelin, some (including ATCC 17616 and the type strain LMG 13010) do not (this study; Esmaeel et al, 2016 ) .…”

Paraburkholderia phytofirmans PsJN-Plants Interaction: From Perception to the Induced Mechanisms

“…These gene clusters have been predicted using Florine workflow (Esmaeel et al, 2016b). Each color of gene clusters represents a different class of metabolites.…”

Recovering genomic clusters of secondary metabolites from lakes: a Metagenomics 2.0 approach

“…The 7 clusters on this genome vary from 8,675 base pairs (bp) to 52,516 bp in size, been only possible to be recovered due to the high completeness of the assembled genome (98.28%). The presence of a great diversity of clusters in Pseudomonas is expected, as many active secondary metabolites (encoded by NRPS) have been previously described in the Pseudomonas genus, ranging from antibiotics and antifungal to siderophores [52][53][54].…”