The
bacterial endosymbiont (Burkholderia rhizoxinica)
of the rice seedling blight fungus (Rhizopus microsporus) harbors a large number of cryptic biosynthesis gene clusters. Genome
mining and sequence similarity networks based on an encoded nonribosomal
peptide assembly line and the associated pyrrole-forming enzymes in
the symbiont indicated that the encoded metabolites are unique among
a large number of tentative pyrrole natural products in diverse and
unrelated bacterial phyla. By performing comparative metabolic profiling
using a mutant generated with an improved pheS Burkholderia counterselection marker, we found that the symbionts’ biosynthetic
pathway is mainly activated under salt stress and exclusively in symbiosis
with the fungal host. The cryptic metabolites were fully characterized
as novel pyrrole-substituted depsipeptides (endopyrroles). A broader
survey showed that endopyrrole production is a hallmark of geographically
distant endofungal bacteria, which produce the peptides solely under
symbiotic conditions.