Genome comparisons provide insights into the role of secondary metabolites in the pathogenic phase of the Photorhabdus life cycle

Abstract

Background: Bacteria within the genus Photorhabdus maintain mutualistic symbioses with nematodes in complicated lifecycles that also involves insect pathogenic phases. Intriguingly, these bacteria are rich in biosynthetic gene clusters that produce compounds with diverse biological activities. As a basis to better understand the life cycles of Photorhabdus we sequenced the genomes of two recently discovered representative species and performed detailed genomic comparisons with five publically available genomes.

Results: Here we report the genomic details of two new reference Photorhabdus species. By then conducting genomic comparisons across the genus, we show that there are several highly conserved biosynthetic gene clusters. These clusters produce a range of bioactive small molecules that support the pathogenic phase of the integral relationship that Photorhabdus maintain with nematodes.

Conclusions: Photorhabdus contain several genetic loci that allow them to become specialist insect pathogens by efficiently evading insect immune responses and killing the insect host.

Keywords: Photorhabdus; Secondary metabolites; Sequencing; Symbiosis.

Fig. 1

Map of highly conserved BGCs (present in at least 5 strains) in Photorhabdus spp. Following antiSMASH analysis, clusters were aligned using Mauve (v2.3.1) to identify homologous sequences. Domain architecture was checked using the conserved domain database from NCBI for each cluster to ensure consistency across the proposed families. Class of compound, names of identified compounds and domain structures are indicated. For all BGCs, see Additional file 5. Grey boxes represent the reported cluster, not identified by antiSMASH (see Methods)

Fig. 2

Schematic summary of the intricate tripartite lifecycle of Photorhabdus highlighting the produced specialized metabolites and predicted functions (indicated by a ‘?’ where unproven associations exist). Nematodes infect insects and release the bacteria inside the hemolymph before undergoing several rounds of development while the insect is killed. The bacteria release several compounds (dashed arrows) that variously affect the insect’s immune response. DAR = dialkylresorcinol, PPY = photopyrone