Evolution of an endofungal Lifestyle: Deductions from the Burkholderia rhizoxinica Genome

Abstract

BackgroundBurkholderia rhizoxinica is an intracellular symbiont of the phytopathogenic zygomycete Rhizopus microsporus, the causative agent of rice seedling blight. The endosymbiont produces the antimitotic macrolide rhizoxin for its host. It is vertically transmitted within vegetative spores and is essential for spore formation of the fungus. To shed light on the evolution and genetic potential of this model organism, we analysed the whole genome of B. rhizoxinica HKI 0454 - a type strain of endofungal Burkholderia species.ResultsThe genome consists of a structurally conserved chromosome and two plasmids. Compared to free-living Burkholderia species, the genome is smaller in size and harbors less transcriptional regulator genes. Instead, we observed accumulation of transposons over the genome. Prediction of primary metabolic pathways and transporters suggests that endosymbionts consume host metabolites like citrate, but might deliver some amino acids and cofactors to the host. The rhizoxin biosynthesis gene cluster shows evolutionary traces of horizontal gene transfer. Furthermore, we analysed gene clusters coding for nonribosomal peptide synthetases (NRPS). Notably, B. rhizoxinica lacks common genes which are dedicated to quorum sensing systems, but is equipped with a large number of virulence-related factors and putative type III effectors.ConclusionsB. rhizoxinica is the first endofungal bacterium, whose genome has been sequenced. Here, we present models of evolution, metabolism and tools for host-symbiont interaction of the endofungal bacterium deduced from whole genome analyses. Genome size and structure suggest that B. rhizoxinica is in an early phase of adaptation to the intracellular lifestyle (genome in transition). By analysis of tranporters and metabolic pathways we predict how metabolites might be exchanged between the symbiont and its host. Gene clusters for biosynthesis of secondary metabolites represent novel targets for genomic mining of cryptic natural products. In silico analyses of virulence-associated genes, secreted proteins and effectors might inspire future studies on molecular mechanisms underlying bacterial-fungal interaction.

Non-pathogenic Rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica

“…Among those, we detected homologs that were reported to be involved in the interaction of plant growth-promoting bacteria with host plants (Supplementary Table S3). In contrast to other, obligate endofungal bacteria that live in symbiosis with their fungal hosts, RrF4 does not have a reduced genome (Lackner et al, 2011;Ghignone et al, 2012;Fujimura et al, 2014;TorresCortés et al, 2015;Naito et al, 2015), which may indicate a facultative symbiosis of RrF4 with P. indica. The high similarity (in size and gene content) of the chromosomal genomes of RrF4 and C58 indicated that RrF4 did not lose any essential genes or partial genetic pathways.…”

“…Nevertheless, at present, we do not know all the factors needed by RrF4 to associate with its fungal host P. indica. Lackner et al (2011) denoted the intrahyphal Burkholderia rhizoxinica as a bacterium with a 'genome in transition' because it showed to some extent a reduced genome size compared with freeliving Burkholderia species which was not as strongly reduced as found in several other endobacteria. Although RrF4 did not show a reduced genome size, changes in the structure and gene content of both, the pTi and pAt plasmids may hint to an adaptation to a specific ecological niche.…”

Bacterial-Fungal Interactions: Hyphens between Agricultural, Clinical, Environmental, and Food Microbiologists

“…The evolutionary consequences of BFIs are generally poorly understood, although in certain circumstances, such as intrahyphal bacteria or horizontal gene transfer between bacteria and fungi, a clear heritable component to the interaction can be discerned. The first complete genome sequence of an intrahyphal bacterium, the rhizoxin-producing bacterium Burkholderia rhizoxinica (207), has revealed a genome size reduction compared to the genome sizes of other Burkholderia bacteria, a characteristic that is common in the genomes of many bacteria that have adapted to obligate or symbiotic associations with eukaryotes (258), although this reduction is less extreme than those of some bacterial symbionts of insects, and those authors suggested that B. rhizoxinica has a "genome in transition" to adaptation to the intrahyphal niche (208). The B. rhizoxinica genome also suggests some metabolic adaptation to an intrahyphal existence by the bacterium and possesses a surprisingly large number of genes that are predicted to be involved in the biosynthesis of nonribosomal peptides (208).…”

“…The first complete genome sequence of an intrahyphal bacterium, the rhizoxin-producing bacterium Burkholderia rhizoxinica (207), has revealed a genome size reduction compared to the genome sizes of other Burkholderia bacteria, a characteristic that is common in the genomes of many bacteria that have adapted to obligate or symbiotic associations with eukaryotes (258), although this reduction is less extreme than those of some bacterial symbionts of insects, and those authors suggested that B. rhizoxinica has a "genome in transition" to adaptation to the intrahyphal niche (208). The B. rhizoxinica genome also suggests some metabolic adaptation to an intrahyphal existence by the bacterium and possesses a surprisingly large number of genes that are predicted to be involved in the biosynthesis of nonribosomal peptides (208). As more intrahyphal bacterial genomes become available, such as that of "Candidatus Glomeribacter gigasporarum" (175), it will be interesting to see if there are common features that are indicative of strains that can live within fungi.…”

“…(Right) Cartoon illustrating the role of Burkholderia rhizoxinica in the nutrition of Rhizopus microcarpus. In contrast to the cyanolichen example, the bacterium is not a primary producer of organic carbon or nitrogen for the fungus (208). However, the bacterial biosynthesis of the toxin rhizoxin is crucial for fungal pathogenicity toward rice seedlings and therefore to the fungal exploitation of plant-derived carbon and nitrogen (298).…”