A lover and a fighter: the genome sequence of an entomopathogenic nematode Heterorhabditis bacteriophora

Abstract

Heterorhabditis bacteriophora are entomopathogenic nematodes that have evolved a mutualism with Photorhabdus luminescens bacteria to function as highly virulent insect pathogens. The nematode provides a safe harbor for intestinal symbionts in soil and delivers the symbiotic bacteria into the insect blood. The symbiont provides virulence and toxins, metabolites essential for nematode reproduction, and antibiotic preservation of the insect cadaver. Approximately half of the 21,250 putative protein coding genes identified in the 77 Mbp high quality draft H. bacteriophora genome sequence were novel proteins of unknown function lacking homologs in Caenorhabditis elegans or any other sequenced organisms. Similarly, 317 of the 603 predicted secreted proteins are novel with unknown function in addition to 19 putative peptidases, 9 peptidase inhibitors and 7 C-type lectins that may function in interactions with insect hosts or bacterial symbionts. The 134 proteins contained mariner transposase domains, of which there are none in C. elegans, suggesting an invasion and expansion of mariner transposons in H. bacteriophora. Fewer Kyoto Encyclopedia of Genes and Genomes Orthologies in almost all metabolic categories were detected in the genome compared with 9 other sequenced nematode genomes, which may reflect dependence on the symbiont or insect host for these functions. The H. bacteriophora genome sequence will greatly facilitate genetics, genomics and evolutionary studies to gain fundamental knowledge of nematode parasitism and mutualism. It also elevates the utility of H. bacteriophora as a bridge species between vertebrate parasitic nematodes and the C. elegans model.

Figure 1. Phylogenetic position of Heterorhabditis relative to other notable Rhabditina.

A. At the base of the tree is the free-living microbivorous Panagrellus (Panagrolaimoidea). Lineages in green are semaphoronts of large, diverse clades of microbivorous nematodes whose members associate with invertebrates at some point in their lifecycle, typically via phoresy and/or necromeny –. Heterorhabditis is a transitional taxon, exhibiting ancestral microbivorous traits, but has also evolved obligate pathenogensis and shares most recent common ancestry with obligate mammalian parasites (Strongyloidea; lineages in red). Modified after –. Taxonomy follows the ranking hypotheses and nomenclature of Hodda, 2011 . B. H. bacteriophora nematodes have evolved a mutualism with insect pathogenic P. luminescens bacteria (green) where each partner cooperates to achieve voracious entomopathogenicity. An infective juvenile regurgitating intestinal symbionts (right) out the pharynx is shown. The movement of the nematode head causes slight misalignment of the fluorescent and differential interference micrograph image overlays.

Figure 2. Genes of insulin/IGF-1 signaling pathway in H. bacteriophora (highlighted in yellow) and C. elegans (all genes).

The genes in red and blue fonts are negative regulator and positive regulator, respectively, of stress resistance, lifespan, and immunity in C. elegan .

Figure 3. Comparison of genes involved in RNA interference pathway in C. elegans, B. malayi, M. hapla, and H. bacteriophora.

Four genes in bold, drsh-1, ego-1, rsd-3, and smg-2 were identified in all four species. sid-1 gene that is required for systemic RNAi in C. elegans was only identified in C. elegans and H. bacteriophora.

Figure 4. Comparison of top 20 Pfam domains in H. bacteriophora genome with those in the 10 nematode species in the study.

The top 20 Pfam domains were identified as the ones having the 20 largest number of occurrence in H. bacteriophora genome.

Figure 5. H. bacteriophora informs C. elegans protein structure function.

Multiple alignment of the EGF-receptor (LET-23) carboxyl tail of Caenorhabditis elegans, briggsae and japonica with H. bacteriophora. 3-way, alignment of the three Caenorhabditis proteins; 4-way, alignment of three Caenorhabditis proteins with Hba-LET-23. *, identity; :, strong similarity; ., weak similarity. Red and green highlight the parts of the protein that have been demonstrated to be important in signaling and localization, respectively. Numbers represent the length of the predicted proteins.