Making the most of "omics" for symbiosis research

Abstract

Omics, including genomics, proteomics, and metabolomics, enable us to explain symbioses in terms of the underlying molecules and their interactions. The central task is to transform molecular catalogs of genes, metabolites, etc., into a dynamic understanding of symbiosis function. We review four exemplars of omics studies that achieve this goal, through defined biological questions relating to metabolic integration and regulation of animal-microbial symbioses, the genetic autonomy of bacterial symbionts, and symbiotic protection of animal hosts from pathogens. As omic datasets become increasingly complex, computationally sophisticated downstream analyses are essential to reveal interactions not evident from visual inspection of the data. We discuss two approaches, phylogenomics and transcriptional clustering, that can divide the primary output of omics studies-long lists of factors-into manageable subsets, and we describe how they have been applied to analyze large datasets and generate testable hypotheses.

Figure 1

Complementary genetic capacity for essential amino acid synthesis by the primary symbiont (Sulcia) and secondary symbiont in three groups of xylem-feeding insects. Solid bars, genes for biosynthetic pathway present on genome. Data collated from McCutcheon et al. (2009); McCutcheon and Moran( & 2010)

Figure 2

Quantitative proteomic analysis of tissue fractions of the pea aphid-Buchnera symbiosis identifies proteins coded by the Buchnera genome enriched in Buchnera cells by hierarchical clustering (red, enriched; green, depleted). Data from Poliakov et al.(2011).

Figure 3

Use of phylogenomics to identify candidate symbiosis-related genes in the bacterium Xenorhabdus nematophila (Enterobacteriaceae), which associates with entomopathogenic nematodes of the genus Steinernema.A) The pool of 4299 coding genes in the X. nematophila genome was reduced by B) subtracting all 1275 genes absent from the congeneric symbiont X. bovienii and C) subtracting 2491 non-symbiotic genes (shared with the free-living Enterobacteriaceae Salmonella enterica Typhimurium LT2 and Escherichia coli K12). D) The remaining 533 genes were divided as “nematode symbiosis-conserved” if they were shared in two con-familial Photorhabdus species that are also nematode symbionts (290 genes), or specific to the nematode host Steinernema (“Steinernema-conserved”) (243 genes) if they were absent in the Photorhabdus species. E) Phylogenomic analyses performed on the two gene groups identified 15 and 9 clusters, respectively, of which 6 and 4 clusters were enriched in genes shared in plant and animal symbionts in the NCBI database (identified by custom metadata mining), yielding 170 and 51 genes for final analysis. F) Schematic of the phylogenetic relationship between Xenorhabdus and other bacteria that provided reference genomes used in the study, all of which are related in the Family Enterobacteriaceae. Data from Chaston et al. (2011).