The chemical defensome of five model teleost fish

Abstract

How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and transcription factors, biotransformation enzymes, transporters, antioxidants, and metal- and heat-responsive genes, and is collectively known as the chemical defensome. Teleost fish is the largest group of vertebrate species and can provide valuable insights into the evolution and functional diversity of defensome genes. We have previously shown that the xenosensing pregnane x receptor (pxr, nr1i2) is lost in many teleost species, including Atlantic cod (Gadus morhua) and three-spined stickleback (Gasterosteus aculeatus), but it is not known if compensatory mechanisms or signaling pathways have evolved in its absence. In this study, we compared the genes comprising the chemical defensome of five fish species that span the teleosteii evolutionary branch often used as model species in toxicological studies and environmental monitoring programs: zebrafish (Danio rerio), medaka (Oryzias latipes), Atlantic killifish (Fundulus heteroclitus), Atlantic cod, and three-spined stickleback. Genome mining revealed evolved differences in the number and composition of defensome genes that can have implication for how these species sense and respond to environmental pollutants, but we did not observe any candidates of compensatory mechanisms or pathways in cod and stickleback in the absence of pxr. The results indicate that knowledge regarding the diversity and function of the defensome will be important for toxicological testing and risk assessment studies.

Figure 1

Chemical defensome genes in five model fish species. The genes were identified by searching gene names and using HMMER searches with Pfam profiles, followed by reciprocal or best-hit blast searches towards the zebrafish proteome. The gene families are organized in categories following Gene Ontology annotations and grouped by their role in the chemical defensome. The size of the disk represents the relative number of genes in the different fish genomes within each group, with the number of genes in a specific gene family as slices.

Figure 2

Phylogenetic tree of NAD(P)H:quinone oxidoreductases (NQO), also known as DT-diaphorase (DTD). Multiple sequence alignment and phylogenetic tree was built using Clustal Omega with standard settings. The tree was drawn using iTol, and rooted with the archaebacterial NQO5.

Figure 3

Transcription of chemical defensome genes in early development of (a) zebrafish (Danio rerio) and (b) stickleback (Gasterasteus aculeatus). Absolute transcription values (log2 scale) of defensome genes, grouped into their functional category, are shown at early morula, late morula, mid gastrula, early organogenesis, and 24 h post hatching (hph).

Figure 4

Transcriptional responses on chemical defensome genes in (a) zebrafish embryo (3.3 h post fertilization (hpf)) and (b) zebrafish larvae (96 hpf) following exposure to benzo(a)pyrene. The transcription is shown as log2 fold change between exposed and control group at each timepoint. The genes are grouped into their functional categories in the chemical defensome and the name of some genes are indicated for clarity.