The chemical defensome: environmental sensing and response genes in the Strongylocentrotus purpuratus genome

Abstract

Metazoan genomes contain large numbers of genes that participate in responses to environmental stressors. We surveyed the sea urchin Strongylocentrotus purpuratus genome for homologs of gene families thought to protect against chemical stressors; these genes collectively comprise the 'chemical defensome.' Chemical defense genes include cytochromes P450 and other oxidases, various conjugating enzymes, ATP-dependent efflux transporters, oxidative detoxification proteins, and transcription factors that regulate these genes. Together such genes account for more than 400 genes in the sea urchin genome. The transcription factors include homologs of the aryl hydrocarbon receptor, hypoxia-inducible factor, nuclear factor erythroid-derived 2, heat shock factor, and nuclear hormone receptors, which regulate stress-response genes in vertebrates. Some defense gene families, including the ABCC, the UGT, and the CYP families, have undergone expansion in the urchin relative to other deuterostome genomes, whereas the stress sensor gene families do not show such expansion. More than half of the defense genes are expressed during embryonic or larval life stages, indicating their importance during development. This genome-wide survey of chemical defense genes in the sea urchin reveals evolutionary conservation of this network combined with lineage-specific diversification that together suggest the importance of these chemical stress sensing and response mechanisms in early deuterostomes. These results should facilitate future studies on the evolution of chemical defense gene networks and the role of these networks in protecting embryos from chemical stress during development.

Fig. 1

Conceptual organization of the chemical defensome. Organic and inorganic toxicants are actively exported, and also subjected to a variety of biotransformative reactions including oxidation, reduction, conjugation, and hydrolysis. Solid lines indicate possible pathways for exogenous toxicants, dotted lines represent possible gene induction in response to stress-activated receptors, and dot-dashed lines indicate possible sources of toxicant-stimulated endogenous production of reactive oxygen. Gene families responsible for the some of the activities are indicated in appropriate boxes, and are abbreviated as found in the text.

Fig. 2

Unrooted Bayesian phylogenetic tree of NFE2-related CNC genes, including vertebrate, tunicate, and sea urchin homologs. Drosophila CNCA serves as the outgroup. Numbers at branch points are the posterior probabilities calculated from 5 million generations of Bayesian MCMC. The approved gene symbols for the human genes designated here by the common names NRF1, NRF2, and NRF3 are NFE2L1, NFE2L2, and NFE2L3, respectively. Species abbreviations are Drome, Drosophila melanogaster, Cioin Ciona intestinalis, Danre Danio rerio, Homsa Homo sapiens, and Strpu Strongylocentrotus purpuratus. The distance bar represents 0.1 amino acid substitutions per site.

Fig. 3

Unrooted Bayesian phylogenetic tree of NR genes involved in toxicant responses in vertebrates. Sequences include vertebrate, tunicate, and sea urchin genes in the NR1J, NR1I, NR1H, NR1C, and NR2B subfamilies. Numbers at branch points are the posterior probabilities calculated from 5 million generations of Bayesian MCMC. Species abbreviations are as in Fig. 2. The distance bar represents 0.1 amino acid substitutions per site.

Fig. 4

Distribution of ABC transporters between ABC families A–H in primate, zebrafish, tunicate, and urchin.

Fig. 5

Unrooted minimum evolution phylogenetic tree of ABCC genes, including vertebrate, tunicate, sea urchin, and Drosophila sequences. Numbers at branch points are bootstrap values resulting from 250 bootstrap replicates. Branches marked with an asterisk exhibit 100% support. Species abbreviations are as in Fig. 2.

Fig. 6

Distribution of genes in families CYP1–CYP4 in human, pufferfish, tunicate, and urchin.

Fig. 7

Gene count comparisons for various classes of defensome genes. The area of each circle is proportional to the total number of genes classified into the defensome. Receptors include bHLH-ZIP, NR, and CNC receptors. Transporters are ABC and OAT transporters; oxidative modification genes include CYP, FMO, and ALDH; conjugative genes are GST, MGST, UGT, SULT, and NAT; antioxidant genes are SOD, CAT, PXR, and GPX. Other genes include MT, AKR, EPHX, and NQO.