Genome-wide identification of 31 cytochrome P450 (CYP) genes in the freshwater rotifer Brachionus calyciflorus and analysis of their benzo[α]pyrene-induced expression patterns

Jeonghoon Han,Duck-Hyun Kim,Hui-Su Kim,Hee-Jin Kim,Steven A.J Declerck,Atsushi Hagiwara,Jae-Seong Lee

doi:10.1016/j.cbd.2017.10.003

Abstract

While marine invertebrate cytochrome P450 (CYP) genes and their roles in detoxification mechanisms have been studied, little information is available regarding freshwater rotifer CYPs and their functions. Here, we used genomic sequences and RNA-seq databases to identify 31 CYP genes in the freshwater rotifer Brachionus calyciflorus. The 31 Bc-CYP genes with a few tandem duplications were clustered into CYP 2, 3, 4, mitochondrial, and 46 clans with two marine rotifers Brachionus plicatilis and Brachionus koreanus. To understand the molecular responses of these 31 Bc-CYP genes, we also examined their expression patterns in response to benzo[α]pyrene (B[α]P). Three Bc-CYP genes (Bc-CYP3044B3, Bc-CYP3049B4, Bc-CYP3049B6) were significantly upregulated (P<0.05) in response to B[α]P, suggesting that these CYP genes can be involved in detoxification in response to B[α]P exposure. These genes might be useful as biomarkers of B[α]P exposure in B. calyciflorus. Overall, our findings expand the repertoire of known CYPs and shed light on their potential roles in xenobiotic detoxification in rotifers.

Highlights

Cytochrome P450s (CYPs) comprise a multigene superfamily belonging to the phase I detoxification system in diverse living organisms (Nelson et al, 1996; Werck-Reichhart and Feyereisen, 2000)
The CYP1 family (CYP1A, CYP1B, CYP1C, and CYP1D) has been well studied for its role in detoxification through the aryl hydrocarbon receptor (AhR)-CYP1 signaling pathway, which is involved in biotransformation of diverse xenobiotics such as benzo[α]pyrene (B[α]P) and polycyclic aromatic hydrocarbons (PAHs) in marine vertebrates (Goksøyr, 1995; Whitlock, 1999; Wang et al, 2006)
Knowledge of CYP complements is limited in freshwater invertebrates except for the water flea Daphnia pulex compared to what is known about CYP complements in vertebrates and marine invertebrates (Nelson, 2009; Baldwin et al, 2009; Han et al, 2017b)

Summary

Introduction

Cytochrome P450s (CYPs) comprise a multigene superfamily belonging to the phase I detoxification system in diverse living organisms (e.g., bacteria, fungi, and animals) (Nelson et al, 1996; Werck-Reichhart and Feyereisen, 2000). The CYP1 family (CYP1A, CYP1B, CYP1C, and CYP1D) has been well studied for its role in detoxification through the aryl hydrocarbon receptor (AhR)-CYP1 signaling pathway, which is involved in biotransformation of diverse xenobiotics such as benzo[α]pyrene (B[α]P) and polycyclic aromatic hydrocarbons (PAHs) in marine vertebrates (Goksøyr, 1995; Whitlock, 1999; Wang et al, 2006). Genome-wide identification of CYP genes and analysis of their transcriptional profiles in freshwater invertebrates are important for better understanding AhR-CYP signaling pathways associated with detoxification mechanisms in aquatic invertebrates. We identified 31 CYP genes from genome sequences and RNA-seq databases of the freshwater rotifer B. calyciflorus and analyzed their expression patterns in response to. Our results contribute to the understanding of molecular defense mechanisms involving CYP genes in response to environmental pollutants in freshwater rotifers

Culture and maintenance

Identification and nomenclature of CYP genes

Phylogenetic analysis

Statistical analysis

Annotation of the 31 Bc-CYP genes and phylogenetic analysis

Amino acid alignments of the conserved domains of Bc-CYP genes