Identification and developmental expression of the full complement of Cytochrome P450 genes in Zebrafish

© The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 11 (2010): 643, doi:10.1186/1471-2164-11-643.Increasing use of zebrafish in drug discovery and mechanistic toxicology demands knowledge of cytochrome P450 (CYP) gene regulation and function. CYP enzymes catalyze oxidative transformation leading to activation or inactivation of many endogenous and exogenous chemicals, with consequences for normal physiology and disease processes. Many CYPs potentially have roles in developmental specification, and many chemicals that cause developmental abnormalities are substrates for CYPs. Here we identify and annotate the full suite of CYP genes in zebrafish, compare these to the human CYP gene complement, and determine the expression of CYP genes during normal development. Zebrafish have a total of 94 CYP genes, distributed among 18 gene families found also in mammals. There are 32 genes in CYP families 5 to 51, most of which are direct orthologs of human CYPs that are involved in endogenous functions including synthesis or inactivation of regulatory molecules. The high degree of sequence similarity suggests conservation of enzyme activities for these CYPs, confirmed in reports for some steroidogenic enzymes (e.g. CYP19, aromatase; CYP11A, P450scc; CYP17, steroid 17a-hydroxylase), and the CYP26 retinoic acid hydroxylases. Complexity is much greater in gene families 1, 2, and 3, which include CYPs prominent in metabolism of drugs and pollutants, as well as of endogenous substrates. There are orthologous relationships for some CYP1 s and some CYP3 s between zebrafish and human. In contrast, zebrafish have 47 CYP2 genes, compared to 16 in human, with only two (CYP2R1 and CYP2U1) recognized as orthologous based on sequence. Analysis of shared synteny identified CYP2 gene clusters evolutionarily related to mammalian CYP2 s, as well as unique clusters. Transcript profiling by microarray and quantitative PCR revealed that the majority of zebrafish CYP genes are expressed in embryos, with waves of expression of different sets of genes over the course of development. Transcripts of some CYP occur also in oocytes. The results provide a foundation for the use of zebrafish as a model in toxicological, pharmacological and chemical disease research.This work was supported by NIH grants R01ES015912 and P42ES007381 (Superfund Basic Research Program at Boston University) (to JJS). MEJ was a Guest Investigator at the Woods Hole Oceanographic Institution (WHOI) and was supported by grants from the Swedish research council Formas and Carl Trygger's foundation. AK was a Post-doctoral Fellow at WHOI, and was supported by a fellowship from the Japanese Society for Promotion of Science (JSPS). JZ and TP were Guest Students at the WHOI and were supported by a CAPES Ph.D. Fellowship and CNPq Ph.D. Sandwich Fellowship (JZ), and by a CNPq Ph.D. Fellowship (TP), from Brazil

Occurrence and Distribution of Diverse Populations of Magnetic Protists in a Chemically Stratified Coastal Salt Pond

Chemical stratification occurs in the water columns and sediments of many aquatic habitats resulting in vertical chemical and redox gradients. Various types of microorganisms are often associated with specific depths and chemical parameters in these situations. For example, magnetite-producing magnetotactic bacteria are known to form horizontal “plates” of cells at the oxic/anoxic transition zone (OATZ) of such environments. Here, we report the presence of populations of diverse magnetic protists in a seasonally chemically stratified, coastal salt pond. The protistan types included several biflagellates, a dinoflagellate, and a ciliate that were each associated with specific depths and thus, specific chemical, microbiological and redox conditions in the water column. Most cells contained crystals of magnetite usually arranged in chains similar to the magnetosomes in the magnetotactic bacteria. The origin of the particles is unknown. There was no evidence of the presence of endosymbiotic magnetotactic bacteria within the protists nor were the protists observed to be engulfing magnetotactic bacteria despite the fact that high numbers of the latter were present at the same depths as the protists. However, this does not exclude ingestion of magnetotactic bacteria as a source of the magnetic particles while others may biomineralize magnetite. Because protists play an important role in the availability of iron for phytoplankton in marine waters by ingesting and reducing colloidal iron particles, the protists described here could play a significant role in iron cycling in chemically stratified anoxic basins, either through endogenous production of magnetic iron oxide and/or iron sulfide particles, or by ingestion of magnetotactic bacteria and the subsequent reduction and dissolution of iron oxide and/or sulfide particles in their magnetosomes