Evolution of the cytochrome P450 superfamily: sequence alignments and pharmacogenetics

doi:10.1016/S1383-5742(97)00040-9

Mutation Research/Reviews in Mutation Research

Volume 410, Issue 3, June 1998, Pages 245-270

https://doi.org/10.1016/S1383-5742(97)00040-9 Get rights and content

Abstract

The evolution of the cytochrome P450 (CYP) superfamily is described, with particular reference to major events in the development of biological forms during geological time. It is noted that the currently accepted timescale for the elaboration of the P450 phylogenetic tree exhibits close parallels with the evolution of terrestrial biota. Indeed, the present human P450 complement of xenobiotic-metabolizing enzymes may have originated from coevolutionary `warfare' between plants and animals during the Devonian period about 400 million years ago. A number of key correspondences between the evolution of P450 system and the course of biological development over time, point to a mechanistic molecular biology of evolution which is consistent with a steady increase in atmospheric oxygenation beginning over 2000 million years ago, whereas dietary changes during more recent geological time may provide one possible explanation for certain species differences in metabolism. Alignment between P450 protein sequences within the same family or subfamily, together with across-family comparisons, aid the rationalization of drug metabolism specificities for different P450 isoforms, and can assist in an understanding of genetic polymorphisms in P450-mediated oxidations at the molecular level. Moreover, the variation in P450 regulatory mechanisms and inducibilities between different mammalian species are likely to have important implications for current procedures of chemical safety evaluation, which rely on pure genetic strains of laboratory bred rodents for the testing of compounds destined for human exposure.

Introduction

The cytochromes P450 (CYP) comprise a superfamily of heme-thiolate enzymes, of which 504 or more individual members have been identified and sequenced, that are primarily associated with the Phase 1 oxygenation of organic compounds, both exogenous and endogenous, in all species investigated thus far, including those of: bacteria, fungi, plants, fish, birds, reptiles, insects and mammalia, including man 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12. The general reaction for P450-mediated mono-oxygenation of a hydrocarbon-based substrate, RH, can be represented as follows: $RH+O_{2} → 2H^{+},2e^{−} P450 ROH+H_{2} O$ where molecular dioxygen is cleaved by the sequential input of two reducing equivalents, supplied by NADPH or NADH, whereupon a single oxygen atom is inserted into the substrate to produce an oxygenated metabolite, ROH, with concomitant generation of water from the second oxygen atom.

P450 isozymes are able to catalyze a considerable variety of oxidations for many structural classes of chemicals, and it has been estimated that the total number of P450 substrates may exceed 200,000 which would include the majority of drugs and other xenobiotics, together with several types of endobiotics such as: steroids, fatty acids, eicosanoids, retinoids and prostaglandins. Although P450s are largely encountered in aerobic organisms, it is possible that they could have origins in anaerobic bacterial species which developed when the earth possessed a reducing atmosphere, but may have, nevertheless, contained sufficient oxygen concentrations to support mixed function oxidase activity generally associated with P450 catalysis. Consequently, since the origin of terrestrial life at around 3850 million years ago [13] it has been estimated that P450 emerged in an ancestral prokaryotic species as early as 3500 million years ago [1].

Section snippets

P450 phylogenetic trees

Over the last ten years or more successive compilations of reported P450 sequences have shown a dramatic increase in known P450 isozymes, and Fig. 1 demonstrates that the number of sequenced P450s published displays an exponential rise, suggesting that many more P450 genes are likely to be characterized in future. Currently, the number of P450s known from cDNA and other sequencing procedures has been reported to be 481, according to the most recent update [2], and is likely to be over 500

Comparison between P450 phylogeny and evolution of species

The generally accepted timescale for the development of biota [29] is summarized in Table 1, which provides a convenient point of comparison with the P450 phylogenetic tree. It is thought that the earliest forms of life were anaerobic bacteria which appeared around 3800 million years ago [13], and the change from an originally reducing atmosphere to an oxidising one occurred about 2000 million years ago, as the evolution of photosynthetic systems gave rise to a steady increase in atmospheric

Genetic polymorphism and pharmacogenetics

Human cytochromes P450 are known to be subject to a certain degree of genetic variation. In particular, there is clear evidence for impaired metabolic functions relating to CYP2D6 and CYP2C19 isoforms in relatively small percentages of certain ethnogeographical populations, whereas similar examples of genetic polymorphism arising from allelic variants in P450 genes are suspected for CYP1A1, CYP1A2, CYP2A6 and CYP2E1 [70]. It is possible that all human P450s are subject to inter-individual

Species differences in metabolism

Although a substantial number of both endogenous and exogenous P450 substrates are metabolized similarly by mammalian species, there are also examples where differences occur which may be due to either the same chemical being metabolized by different isoforms or by orthologous P450s within the same family/subfamily. For example, phenobarbital treatment increases the toxicity of paracetamol (acetamidophen) in rat and mouse, but decreases the toxicity of this chemical in the hamster [91].

Sequence alignments and P450 models

One method for rationalizing P450 substrate specificity and species differences in metabolism is to construct molecular models of either the putative active sites 97, 98, 99 or of the entire P450 enzymes of relevance 8, 100, 101, 102, 103, 104. In order to accomplish this one requires a relatively homologous P450 crystal structure, as a starting template, and a means of carrying out the molecular mutagenesis of the relevant amino acid residues identified by protein sequence alignment of the

Acknowledgements

The financial support of GlaxoWellcome, Merck, Sharp and Dohme, and the University of Surrey Foundation Fund is gratefully acknowledged by one of us (DFVL).

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Evolution of the cytochrome P450 superfamily: sequence alignments and pharmacogenetics

Abstract

Introduction

Section snippets

P450 phylogenetic trees

Comparison between P450 phylogeny and evolution of species

Genetic polymorphism and pharmacogenetics

Species differences in metabolism

Sequence alignments and P450 models

Acknowledgements

Trends Genet.

Biochem. Pharmacol.

Methods Enzymol.

FEBS Lett.

J. Mol. Biol.

J. Biol. Chem.

J. Biol. Chem.

Mut. Res.

Methods Enzymol.

Methods Enzymol.

Methods Enzymol.

Methods Enzymol.

Toxicology

The P450 superfamily: update on new sequences, gene mapping, accession numbers, early trivial names of enzymes and nomenclature

DNA Cell Biol.

P450 superfamily: update on new sequences, gene mapping, accession numbers and nomenclature

Pharmacogenetics

The P450 superfamily: updated listing of all genes and recommended nomenclature for the chromosomal loci

DNA

Evolution of the cytochrome P450 genes

Xenobiotica

Evolution of cytochrome P450 proteins

Mol. Biol. Evol.

P450 genes: structure, evolution and regulation

Annu. Rev. Biochem.

Evidence for life on earth before 3800 million years ago

Nature

Evolution, structure and gene regulation of cytochrome P450

Front. Biotransformation

Evolution of the P450 gene superfamily and regulation of the murine CYP1A1 gene

Biochem. Soc. Trans.

Crystal structure of hemoprotein domain of P450BM-3, a prototype for microsomal P450s

Science

Three-dimensional models of human and other mammalian P450s constructed from an alignment with P450102 (P450bm3)

Xenobiotica

Crystal structure and refinement of cytochrome P450terp at 2.3 Å

J. Mol. Biol.

Structure of cytochrome P450eryF involved in erythromycin biosynthesis

Structural Biol.

Catalytic mechanism of cytochrome P450: evidence of a distal charge relay

J. Am. Chem. Soc.

Late Proterozoic rise in atmospheric oxygen concentration inferred from phylogenetic and sulphur-isotope studies

Nature

Breathing room for early animals

Nature

The early evolution of eukaryotes: a geological perspective

Science

Mitochondrial origins

Proc. Natl. Acad. Sci. U.S.A.

Bacterial evolution

Microbiol. Rev.

Formation of amide bonds without a condensation agent and implications for origin of life

Nature

Doing without oxygen

Biologist

Life in boiling water

Chem. Britain

On the nature of global classification

Proc. Natl. Acad. Sci. U.S.A.

Three-dimensional models of human and other mammalian P450s constructed from an alignment with P450102 (P450_bm3)

Crystal structure and refinement of cytochrome P450_terp at 2.3 Å

Structure of cytochrome P450_eryF involved in erythromycin biosynthesis