The rat clofibrate-inducible CYP4A gene subfamily. I. Complete intron and exon sequence of the CYP4A1 and CYP4A2 genes, unique exon organization, and identification of a conserved 19-bp upstream element

A novel murine P-450 gene, Cyp4a14, is part of a cluster of Cyp4a and Cyp4b, but not of CYP4F, genes in mouse and humans

Genomic clones for Cyp4a12 and a novel member of the murine Cyp4a gene family were isolated. The novel gene, designated Cyp4a14, has a GC rich sequence immediately 5' of the transcription start site, and is similar to the rat CYP4A2 and CYP4A3 genes. The Cyp4a14 gene spans approximately 13 kb, and contains 12 exons; sequence similarity to the rat CYP4A2 gene sequence falls off 300 bp upstream from the start site. In view of the known sex-specific expression of the rat CYP4A2 gene, the expression and inducibility of Cyp4a14 was examined. The gene was highly inducible in the liver when mice were treated with the peroxisome proliferator, methylclofenapate; induction levels were low in control animals and no sex differences in expression were observed. By contrast, the Cyp4a12 RNA was highly expressed in liver and kidney of control male mice but was expressed at very low levels in liver and kidney of female mice. Testosterone treatment increased the level of this RNA in female liver slightly, and to a greater extent in the kidney of female mice. In agreement with studies on the cognate RNA, expression of Cyp4a12 protein was male-specific in the liver of control mice and extremely high inducibility of Cyp4a10 protein, with no sex differences, was also demonstrated. In view of the overlapping patterns of inducibility of the three Cyp4a genes, we investigated whether the three genes were co-localized in the genome. Two overlapping yeast artificial chromosome (YAC) clones were isolated, and the three Cyp4a genes were shown to be present on a single YAC of 220 kb. The Cyp4a genes are adjacent to the Cyp4b1 gene, with Cyp4a12 most distant from Cyp4b1. The clustering of these two gene subfamilies in the mouse was replicated in the human, where the CYPA411 and CYP4B1 genes were present in a single YAC clone of 440 kb. However, the human CYP4F2 gene was mapped to chromosome 19. Phylogenetic analysis of the CYP4 gene families demonstrated that CYP4A and CYP4B are more closely related than CYP4F.

Mapping of rat chromosome 5 markers generated from chromosome-sorted DNA

Nineteen markers for rat Chromosome 5 (Chr) were generated by screening chromosome-sorted DNA libraries and were subsequently mapped by linkage to known markers by use of five F2 rat populations. Along with existing markers, these newly produced markers are potentially useful for fine mapping of certain quantitative trait loci for blood pressure and for obesity.

The cytochrome P450 4 (CYP4) family

1. The CYP4 family consists of 11 subfamilies (CYP4A-CYP4M), which encode constitutive and inducible isozymes expressed in both mammals and insects. 2. The CYP4A subfamily encodes several cytochrome P450 enzymes that are capable of hydroxylating the terminal omega-carbon and, to a lesser extent, the (omega-1) position of saturated and unsaturated fatty acids, as well as enzymes active in the omega-hydroxylation of various prostaglandins. 3. The CYP4A1, A2 and A3 genes, the most extensively studied members of the CYP4 family, are expressed constitutively in rat liver and kidney and their expression is induced by a class of chemicals known as peroxisome proliferators, which includes the hypolipidemic drug, clofibrate. 4. Induction of CYP4A expression by clofibrate is due to transcriptional activation, mediated possibly via a peroxisome proliferator activated receptor (PPAR). 5. CYP4A gene expression is hormonally regulated. 6. The CYP4A1-3 genes are expressed constitutively and following induction in pregnant and lactating rats. 7. Translactational and transplacental induction of the CYP4A1-3mRNAs and proteins has been demonstrated. 8. There is a close association between microsomal CYP4A1 induction, peroxisome proliferation and induction of the peroxisomal fatty acid metabolizing system. 9. The CYP4A subfamily may be involved in the metabolism of arachidonic acid leading to the formation of physiologically important metabolites involved in such processes as blood flow in the kidney, cornea and brain.

The cDNA cloning and transient expression of a chicken gene encoding cytochrome P-450scc

A cDNA clone, pcSCC1, isolated from a chicken adrenal gland library showed about 62% nucleotide sequence similarity to those of mammalian and rainbow trout P-450scc cDNAs and was proved to be the clone for chicken P-450scc by the enzymatic activity of converting 25-hydroxycholesterol to pregnenolone demonstrated in the transfected COS-7 cells. Comparison of deduced amino acid sequences shows significant conservation of heme- and steroid-binding domains but little similarity in the putative N-terminal presequence region among chicken, trout and mammals. The chicken cDNA lacks a polyadenylation signal in its 3'-UTR. Sequencing of a 3' end region of the P-450scc gene (CYP11A1) suggests that a region containing the polyadenylation signal is spliced out from the pre-mRNA.

Renal cytochrome P4504A activity and salt sensitivity in spontaneously hypertensive rats

Differences in the renal metabolism of arachidonic acid by cytochrome P450 have been reported in the spontaneously hypertensive rat (SHR) and Wistar-Kyoto rats, but the contribution of this system to the development of hypertension is unclear. The present study compared renal P450 activity and blood pressure in SHR and Brown-Norway rats (BN) under control conditions and in response to an elevation in sodium intake; genetic linkage analysis was performed in an F2 population (n=219) derived from these strains. Basal renal P4504A enzyme activity measured by conversion of [C(14)]arachidonic acid to 20-hydroxyeicosatetraenoic acid (20-HETE) was significantly greater in the kidneys of adult SHR (n=7) than of BN (n=8) (82 +/- 7 versus 60 +/- 5 pmol/min per milligram protein). Renal 20-HETE production fell 45 percent in SHR and 22 percent in BN in which salt intake was elevated by drinking of saline instead of water for 2 weeks. Mean arterial pressure averaged 157 +/- 3mm Hg in SHR (n = 9) and 100 +/- 2 mm Hg in BN fed a normal salt diet, and it rose to 170 +/- 7 mm Hg (P<.05) in SHR and fell to 90 +/- 3 mm Hg (P<.05) in BN (n=8) after sodium intake was elevated. A polymorphic marker, D5Rjr1, that spanned a repeated element in the P4504A gene on chromosome 5, where all three P4504A isoforms are located, was used for genotyping of the F2 population. The P4504A genotype did not cosegregate with baseline mean arterial pressure in the F2 population; however, significant linkage was observed with the change in mean arterial pressure after sodium intake of the rats was elevated. The degree of linkage differed in male and female rats, and the highest LOD score (3.6) was observed in male F2 rats with a BN grandfather. These findings suggest that the difference in renal P450 activity in SHR and BN does not contribute to the development of hypertension in this F2 population, but it may play some role in determining the blood pressure response to an elevation in salt intake.

Cytochrome P4504A genotype cosegregates with hypertension in Dahl S rats

Recent studies indicate that the production of 20-HETE by a P4504A2 enzyme in the outer medulla of the kidney is reduced in Dahl salt-sensitive (SS/Jr) rats, but the contribution of this abnormality to the elevation in loop Cl- transport and development of hypertension in this model is unknown. THe present study found that alleles at the locus for the P4504A2 gene cosegregate with blood pressure in an F2 population (n=151) derived from a cross between SS/Jr and Lewis rats (P < .0001). The P4504A2 locus is located in a region on rat chromosome 5 where a blood pressure quantitative trait locus was previously detected. Systolic blood pressure averaged 201 +/- 6 mm Hg in rats with the SS genotype (n=36), 192 +/- 4 mm Hg in SL genotype rats (n=77), and 169 +/- 3 mm Hg in LL genotype rats (n=38). In further studies, we confirmed that there are phenotypic differences in the expression of the P4504A2 gene in the kidneys of SS/Jr and Lewis rats. Although the production of 20-HETE from 14C-arachidonic acid was similar in microsomes prepared from the renal cortex of SS/Jr and Lewis rats (54 +/- 3 versus 55 +/- 3 pmol/min/mg protein), the production of 20-HETE in microsomes prepared from the outer medulla (OM) was markedly reduced in SS/Jr rats (2.8 +/- 0.8 versus 6.7 +/- 1 pmol/min/mg protein). The diminished production of 20-HETE in the OM was due to a threefold reduction in the level of P4504A2 protein. These results suggest that an altered expression of the P4504A2 enzyme in the OM may contribute to the development of hypertension in SS/Jr rats.

Translactational induction of CYP4A expression in 10.5-day neonatal rats by the hypolipidemic drug clofibrate

Lactating mothers of 7.5-day neonatal rats were injected intraperitoneally with 500 mg kg-1 clofibrate for 3 consecutive days at 24-hour intervals; 24 hours after the final injection, the maternal cytochrome P450 4A (CYP4A) mRNA levels had risen 14- and 2.5-fold above the constitutive levels of expression seen in the liver and kidney, respectively. Lactational transfer of clofibrate to the suckling 10.5-day litter was demonstrated by the 15- and 5-fold elevation observed in the neonatal hepatic and renal CYP4A mRNAs, respectively, following suckling from drug-induced mothers. A significant decrease in the relative liver weights of these neonatal pups was seen following clofibrate exposure via maternal milk, in total contrast to the normally observed increase in liver/body weight ratios of rats treated with clofibrate. Western blot analysis using a polyclonal goat anti-rat CYP4A1 antibody also demonstrated a rise in the CYP4A protein levels in both the mothers and their litters following maternal clofibrate treatment.

Identification and characterization of DNA elements implicated in the regulation of CYP4A1 transcription

We have identified a peroxisome proliferator response element (PPRE) approx. 4300 nucleotide upstream of the rat cytochrome P-450 CYP4A1 gene. Two members of the steroid-hormone-receptor superfamily, the peroxisome proliferator-activated receptor-alpha (PPAR alpha) and the retinoid X receptor-alpha (RXR alpha), bind specifically to this element as a heterodimer, and this element confers responsiveness to the peroxisome proliferator Wyeth-14,643 when tested in co-transfection assays. A second element, located 35 nucleotides further upstream, fails to bind PPAR alpha/RXR alpha heterodimers and is unresponsive to Wy-14,643 in co-transfection assays. Both elements are, however, responsive to 9-cis-retinoic acid in the presence of RXR alpha, when tested in the co-transfection assay. As RXR alpha fails to bind to either element as a homodimer, we suggest that RXR alpha interacts with PPAR alpha to regulate transcription via the proximal element, and interacts with some other cellular factor to regulate transcription via the more distal element. This is consistent with previous reports that a number of peroxisome proliferator-regulated genes contain PPRE-like elements as part of their regulatory sequences, which may be recognized by several receptor combinations. This provides further evidence that PPARs and their co-factors are important in mediating the pleiotropic action of peroxisome proliferators.

Transient induction of fatty acid synthase in rat liver after removal of a peroxisome proliferator

Removal of a peroxisome proliferator from the diet triggered the degradation of peroxisomes and induced the transient expression of a 220 kDa soluble protein in rat liver. The 220 kDa protein was purified by conventional methods and analyzed by amino acid sequencing. A total of 99 amino acid residues in 4 lysylendopeptidase-digested peptides completely matched those in rat fatty acid synthase. The transient induction of fatty acid synthase mRNA during peroxisome degradation was confirmed by Northern blotting.

Molecular cloning of the rat analogue of human CD59: structural comparison with human CD59 and identification of a putative active site

We have previously described the purification and partial characterization of the rat analogue of the human complement regulatory molecule CD59 [Hughes, Piddlesden, Williams, Harrison and Morgan (1992) Biochem. J. 284, 169-176]. We present here the molecular cloning and full sequence analysis of this molecule. A PCR-based approach utilizing primers designed from the amino-terminal protein sequence was used to isolate a full-length cDNA clone from a rat kidney cDNA library. This clone encoded a 92 bp 5'-flanking sequence, a 66 bp signal peptide and a 315 bp coding region containing putative glycosylation and GPI-anchor signals. The 3' untranslated flanking region was approximately 1.1 kbp long and included the poly-A tail and a CATA repeating sequence. The coding region was 58% identical with the human cDNA at the nucleotide level and 44% identical at the amino acid level. Despite this relatively low overall sequence conservation, several highly conserved stretches were apparent, particularly in the N-terminal portion of the molecule, in the cysteine-rich region immediately preceding the site of glycolipid attachment and in the C-terminal peptide removed during glycolipid attachment. An N-glycosylation site was identified at Asn-16 and a putative glycosylphosphatidylinositol anchor addition site at Asn-79, indicating that the mature processed protein was two residues longer than human CD59. Comparison of the sequences of rat and human CD59, together with consideration of the published three-dimensional structure of human CD59 and functional data, implicates specific regions of the protein in interactions with C-8 and/or C-9.

Induction of cytochrome P450 isozymes in rat renal microsomes by cyclosporin A

To examine the effects of cyclosporin A (CsA) on renal cytochrome P450 forms, CsA was administered to rats, and the renal levels of P450 were determined by immunoblotting. CsA treatment for 17 days increased total renal P450 content by 40% with a concomitant elevation of the omega- and (omega-1)-hydroxylation activities of lauric acid. Arachidonic acid omega-hydroxylation activity was also induced 2-fold by treatment with CsA for 17 days. Among the P450 forms, CYP4A2 was induced significantly, whereas CYP2C23, CYP4A1 and CYP4A8 were unaffected. These changes were accompanied by slight but significant increases in blood urea nitrogen and systolic blood pressure. These data suggest that CsA increased arachidonic acid omega-hydroxylation activity by the induction of CYP4A2. The specific induction of CYP4A2 may be related to CsA-induced nephrotoxicity and elevated blood pressure, because omega-hydroxyarachidonic acid is a potent vasoconstrictor.

Dehydroepiandrosterone 3 beta-sulphate is an endogenous activator of the peroxisome-proliferation pathway: induction of cytochrome P-450 4A and acyl-CoA oxidase mRNAs in primary rat hepatocyte culture and inhibitory effects of Ca(2+)-channel blockers

The role of steroids related to the adrenal androgen dehydroepiandrosterone (5-androstene-3 beta-ol-17-one; DHEA) in regulating the expression of peroxisomal and cytochrome P-450 4A (CYP4A) enzymes active in fatty acid metabolism was assessed using a primary rat hepatocyte culture system. Exposure of hepatocytes to the peroxisome proliferator, clofibric acid (10-250 microM), for 48-96 h led to substantial increases in CYP4A protein, CYP4A1, CYP4A2 and CYP4A3 mRNAs, and the mRNAs encoding both forms of peroxisomal acyl-CoA oxidase (ACOX-I and ACOX-II), as judged by Northern-blot analysis using gene-specific oligonucleotide probes. Although DHEA treatment in vivo is effective in inducing these mRNAs in rat liver, it had no effect in the cultured hepatocytes. In contrast, treatment of the cells with DHEA 3 beta-sulphate (DHEA-S; 10-250 microM) stimulated major increases in CYP4A and ACOX mRNA levels. Examination of several analogues indicated a preference for 3 beta-sulphate over 17 beta-sulphated steroids and the inactivity of a 3 alpha-hydroxy-17 beta-sulphate derivative (DHEA-S > 5-androstene-3 beta,17 beta-diol 3-sulphate approximately 5 alpha-androstene-3 beta-ol-17-one 3-sulphate > 5-androstene-3 beta, 17 beta,17 beta-diol 17-sulphate approximately 5 beta-androstane-3 alpha-ol-17-one 3-sulphate >> 5 alpha-androstane-3 alpha, 17 beta-diol 17-sulphate). Induction of CYP4A mRNAs by either DHEA-S or clofibric acid was partially blocked by structurally diverse Ca(2+)-channel antagonists (nicardipine, nifedipine and diltiazem; 50 microM), suggesting that both the steroidal and fibrate classes of CYP4A inducers stimulate peroxisomal-proliferative responses via a Ca(2+)-dependent pathway. Retinoic acid alone slightly induced CYP4A mRNAs but did not enhance the induction by clofibrate or DHEA-S. As DHEA-S corresponds to a physiologically important major circulating androgen, these findings suggest that it may serve as an endogenous regulator of hepatic peroxisome enzyme levels. They further suggest that Ca(2+)-channel blockers may be useful pharmacological tools for the further study of the underlying cellular mechanism whereby endogenous steroids and fibrate drugs induce peroxisome proliferation, and the relationship of these events to activation of the peroxisome proliferator-activated receptor.

Deduced amino acid sequence of a murine cytochrome P-450 Cyp4a protein: developmental and hormonal regulation in liver and kidney

Proteins from the cytochrome P-450 CYP4A gene family metabolise hormones such as prostaglandins and other fatty acids, and are induced by peroxisome proliferators such as the hypolipidaemic drugs clofibrate and ciprofibrate. In order to better understand the function and regulation of these enzymes we have cloned a murine cDNA, Cyp4a-10, whose deduced amino acid sequence shares 92% sequence identity with rat CYP4A1. The developmental and hormonal regulation of this protein and other members of the murine Cyp4a gene family were then studied using a polyclonal antibody to rat CYP4A1. The expression of Cyp4a proteins in liver and kidney develop gradually from birth and are sexually differentiated in mature animals; growth hormone appears to be involved in regulating expression of hepatic Cyp4a proteins. The administration of phenobarbital and dexamethasone affected the expression of Cyp4a proteins in the liver, but not in the kidney, where testosterone was the key regulatory factor, demonstrating interesting tissue-specific effects in the regulation of these enzymes.

Cluster of cytochrome P450 genes on the X chromosome of Drosophila melanogaster

A new cytochrome P450 gene was found within the wap1-prune genetic region of the Drosophila melanogaster X chromosome. It encodes a putative cytochrome P450 of subfamily 4D and has been designated CYP4D2. CYP4D2 has a complex exon-intron structure. Both the heme-binding motif and a region diagnostic for family 4 are not interrupted by introns. CYP4D2 lies 20 kb proximal to the previously described CYP4D1 gene (Gandhi et al., 1992). In addition to CYP4D1 and CYP4D2, two other DNA fragments homologous to P450 genes are detected within the wap1-prune region.

Impact of cytochrome P450 system on lipoprotein metabolism. Effect of abnormal fatty acids (3-thia fatty acids)

Fatty acid omega-hydroxylation, peroxisomal and mitochondrial fatty acid oxidation and related lipid-metabolizing enzymes are constitutive activities of mammalian cells. The past 5 years have witnessed an increased interest in the modulation of these pathways and functions by a new group of abnormal fatty acids (sulfur-substituted fatty acid analogs), due to the metabolic and nutritional aspects related to human health and disease, and possible treatment of certain inherited peroxisomal and mitochondrial disorders. The purpose of this review is to present an overview of current knowledge in the field and to provide an account of recent developments, particularly with respect to the chemical nature of the biologically active factors and their possible mechanism of action.

Human 25-hydroxyvitamin D 24-hydroxylase cytochrome P450 subunit maps to a different chromosomal location than that of pseudovitamin D-deficient rickets

We have cloned part of the human 25-OHD 24-hydroxylase cytochrome P450 (P450cc24) cDNA. The characterized sequence consists of 776 bp of the coding and 720 bp of the 3'-untranslated region interrupted by an intron. In the coding region we found 79.8% similarity in DNA and 87.5% in deduced amino acid sequences between human and rat, with no similarity in the 3'-untranslated region. By Southern blot hybridization of DNA from human-hamster somatic cell hybrids and by in situ immunofluorescence hybridization, we mapped P450cc24 to human chromosome 20q13.1. This location of P450cc24 is different from that of pseudovitamin D-deficient rickets (PDDR), previously assigned to chromosome 12q14 by linkage analysis, thus excluding it as a target of the PDDR mutation. Since it is likely that PDDR is caused by a mutation in the 25-OHD 1 alpha-hydroxylase P450 subunit (P450cc1 alpha) our results do not support the hypothesis that the two cytochromes are encoded by a single gene.

Molecular evolution of P450 superfamily and P450-containing monooxygenase systems

This paper reviews the classification of the P450 superfamily which is mainly based on sequence homology. The widely accepted classification by Nebert et al. [(1991) DNA Cell Biol. 10, 1-14] as well as the results of a 'two-step' multiple sequence alignment technique show that the molecular evolution of P450s, in contrast to that of many protein families, does not follow phylogeny. The data suggest that during the evolution of P450s, gene duplications and gene fusions, horizontal gene transfer and intron loss events have occurred. 'Weak' and 'strong' hierarchies in the clustering of P450 sequences were revealed. A novel evolutionary tree of the P450 superfamily has been constructed using a multiple alignment of consensus sequences. The simple classification of known P450-containing monooxygenase systems into three-, two- and one-component systems is further discussed. Particularly, the multidomain enzyme, nitric oxide synthase (NOS), should be classified as an example of a eukaryotic one-component P450 system since its N-terminal (haem) domain exhibits similarity with microsomal P450s.

Characterization of cytochromes P450 in liver and kidney of rats treated with di-(2-ethylhexyl)phthalate

A polyclonal antibody was made to a liver cytochrome P450 purified from di-(2-ethyl-hexyl)phthalate (DEHP)-treated Sprague-Dawley rats and was used to identify the CYP4A forms in liver and kidney cortex microsomes of control rats and rats treated with this peroxisome proliferator. Three clearly separated major protein bands were recognized on western blots in liver microsomes of control male rats or male rats treated with a single dose of DEHP, which, based on the description of relative mobility, tissue specificity, and sex dependent expression of CYP4A forms (Sundseth and Waxman (1992). J. Biol. Chem., 267, 801-810), correspond to the migration pattern of forms 4A1, 4A2, and 4A3 in clofibrate-treated rats. The administration of DEHP for 2 or 3 days caused a loss of resolution of two of the protein bands. The protein band corresponding to 4A2 was absent in liver or kidney cortex microsomes of DEHP-treated or control female rats and was not always visible in the livers of control male rats. The purified P450DEHP supported the hydroxylation of arachidonic acid at both the 19- and 20-carbon atoms with turnover rates of 1.4 +/- 0.2 and 22.7 +/- 2.5 nmoles per minute per nmol P450, respectively. No measurable amounts of hydroxylated products were obtained when prostaglandin E1, leukotriene B4, or testosterone were used as substrates. Another member of the CYP4 family, 4B1 from rabbit lung microsomes, was also recognized by this antibody on western blot analysis; however, rabbit lung form 4A4 showed only minimal cross-reactivity with this antibody.

Repression of cytochrome P450 by cytokines: IL-1 beta counteracts clofibric acid induction of CYP4A in cultured fetal rat hepatocytes

Interleukin-1 is known to repress a number of hepatic drug-metabolizing enzymes in rats and humans. The effect of interleukin-1 beta on lauric acid 12-hydroxylase (CYP4A family) was studied in cultured fetal rat hepatocytes after clofibric acid induction. Dexamethasone was used as an agent promoting differentiation and long-term maintenance of active hepatocytes. Dexamethasone and clofibric acid in combination allowed maximal (13.5-fold) induction of CYP4A1. Lauric acid 12-hydroxylase activity was found to increase with time in culture. Interleukin-1 beta adversely affected P4504A clofibric acid-induced activity, totally eliminating the effect of induction at doses exceeding 5 ng/ml. This repression/inhibition was dose-dependent. The mechanism by which interleukin-1 beta prevents the development of cytochrome P4504A activity is unclear.

Identification of a new, abundant superfamily of mammalian LTR-transposons

A new superfamily of mammalian transposable genetic elements is described with an estimated 40,000 to 100,000 members in both primate and rodent genomes. Sequences known before as MT, ORR-1, MstII, MER15 and MER18 are shown to represent (part of) the long terminal repeats of retrotransposon-like elements related to THE1 in humans. These transposons have structural similarities to retroviruses. However, the putative product of a 1350 base pair open reading frame detected in the consensus internal sequence of THE1 does not resemble retroviral proteins. The elements are named 'Mammalian apparent LTR-retrotransposons' (MaLRs). The internal sequence is usually found to be excised. Their presence in rodents, artiodactyls, lagomorphs, and primates, the divergence of the individual elements from their consensus, and the existence of a probably orthologous element in mouse and man suggest that the first MaLRs were distributed before the radiation of eutherian mammals 80-100 million years ago. MaLRs may prove to be very helpful in determining the evolutionary branching pattern of mammalian orders and suborders.

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

We provide here a list of 221 P450 genes and 12 putative pseudogenes that have been characterized as of December 14, 1992. These genes have been described in 31 eukaryotes (including 11 mammalian and 3 plant species) and 11 prokaryotes. Of 36 gene families so far described, 12 families exist in all mammals examined to date. These 12 families comprise 22 mammalian subfamilies, of which 17 and 15 have been mapped in the human and mouse genome, respectively. To date, each subfamily appears to represent a cluster of tightly linked genes. This revision supersedes the previous updates [Nebert et al., DNA 6, 1-11, 1987; Nebert et al., DNA 8, 1-13, 1989; Nebert et al., DNA Cell Biol. 10, 1-14 (1991)] in which a nomenclature system, based on divergent evolution of the superfamily, has been described. For the gene and cDNA, we recommend that the italicized root symbol "CYP" for human ("Cyp" for mouse), representing "cytochrome P450," be followed by an Arabic number denoting the family, a letter designating the subfamily (when two or more exist), and an Arabic numeral representing the individual gene within the subfamily. A hyphen should precede the final number in mouse genes. "P" ("p" in mouse) after the gene number denotes a pseudogene. If a gene is the sole member of a family, the subfamily letter and gene number need not be included. We suggest that the human nomenclature system be used for all species other than mouse. The mRNA and enzyme in all species (including mouse) should include all capital letters, without italics or hyphens. This nomenclature system is identical to that proposed in our 1991 update. Also included in this update is a listing of available data base accession numbers for P450 DNA and protein sequences. We also discuss the likelihood that this ancient gene superfamily has existed for more than 3.5 billion years, and that the rate of P450 gene evolution appears to be quite nonlinear. Finally, we describe P450 genes that have been detected by expressed sequence tags (ESTs), as well as the relationship between the P450 and the nitric oxide synthase gene superfamilies, as a likely example of convergent evolution.

Characterization of a rabbit gene encoding a clofibrate-inducible fatty acid omega-hydroxylase: CYP4A6

CYP4A6 mRNAs are induced in the rabbit liver and kidney following treatment with the antihyperlipidemic drug clofibrate. As a first step toward the elucidation of the mechanism controlling the induction of this and other CYP4A genes by clofibrate and other peroxisome proliferators, we have cloned and characterized the CYP4A6 gene. Genomic DNA containing the first 12 exons encoding CYP4A6 was isolated as three recombinant lambda phage, two of which were overlapping. The sequence of more than 1000 bp of the 5' upstream region as well as of the first 12 exons has been determined. These 12 exons encode all but approximately 80 bp at the 3' terminus of CYP4A6. Intron/exon junctions within the coding region of the gene are conserved relative to the rat CYP4A1 and CYP4A2 genes. Primer extension analysis indicates that transcription is initiated 33 bp upstream of the start codon. The CYP4A6 promoter region, like that of the rat CYP4A1 and CYP4A2 genes, does not contain a consensus TATA box. However, a consensus Sp1 recognition element is apparent at -46 bp upstream of the transcription start site. In addition, a sequence related to one of two regulatory elements that control the induction of the rat acyl-CoA oxidase gene by ciprofibrate is present upstream of the CYP4A6 promoter.

Characterization of a cytochrome P450 from di(2-ethylhexyl) phthalate-treated rats which hydroxylates fatty acids

A cytochrome P450 was purified from liver microsomes of rats treated with di(2-ethylhexyl) phthalate (DEHP). DEHP is a member of a group of structurally diverse compounds which have been classified as peroxisome proliferators and are inducers of cytochromes P450 which hydroxylate lauric acid and other fatty acids. The P450 isolated from DEHP-treated rats (P450DEHP) was observed to have a Mr value of 51 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and a maximum absorbance of 452 nm in its reduced carbon monoxide bound state. The amino terminal residue for P450DEHP was alanine and an 18-amino acid segment at the N-terminal region was identified. The N-terminal amino acid for the P450 4A1 from clofibrate-treated rats is methionine and alignment of the N-terminal segment of the P450DEHP with P450 4A1 indicated that the first four amino acids were absent. There were two amino acid differences between the two P450s in this 18-amino acid segment; in P450DEHP an alanine and a phenylalanine were substituted for serines in P450 4A1. The P450DEHP was found to catalyze the hydroxylation of several saturated fatty acids, having the highest turnover activity with laurate (82.1 nmol 12-OH-laurate formed/min/nmol P450). Myristate, palmitate, and stearate were also metabolized but at decreasing rates. Cytochrome b5 stimulated laurate 12-hydroxylation 10-fold in a reconstituted system. Laurate was not metabolized at its 11-carbon atom; however, the longer chain length fatty acids were metabolized at the (omega-1)-carbon atom in addition to the omega-carbon atom. A polyclonal antibody to the P450DEHP recognized three protein bands in liver microsomes from control and DEHP-treated rats on Western blot analysis, but only two protein bands from phenobarbital-treated rats.

The mouse peroxisome proliferator activated receptor recognizes a response element in the 5' flanking sequence of the rat acyl CoA oxidase gene

Peroxisome proliferators are a diverse group of chemicals, including several hypolipidaemic drugs, that activate a nuclear hormone receptor termed the peroxisome proliferator activated receptor (PPAR). The peroxisomal enzyme acyl CoA oxidase (ACO) is the most widely used marker of peroxisome proliferator action. We have examined the 5' flanking region of the rat ACO gene for sequences that mediate the transcriptional effect of peroxisome proliferators and have identified an element located 570 bp upstream of the ACO gene that confers responsiveness to the hypolipidaemic peroxisome proliferator Wy-14,643. This peroxisome proliferator response element (PPRE) contains a direct repeat of the sequence motifs TGACCT and TGTCCT and binds PPAR. These data therefore indicate an important role of PPAR in mediating the action of peroxisome proliferators including the induction of ACO.

Purification and NH2-terminal amino acid sequences of human and rat kidney fatty acid omega-hydroxylases

A cytochrome P-450 (P-450), designated P-450HK omega, has been isolated and purified from human kidney microsomes to a specific content of 13 nmoles of P-450/mg of protein. P-450HK omega showed an apparent molecular weight of 52,000 on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Absolute spectra of the oxidized form indicated that this P-450 was largely in the low-spin state and partly in the high-spin state. It catalyzed the omega- and (omega-1)-hydroxylation of fatty acids such as laurate, myristate, and palmitate, with no activity toward prostaglandin A1, benzphetamine, 7-ethoxycoumarin, or 7-ethoxyresorufin. The first 35 NH2-terminal amino acid sequence of P-450HK omega had about 70% homology with those of rabbit kidney fatty acid omega-hydroxylases of the P-450 IVA gene subfamily, P-450ka-1, P-450ka-2, and P-450kd, except for four undetermined residues. Moreover, Western blot and immuno-inhibition studies showed that P-450HK omega reacted with an antibody against the rabbit kidney fatty acid omega-hydroxylase. The results suggest that P-450HK omega is a member of the same P-450 gene family (IVA subfamily) as the rabbit enzymes. In addition, the terminal sequence of P-450HK omega also showed 54% homology with that of P-450k-2, a fatty acid omega-hydroxylase from rat kidney microsomes. To our knowledge, this is the first time that a P-450 specific for fatty acid omega-hydroxylase activity has been isolated to homogeneity from human tissues.

Induction of omega-oxidation of monocarboxylic acids in rats by acetylsalicylic acid

The accumulation of dicarboxylic acids, particularly long chain, is a prominent feature of Reye's syndrome and diseases of peroxisomal metabolism. We assessed the omega-oxidation of a spectrum of fatty acids in rats and asked whether pretreatment of rats with aspirin, which is known to predispose children to Reye's syndrome, would affect omega-oxidation of long chain fatty acids. We found that aspirin increased liver free fatty acids and increased the capacity for omega-oxidation three- to sevenfold. Omega-oxidation of long chain substrate was stimulated to a greater degree than medium chain substrate and was apparent within one day of treatment, at serum aspirin concentrations below the therapeutic range in humans. The apparent Km for lauric acid was 0.9 microM and 12 microM for palmitate. We also found a difference in the storage stability of activity toward medium and long chain substrate. Saturating concentrations of palmitate had no effect on the formation of dodecanedioic acid, whereas laurate decreased but never eliminated the omega-oxidation of palmitate. 97% of the total laurate omega-oxidative activity recovered was found in the microsomes, but 32% of palmitate omega-oxidative activity was present in the cytosol. These results demonstrate that aspirin is a potent stimulator of omega-oxidation and suggest that there may be multiple enzymes for omega-oxidation with overlapping substrate specificity.

A novel rat hepatic clofibrate-inducible cytochrome P450 that is not a lauric acid hydroxylase

2-Methoxy-6-[1-methylethyl]naphthalene (MMEN) was hydroxylated in an NADPH-dependent manner to the (omega-1)-alcohol and the (R)-omega- and (S)-omega-alcohols by rat hepatic microsomes. (S)-omega-Hydroxylation was selectively induced 7-fold by clofibrate treatment. Phenobarbital, 3-methyl-cholanthrene, dexamethasone, cholestyramine, and MMEN did not induce this activity to the same extent. Incubation of the racemic omega-alcohols with microsomes isolated from rats resulted in a greater rate of degradation of the (S)- than the (R)-omega-alcohol confirming (S)-omega-hydroxylation to be an initial catalytic event. MMEN and lauric acid were not competitive inhibitors of each other in microsomes from clofibrate-treated rats, indicating the (S)-omega-MMEN hydroxylase to be a different enzyme from the characterized clofibrate-inducible lauric acid hydroxylases, CYP4A1 and CYP4A3. This was confirmed by the observations that (1) lauric acid hydroxylation was inhibited by 0.02% Tween 20 or Tween 80 and 25 microM capric or myristic acids, whereas omega-MMEN hydroxylation was not, (2) omega-MMEN hydroxylation was inhibited by ketoconazole, cholesterol and acetone, whereas lauric acid hydroxylation was not, and (3) CYP4A1 and CYP4A3 expressed in Hep G2 cells did not catalyze MMEN hydroxylation. Microsomes from the lungs of rabbits treated with progesterone and kidney of untreated rats did not support selective (S)-omega-MMEN hydroxylation, indicating that this activity is not associated with CYP4A4 or CYP4A2, respectively. Leukotriene B4 (LTB4) hepatic microsomal hydroxylation was not inhibited by MMEN and microsomes from human neutrophils did not support the reaction. These data identify a hitherto uncharacterized cytochrome P450 which is selectively induced by clofibrate and does not catalyze the omega-hydroxylation of the fatty acids or prostaglandins investigated. It is proposed that the enzyme catalyzing the selective (S)-omega-hydroxylation of MMEN is a novel rat P450 and that it is either a new member of the CYP4 family or a clofibrate-inducible P450 from another gene family.

Effects of ethanol and clofibrate on expression of cytochrome P-450 enzymes and epoxide hydrolase in cultures and cocultures of rat hepatocytes

Cultured and cocultured rat hepatocytes were used to study the effects of ethanol and clofibrate on cytochrome P-450 (P-450) enzymes and epoxide hydrolase. We showed that in the presence of ethanol, clofibrate or both compounds, rat hepatocytes were able to express, after 3 days of pure culture, quantitatively and qualitatively reasonable levels of most cytochrome P-450 enzymes and epoxide hydrolase, compared to freshly isolated hepatocytes. However, ethanol induced the P-450IA subfamily, and clofibrate the P-450-IVA subfamily. In cocultures, after 6 days, most P-450 enzymes were still expressed while P-450IIC11 was completely lost. Ethanol and clofibrate had the same effect as in pure culture. These results show, by modifying culture medium conditions and cell-cell interactions, that it is possible to maintain reasonable xenobiotic-metabolizing-enzyme expression; however, these conditions have to be improved in order to preserve better P-450 expression. The mechanism of these effects and the inducibility of these systems remain to be elucidated by a study at molecular level.

A gene structure of testosterone 6 beta-hydroxylase (P450IIIA)

Genomic clones of a rat testosterone 6 beta-hydroxylase have been isolated and characterized as the first gene (P450/6 beta A) among P450IIIA subfamily. This gene spans about 25Kb and consists of 13 exons, which is the largest number of exons among cytochrome P-450 genes reported previously. The nucleotide sequence of the exon region showed high similarity to those of P450PCN2 and P450PCN1 cDNA (Gonzalez, F.J. et al. (1987) Mol. Cell. Biol. 2969-2974), but several replacements and deletions of nucleotide were found between the P450/6 beta A gene and both cDNAs, indicating the existence of multiple P450IIIA genes in rats.

Cytochrome P450 family 4 in a cockroach: molecular cloning and regulation by regulation by hypertrehalosemic hormone

Hypertrehalosemic hormone (a carbohydrate-mobilizing neuroendocrine decapeptide) and starvation markedly increased levels of a cockroach (Blaberus discoidalis) fat body cytochrome P450 message. The gene represented by the cloned P450 cDNA has been named CYP4C1 (cytochrome P450 family 4, subfamily C, gene 1), a newly identified member of the ubiquitous cytochrome P450 monooxygenase gene superfamily. Blaberus CYP4C1 (511 amino acids, Mr = 58,485) has a hydrophobic NH2 terminus and a sequence near the COOH terminus that is homologous to the cysteine-containing heme-binding region definitive of cytochromes P450. The cockroach sequence is 32-36% identical to mammalian family 4A and 4B enzymes. It contains a 13-residue sequence characteristic of family 4 but not other P450s. This study suggests that CYP4C1 is hormonally regulated in association with energy substrate mobilization and supports the idea that family 4 is an old and widespread gene family.

Localization and differential induction of cytochrome P450IVA and acyl-CoA oxidase in rat liver

The peroxisome proliferators are structurally diverse chemicals which induce hyperplasia, hypertrophy and the proliferation of peroxisomes in the rodent liver. Cytochrome P450IVA1 and peroxisomal enzymes, such as acyl-CoA oxidase, are induced and are early markers of treatment with peroxisome proliferators. In this study, rats were dosed intraperitoneally with the potent peroxisome proliferator methylclofenapate and the hepatic induction response was studied. There was no significant change in the enzyme activities of laurate hydroxylase (cytochrome P450IVA1) or acyl-CoA oxidase in the first 8 h after treatment, but the activities had doubled at 24 h, suggesting that these enzymes are not involved in the mediation of early events in peroxisome proliferation. Hepatic cytochrome P450IVA1 mRNA was significantly increased at 6 and 8 h after treatment, rising to 15-fold above control values at 30 h. In contrast, acyl-CoA oxidase mRNA showed no significant change in the first 8 h, but increased to 13-fold above control values at 24 and 30 h, thereby demonstrating different kinetics of induction of the two mRNAs. In order to determine whether cytochrome P450IVA1 and peroxisomal enzymes were included in the same cells, rats were treated daily with sub-maximal (2 or 5 mg/kg) and maximal (25 mg/kg) inducing doses of methylclofenapate for 4 days. The lobular distribution of induced proteins was determined immunocytochemically with antibodies raised against P450IVA1 and acyl-CoA oxidase. Livers from control animals showed minimal staining for both proteins. However, in the livers of animals treated with 2 or 5 mg of methylclofenapate/kg, both acyl-CoA and P450IVA immunostaining was increased, mainly in the centrilobular area. Immunostaining of serial sections revealed that these proteins were induced in the same region of the lobule. A maximal inducing dose of methylclofenapate (25 mg/kg) caused panlobular induction of both proteins. The results demonstrate that these proteins are induced in a dose-dependent manner in the same, spatially distinct, sensitive region of the liver lobule.

Isolation of preferentially expressed genes in the kidneys of hypertensive rats

By differential hybridization, three complementary DNAs designated as S3, S2, and SA were isolated, and the corresponding messenger RNAs (mRNAs) were differentially expressed between the kidneys of spontaneously hypertensive rats (SHR) and normotensive Wistar-Kyoto (WKY) rats. S3 is identical to cytochrome P450 IV A2. SA encoded a protein of 546 amino acid residues, and its carboxyl terminal region had a slight homology to luciferase. No homologous sequence has been reported in S2 sequences. S3 mRNA was about four times more abundantly expressed in the kidneys of 28-day-old SHR than in those of age-matched WKY rats, but there was no difference at age 16 weeks. A low NaCl diet positively modulated the expression of the S3 gene. S2 mRNA was almost undetectable in the kidneys of 28-day-old WKY rats but was clearly detected in those of age-matched SHR. The expression level of S2 mRNA in the livers of 16-week-old SHR was about five times higher than that of age-matched WKY rats. The expression of S2 mRNA in the livers was modulated by dietary NaCl and captopril. SA mRNA was more than 10 times more abundantly expressed in the kidneys of SHR than in those of WKY rats from age 4 weeks. With the administration of captopril, the expressions of SA mRNA in the livers of SHR were positively modulated. Because these three genes are not only differentially expressed between SHR and WKY rats but also related to sodium metabolism or blood pressure control, the identification of these genes may provide important probes to examine the mechanisms of hypertension.

The P450 superfamily: update on new sequences, gene mapping, and recommended nomenclature

We provide here a list of 154 P450 genes and seven putative pseudogenes that have been characterized as of October 20, 1990. These genes have been described in a total of 23 eukaryotes (including nine mammalian and one plant species) and six prokaryotes. Of 27 gene families so far described, 10 exist in all mammals. These 10 families comprise 18 subfamilies, of which 16 and 14 have been mapped in the human and mouse genomes, respectively; to date, each subfamily appears to represent a cluster of tightly linked genes. We propose here a modest revision of the initially proposed (Nebert et al., DNA 6, 1-11, 1987) and updated (Nebert et al., DNA 8, 1-13, 1989) nomenclature system based on evolution of the superfamily. For the gene we recommend that the italicized root symbol CYP for human (Cyp for mouse), representing cytochrome P450, be followed by an Arabic number denoting the family, a letter designating the subfamily (when two or more exist), and an Arabic numeral representing the individual gene within the subfamily. A hyphen should precede the final number in mouse genes. We suggest that the human nomenclature system be used for other species. This system is consistent with our earlier proposed nomenclature for P450 of all eukaryotes and prokaryotes, except that we are discouraging the future use of cumbersome Roman numerals.

On the mechanism of induction of microsomal cytochrome P450IVA1 and peroxisome proliferation in rat liver by clofibrate

The time course of induction of microsomal and peroxisomal lipid-metabolizing enzymes in male Wistar rat liver has been investigated following a single i.p. dose of clofibrate (250 mg/kg). The microsomal enzyme, cytochrome P450IVA1, demonstrated a biphasic response to sodium clofibrate administration, the biphasic response consisting of an initial small response, peaking at approximately 30 min post-dose and returning to near baseline values after 2 hr. A second major induction of cytochrome P450IVA1 occurred between 18 and 24 hr post-dose. This biphasic phenomenon for cytochrome P450IVA1 was observed for the enzyme activity (lauric acid hydroxylase), immunodetectable protein (using a specific ELISA method) and at the mRNA level (using a 2.1 kilobase cytochrome P450IVA1 cDNA probe). In contrast, peroxisomal fatty acid beta-oxidation enzymes responded in a monophasic manner to clofibrate administration, peaking approximately 24 hr post-dose. Accordingly, microsomal cytochrome P450IVA1 was induced before the peroxisomal enzymes of fatty acid beta-oxidation. The effect of cycloheximide on the induction of peroxisome proliferation by clofibrate was additionally investigated. The prior administration of cycloheximide to Wistar rats ablated the clofibrate-dependent induction of both cytochrome P450IVA1 and peroxisomal-dependent lipid metabolism and also blocked the corresponding synthesis of enzyme proteins. Cycloheximide additionally inhibited the clofibrate-dependent increase in peroxisomal acyl-CoA oxidase mRNA, but was without effect on the induced cytochrome P450IVA1 mRNA levels, indicating a protein or enzyme dependency for the phenomenon of peroxisome proliferation. Taken collectively, our data strongly argues that the regulation of microsomal cytochrome P450IVA1 and peroxisomal fatty acid beta-oxidation enzymes are closely related, possibly through the initial, clofibrate-dependent regulation of cytochrome P450IVA1.

Cloning and characterization of a novel member of the cytochrome P450 subfamily IVA in rat prostate

To isolate cDNAs for forms of cytochrome P450 from rat prostate, a lambda gt11 cDNA library from this tissue was screened with a mixture of oligonucleotide probes directed against the conserved heme binding region of different P450 isozymes. A cDNA clone (PP1) encoding a part of a novel form of cytochrome P450 was isolated and the deduced amino acid sequence showed 76% identity with cytochrome P450 IVA1, indicating that PP1 is a member of the same subfamily. Northern blot analysis of total RNA from prostates of untreated rats revealed that two mRNAs of approximately 2.8 and 2.2 kb hybridize to PP1. The level of mRNA was induced fivefold above the level in intact animals by androgen treatment of castrated rats. Analysis of poly(A)+RNA levels in different tissues on Northern blots showed high constitutive expression of PP1 in the kidney, but no signal was detectable with RNA from liver; a weak signal was detected in the retina. Subsequent screening of a rat kidney cDNA library led to the isolation of the full-length clone KP1, which differs from Pp1 only in three nucleotide positions. KP1 is 1,957 bp long and contains a 1,527-bp-long open reading frame encoding a protein of 508 amino acids. In situ hybridization of rat kidney sections with PP1 showed that this P450 form is expressed in the outer stripe of the outer medulla, indicating its localization in the proximal tubules.

Identification of a new P450 expressed in human lung: complete cDNA sequence, cDNA-directed expression, and chromosome mapping

A cDNA coding for a P450 expressed in human lung was isolated from a lambda gt11 library constructed from human lung mRNA using a cDNA probe to rat P450 IVA1. The cDNA-deduced amino acid sequence of this P450, designated IVB1, consisted of 511 amino acids and had a calculated molecular weight of 59,558. The IVB1 amino acid sequence bore 51%, 53%, and 52% similarities to rat IVA1, IVA2, and rabbit P450p-2, respectively. Comparison of the primary amino acid sequence of human IVB1 with rat IVA and rabbit p-2 P450 sequences revealed a region of absolute sequence identity of 17 amino acids between residues 304 and 320. However, the functional significance of this conserved sequence is unknown. Human IVB1 also appears to be related to P450 isozyme 5 that has been extensively characterized in rabbits. The IVB1 cDNA was inserted into a vaccinia virus expression vector and the enzyme expressed in human cell lines. The expressed enzyme had an absorption spectrum with a lambda max at 450 nm when reduced and complexed with carbon monoxide, typical of other cytochrome P450s. Unlike rabbit P450 isozyme 5, however, human IVB1 was unable to activate the promutagen 2-aminofluorene. Human lung microsomal P450s were also unable to metabolize this compound despite the presence of IVB1 mRNA in three out of four human lungs analyzed. In contrast to its expression in lung, IVB1 mRNA was undetectable in livers from 14 individuals, including those from which the lungs were derived. IVB1-related mRNA was also expressed in rat lung and was undetectable in untreated rat liver.(ABSTRACT TRUNCATED AT 250 WORDS)

The rat clofibrate-inducible CYP4A subfamily. II. cDNA sequence of IVA3, mapping of the Cyp4a locus to mouse chromosome 4, and coordinate and tissue-specific regulation of the CYP4A genes

A novel P450 cDNA, designated IVA3, was isolated from a lambda gt11 cDNA library from clofibrate-treated rat liver by screening with the lauric acid omega-hydroxylase, IVA1, cDNA probe. This cDNA encoded a protein with 507 amino acids and a calculated Mr of 58,239. The IVA3 cDNA shared 65% and 97% nucleotide and 72% and 96% DNA-deduced amino acid sequence similarities with IVA1 and IVA2, respectively. The CYP4A gene family, designated the Cyp4a locus, was mapped to mouse chromosome 4 using a panel of mouse-hamster somatic cell hybrids. Levels of the IVA mRNAs were analyzed in rat tissues and cell cultures after treatment with the hypolipidemic drug clofibrate. The IVA1, IVA2, and IVA3 mRNAs were present at very low levels in the livers of untreated rats and markedly induced in rats treated with clofibrate. Dose-response and time-course studies revealed that all three genes were regulated coordinately in liver. In contrast to the coordinate induction in liver, only the CYP4A3 gene was induced in the rat hepatoma cell line McA-RH7777. In the kidney, IVA1 and IVA3 mRNAs were present at low levels and were induced by clofibrate in a manner similar to that in liver. In contrast, the IVA2 mRNA was expressed in the kidney of untreated rats at a level similar to that of the maximally induced IVA2 mRNA in liver. These data indicate that the CYP4A1, CYP4A2, and CYP4A3 genes are regulated coordinately in liver while only CYP4A2 is activated constitutively in kidney.