Rapid Birth–Death Evolution Specific to Xenobiotic Cytochrome P450 Genes in Vertebrates

Genes vary greatly in their long-term phylogenetic stability and there exists no general explanation for these differences. The cytochrome P450 (CYP450) gene superfamily is well suited to investigating this problem because it is large and well studied, and it includes both stable and unstable genes. CYP450 genes encode oxidase enzymes that function in metabolism of endogenous small molecules and in detoxification of xenobiotic compounds. Both types of enzymes have been intensively studied. My analysis of ten nearly complete vertebrate genomes indicates that each genome contains 50–80 CYP450 genes, which are about evenly divided between phylogenetically stable and unstable genes. The stable genes are characterized by few or no gene duplications or losses in species ranging from bony fish to mammals, whereas unstable genes are characterized by frequent gene duplications and losses (birth–death evolution) even among closely related species. All of the CYP450 genes that encode enzymes with known endogenous substrates are phylogenetically stable. In contrast, most of the unstable genes encode enzymes that function as xenobiotic detoxifiers. Nearly all unstable CYP450 genes in the mouse and human genomes reside in a few dense gene clusters, forming unstable gene islands that arose by recurrent local gene duplication. Evidence for positive selection in amino acid sequence is restricted to these unstable CYP450 genes, and sites of selection are associated with substrate-binding regions in the protein structure. These results can be explained by a general model in which phylogenetically stable genes have core functions in development and physiology, whereas unstable genes have accessory functions associated with unstable environmental interactions such as toxin and pathogen exposure. Unstable gene islands in vertebrates share some functional properties with bacterial genomic islands, though they arise by local gene duplication rather than horizontal gene transfer.     

Genetics of cytochrome P450 in two insecticide-resistant strains of the housefly,Musca domestica L.

A susceptible strain of Musca domestica containing visible mutant markers on chromosomes II, III, and V was crossed with multiresistant R-Fc and R-diazinon strains. F₁ flies were backcrossed to the mutant parent, resultant progenies were isolated according to phenotype, and substrains were established. The level of resistance to diazinon, aldrin epoxidase activity, and cytochrome P450 difference spectra of microsomes from each substrain were measured. Titers of cytochrome P450, measured as CO spectra, as well as type I, type II, and type III cytochrome P450 substrate difference spectra were compared in microsomal preparations obtained from phenotypes containing vatious resistant chromosome combinations. In both resistant strains, high levels of cytochrome P450 were controlled by a gene(s) on chromosome II. In R-diazinon, qualitative spectral changes were also controlled by chromosome II, whereas in R-Fc both chromosomes II and V contributed to qualitative changes in cytochrome P450. Both quantitative and qualitative characteristics were intermediate in heterozygous flies, suggesting incomplete dominance for their inheritance. Findings are discussed in relation to known genetics of microsomal resistance to insecticides.     

Musca domestica L D.

Field strains of the house fly (Musca domestica L. Diptera: Muscidae) were collected in April and September 2002 from cow farms (Antalya, Izmir) and garbage dumps (Adana, Ankara, Istanbul, Sanliurfa) in Turkey. The resistance levels of first to fifth generation offspring were evaluated against six insecticides (cypermethrin, cyphenothrin, deltamethrin, permethrin, resmethrin, fenitrothion). Resistance levels for pyrethroid group insecticides ranged from 23.27 (permethrin-Istanbul fall strain) to 633.09 (cypermethrin-Izmir spring strain) and for fenitrothion ranged from 5.78 (Istanbul fall strain) to 51.04 (Antalya spring strain). Our results showed that pyrethroid resistance was high and changed from spring to fall in relation to usage and application frequencies of these compounds at the study sites. Although fenitrothion resistance levels were determined to be lower than pyrethroids, these levels were still high and led to control failure. Flies from cow farms were more resistant than those from garbage dumps, but resistance levels for Sanliurfa and Adana strains were also high in relation to usage of different insecticides for agricultural purposes. Although resistance levels against different pyrethroids decreased from spring to fall, these levels still indicated the presence of a strong selective pressure on the populations.     

Kynurenine hydroxylase in Musca domestica L.

1. Kynurenine hydroxylase activity was assayed in extracts of Musca domestica L. 2. During the life cycle of the fly, there is a peak of enzyme activity shortly after pupation. 3. Eye-color mutants, rb2, rb1; rb2 and cm, show reduced activity during pupal stages. 4. An ocra mutant lacks this activity. 5. The rb1 and rb2 mutations were separated from the rb1; rb2 strain. From measurements of the xanthommatin content, the rb1 mutation was suggested to enhance the expression of the rb2 gene.     

Cytochrome P-450 difference spectra of microsomes from several insecticide-resistant and -susceptible strains of the housefly, Musca domestica L

Cytochrome P-450 difference spectra were obtained with microsomes prepared from several strains of the housefly, Musca domestica, that were susceptible or resistant to insecticides. Based on Type I, Type II and Type III spectral interactions, both quantitative and qualitative variations are apparent among strains. Cytochrome P-450 from Fc and dimethoate strains had spectral characteristics which were most different from those of susceptible strains. No correlation could be made between strains having known high mixed-function oxidase activity and any single cytochrome P-450 spectral characteristic.     

Cytochrome P450 Genes from the Sacred Lotus Genome

Cytochrome P450 monooxygenases (P450s) in the sacred lotus (Nelumbo nucifera) genome have been identified and named according to systematic P450 nomenclatures. Comparisons of these sequences with those in the papaya and grape CYPomes have indicated that gene blooms exist in the CYP89, CYP94, CYP96 and CYP714 families and that less dramatic expansions exist in the CYP71 and CYP72 families. Expansions in the CYP94 and CYP96 families may be associated with generation of the extremely hydrophobic leaf surfaces associated with the “lotus effect” in this water-adapted species, since these families are known to hydroxylate fatty acids and alkanes in the wax biosynthetic pathways of other plant species. Evolution of the CYP719 and CYP80 families may be associated with production of a number of benzylisoquinoline and aporphine alkaloids. Structures for anonaine and roemerine, two of the most abundant aporphine alkaloids in lotus leaves and seeds, contain methylenedioxy bridges that are known to be generated by members of the CYP719 family. With only one CYP719A22 gene existing in the lotus genome, it is likely that it is involved in making aporphine alkaloids. The fact that CYP719 has not previously been seen in angiosperm phylogeny below the order of Ranunculales suggests that its presence in lotus (in the Proteales) presents an evolutionary terminus prior to its loss in more recent eudicot species. With several CYP80 family genes existing in the lotus genome, there are multiple candidates for those involved in conducting benzylisoquinoline alkaloid synthesis.     

细胞色素P450基因及其在植物改良中的应用

细胞色素P450是一类含血红素的氧化还原酶类,它参与多种生化反应,在防御生物免受病虫害及逆境胁迫等方面具有重要作用。生物基因组序列分析表明,它是一个基因超家族。许多细胞色素P450基因已被鉴定和克隆,并应用于植物遗传改良;在转基因培育多抗性植物、创造植物雄性不育系,提高植物降解化学农药残留等污染物的能力和有效生产具有药用价值的化合物等方面已取得可喜进展,显示出广阔的应用前景。 Abstract:Cytochrome P450s are heme-containing mixed-function oxidases,involving in lots of biochemical reactions.They play an important role in preventing plants from pathogen and insect attacks and environmental stress.Sequence analysis of genomes has revealed that P450 is a gene super-family.Many cytochrome P450s have been characterized and cloned.Some of them have been used in plant genetic improvement.A great progress has been made in using these P450 genes to create the transgenic plants with multiple resistances,male sterility,higher capability to dissolve toxic chemicals and pollutants and effective productivity of high valuable compounds,indicating P450 genes have a broad prospect with great potential application.     

植物细胞色素P450基因的异源表达系统研究进展

细胞色素P450氧化酶是一类具有多种催化功能含血红素的氧化酶系。由于参与多种类型的氧化反应,在植物生命活动中有重要功能,其研究一直受到重视。自1990年第一个植物P450基因成功克隆以来,到2002年年底,已有600多个P450基因被克隆,有100多个基因在细菌、酵母、杆状病毒昆虫细胞等异源表达系统中成功表达并鉴定了功能。拟对植物P450的大肠杆菌、酵母、杆状病毒昆虫细胞表达系统的特点进行比较,对在各表达系统中成功表达并进行了功能鉴定的植物P450进行归纳,并对目前植物P450异源表达的现状和应用进行概述。     

不同杀虫剂处理对赤拟谷盗P450基因诱导表达特性影响

害虫细胞色素P450基因可被杀虫剂迅速诱导,然而当前对不同杀虫剂处理下赤拟谷盗P450基因诱导表达特性的研究较少。本研究首先通过序列比对选取了来自不同家族的8个赤拟谷盗P450基因CYP4G7、CYP4Q4、CYP4BR3、CYP12H1、CYP6BK11、CYP9D4、CYP9Z5和CYP345A1,然后采用四种不同杀虫剂氯氰菊酯、氟氯氰菊酯、氯菊酯和吡虫啉对赤拟谷盗20 d幼虫进行生物测定,再根据生测结果以四个药剂亚致死剂量分别处理幼虫,并采用荧光定量PCR分析8个P450基因的表达特性。结果表明,CYP4G7和CYP345A1可以分别被氯氰菊酯(分别上调1.97倍和2.06倍)、氟氯氰菊酯(2.00倍和2.03倍)和氯菊酯(1.73倍和1.81倍)显著诱导,而CYP4BR3和CYP345A1可以被吡虫啉(分别上调1.99倍和1.93倍)显著诱导。本研究结果表明赤拟谷盗P450基因的显著诱导与基因家族类型以及农药品种有关。     

Comparison of Cytochrome P450 Genes from Six Plant Genomes

Plants depend on cytochrome P450 (CYP) enzymes for nearly every aspect of their biology. In several sequenced angiosperms, CYP genes constitute up to 1% of the protein coding genes. The angiosperm sequence diversity is encapsulated by 59 CYP families, of which 52 families form a widely distributed core set. In the 20 years since the first plant P450 was sequenced, 3,387 P450 sequences have been identified and annotated in plant databases. As no new angiosperm CYP families have been discovered since 2004, it is now apparent that the sampling of CYP diversity is beginning to plateau. This review presents a comparison of 1,415 cytochrome P450 sequences from the six sequenced genomes of Vitis vinifera (grape), Carica papaya (papaya), Populus trichocarpa (poplar), Oryza sativa (rice), Arabidopsis thaliana (Arabidopsis or mouse ear’s cress) and Physcomitrella patens (moss). An evolutionary analysis is presented that tracks land plant P450 innovation over time from the most ancient and conserved sequences to the newest dicot-specific families. The earliest or oldest P450 families are devoted to the essential biochemistries of sterol and carotenoid synthesis. The next evolutionary radiation of P450 families appears to mediate crucial adaptations to a land environment. And, the newest CYP families appear to have driven the diversity of angiosperms in mediating the synthesis of pigments, odorants, flavors and order-/genus-specific secondary metabolites. Family-by-family comparisons allow the visualization of plant genome plasticity by whole genome duplications and massive gene family expansions via tandem duplications. Molecular evidence of human domestication is quite apparent in the repeated P450 gene duplications occurring in the grape genome.     

Cytochrome P450 pattern revision.

The pattern suggested for the structure-function superfamily of cytochromes P450 is composed by combining the conserved amino acid motifs. The sizes of P450 cytochromes were estimated according to their length. The empirical coefficients reflecting the peculiarities of the primary structure of these enzymes are calculated. We propose an approach for determining novel proteins sequences to the mentioned superfamily on the ground of the complex of these parameters. A number of the hypothetical proteins from the international databases is related to the cytochromes P450 by means of our pattern.     

Kinetic mechanism of cytochrome P450 reductase from the house fly (Musca domestica).

Recombinant house fly (Musca domestica) cytochrome P450 reductase has been purified by anion exchange and affinity chromatography. Steady-state kinetics of cytochrome c reductase activity revealed a random Bi-Bi mechanism with formation of a ternary P450 reductase-NADPH-electron acceptor complex as catalytic intermediate. NADP(H) binding is essential for fast hydride ion transfer to FAD, as well as for electron transfer from FMN to cytochrome c. Reduced cytochrome c had no effect on the enzyme activity, while NADP+ and 2'-AMP inhibited P450 reductase competitively with respect to NADPH and noncompetitively with respect to cytochrome c. The affinity of the P450 reductase to NADPH is 10 times higher than to NADP+ (Kd of 0.31 and 3.3 microM, respectively). Such an affinity change during catalysis could account for a +30 mV shift of the redox potential of FAD. Cys560 was substituted for Tyr by site-directed mutagenesis. This mutation decreased enzyme affinity to NADPH 35-fold by decreasing the bimolecular rate constant of nucleotide binding with no detectable effect on the kinetic mechanism. The affinity of the C560Y mutant enzyme to NADP+ decreased 9-fold compared to the wild-type enzyme, while the affinity to 2'-AMP was not significantly affected, suggesting that Cys560 is located in the nicotinamide binding site of the active, full-size enzyme in solution.     

Simultaneous purification of a cytochrome P-450 and cytochrome b5 from the house fly,Musca domestica L.

Cytochrome P-450, cytochrome b₅ and cytochrome P-450 reductase were purified from house fly abdomens using high performance liquid chromatography (HPLC). Using a new technique, cytochrome P-450 was separated from the bulk of other proteins after polyethylene glycol fractionation and hydrophobic interaction chromatography (HIC) using a phenyl-5PW column. This technique resulted in 91% recovery of the cytochrome P-450s in a single concentrated fraction that also contained the remaining cytochrome b₅ and cytochrome P-450 reductase activity. Further purification by anion exchange on a DEAE-5SW column resolved the cytochrome P-450s, cytochrome b₅ and cytochrome P-450 reductase into individual fractions. The ion exchange step yielded one fraction that contained a high specific content of P-450 (14.4 nmol/mg protein). This cytochrome P-450 fraction ran as a single band at 54.3 kDa in sodium dodecyl sulfate polyacrylamide (SDS-PAGE) gel electrophoresis and had a carboxy ferrocytochrome absorbance maximum at 447 nm.Further purification of the anion exchange cytochrome b₅ fraction, by C8 reverse phase HPLC, resulted in a cytochrome b₅ fraction with a specific content of 51.8 nmol/mg protein and an apparent molecular mass of 19.7 kDa by SDS-PAGE. The anion exchange HPLC fraction containing the cytochrome P-450 reductase activity was further purified by NADP-agarose affinity chromatography. This step yielded cytochrome P-450 reductase with an apparent molecular mass of 72 kDa.     

人细胞色素P450在大肠杆菌中的功能表达

研究人细胞色素P450（P450,CYP）在大肠杆菌中的功能表达对新药研发,临床药物治疗和药物早期ADME/T性质研究均有重要意义。异源表达人P450使用最多的宿主是大肠杆菌E.coli,然而要获得足量的有催化活性的P450仍是一个难题。结合作者近年研究,对异源表达的研究意义,P450在E.coli中功能表达的策略,高效表达的影响因素和共表达等方面做一评述,指出今后的研究应用方向。     

Expression of a Ripening-Related Avocado (Persea americana) Cytochrome P450 in Yeast

One of the mRNAs that accumulates during the ripening of avocado (Persea americana Mill. cv Hass) has been previously identified as a cytochrome P450 (P450) monooxygenase and the corresponding gene designated CYP71A1. In this report we demonstrate that during ripening the accumulation of antigenically detected CYP71A1 gene product (CYP71A1) correlates with increases in total P450 and two P450-dependent enzyme activities: para-chloro-N-methylaniline demethylase, and trans-cinnamic acid hydroxylase (tCAH). To determine whether both of these activities are derived from CYP71A1, we have expressed this protein in yeast (Saccharomyces cerevisiae) using a galactose-inducible yeast promoter. Following induction, the microsomal fraction of transformed yeast cells undergoes a large increase in P450 level, attributable almost exclusively to the plant CYP71A1 protein. These membranes exhibit NADPH-dependent para-chloro-N-methylaniline demethylase activity at a rate comparable to that in avocado microsomes but have no detectable tCAH. These results demonstrate both that the CYP71A1 protein is not a tCAH and that a plant P450 is fully functional upon heterologous expression in yeast. These findings also indicate that the heterologous P450 protein can interact with the yeast NADPH:P450 reductase to produce a functional complex.