The cytochrome P450 gene superfamily in Drosophila melanogaster: annotation, intron-exon organization and phylogeny

The cytochrome P450 gene superfamily is represented by 90 sequences in the Drosophila melanogaster genome. Of these 90 P450 sequences, 83 code for apparently functional genes whereas seven are apparent pseudogenes. More than half of the genes belong to only two families, CYP4 and CYP6. The CYP6 family is insect specific whereas the CYP4 family includes sequences from vertebrates. There are eight genes coding for mitochondrial P450s as deduced from their homology to CYP12A1 from the house fly. The genetic map of the distribution of D. melanogaster P450 genes shows (a) the absence of P450 genes on the chromosome 4 and Y, (b) more than half of the P450 genes are found on chromosome 2, and (c) the largest cluster contains nine genes. Sequence alignments were used to draw phylogenetic trees and to analyze the intron-exon organization of each functional P450 gene. Only five P450 genes are intronless. We found 57 unique intron positions, of which 23 were phase zero, 19 were phase one and 15 were phase two. There was a relatively good correlation between intron conservation and phylogenetic relationship between members of the P450 subfamilies. Although the function of many P450 proteins from vertebrates, fungi, plants and bacteria is known, only a single P450 from D. melanogaster, CYP6A2, has been functionally characterized. Gene organization appears to be a useful tool in the study of the regulation, the physiological role and the function of these P450s.     

Characterization of the CYP4A11 gene,a second CYP4A gene in humans

Comparison between the cDNA sequence of CYP4A11 and that deduced from a published genomic clone suggested the presence of an additional CYP4A gene in humans, CYP4A22. PCR amplification of genomic DNA yielded overlapping clones covering 13kb of genomic DNA and extending from 1003bp upstream from CYP4A11 translation initiation to 135bp upstream of the mRNA polyadenylation signal. Sequence and Southern blot analysis showed the presence in humans of two highly homologous CYP4A genes, CYP4A11 and CYP4A22. These two genes share 96% sequence identity and have similar intron/exon sizes and distribution. Short nucleotide insertions (< or =10bp) in introns 1, 3, 9, and 11, and deletions (< or =18bp) in introns 4, 6, and 11 differentiate the two genes. RT-PCR amplification of human kidney RNA followed by restriction fragment analysis showed that CYP4A11 is the predominant isoform expressed in kidney.     

The chimeric gene linked to glucocorticoid-suppressible hyperaldosteronism encodes a fused P-450 protein possessing aldosterone synthase activity.

Glucocorticoid-suppressible hyperaldosteronism (GSH) is one variety of primary aldosteronism with hypertension and is inherited in an autosomal dominant mode. A recent report has indicated that GSH is caused by a gene duplication arising from unequal crossing over between the two genes, CYP11B1 and CYP11B2, encoding P-450(11 beta) and P-450C18, respectively (Lifton et al. Nature (1992) 355, 262-265). The nucleotide sequence analysis in the present study has demonstrated that unequal crossing over in the chimeric gene formed by the gene duplication occurs within the region from the 3'-portion of exon 4 through the 5'-portion of intron 4 in Australian GSH patients. Namely, the chimeric gene encodes a fused P-450 protein consisting of the amino-terminal side of P-450(11 beta) (encoded by exons 1-4 of CYP11B1) and the carboxyl-terminal side of P-450C18 (encoded by exons 5-9 of CYP11B2). When a cDNA corresponding to the chimeric gene is transfected into COS-7 cells, the fused P-450 protein expressed in the mitochondria exhibits steroid 18-hydroxylase or aldosterone synthase activity. These results provide the molecular genetic basis for the characteristic biochemical phenotype of GSH patients.     

三种杀虫剂亚致死剂量对草地贪夜蛾细胞色素P450基因表达的影响

【目的】为明确杀虫剂亚致死剂量对草地贪夜蛾Spodoptera frugiperda细胞色素P450基因表达的影响。【方法】本研究采用叶片浸渍法测定了3种杀虫剂[氯虫苯甲酰胺、甲氨基阿维菌素苯甲酸盐和苏云金杆菌Bacillus thuringiensis(Bt)]对草地贪夜蛾2龄幼虫的毒力,以及通过实时荧光定量PCR(real-time quantitative PCR, RT-qPCR)技术测定了这3种杀虫剂亚致死剂量(LC_(10))处理后48 h时草地贪夜蛾2龄幼虫16个P450基因的表达量。【结果】氯虫苯甲酰胺、甲氨基阿维菌素苯甲酸盐和Bt对草地贪夜蛾2龄幼虫的LC_(10)值分别为0.931, 0.283和1 089.688 mg/L。2龄幼虫受LC_(10)氯虫苯甲酰胺胁迫后,13个P450基因(CYP4G75,CYP6AB12,CYP6B50,CYP321A7,CY321A8,CYP321A9,CYP321A10,CYP321B1,CYP337B5,CYP9A59,CYP9A58,CYP6AE44及CYP6AE43)表达上调,其中CYP6AE44表达量为对照的34.60倍;2龄幼虫受LC_(10)甲维盐胁迫后,11个P450基因(CYP4G75,CYP6AB12,CYP321A7,CY321A8,CYP321A9,CYP321A10,CYP321B1,CYP337B5,CYP9A58,CYP6AE44及CYP6AE43)表达上调,其中CYP321B1表达量为对照的28.70倍;2龄幼虫受LC_(10)Bt胁迫后,11个P450基因(CYP4G75,CYP6AB12,CYP6AN4,CYP321A7,CY321A8,CYP321A9,CYP321A10,CYP321B1,CYP337B5,CYP6AE44及CYP6AE43)表达上调,其中CYP6AE44表达量为对照的40.80倍。【结论】草地贪夜蛾2龄幼虫的多个P450基因受这3种杀虫剂亚致死剂量处理后表达上调,其中CYP4G75,CYP6AB12,CYP321A7,CY321A8,CYP321A9,CYP321A10,CYP321B1,CYP321B5,CYP6AE44及CYP6AE43均能被这3种杀虫剂诱导表达。     

Comparison of P450s from human and fugu: 420 million years of vertebrate P450 evolution

The fugu (pufferfish) genome has been sequenced, and a second genome assembly was released 17 May 2002. Exhaustive searches were made to identify all P450 genes and pseudogenes from the earlier release of 26 October 2001. P450 genes assembled as completely as possible from these data were used to do additional searches of the newer assembly and all P450 genes and pseudogenes in the available fugu sequence data have been identified, compared to human P450s, and assigned names. There are 54 P450 genes in fugu and 1 nearly intact pseudogene (CYP3A50P). CYP1A is missing much of its N-terminal half; however, 45 P450 genes are completely assembled. Eight others are lacking only one or two exons or less. CYP2X4 is known only from an EST. This may be a 55th P450 gene if it represents an accurate sequence. In addition to 2X4, there are 16 other pseudogene fragments or small pieces of P450 genes. At the P450 family level, 17 of 18 mammalian families are found in fugu. CYP39 is the only CYP family missing and it is not seen in any other fish sequence data either. The CYP2 family shows the largest degree of divergence. In the CYP2 family, only CYP2R1 and CYP2U1 are conserved as recognizable subfamilies across species. Intron-exon boundaries are largely preserved across 420 million years of evolution.     

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。     

Intron-exon organization and phylogeny in a large superfamily, the paralogous cytochrome P450 genes of Arabidopsis thaliana

The cytochrome P450 gene superfamily is represented by 80 genes in animal genomes and perhaps more than 300 genes in plant genomes. We analyzed about half of all Arabidopsis P450 genes, a very large dataset of truly paralogous genes. Sequence alignments were used to draw phylogenetic trees, and this information was compared with the intron-exon organization of each P450 gene. We found 60 unique intron positions, of which 37 were phase 0 introns. Our results confirm the polyphyletic origin of plant P450 genes. One group of these genes, the A-type P450s, are plant specific and characterized by a simple organization, with one highly conserved intron. Closely related A-type P450 genes are often clustered in the genome with as many as a dozen genes (e.g., of the CYP71 subfamily) on a short stretch of chromosome. The other P450 genes (non-A-type) form several distinct clades and are characterized by numerous introns. One such clade contains the two CYP51 genes, which are thought to encode obtusifoliol 14a demethylase. The two CYP51 genes have a single intron that is not shared with CYP51 genes from vertebrates or fungi, or with any other Arabidopsis P450 gene. Only a few of the Arabidopsis P450 genes are intronless (e.g., the CYP710A and CYP96A subfamilies). There was a relatively good correlation between intron conservation and phylogenetic relationships between members of the P450 subfamilies. Gene organization appears to be a useful tool in establishing the evolutionary relatedness of P450 genes, which may help in predictions of P450 function.     

Cloning of CYP9G2 from the diamondback moth, Plutella xylostella (Lepidoptera: Yponomeutidae).

Cytochrome P450s constitute a superfamily of hemoproteins, important in the metabolism of endogenous and xenobiotic compounds. The full-length cDNA of a novel cytochrome P450, CYP9G2, was isolated from a cDNA library. The cDNA is 2143 bp in length and contains an open reading frame from 50 to 1615 bp, encoding a protein of 521 amino acid residues. The putative P450 protein contains a highly hydrophobic N terminus and a P450 protein signature motif, FG/S*G*R*C*G***A/G, known as the important ligand for heme binding, analysis of the NH2-terminal sequence indicated that CYP9G2 is a microsomal P450. Using polymerase chain reaction with primers specific to CYP9G2, the genomic structure of CYP9G2 was analyzed, and it was found that the gene contains seven introns and eight exons within the coding region, all the sequences of the exon-intron junctions are consistent with the AG-GT rule. Multiple alignment indicated that CYP9G2 is most similar to CYP9E2 from the Blattella germanica (42.7% identity), it is also similar to the insect P450s in family 9, including CYP9L1 from Anopheles gambiae (38.7%) and CYP9A1 from Heliothis virescens (39.5%).     

Inducible P450s of the CYP9 family from larval Manduca sexta midgut

Several related cytochrome P450 cDNAs belonging to the CYP9 family have been cloned from the midgut of larval tobacco hornworms, Manduca sexta. The first P450, CYP9A2, was obtained by RT-PCR using degenerate primers. Northern blot analysis of expression in the midgut using the CYP9A2 probe revealed a significant induction by a variety of chemicals. Diets supplemented with the wild tomato compound 2-undecanone caused a dose-dependent induction which peaked after 48 h. Induction was also observed after addition to the diet of indole-3-carbinol, phenobarbital, 2-tridecanone and xanthotoxin. Neither alpha-pinene, clofibrate nor nicotine were effective inducers. The CYP9A2 probe hybridized to two mRNA species, one of 2. 0 kb and another of 4.2 kb, suggesting cross-hybridization to other P450 mRNAs. Additional P450 clones of the CYP9 family were then obtained and sequenced. Northern hybridization revealed that the 4.2 kb band also hybridized to CYP9A4 whereas the 2.0 kb hybridized to CYP9A5. Despite being 91% identical, CYP9A4 and CYP9A5 were induced differentially by clofibrate and xanthotoxin. Multiple P450 genes from various families are therefore induced in Lepidoptera in response to plant allelochemicals or xenobiotics.     

苹果蠹蛾细胞色素P450基因CYP332A19和CYP337B19的克隆及表达分析

【目的】本研究旨在通过克隆苹果蠹蛾Cydia pomonella细胞色素P450基因CYP332A19和CYP337B19,并对其进行序列和表达分析,以更好地了解这两个P450基因在植物次生物质解毒方面的作用,为进一步的功能研究提供依据。【方法】采用本地BLAST搜索苹果蠹蛾转录组数据库获得细胞色素P450基因cDNA序列,采用RT-PCR技术克隆目的基因的编码区。利用生物信息学软件分析目的基因的序列特征及与其他近缘物种的P450基因的系统进化关系。采用RT-qPCR技术测定目的基因在苹果蠹蛾不同发育阶段(卵、1-5龄幼虫、蛹和成虫)、4龄幼虫不同组织(头部、表皮、脂肪体、中肠和马氏管)以及4龄幼虫分别取食添加0.1%香豆素和0.5%槲皮素的人工饲料2 d后的表达水平。【结果】克隆获得苹果蠹蛾细胞色素P450基因CYP332A19(GenBank登录号: MF574708)和CYP337B19(GenBank登录号: MF574697)的全长cDNA序列,开放阅读框(ORF)分别长1 518和1 491 bp,分别编码505和496个氨基酸,其蛋白质分子量分别为58.586和57.734 kD,理论等电点分别为8.99和7.61。结构域分析显示,CYP332A19和CYP337B19中均包含包括血色素结合区在内的5个保守的细胞色素P450结构域。系统发育树显示,苹果蠹蛾CYP332A19与苹淡褐卷蛾Epighyas postvittana CYP332A9等CYP332A基因聚在一枝,而CYP337B19与稻纵卷叶螟Cnaphalocrocis medinalis CYP337B12和六星灯蛾Zygaena filipendulae CYP337B11等CYP337B基因聚在另一枝。RT-qPCR分析结果表明,CYP332A19和CYP337B19在苹果蠹蛾幼虫期的表达水平高于卵期的,分别在4龄幼虫脂肪体和中肠中的表达量最高。取食分别含0.1%香豆素和0.5%槲皮素的人工饲料2 d后,4龄幼虫体内的CYP332A19和CYP337B19相对表达量显著高于对照组(取食含2%DMSO的人工饲料)。【结论】CYP332A19和CYP332B19分别在苹果蠹蛾幼虫脂肪体和中肠中高表达,且在取食含香豆素和槲皮素的人工饲料的苹果蠹蛾幼虫体内表达量升高,说明这两个基因可能参与苹果蠹蛾对外源物质的解毒代谢过程。本研究的结果有助于我们了解苹果蠹蛾对寄主次生物质解毒代谢机理,为苹果蠹蛾防治提供新思路。     

淡色库蚊细胞色素P450基因研究

采用一对昆虫细胞色素P450简并引物,以反转录-聚合酶链反应从淡色库蚊对溴氰菊酯敏感品系和抗性品系成虫RNA扩增到约485 bp和510 bp两个片段,将这两个片段与PinPoint^TMXa-1 T质粒重组,然后克隆至大肠杆菌JM109菌株,筛选获得68个阳性克隆;其中24个阳性克隆测序后与GenBank资料对照,显示为细胞色素P450新序列;分子系统学研究显示,24个新基因（等位基因）分别属CYP4家族CYP4C、CYP4D、CYP4H和CYP4J等4个亚家族,其已由细胞色素P450命名委员会命名和GenBank登录上网;其中CYP4C23可能是一个假基因,CYP4H13具有一段58个碱基长度的内含子,CYP4J4V1在近3′端具有一个终止密码子TAG.     

Chimpanzee fetal G gamma and A gamma globin gene nucleotide sequences provide further evidence of gene conversions in hominine evolution

The fetal globin genes G gamma and A gamma from one chromosome of a chimpanzee (Pan troglodytes) were sequenced and found to be closely similar to the corresponding genes of man and the gorilla. These genes contain identical promoter and termination signals and have exons 1 and 2 separated by the conserved short intron 1 (122 bp) and exons 2 and 3 separated by the more rapidly evolving, larger intron 2 (893 bp and 887 bp in chimpanzee G gamma and A gamma, respectively). Each intron 2 has a stretch of simple sequence DNA (TG)n serving possibly as a "hot spot" for recombination. The two chimpanzee genes encode polypeptide chains that differ only at position 136 (glycine in G gamma and alanine in A gamma) and that are identical to the corresponding human chains, which have aspartic acid at position 73 and lysine at 104 in contrast to glycine and arginine at these respective positions of the gorilla A gamma chain. Phylogenetic analysis by the parsimony method revealed four silent (synonymous) base substitutions in evolutionary descent of the chimpanzee G gamma and A gamma codons and none in the human and gorilla codons. These Homininae (Pan, Homo, Gorilla) coding sequences evolved at one-tenth the average mammalian rate for nonsynonymous and one-fourth that for synonymous substitutions. Three sequence regions that were affected by gene conversions between chimpanzee G gamma and A gamma loci were identified: one extended 3' of the hot spot with G gamma replaced by the A gamma sequence, another extended 5' of the hot spot with A gamma replaced by G gamma, and the third conversion extended from the 5' flanking to the 5' end of intron 2, with G gamma replaced here by the A gamma sequence. A conversion similar to this third one has occurred independently in the descent of the gorilla genes. The four previously identified conversions, labeled C1-C4 (Scott et al. 1984), were substantiated with the addition of the chimpanzee genes to our analysis (C1 being shared by all three hominines and C2, C3, and C4 being found only in humans). Thus, the fetal genes from all three of these hominine species have been active in gene conversions during the descent of each species.      

中华按蚊CYP6Y亚家族基因的鉴定和生物信息学分析

【目的】鉴定中华按蚊Anopheles sinensis CYP6Y亚家族基因,分析它们的结构和特征,推测其可能的功能。【方法】以冈比亚按蚊An. gambiae CYP6Y1作为询问序列,通过双向Blast方法检索中华按蚊转录组中CYP6Y亚家族基因,并通过生物信息学方法分析基因结构、特征及可能的功能。【结果】从中华按蚊转录组测序数据中鉴定出2条CYP6Y亚家族基因,分别命名为AsCYP6Y1（GenBank登录号：KF709397）和AsCYP6Y2（GenBank登录号：KF709398）。序列分析显示,AsCYP6Y1和AsCYP6Y2全长分别为1 713 bp和1 815 bp,分别编码502和526个氨基酸。基因结构分析显示,该亚家族基因仅含有1个相位1型内含子并与其他P450基因形成保守的共线性分布。蛋白结构分析显示,这2个基因编码的蛋白含P450特有的5个特征序列和6个底物结合位点,且均不存在信号肽,其亚细胞定位为细胞质。3D结构分析显示,AsCYP6Y1有18条α螺旋和13股反向平行的β折叠,AsCYP6Y2有19条α螺旋和11股反向平行的β折叠。通过同样的方法,在达林按蚊An. darlingi中也鉴定出2个CYP6Y亚家族基因。系统进化分析显示,AsCYP6Y1和AsCYP6Y2分别与其他3种按蚊的CYP6Y1和CYP6Y2聚成一支,Bootstrap值均大于90%。替换率分析显示,中华按蚊AsCYP6Y1和AsCYP6Y2与其他3种按蚊同源基因的Ka/Ks均小于1。相对进化速率分析显示,中华按蚊CYP6Y和CYP6M亚家族的相对进化速率均显著快于CYP6P亚家族,而CYP6Y和CYP6M亚家族之间没有显著差异。【结论】在中华按蚊和达林按蚊中存在2个CYP6Y亚家族基因,之前在冈比亚按蚊和不吉按蚊An. funestus中也发现2个CYP6Y亚家族基因,表明CYP6Y亚家族基因可能在按蚊属广泛存在,且可能为按蚊属昆虫所特有。