家蚕（Bombyx mori）全基因组细胞色素P450基因结构与进化分析及CYP18A1克隆与功能研究
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摘要
细胞色素P450酶系义称作多功能氧化酶(MFO),是广泛存在于所有需氧生物体中的一类代谢酶系,细胞色素P450基因起源于35亿年前的一个共同祖先,是最古老和最庞大的超基因家族之一,在生命的过程中,它对内源物质的代谢与转化或外源化合物的活化与降解等进行催化和调控。在昆虫基因组中大约有100个左右的P450s,它们的作用涉及生长、发育、取食等过程,其对异生物质的代谢特性导致了昆虫对杀虫剂的抗药性和对植物有毒物质的耐受性,它还参与了昆虫体内保幼激素、蜕皮激素和脂肪酸等内源化合物的合成与代谢。
家蚕(Bombyx mori)是鳞翅目昆虫的模式生物,鳞翅目是昆虫中的第二大目,其中许多是极具危害性的农业害虫。随着生物技术的发展,家蚕已经成为一个重要的生物反应器用于生产重组蛋白。鳞翅目昆虫基因组信息不但对蚕丝业的改良产生了重大影响,而且也促进了新的害虫防治技术的发展。本研究基于家蚕基因组精细图和EST、全基因组基因芯片数据,对家蚕细胞色素P450基因进行了生物信息学及比较基因组学研究,开展了其中CYP9A基因簇的结构与进化分析,采用RNAi技术对家蚕中被推定为蜕皮激素C_(26)-羟基化酶的直向同源基因CYP18A1进行了功能研究。本论文的主要研究结果如下:
1.家蚕细胞色素P450基因的基因组学分析
将人、拟南芥、果蝇及盘基网柄菌等其它24个物种中已知的P450s在家蚕基因组精细图数据库中进行同源检索分析,以鉴定家蚕细胞色素P450基因。结果显示,家蚕基因组中存在84个细胞色素P450基因,其中有78个功能基因,6个假基因,并发现其中有8个基因簇的存在,最大的基因簇包含有9个P450s。假基因和基因簇的存在均属首次报道。
首次绘制了家蚕P450s的基因图谱,其中80个P450s可定位到19条不同的染色体上。此次首先报道的6个假基因,包括2个基因缺失突变,3个因片段滑移而产生阅读框内的移码突变,1个基因碎片。它们主要分布于基因数量大量扩增的Clan3和Clan4,而且有5个位于基因簇中,这充分显示了它们与基因复制的直接联系。
通过对预测P450s序列延伸,获得了70个具有完全开放阅读框的功能基因全长序列。并根据预测序列建立了系统发生树,将它们按昆虫P450集团、家族、亚家族分类,78个功能基因可分为26个家族,47个亚家族。提交国际细胞色素P450委员会后被分别予以正式命名。
84个预测基因有40个基因至少有1条EST序列为其表达证据。其中,来自Clan2和线粒体集团的P450s有EST证据的比例要明显高于其它2个集团,说明这些基因对家蚕正常的发育变态至关重要。家蚕全基因组芯片数据分析表明不同家蚕P450s之间具有组织和时期表达的差异性与特异性,未表达基因应更具昆虫P450s的诱导表达特点。
本研究还首次利用wise2程序对每个预测家蚕P450s进行内含子-外显子结构的分析,绘制了首张全基因组家蚕P450s结构图,通过它们的系统发生关系分析得知,基因结构和系统发生关系之间总体上存在紧密联系,即:进化关系越近,基因结构越相似,进化关系越远,基因结构差异越大。
2.昆虫P450s的比较基因组学分析
果蝇是目前昆虫P450s功能研究得最为清楚的模式昆虫,它和家蚕分别作为双翅目与鳞翅目昆虫的代表,P450s的数量也基本相当。通过利用这2种昆虫的功能基因建立系统发生树,发现了2物种间存在10对直向同源基因,但在基因数量大量扩增的Clan3与Clan4中,已很难找出直向同源基因,这2个集团基因在进化树的进化枝上表现出了种属特异性,即:在独立的进化枝上聚合的基因绝大多数是来自同一昆虫。我们推测这些基因在不同种类昆虫中的分化,是为了应对昆虫各自不同的生存环境与取食对象的选择压力所致。此外,在家蚕和果蝇的P450功能基因在Clan3与Clan4的数量和种类分布上存在明显差异,推测家蚕等鳞翅目昆虫可能没有像果蝇等双翅目昆虫那样对有毒物质的强代谢能力,替而代之是更多地依赖于多样选择和增强反防御能力等主动防御方式来提高自身对环境的适应能力。
通过比较基因组学方法,研究发现直向同源基因CYP18A1和CYP306A1在家蚕、果蝇与蜜蜂中存在线性保守,其基因位置与结构的同源性。暗示了它们功能上的相似性。
首次根据果蝇、蜜蜂与家蚕P450s内含子-外显子结构,按不同集团的划分对来自3种不同昆虫的P450s进行了基因结构的比较分析。结果发现这些基因中存在大量的特异性内含子,在家蚕和蜜蜂中存在0相跨集团保守内含子,但在3个昆虫中均存在的跨集团保守内含子是1相内含子,这些实际观察到的情况还不能很好回答内含子起源的问题。横向同源基因大量扩增,进化最迅速,功能多样,表现出环境应答基因特点的Clan3基因虽然由昆虫特有的P450s所组成,分化时间在3亿年以内,但跨不同昆虫的保守内含子最少。而在功能保守的Clan2和线粒体集团,特别是线粒体集团,则存在数量较多的跨昆虫保守内含子;从线虫、人与昆虫的P450s比较来看,尽管它们的分化时间已超过7亿年,仍然在这2集团中存在一定数量的保守内含子,说明这些功能保守的基因虽然在氨基酸序列保守性方面发生了明显的差异,已不属于同一家族的基因,但与功能相关的结构域仍然高度保守,导致了编码该保守序列的DNA结构即形成的内含子与外显子的结构保守性也很高。
果蝇、蜜蜂与家蚕的基因组大小分别为132Mb、262Mb和432Mb。果蝇P450s的内含子数量最少,大小最小,家蚕的内含子数量最多,大小最大,蜜蜂则居于其中,这刚好和这3种昆虫基因组大小相一致。表明随着基因组增大,基因的内含子含量也随之增多。
3.家蚕CYP9A基因簇基因的克隆与复制机制研究
通过RT-PCR方法,克隆得到了家蚕4个CYP9A基因,分别被国际P450委员会命名为CYP9A19,CYP9A20,CYP9A21,CYP9A22。它们具有完全相同大小的开放阅读框,均有9个内含子,10个外显子,内含子的插入位点与相位完全保守。3个同转录方向的基因串联重复,而另1个反方向转录的基因被4个串联的乙醇脱氢酶基因所间隔而位于同一Scaffold的下游,呈现出明显的基因重复的结构特征,这是关于家蚕细胞色素P450s基因簇的第一个报道。
同源性分析表明,家蚕CYP9As和已分离的昆虫CYP9As有很高的序列相似性,而且和美国棉铃虫的CYP9A12v3和CYP9A14具有完全保守的内含子插入位点,所对应的各外显子长度几乎完全相同。昆虫CYP9As的系统进化分析表明,家蚕的4个CYP9As是由3次不同的复制事件而来。其中,CYP9A22和棉铃虫的CYP9A14的同源性超过了和家蚕本身CYP9As的同源性,应是最古老的基因,CYP9A19和CYP9A21的序列相似性超过了94%,而且5'端旁侧序列也存在相当高的同源性,应是最近基因复制事件的产物。
从家蚕CYP9A基因的表达分析来看,这4个基因均选择性地在外源化合物进入蚕体的主要入口组织脂肪体、中肠及体壁中表达,表明它们可能与异生性化合物代谢有关,同时它们也在其他组织和器官中表达,推测它们参与了内源性物质调节。通过4个基因间的特异性表达方式和它们系统发生关系表明,基因复制发生时间与基因的表达分化之间存在相当紧密的相关关系。即:分化时间越远则表达筹异越大。
4.家蚕CYP18A1的克隆与功能研究
蜕皮激素对昆虫生长、发育和繁殖有重要调控作用,尤其对蜕皮和变态过程。根据信息分析的结果,我们克隆了家蚕中被推定为蜕皮激素C_(26)羟基化酶的直向同源基因CYP18A1,该基因包括5'-UTR在内有1737bp,编码541个氨基酸,在GenBank上的对应登录号为EF421988。它和已经分离的其它物种的直向同源基因,特别是海灰翅夜蛾的有较高的同源性。在和包括哺乳动物中与类固醇合成和代谢有关P450s在内的基因进行系统发生关系分析时发现,哺乳动物中与类固醇代谢有关的CYP2基因和家蚕CYP18A1有较为相近的进化关系,这可能暗示着与甾类化合物代谢相关基因在远源物种分化后,仍保持着序列与功能的保守性。
无论表达谱分析还是家蚕全基因组芯片数据均表明该基因在上簇第2天有相对较高的转录水平,与家蚕体内相应的蜕皮激素峰值时间有很高的一致性,从而进一步印证了以前的研究对该昆虫直向同源基因功能的推断,即蜕皮激素应一样参与了家蚕的CYP18A的转录调控,该基因与家蚕蜕皮激素代谢也可能有一定的关系。
结合组织、时间表达谱分析,以体外注射的方式,通过在5龄中后期及老熟前期连续向蚕体导入体外合成的CYP18A1对应的dsRNA,获得了发育偏快的表型。说明家蚕CYP18A1基因可能与家蚕的发育变态相关。该基因功能的发现和进一步深入研究可会为昆虫害虫防治提供新的作用靶标和控制策略。
Cytochrome P450 enzymes(mixed function oxidases)are a complex family of heme-containing enzymes found in virtually all aerobic organisms,which is one of the oldest and largest gene superfamilies.Cytochrome P450(P450s)evolved from a common ancestor which has existed for more than 3.5 billion years.Many functions are attributed to cytochrome P450s including the metabolism of a wide variety of both endogenous substrates and xenobiotics.The genome of each insect species may carry a hundred or so different P450 genes.They do many things:P450.enzymes are found in the biosynthetic and metabolic pathways of ecdysteroids and juvenile hormones,they also metabolize insecticides,resulting either in bioactivation or,more often,in detoxification,the latter process being enhanced in many strains with metabolic resistence to insecticides.Furthermore, P450 metabolism of certain plant chemicals is often the key to the adaptation of insect herbivores to their host plants.
Silkworm(Bombyx raori)is the model organism for Lepidoptera,the second biggest order in insects,which includes the most disruptive agricultural pests.With the development of biotechnology,B.mori has been used as an important bioreactor for the production of recombinant proteins.Lepidopteran genome information not only makes a strong impact on improving sericulture, but also facilitates the development of new pest controls.On basis of the completing genome sequence database of silkworm,coupled with its ESTs and the whole genome microarray,we studied the silkworm cytochrome P450 by analysis of bioinformation and comparative genomics.We also analyzed the structure and evolution of the CYP9A cluster and studied on the cloning and function of orthologous CYP18A1,a candidate for the ecdysone 26-hydroxylase.The main results present as follows.
1.Analysis of cytochrome P450s in a completing silkworm genome sequence
The cytochrome P450s in 24 species available from GenBank or P450 homepage were used to scanne the completing silkworm genome sequence,we identified 84 putative cytochrome P450s in silkworm genome.Among of them,78 appear to be functional P450 genes,six are probable pseudogenes.The genetic map shows that 80 P450s are distributed on 19 chromosomes,eight clusters with over three genes are organized in silkworm genome,with up to 9 member genes in the largest cluster.Of six probable pseudogenes,2 are characterized by deletions,3 by the presence of several stop codons in the open reading frame(ORF)and one separated from their parent loci but never represented a functional gene.Five probable pseudogenes are distributed into the different clusters,maybe they are duplications in the different evolutionary events.This constructs first report on gene clusters and pseudogenes in P450S superfamily of the silkworm.
These insect conserved motifs of the protein were used as milestones in the gradual elaboration of full-length P450 sequences.As a result,70 functional P450s with complete open reading frame are identified by Wise2 and EST assembly.All them were named by the P450 Nomenclature Committee,78 functional P450-like genes can be classified into 26 families and 47 subfamilies,and were used to BLAST search against the ESTs database,40 genes have at least one EST,while 44 genes are not represented in the EST collection.Among of them,more P450s from Clan2 and Mito.CYP.clan,especially P450s involved in ecdysteroid biosynthesis,have ESTs as expression evidence than the other P450s from Clan3 and Clan4,which suggest that these P450s from Clan2 and Mito.CYP are essential housekeeping genes which require a high fidelity because of functional constrains.The whole genome microarray also reveals that the different P450s have distinct pattern of temporal and tissue-specific expression.Others unexpressed should be inducible expression.
We have drawn the first map of silkworm P450 intron positions and phases compared to the phylogenetic tree.There is a relatively good correlation between intron conservation and phylogenetic relationship between members of the P450 subfamilies.The orthologous CYP15C1 is also identified,which catalyzes epoxidation of methyl famesoate to juvenile hormoneⅢin cockroach corpora allata.
2.Comparative genomics analysis of P450s among different insects
The silkworm and the fruit fly(Drosophila melanogaster),which is the most well-studied model organism for insect,a lepidoptera,a diptera,are complete metamorphosis insects,and they almost contain the same numbers of P450s.We have presumed 10 orthologous gene pairs by phylogenetic analysis,and 5 gene pairs among them are involved in ecdysteroid biosynthesis,which require a high fidelity because of functional constrains,and almost retain stringently as 1:1 orthologs.But P450s in Clan3 and Clan4 are the most numerous among insect P450s,it is difficult to find the distinct orthologous gene pairs.They form different separate species-specific clusters in the phylogenetic tree,which is presumedly related to their habitat and ecological niche.Almost all P450s of silkworm in Clan3 are cluster into one clade with CYP6B found in the metabolism of certain plant chemicals,whereas P450s of housefly in this clan are cluster into a different clade with CYP6A related to metabolic resistence to insecticides.Furthermore,there are distinct number and subfamily difference in P450s of Clan3 and Clan4,We can presume that silkworm may not confer an strong metabolic resistance to xenobiotics,instead,it depend much more on additional selective ability of their varied food sources and environment to cope with the ever-changing environment.
By comparative genomics analysis,we find there is conserved arrangement of CYP306A1 and CYP18.41 among the three insects.Together,the tight linkage and conserved intron-exon organization indicate an orthologous relationship.
Based on the data.on intron-exon organization of P450s in D.melanogaster and Apis,along with the analysis of P450s in silkworm,we draw comparisons between P450s from different insect P450 Clans.The different P450s contain a large member of unique intron positions and phases,the very few introns of insect P450s conserved across CYP Clan are phase 1 introns,while there is phase 0 conserved across CYP Clan intron.The observed results were not what the "intron-early or intron-late" scenario expected.Fewer introns are conserved from insect CYP genes in Clan3 which appear to share the characteristics of "environment response genes" and are related to functional diversity,while a lot of conserved introns of insect CYP genes from Clan2 and mitochondrial P450 which are involved in essential physiological functions have their counterparts in other insect P450s. As compared with other animal phyla P450s,some intron insertion sites of are conserved,although the three phyla diverged some 700.MAY.The result revealed that the conserved intron-exon structure play a vital part in conservation of gene function.
Assuming the genome sizes of B.mori,D.melanogaster and A.mellifera are 432Mb,132Mb and 262Mb,respectively.The intron number per gene and the intron sizes are different,B.mori＞A. rnellifera＞D.melanogaster.There is a tendency that they all increase with genome sizes
3.Characterization of multiple CYP9A genes and their putative evolution mechanism All four of CYP9A subfamily members in the silkworm were cloned by RT-PCR and designated as CYP9A19-CYP9A22 by the P450 Nomenclature Committee,respectively.Each of the genes contains an ORF of 1593bp in identical length and encodes a putative polypeptide of 531 amino acids.Both of nucleic acid and amino acid sequences share very high identities to each other. Alignment with the cDNA sequences revealed that these paralogs share an identical genomic structure,each comprising 10 exons and 9 introns of variable sizes.The locations of their introns are absolutely conserved,CYP9A19,CYP9A20 and CYP9A21 form a tandem cluster,whereas CYP9A22 separated from the cluster by four tandem alcohol dehydrogenase-like genes.Phylogenetic relationships and structural comparisons indicated that these paralogs arose as a result of gene duplication events.CYP9A22 with oppositional orientation forms a separate one with the members from different organisms in lepidopteran insect,which is more similar to CYP9A14(63%amino acid identical)from H.armigera than to members of its own,indicating an duplication which occur most early than the other two tandem duplicate events.In contrast,CYP9A19 and CYP9A21 displayed not only a high degree of sequence similarity in the coding region,but also in the 5'-flanking region, which further confirmed that they probably arose from the most recent duplication event.The analysis of the tissue-related expressions show that all CYP9A genes in silkworm selectively expressed in "first line of defense" tissue such as midgut,exoskeleton and subcuticular fat body, which coincides with the most commonly Clan3 function involved in xenobiotics metabolism and resistance.The other tissue-related expressions do not exclude a physiological function towards endogenous substmtes.The differentially expression patterns of four duplicates in silkworm CYP9A subfamily and their phylogenetic relationships also confirm the inference that there is a positive correlation between expression divergence and the age of duplicate genes.
4.cDNA cloning and function study on P450 gene CYP18A1 in the silkworm,B.mori Fundamental events in the life of insects such as growth,development and reproduction are regulated by ecdysteroids(molting hormone),especially during molting and metamorphosis development.The orthologous CYP18A1 gene,which are a candidate for the ecdysone 26-hydroxylase,was identified from B.mori.A gene containing 1 737 bp is assembled on the basis of several ESTs,which extended into 5'-UTR.It contains an ORF of 1 623 bp encoding 541 amino acids,termed as B.rnori CYP18A1 by the P450 nomenclature committee(GenBank accession number:EF421988).It shares high identities with other orthologs including Spodoptera littoralis CYP18A1 genes.The result of RT-PCR and the whole genome microarray revealed that B.mori CYP18A1 not only acquired a temporal and tissue-specific expression profile,but also exhibited a distinct expression pattern which closely coincided with the reported peak of ecdysteroid in the haemolymphs of B.mori.This further suggests orthologous CYP18A1 gene in insects is closely related to ecdysteroid homeostasis.The phylogenetic relationship of genes involved in ecdysteroids shows a close relationship between the silkworm CYP18A1 and the members of the CYP2 family, including some mammalian sterorid-metabolising P450s.
Based on the analysis of RT-PCR,we prepared dsRNA and performed RNAi(RNA interference)experiment in the silkworm larva.RNAi mediated knockdown drastically reduced CYP18A1 expression and led to the presence of excessive early mature silkworms and moth.Result revealed that the silkworm CYP18A1 is essential for molting and metamorphosis development.The result futher indicates silkworm CYP18A1 has involved in metabolic pathways of ecdysteroids, which may provide novel targets for exploitation in the development of new pest control strategies.
家蚕(Bombyx mori)是鳞翅目昆虫的模式生物,鳞翅目是昆虫中的第二大目,其中许多是极具危害性的农业害虫。随着生物技术的发展,家蚕已经成为一个重要的生物反应器用于生产重组蛋白。鳞翅目昆虫基因组信息不但对蚕丝业的改良产生了重大影响,而且也促进了新的害虫防治技术的发展。本研究基于家蚕基因组精细图和EST、全基因组基因芯片数据,对家蚕细胞色素P450基因进行了生物信息学及比较基因组学研究,开展了其中CYP9A基因簇的结构与进化分析,采用RNAi技术对家蚕中被推定为蜕皮激素C_(26)-羟基化酶的直向同源基因CYP18A1进行了功能研究。本论文的主要研究结果如下:
1.家蚕细胞色素P450基因的基因组学分析
将人、拟南芥、果蝇及盘基网柄菌等其它24个物种中已知的P450s在家蚕基因组精细图数据库中进行同源检索分析,以鉴定家蚕细胞色素P450基因。结果显示,家蚕基因组中存在84个细胞色素P450基因,其中有78个功能基因,6个假基因,并发现其中有8个基因簇的存在,最大的基因簇包含有9个P450s。假基因和基因簇的存在均属首次报道。
首次绘制了家蚕P450s的基因图谱,其中80个P450s可定位到19条不同的染色体上。此次首先报道的6个假基因,包括2个基因缺失突变,3个因片段滑移而产生阅读框内的移码突变,1个基因碎片。它们主要分布于基因数量大量扩增的Clan3和Clan4,而且有5个位于基因簇中,这充分显示了它们与基因复制的直接联系。
通过对预测P450s序列延伸,获得了70个具有完全开放阅读框的功能基因全长序列。并根据预测序列建立了系统发生树,将它们按昆虫P450集团、家族、亚家族分类,78个功能基因可分为26个家族,47个亚家族。提交国际细胞色素P450委员会后被分别予以正式命名。
84个预测基因有40个基因至少有1条EST序列为其表达证据。其中,来自Clan2和线粒体集团的P450s有EST证据的比例要明显高于其它2个集团,说明这些基因对家蚕正常的发育变态至关重要。家蚕全基因组芯片数据分析表明不同家蚕P450s之间具有组织和时期表达的差异性与特异性,未表达基因应更具昆虫P450s的诱导表达特点。
本研究还首次利用wise2程序对每个预测家蚕P450s进行内含子-外显子结构的分析,绘制了首张全基因组家蚕P450s结构图,通过它们的系统发生关系分析得知,基因结构和系统发生关系之间总体上存在紧密联系,即:进化关系越近,基因结构越相似,进化关系越远,基因结构差异越大。
2.昆虫P450s的比较基因组学分析
果蝇是目前昆虫P450s功能研究得最为清楚的模式昆虫,它和家蚕分别作为双翅目与鳞翅目昆虫的代表,P450s的数量也基本相当。通过利用这2种昆虫的功能基因建立系统发生树,发现了2物种间存在10对直向同源基因,但在基因数量大量扩增的Clan3与Clan4中,已很难找出直向同源基因,这2个集团基因在进化树的进化枝上表现出了种属特异性,即:在独立的进化枝上聚合的基因绝大多数是来自同一昆虫。我们推测这些基因在不同种类昆虫中的分化,是为了应对昆虫各自不同的生存环境与取食对象的选择压力所致。此外,在家蚕和果蝇的P450功能基因在Clan3与Clan4的数量和种类分布上存在明显差异,推测家蚕等鳞翅目昆虫可能没有像果蝇等双翅目昆虫那样对有毒物质的强代谢能力,替而代之是更多地依赖于多样选择和增强反防御能力等主动防御方式来提高自身对环境的适应能力。
通过比较基因组学方法,研究发现直向同源基因CYP18A1和CYP306A1在家蚕、果蝇与蜜蜂中存在线性保守,其基因位置与结构的同源性。暗示了它们功能上的相似性。
首次根据果蝇、蜜蜂与家蚕P450s内含子-外显子结构,按不同集团的划分对来自3种不同昆虫的P450s进行了基因结构的比较分析。结果发现这些基因中存在大量的特异性内含子,在家蚕和蜜蜂中存在0相跨集团保守内含子,但在3个昆虫中均存在的跨集团保守内含子是1相内含子,这些实际观察到的情况还不能很好回答内含子起源的问题。横向同源基因大量扩增,进化最迅速,功能多样,表现出环境应答基因特点的Clan3基因虽然由昆虫特有的P450s所组成,分化时间在3亿年以内,但跨不同昆虫的保守内含子最少。而在功能保守的Clan2和线粒体集团,特别是线粒体集团,则存在数量较多的跨昆虫保守内含子;从线虫、人与昆虫的P450s比较来看,尽管它们的分化时间已超过7亿年,仍然在这2集团中存在一定数量的保守内含子,说明这些功能保守的基因虽然在氨基酸序列保守性方面发生了明显的差异,已不属于同一家族的基因,但与功能相关的结构域仍然高度保守,导致了编码该保守序列的DNA结构即形成的内含子与外显子的结构保守性也很高。
果蝇、蜜蜂与家蚕的基因组大小分别为132Mb、262Mb和432Mb。果蝇P450s的内含子数量最少,大小最小,家蚕的内含子数量最多,大小最大,蜜蜂则居于其中,这刚好和这3种昆虫基因组大小相一致。表明随着基因组增大,基因的内含子含量也随之增多。
3.家蚕CYP9A基因簇基因的克隆与复制机制研究
通过RT-PCR方法,克隆得到了家蚕4个CYP9A基因,分别被国际P450委员会命名为CYP9A19,CYP9A20,CYP9A21,CYP9A22。它们具有完全相同大小的开放阅读框,均有9个内含子,10个外显子,内含子的插入位点与相位完全保守。3个同转录方向的基因串联重复,而另1个反方向转录的基因被4个串联的乙醇脱氢酶基因所间隔而位于同一Scaffold的下游,呈现出明显的基因重复的结构特征,这是关于家蚕细胞色素P450s基因簇的第一个报道。
同源性分析表明,家蚕CYP9As和已分离的昆虫CYP9As有很高的序列相似性,而且和美国棉铃虫的CYP9A12v3和CYP9A14具有完全保守的内含子插入位点,所对应的各外显子长度几乎完全相同。昆虫CYP9As的系统进化分析表明,家蚕的4个CYP9As是由3次不同的复制事件而来。其中,CYP9A22和棉铃虫的CYP9A14的同源性超过了和家蚕本身CYP9As的同源性,应是最古老的基因,CYP9A19和CYP9A21的序列相似性超过了94%,而且5'端旁侧序列也存在相当高的同源性,应是最近基因复制事件的产物。
从家蚕CYP9A基因的表达分析来看,这4个基因均选择性地在外源化合物进入蚕体的主要入口组织脂肪体、中肠及体壁中表达,表明它们可能与异生性化合物代谢有关,同时它们也在其他组织和器官中表达,推测它们参与了内源性物质调节。通过4个基因间的特异性表达方式和它们系统发生关系表明,基因复制发生时间与基因的表达分化之间存在相当紧密的相关关系。即:分化时间越远则表达筹异越大。
4.家蚕CYP18A1的克隆与功能研究
蜕皮激素对昆虫生长、发育和繁殖有重要调控作用,尤其对蜕皮和变态过程。根据信息分析的结果,我们克隆了家蚕中被推定为蜕皮激素C_(26)羟基化酶的直向同源基因CYP18A1,该基因包括5'-UTR在内有1737bp,编码541个氨基酸,在GenBank上的对应登录号为EF421988。它和已经分离的其它物种的直向同源基因,特别是海灰翅夜蛾的有较高的同源性。在和包括哺乳动物中与类固醇合成和代谢有关P450s在内的基因进行系统发生关系分析时发现,哺乳动物中与类固醇代谢有关的CYP2基因和家蚕CYP18A1有较为相近的进化关系,这可能暗示着与甾类化合物代谢相关基因在远源物种分化后,仍保持着序列与功能的保守性。
无论表达谱分析还是家蚕全基因组芯片数据均表明该基因在上簇第2天有相对较高的转录水平,与家蚕体内相应的蜕皮激素峰值时间有很高的一致性,从而进一步印证了以前的研究对该昆虫直向同源基因功能的推断,即蜕皮激素应一样参与了家蚕的CYP18A的转录调控,该基因与家蚕蜕皮激素代谢也可能有一定的关系。
结合组织、时间表达谱分析,以体外注射的方式,通过在5龄中后期及老熟前期连续向蚕体导入体外合成的CYP18A1对应的dsRNA,获得了发育偏快的表型。说明家蚕CYP18A1基因可能与家蚕的发育变态相关。该基因功能的发现和进一步深入研究可会为昆虫害虫防治提供新的作用靶标和控制策略。
Cytochrome P450 enzymes(mixed function oxidases)are a complex family of heme-containing enzymes found in virtually all aerobic organisms,which is one of the oldest and largest gene superfamilies.Cytochrome P450(P450s)evolved from a common ancestor which has existed for more than 3.5 billion years.Many functions are attributed to cytochrome P450s including the metabolism of a wide variety of both endogenous substrates and xenobiotics.The genome of each insect species may carry a hundred or so different P450 genes.They do many things:P450.enzymes are found in the biosynthetic and metabolic pathways of ecdysteroids and juvenile hormones,they also metabolize insecticides,resulting either in bioactivation or,more often,in detoxification,the latter process being enhanced in many strains with metabolic resistence to insecticides.Furthermore, P450 metabolism of certain plant chemicals is often the key to the adaptation of insect herbivores to their host plants.
Silkworm(Bombyx raori)is the model organism for Lepidoptera,the second biggest order in insects,which includes the most disruptive agricultural pests.With the development of biotechnology,B.mori has been used as an important bioreactor for the production of recombinant proteins.Lepidopteran genome information not only makes a strong impact on improving sericulture, but also facilitates the development of new pest controls.On basis of the completing genome sequence database of silkworm,coupled with its ESTs and the whole genome microarray,we studied the silkworm cytochrome P450 by analysis of bioinformation and comparative genomics.We also analyzed the structure and evolution of the CYP9A cluster and studied on the cloning and function of orthologous CYP18A1,a candidate for the ecdysone 26-hydroxylase.The main results present as follows.
1.Analysis of cytochrome P450s in a completing silkworm genome sequence
The cytochrome P450s in 24 species available from GenBank or P450 homepage were used to scanne the completing silkworm genome sequence,we identified 84 putative cytochrome P450s in silkworm genome.Among of them,78 appear to be functional P450 genes,six are probable pseudogenes.The genetic map shows that 80 P450s are distributed on 19 chromosomes,eight clusters with over three genes are organized in silkworm genome,with up to 9 member genes in the largest cluster.Of six probable pseudogenes,2 are characterized by deletions,3 by the presence of several stop codons in the open reading frame(ORF)and one separated from their parent loci but never represented a functional gene.Five probable pseudogenes are distributed into the different clusters,maybe they are duplications in the different evolutionary events.This constructs first report on gene clusters and pseudogenes in P450S superfamily of the silkworm.
These insect conserved motifs of the protein were used as milestones in the gradual elaboration of full-length P450 sequences.As a result,70 functional P450s with complete open reading frame are identified by Wise2 and EST assembly.All them were named by the P450 Nomenclature Committee,78 functional P450-like genes can be classified into 26 families and 47 subfamilies,and were used to BLAST search against the ESTs database,40 genes have at least one EST,while 44 genes are not represented in the EST collection.Among of them,more P450s from Clan2 and Mito.CYP.clan,especially P450s involved in ecdysteroid biosynthesis,have ESTs as expression evidence than the other P450s from Clan3 and Clan4,which suggest that these P450s from Clan2 and Mito.CYP are essential housekeeping genes which require a high fidelity because of functional constrains.The whole genome microarray also reveals that the different P450s have distinct pattern of temporal and tissue-specific expression.Others unexpressed should be inducible expression.
We have drawn the first map of silkworm P450 intron positions and phases compared to the phylogenetic tree.There is a relatively good correlation between intron conservation and phylogenetic relationship between members of the P450 subfamilies.The orthologous CYP15C1 is also identified,which catalyzes epoxidation of methyl famesoate to juvenile hormoneⅢin cockroach corpora allata.
2.Comparative genomics analysis of P450s among different insects
The silkworm and the fruit fly(Drosophila melanogaster),which is the most well-studied model organism for insect,a lepidoptera,a diptera,are complete metamorphosis insects,and they almost contain the same numbers of P450s.We have presumed 10 orthologous gene pairs by phylogenetic analysis,and 5 gene pairs among them are involved in ecdysteroid biosynthesis,which require a high fidelity because of functional constrains,and almost retain stringently as 1:1 orthologs.But P450s in Clan3 and Clan4 are the most numerous among insect P450s,it is difficult to find the distinct orthologous gene pairs.They form different separate species-specific clusters in the phylogenetic tree,which is presumedly related to their habitat and ecological niche.Almost all P450s of silkworm in Clan3 are cluster into one clade with CYP6B found in the metabolism of certain plant chemicals,whereas P450s of housefly in this clan are cluster into a different clade with CYP6A related to metabolic resistence to insecticides.Furthermore,there are distinct number and subfamily difference in P450s of Clan3 and Clan4,We can presume that silkworm may not confer an strong metabolic resistance to xenobiotics,instead,it depend much more on additional selective ability of their varied food sources and environment to cope with the ever-changing environment.
By comparative genomics analysis,we find there is conserved arrangement of CYP306A1 and CYP18.41 among the three insects.Together,the tight linkage and conserved intron-exon organization indicate an orthologous relationship.
Based on the data.on intron-exon organization of P450s in D.melanogaster and Apis,along with the analysis of P450s in silkworm,we draw comparisons between P450s from different insect P450 Clans.The different P450s contain a large member of unique intron positions and phases,the very few introns of insect P450s conserved across CYP Clan are phase 1 introns,while there is phase 0 conserved across CYP Clan intron.The observed results were not what the "intron-early or intron-late" scenario expected.Fewer introns are conserved from insect CYP genes in Clan3 which appear to share the characteristics of "environment response genes" and are related to functional diversity,while a lot of conserved introns of insect CYP genes from Clan2 and mitochondrial P450 which are involved in essential physiological functions have their counterparts in other insect P450s. As compared with other animal phyla P450s,some intron insertion sites of are conserved,although the three phyla diverged some 700.MAY.The result revealed that the conserved intron-exon structure play a vital part in conservation of gene function.
Assuming the genome sizes of B.mori,D.melanogaster and A.mellifera are 432Mb,132Mb and 262Mb,respectively.The intron number per gene and the intron sizes are different,B.mori＞A. rnellifera＞D.melanogaster.There is a tendency that they all increase with genome sizes
3.Characterization of multiple CYP9A genes and their putative evolution mechanism All four of CYP9A subfamily members in the silkworm were cloned by RT-PCR and designated as CYP9A19-CYP9A22 by the P450 Nomenclature Committee,respectively.Each of the genes contains an ORF of 1593bp in identical length and encodes a putative polypeptide of 531 amino acids.Both of nucleic acid and amino acid sequences share very high identities to each other. Alignment with the cDNA sequences revealed that these paralogs share an identical genomic structure,each comprising 10 exons and 9 introns of variable sizes.The locations of their introns are absolutely conserved,CYP9A19,CYP9A20 and CYP9A21 form a tandem cluster,whereas CYP9A22 separated from the cluster by four tandem alcohol dehydrogenase-like genes.Phylogenetic relationships and structural comparisons indicated that these paralogs arose as a result of gene duplication events.CYP9A22 with oppositional orientation forms a separate one with the members from different organisms in lepidopteran insect,which is more similar to CYP9A14(63%amino acid identical)from H.armigera than to members of its own,indicating an duplication which occur most early than the other two tandem duplicate events.In contrast,CYP9A19 and CYP9A21 displayed not only a high degree of sequence similarity in the coding region,but also in the 5'-flanking region, which further confirmed that they probably arose from the most recent duplication event.The analysis of the tissue-related expressions show that all CYP9A genes in silkworm selectively expressed in "first line of defense" tissue such as midgut,exoskeleton and subcuticular fat body, which coincides with the most commonly Clan3 function involved in xenobiotics metabolism and resistance.The other tissue-related expressions do not exclude a physiological function towards endogenous substmtes.The differentially expression patterns of four duplicates in silkworm CYP9A subfamily and their phylogenetic relationships also confirm the inference that there is a positive correlation between expression divergence and the age of duplicate genes.
4.cDNA cloning and function study on P450 gene CYP18A1 in the silkworm,B.mori Fundamental events in the life of insects such as growth,development and reproduction are regulated by ecdysteroids(molting hormone),especially during molting and metamorphosis development.The orthologous CYP18A1 gene,which are a candidate for the ecdysone 26-hydroxylase,was identified from B.mori.A gene containing 1 737 bp is assembled on the basis of several ESTs,which extended into 5'-UTR.It contains an ORF of 1 623 bp encoding 541 amino acids,termed as B.rnori CYP18A1 by the P450 nomenclature committee(GenBank accession number:EF421988).It shares high identities with other orthologs including Spodoptera littoralis CYP18A1 genes.The result of RT-PCR and the whole genome microarray revealed that B.mori CYP18A1 not only acquired a temporal and tissue-specific expression profile,but also exhibited a distinct expression pattern which closely coincided with the reported peak of ecdysteroid in the haemolymphs of B.mori.This further suggests orthologous CYP18A1 gene in insects is closely related to ecdysteroid homeostasis.The phylogenetic relationship of genes involved in ecdysteroids shows a close relationship between the silkworm CYP18A1 and the members of the CYP2 family, including some mammalian sterorid-metabolising P450s.
Based on the analysis of RT-PCR,we prepared dsRNA and performed RNAi(RNA interference)experiment in the silkworm larva.RNAi mediated knockdown drastically reduced CYP18A1 expression and led to the presence of excessive early mature silkworms and moth.Result revealed that the silkworm CYP18A1 is essential for molting and metamorphosis development.The result futher indicates silkworm CYP18A1 has involved in metabolic pathways of ecdysteroids, which may provide novel targets for exploitation in the development of new pest control strategies.
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