DEAD／H盒超家族新成员—人DDX36和小鼠Ddx36基因的分子克隆和特性

果蝇的基因组序列已经测定 ,因此它是结构基因组学和功能基因组学研究的最为理想的一种模式生物。果蝇中具有RNA和DNA解旋酶功能的非雄基因 (maleless,mle) ,在果蝇的生殖细胞中参与基因的转录后调节。从果蝇非雄基因的全序列出发 ,使用同源克隆的策略克隆了具有长的DNA/RNA解旋酶盒 (DEAD/DEAHbox)的人和小鼠新的同源基因 ,分别命名为DDX36和Ddx36。这两个基因属于DEAD/H盒超家族新成员。人的DDX36与果蝇非雄基因在氨基酸序列上有 37%的一致性和 5 8%相似性 ,与新克隆的小鼠Ddx36在氨基酸序列上有 91 %的一致性和 94 %相似性。1 6种组织的Northern杂交结果显示 ,在睾丸中有一条信号非常强 3 .8kb的杂交带 ,其余组织中不表达或仅可见一条非常微弱的 3.8kb的杂交带。定位分析表明该基因位于染色体 3q2 5 .1～ 3q2 5 .2 ;结构分析初步确定有 2 6个外显子和 2 5个内含子。DDX36和Ddx36基因可能与性别分化、精子发生和男性生育有关     

肝脏特异性CD36基因敲除小鼠的制备及鉴定

目的:运用Cre/Loxp重组酶系统构建肝脏特异性CD36基因敲除小鼠并进行鉴定和验证,为研究CD36的生物学功能奠定基础。方法:构建CD36打靶载体,电转转染胚胎干细胞,通过长链PCR筛选出正确同源重组的阳性克隆,阳性胚胎干细胞克隆经扩增后,注射入C57BL/6J小鼠的囊胚中,获得嵌合小鼠,再与Flp小鼠交配筛选获得Flox杂合子小鼠,该小鼠与引进的Alb-Cre小鼠交配,在F3代获得CD36fl/fl:Alb-Cre+基因型小鼠,即为肝脏特异性CD36敲除小鼠。采用PCR鉴定小鼠基因型,PCR、实时荧光定量PCR和Western blot验证小鼠肝脏CD36敲除效果,Western blot检测小鼠肾脏、脂肪和心肌组织CD36表达情况,HE染色观察小鼠肝脏形态学改变。结果:建立了CD36基因的Flox杂合子小鼠,与Alb-Cre小鼠交配后,在F3代筛选出CD36fl/fl:AlbCre-和CD36fl/fl:Alb-Cre+基因型小鼠,DNA水平证实CD36fl/fl:Alb-Cre+基因型小鼠肝脏CD36基因通过Cre/Loxp重组酶系统被敲除。与CD36fl/fl:Alb-Cre-基因型小鼠相比,CD36fl/fl:Alb-Cre+基因型小鼠肝脏CD36mRNA和蛋白表达水平显著降低,肾脏、脂肪和心肌组织CD36蛋白表达无差别,肝脏形态学特征无明显差异。结论:通过Cre/Loxp重组酶系统成功构建了肝脏特异性CD36基因敲除小鼠,为研究CD36在肝脏代谢和肝脏疾病中的功能提供了动物模型。     

绵羊ARHGAP36全长cDNA的克隆及其蛋白在睾丸精细管中的分布检测

ARHGAP36是Rho GAPs家族的一员,在成神经管细胞瘤中超表达,可能参与调节细胞增殖。为了研究ARHGAP36在羊精子发生过程中的作用,采用RACE(rapid amplification of c DNA ends)技术从绵羊睾丸组织中克隆了SARHGAP36的c DNA全长序列。内部区域c DNA序列与5’RACE和3’RACE扩增的两端序列测序后拼接,得到了2698 bp的绵羊ARHGAP36 c DNA全长,其中包含一个长1593 bp的开放阅读框(ORF),编码530 aa,与Uni Prot中预测的牛ARHGAP36氨基酸序列(A7MB27)同源性为98%,说明我们克隆的c DNA是Rho GAP家族的成员ARHGAP36。对所克隆的绵羊ARHGAP36的氨基酸序列和Uni Prot数据库中所收集的所有其它ARHGAP成员的氨基酸序列比对分析显示,ARHGAP36没有其它ARHGAP成员都有的标志性"精氨酸指"基序,而它的对应基序中的保守精氨酸残基被苏氨酸替代了,暗示ARHGAP36很可能并不依靠酶催化活性发挥其功能。当把所克隆的c DNA与Gen Bank中发布的绵羊arhgap36序列比对时发现绵羊arhgap36基因组测序结果的第一个外显子中缺少一小段DNA,导致如果用该基因组序列预测绵羊ARHGAP36的c DNA,无法得到能编码正确氨基酸的c DNA,因此,实验为进一步研究ARHGAP36这个特殊ARHGAP成员的功能提供了正确的c DNA序列。绵羊睾丸总蛋白Western blot检测发现绵羊睾丸内的ARHGAP36有3种长度,免疫组织化学检测发现ARHGAP36蛋白在绵羊睾丸精细管中的精子发生过程中各类细胞中都有分布。     

大鼠肝癌模型中Piwil4、Mael和Ddx4基因mRNA和蛋白表达水平及其与肿瘤检测的关系

PIWI和piRNA的表达水平与肿瘤类型密切相关。Piwil2 mRNA在肝癌中的表达量比肿瘤周围的肝脏组织的表达量高。PIWI/piRNA通路基因Piwil4、Mael和Ddx4为候选癌基因,在多种癌组织中表达,而在肝癌组织中的研究尚无报道。为探讨Piwil4、Mael和Ddx4基因在肝癌组织中表达水平变化的影响,建立了大鼠肝癌模型,并提取血清用ELISA方法检测肿瘤标记物,采用实时荧光定量PCR、蛋白质免疫印迹方法和免疫组织化学方法检测正常肝组织与模型组肝组织中Piwil4、Mael和Ddx4基因mRNA转录和蛋白表达水平。结果表明,大鼠肝癌动物模型血清中肿瘤标记物含量明显升高。Piwil4、Mael和Ddx4基因mRNA及蛋白在肝癌模型组织中高表达。研究表明,肝癌模型组织中Piwil4、Mael和Ddx4基因表达水平有望作为肝癌检测的一种分子标志物。     

辣椒CaNAC36转录因子耐盐性分析

【目的】辣椒是中国种植面积最大的蔬菜作物,随着土地盐碱化问题的日趋严重,加强辣椒耐盐机制研究对促进产业可持续发展具有重要意义。因而,急需加快辣椒耐盐相关关键基因的功能研究。【方法】研究组前期挖掘到与辣椒耐盐性相关的转录因子CaNAC36,在此基础上,以耐盐辣椒PI201224和敏盐辣椒PI438643为供试品种,克隆获得CaNAC36全长gDNA和cDNA序列,通过荧光定量分析CaNAC36及可能的互作基因在盐胁迫条件下不同组织部位的表达情况,并进一步结合生物信息学分析探究CaNAC36及其互作基因之间存在的潜在关系。【结果】结果表明,CaNAC36序列在耐盐和敏盐材料中DNA和cDNA同源性分别为99.86%和100%;荧光定量的结果表明,CaNAC36在耐盐材料根和茎组织中表现为诱导上调表达,在敏盐材料根和叶中表现为诱导下调表达;对可能与CaNAC36存在互作关系的48个基因的注释信息进行分析后,发现跨膜蛋白、转运蛋白、水孔蛋白、氯离子通道蛋白、解毒蛋白等14个基因可能与CaNAC36存在功能互作。进一步分析发现,在PI201224和PI438643盐胁迫处理不同时间点、不同组织中,5个相关基因（Capana08g002748、Capana00g004514、Capana09g000275、Capana07g001450、Capana02g001031）的表达呈现显著差异。同时发现,CaNAC36及5个关联基因启动子域含有大量的逆境相关顺式作用元件。【结论】结合基因克隆、基因表达水平分析以及生物信息学分析,表明CaNAC36是辣椒响应盐胁迫的重要转录因子,并可能与其他基因相互作用以提高植株的耐盐性,可为深度研究辣椒耐盐性以及选育耐盐品种提供数据支撑。     

水稻OsRPL36A基因的表达特性研究

【目的】核糖体蛋白（ribosomal protein,RP）是参与蛋白质合成及基因表达调控的一种重要因子,在植物生长发育和胁迫响应过程中具有重要的作用。研究在水稻中克隆了1个核糖体蛋白家族基因OsRPL36A,并对其生物学功能进行初步研究,为后续OsRPL36A基因功能研究提供理论依据和研究方向。【方法】利用生物信息学技术分析OsRPL36A基因结构、顺式作用元件和演化过程;同时利用实时荧光定量PCR（quantitative real-time PCR,qRT-PCR）技术分析OsRPL36A的组织表达特异性、节律表达模式、及其对不同激素和非生物胁迫的响应情况。【结果】（1）OsRPL36A的编码区全长为297 bp,共编码98个氨基酸,属于核糖体蛋白L36超基因家族。（2）OsRPL36A的启动子区包含3个节律表达相关元件、10个光响应元件、14个激素响应元件和27个环境胁迫响应元件。（3）OsRPL36A在叶片中的表达量相对高于其他组织;具有典型的节律表达模式;且受IAA、高温、低温和渗透胁迫等诱导表达。【结论】OsRPL36A在叶中高表达,具有典型节律表达模式,对IAA显著响应,可能参与热激、低温、盐害和渗透胁迫响应。     

利用DNA免疫技术制备果蝇GBB多克隆抗体及其表达模式的分析

TGF-β信号家族在生物体生命活动中具有多种发育和生理功能。研究该信号家族在生物体内的表达模式具有重要的意义。gbb是TGF-β信号成员bmp7的果蝇同源基因,为了进一步研究gbb对胚胎发育的影响,本文采用DNA免疫技术制备得到果蝇GBB多克隆抗体。首先提取果蝇总RNA,反转录得到cDNA文库,以该文库为模板克隆出gbb基因编码区序列,构建成真核表达质粒pCAGGS-P7/gbb。采用DNA免疫技术免疫BALB/c小鼠,取心血分离血清制备了GBB多克隆抗体。免疫印迹试验表明制备的GBB多克隆抗体有效,果蝇胚胎免疫荧光分析表明GBB在果蝇胚胎发育0～9 h无明显表达,9 h之后开始高效表达。     

人白细胞介素-36受体拮抗剂基因的克隆及序列分析

[目的]构建人白细胞介素-36受体拮抗剂(interleukin-36 receptor antagonist,IL-36Ra)的真核表达载体,并对其基因全长编码区进行分析。[方法]提取总RNA,逆转录出IL-36Ra c DNA序列。设计人IL-36Ra基因的上游引物和下游引物。利用热启动PCR扩增目的基因,将扩增出的IL-36Ra基因编码区通过限制性内切酶酶切后,把酶切的目的片段与载体pc DNA3.1连接,转化到感受态细胞大肠杆菌DH5α中。通过氨苄青霉素抗性筛选、双酶切及菌落PCR鉴定,最后选取阳性克隆进行测序。[结果]重组载体pc DNA3.1-h IL-36Ra经菌落PCR和酶切鉴定,最后通过序列分析证实,其序列与Gen Bank中数据一致。[结论]人IL-36Ra基因的重组真核表达载体pc DNA3.1-h IL-36Ra的成功构建,为进一步研究IL-36Ra在免疫性疾病中的作用奠定了实验基础。     

睾丸生精细胞凋亡相关基因TSARG1与Mtsarg1的分子克隆及Mtsarg1基因的表达谱分析

从已获得的在隐睾和正常睾丸对照中表达量有明显差异的EST片段（GenBank登录号：BE644538）出发,利用生物信息学和实验技术,克隆了小鼠睾丸生精细胞凋亡相关新基因Mtsarg1及相应的人类新基因TSARG1,Gen-Bank登录号分别为AF399971和AY032925。小鼠Mtsargl与人类TSARGl基因在氨基酸水平有55％的一致性和61％相似性,与其他已知蛋白质无明显同源性。小鼠10种组织的RT-PCR分析结果表明,Mtsargl基因在睾丸中高表达,在附睾中呈微弱表达,在其他组织不表达,提示Mtsargl和TSARGl基因在生精细胞凋亡或精子发生中具有潜在的重要作用。     

Expression of two dead box genes (DDX1 and DDX6) is independent of that of MYCN in human neuroblastoma cell lines.

To examine whether two DEAD box genes, DDX1 and DDX6, would have some roles in the progression of tumors, we investigated the correlation of the expression of these genes with that of MYCN in neuroblastomas either with or without MYCN amplification. The mRNA of MYCN was observed only in the cell lines with amplification of MYCN. The mRNAs of DDX1 and DDX6 were found in all the cell lines examined, but the correlation between the mRNA levels of DDX1 or DDX6 and MYCN was poor. These findings suggest that the expression of neither DEAD box gene is correlated with the gene expression of MYCN.     

Cloning and expression analysis of the chicken DEAD box gene DDX1

DEAD box proteins are putative RNA unwinding proteins found in organisms ranging from mammals to bacteria. While some DEAD box genes expressed in higher eukaryotes are ubiquitous, others have distribution profiles that suggest a cell-, tissue-, or developmental-specific role. The DEAD box gene, DDX1, was identified by differential screening of a subtracted retinoblastoma cDNA library. A limited survey of human fetal tissues indicated that DDX1 mRNA has a widespread distribution but is not uniformly expressed in all tissues. To further document the spatial and temporal distribution of DDX1 during embryonic development, we cloned the chicken DDX1 cDNA. The predicted amino acid sequence of chicken DDX1 was 93% identical to that of human DDX1. All DEAD box motifs, as well as a SPRY domain, were present in chicken DDX1. Northern and Western blot analyses showed highest levels of DDX1 at early stages of development. Tissue maturation was generally accompanied by a decrease in expression, although DDX1 levels remained elevated in late embryonic retina and brain. In situ hybridization of retinal tissue sections revealed widespread distribution of DDX1 mRNA at early developmental stages with preferential expression in amacrine and ganglion cells of the differentiated tissue. Preferential expression of DDX1 was also observed in specific areas of the brain in older embryos, such as the external granule layer of the cerebellum. These results suggest a specific role for DDX1 in subsets of differentiated cells as well as a more general role in undifferentiated cells.     

Gene structure of the human DDX3 and chromosome mapping of its related sequences.

The human DDX3 gene (GenBank accession No. U50553) is the human homologue of the mouse Ddx3 gene and is a member of the gene family that contains DEAD motifs. Previously, we mapped the gene to the Xp11.3-11.23. In this report, we describe the structural organization of the human DDX3 gene. It consisted of 17 exons that span approximately 16 kb. An Alu element was present in the intron 13. Its organization was the same as that of the human DBY gene, a closely related sequence present on the Y chromosome. We also identified two processed pseudogenes (DDX3) with a sequence that is highly homologous to those of DDX3 cDNAs, but contain a translation termination codon within its open-reading frame. Pseudogenes are mapped on human chromosomes 4 and X, respectively. In this paper, we discuss the relationships between DDX3 and its related sequences that have been isolated.     

Ddx42p--a human DEAD box protein with RNA chaperone activities

The human gene ddx42 encodes a human DEAD box protein highly homologous to the p68 subfamily of RNA helicases. In HeLa cells, two ddx42 poly(A)⁺ RNA species were detected both encoding the nuclear localized 938 amino acid Ddx42p polypeptide. Ddx42p has been heterologously expressed and its biochemical properties characterized. It is an RNA binding protein, and ATP and ADP modulate its RNA binding affinity. Ddx42p is an NTPase with a preference for ATP, the hydrolysis of which is enhanced by various RNA substrates. It acts as a non-processive RNA helicase. Interestingly, RNA unwinding by Ddx42p is promoted in the presence of a single-strand (ss) binding protein (T4gp32). Ddx42p, particularly in the ADP-bound form (the state after ATP hydrolysis), also mediates efficient annealing of complementary RNA strands thereby displacing the ss binding protein. Ddx42p therefore represents the first example of a human DEAD box protein possessing RNA helicase, protein displacement and RNA annealing activities. The adenosine nucleotide cofactor bound to Ddx42p apparently acts as a switch that controls the two opposing activities: ATP triggers RNA strand separation, whereas ADP triggers annealing of complementary RNA strands.     

DDX4 (VASA) is conserved in germ cell development in marsupials and monotremes

DDX4 (VASA) is an RNA helicase expressed in the germ cells of all animals. To gain greater insight into the role of this gene in mammalian germ cell development, we characterized DDX4 in both a marsupial (the tammar wallaby) and a monotreme (the platypus). DDX4 is highly conserved between eutherian, marsupial, and monotreme mammals. DDX4 protein is absent from tammar fetal germ cells but is present from Day 1 postpartum in both sexes. The distribution of DDX4 protein during oogenesis and spermatogenesis in the tammar is similar to eutherians. Female tammar germ cells contain DDX4 protein throughout all stages of postnatal oogenesis. In males, DDX4 is in gonocytes, and during spermatogenesis it is present in spermatocytes and round spermatids. A similar distribution of DDX4 occurs in the platypus during spermatogenesis. There are several DDX4 isoforms in the tammar, resulting from both pre- and posttranslational modifications. DDX4 in marsupials and monotremes has multiple splice variants and polyadenylation motifs. Using in silico analyses of genomic databases, we found that these previously unreported splice variants also occur in eutherians. In addition, several elements implicated in the control of Ddx4 expression in the mouse, including RGG (arginine-glycine-glycine) and dimethylation of arginine motifs and CpG islands within the Ddx4 promoter, are also highly conserved. Collectively these data suggest that DDX4 is essential for the regulation of germ cell proliferation and differentiation across all three extant mammalian groups-eutherians, marsupials, and monotremes.     

Analog sensitive chemical inhibition of the DEAD‐box protein DDX3

Proper maintenance of RNA structure and dynamics is essential to maintain cellular health. Multiple families of RNA chaperones exist in cells to modulate RNA structure, RNA–protein complexes, and RNA granules. The largest of these families is the DEAD‐box proteins, named after their catalytic Asp‐Glu‐Ala‐Asp motif. The human DEAD‐box protein DDX3 is implicated in diverse biological processes including translation initiation and is mutated in numerous cancers. Like many DEAD‐box proteins, DDX3 is essential to cellular health and exhibits dosage sensitivity, such that both decreases and increases in protein levels can be lethal. Therefore, chemical inhibition would be an ideal tool to probe the function of DDX3. However, most DEAD‐box protein active sites are extremely similar, complicating the design of specific inhibitors. Here, we show that a chemical genetic approach best characterized in protein kinases, known as analog‐sensitive chemical inhibition, is viable for DDX3 and possibly other DEAD‐box proteins. We present an expanded active‐site mutant that is tolerated in vitro and in vivo, and is sensitive to chemical inhibition by a novel bulky inhibitor. Our results highlight a course towards analog sensitive chemical inhibition of DDX3 and potentially the entire DEAD‐box protein family.     

Evolution of the DEAD box helicase family in chicken: chickens have no DHX9 ortholog

Viral RNA represents a pattern molecule that can be recognized by RNA sensors in innate immunity. Humans and mice possess cytoplasmic DNA/RNA sensors for detecting viral replication. There are a number of DEAD (Asp‐Glu‐Ala‐Asp; DExD/H) box‐type helicases in mammals, among which retinoic acid‐inducible gene 1 (RIG‐I) and melanoma differentiation‐associated protein 5 (MDA50) are indispensable for RNA sensing; however, they are functionally supported by a number of sensors that directly bind viral RNA or replicative RNA intermediates to convey signals to RIG‐I and MDA5. Some DEAD box helicase members recognize DNA irrespective of the origin. These sensors transmit IFN‐inducing signals through adaptors, including mitochondrial antiviral signaling. Viral double‐stranded RNAs are reportedly sensed by the helicases DDX1, DDX21, DHX36, DHX9, DDX3, DDX41, LGP2 and DDX60, in addition to RIG‐I and MDA5, and induce type I IFNs, thereby blocking viral replication. Humans and mice have all nucleic acid sensors listed here. In the RNA sensing system in chicken, it was found in the present study that most DEAD box helicases are conserved; however, DHX9 is genetically deficient in addition to reported RIG‐I. Based on the current genome databases, similar DHX9 deficiency was observed in ducks and several other bird species. Because chicken, but not duck, was found to be deficient in RIG‐I, the RNA‐sensing system of chicken lacks RIG‐I and DHX9 and is thus more fragile than that of duck or mammal. DHX9 may generally compensate for the function of RIG‐I and deficiency of DHX9 possibly participates in exacerbations of viral infection such as influenza in chickens.     

Association of human DEAD box protein DDX1 with a cleavage stimulation factor involved in 3'-end processing of pre-MRNA

DEAD box proteins are putative RNA helicases that function in all aspects of RNA metabolism, including translation, ribosome biogenesis, and pre-mRNA splicing. Because many processes involving RNA metabolism are spatially organized within the cell, we examined the subcellular distribution of a human DEAD box protein, DDX1, to identify possible biological functions. Immunofluorescence labeling of DDX1 demonstrated that in addition to widespread punctate nucleoplasmic labeling, DDX1 is found in discrete nuclear foci approximately 0.5 microm in diameter. Costaining with anti-Sm and anti-promyelocytic leukemia (PML) antibodies indicates that DDX1 foci are frequently located next to Cajal (coiled) bodies and less frequently, to PML bodies. Most importantly, costaining with anti-CstF-64 antibody indicates that DDX1 foci colocalize with cleavage bodies. By microscopic fluorescence resonance energy transfer, we show that labeled DDX1 resides within a F?rster distance of 10 nm of labeled CstF-64 protein in both the nucleoplasm and within cleavage bodies. Coimmunoprecipitation analysis indicates that a proportion of CstF-64 protein resides in the same complex as DDX1. These studies are the first to identify a DEAD box protein associating with factors involved in 3'-end cleavage and polyadenylation of pre-mRNAs.