Isolation and sequence analysis of the Sox-1, -2, -3 homologs in Trionyx sinensis and Alligator sinensis having temperature-dependent sex determination

Members of the Sox gene family are characterized by an HMG-box that shows sequence similarity with that of the mouse testis-determining gene Sry. Using degenerate primers PCR, seven and eight HMG-box motifs of Sry-related genes were cloned and sequenced from genomic DNA of Trionyx sinensis (termed TS41-47) and Alligator sinensis (AS41-48) with TSD (temperature-dependent sex determination). Among 15 Sry-related genes, TS41, TS42, AS41, and AS42 shared 80, 72, 81, and 79% amino acid identity, respectively, with each HMG-box domain of the mouse Sox-1, -2, and -3 genes by Blast analysis. Molecular phylogenetic analysis showed that the clustering of TS41-42 and AS41-42 was distant to the clustering of the nonreptilian vertebrate Sox-1, -2, -3 homologs, including fish, amphibian, bird, and mammals. The amino acid identity among TS41-42, AS41-42, and the nonreptilian vertebrate Sox-1, -2, -3 homologs is lower than identities among the Sox-1, -2, -3 homologs, suggesting that the sequence changes in TS41-42 of Trionyx sinensis and AS41-42 of Alligator sinensis might have occurred after the diversification of amniotes.     

Sox9在温度依赖型性别决定中的功能初探

在一些爬行动物中,个体的性别完全取决于胚胎发育过程中的环境温度,称之为温度依赖型性别决定(temperaturedependent sex determination,TSD).TSD的分子机制长期是个谜,特别是调控早期性腺分化的分子基础仍不清楚.本文通过表达分析和基因敲低手段研究了Sox9基因在红耳龟雄性性腺分化中的生物学功能,为TSD动物的性别决定和性腺发育的分子机制的研究奠定了基础.qRT-PCR显示,从性腺分化前的17期起,Sox9呈现产雄温度(male-producing temperature,MPT)性腺特异性高表达,而在产雌温度(female-producing temperature,FPT)性腺中表达水平极低.免疫组化进一步证实了SOX9蛋白的MPT特异性表达趋势,其定位于Sertoli前体细胞核中.温度置换实验显示,与MPT性腺相比,MPT→FPT性腺中(16期置换)的Sox9表达量从17期起就显著降低,表明Sox9能快速响应温度变化.同时MPT性腺经过雌激素处理后,Sox9表达量亦快速下调.功能缺失研究显示,经过Sox9-RNAi处理后,90.9%(20/22)的MPT性腺结构明显雌性化,皮质区高度发育,髓质区退化,揭示Sox9的敲低能导致雄性向雌性性逆转.上述研究表明,Sox9是红耳龟早期睾丸分化的关键调控因子,参与TSD的雄性分化通路.     

苹果乙烯不敏感基因EIN2片段的克隆及序列分析

分别以苹果果实总DNA和cDNA为模板,采用PCR、RT-PCR方法扩增、克隆乙烯不敏感基因(ethyleneinsensitive 2,EIN2),并利用生物信息学方法分析其核苷酸序列和蛋白质结构。结果表明:(1)以DNA和cDNA为模板的扩增结果完全相同,扩增的EIN2基因片段为4 378bp,尚未发现有内含子,开放阅读框全长3 282bp,编码1 093个氨基酸;苹果EIN2相对分子质量为118.9kD,等电点为5.52,其蛋白可能为脂溶性疏水蛋白。(2)所克隆苹果EIN2基因编码的氨基酸序列与拟南芥(AAD41077.1)、碧桃(ACY78397.1)和葡萄(CAN66374.1)EIN2基因编码的氨基酸序列一致性分别为52%、79%、62%。(3)构建的EIN2基因进化树显示,拟南芥、小盐芥、甜瓜、杨毛果EIN2基因亲缘关系较近,聚为一类;葡萄为一类;蒺藜苜蓿为一类;碧桃、矮牵牛、西红柿聚为一类;苹果单独为一类。而且苹果EIN2基因与碧桃等同源基因的亲缘关系相对较近,与拟南芥、小盐芥同源基因的亲缘关系相对较远。     

玉米生物钟基因ZmPRR1-2的克隆及表达分析

为探究玉米生物钟基因ZmPRR1-2的功能及表达特性,解析玉米光周期途径调控开花的机理,该研究以玉米骨干自交系‘黄早4’为材料,克隆ZmPRR1-2基因的cDNA序列并进行生物信息学分析;利用qRT-PCR技术对该基因进行组织特异性表达分析和48 h的昼夜节律表达分析。结果表明：(1)成功克隆获得ZmPRR1-2基因的编码区全长1 554 bp,编码517个氨基酸,编码的蛋白属于PRR基因家族,含有1个REC结构域和1个CCT结构域,多序列比对和系统进化分析显示ZmPRR1-2基因在禾本科植物中高度保守;ZmPRR1-2蛋白属亲水性蛋白,不包含跨膜结构域和信号肽。(2)ZmPRR1-2基因在玉米叶片中的表达量最高,显著高于其他7个组织,表明该基因主要在叶片中发挥功能,而在果穗和花丝中表达量相对较低,且显著低于雄穗中的表达量。(3)昼夜节律表达分析显示,在短日照条件下,ZmPRR1-2基因的表达量于光照3 h后开始逐渐上升,在光照结束后3 h时达到表达高峰;在长日照条件下,于光照6 h后ZmPRR1-2基因的表达量才开始逐渐上升,且在光照结束时达到表达高峰。研究认为,ZmPRR1-2基因...     

富士苹果MdAPETALA2基因的克隆与表达分析

基于苹果基因组测序序列,从‘长富6号’富士苹果中分离了MdAPETALA2基因序列,通过生物信息学方法分析结构特征,利用实时荧光定量RT-PCR技术研究其在不同器官中的表达特性。结果表明:(1)MdAPETA-LA2基因cDNA序列为1 614bp,该基因最大开放阅读框为1 389bp,编码462个氨基酸,含有2个保守的AP2结构域和核定位信号;其编码区含有8个内含子和9个外显子;启动子区域含有许多光响应元件,如ATCT-motif、G-Box、GA-motif、I-box、Sp1、TCCC-motif等,以及水杨酸响应元件、赤霉素响应元件、防御和逆境响应元件等。(2)MdAPETALA2基因在苹果各种器官中均有表达,但不同组织中表达量存在差异,在种子中的表达量最高,其次是根和花,在叶和茎中的表达量最低;在花药中的表达量最大,其次是花托和子房,在花瓣、花梗和花柱中的表达量相对较少。(3)苹果MdAPETALA2基因属于AP2亚族,可能在种子的发育过程中起着非常重要的作用。     

梭梭糖基转移酶基因克隆及序列分析

以梭梭叶片为材料,根据其他植物糖基转移酶基因的保守序列设计引物,采用同源基因克隆及RACE-PCR方法克隆到2个同源的序列,分别命名为 HaUGT1和 HaUGT2。基因测序结果显示, HaUGT1基因编码区长1 485 bp,编码495个氨基酸; HaUGT2基因编码区长1 185 bp,编码394个氨基酸。HaUGT1和HaUGT2蛋白具有保守的PSPG 基序、UDP-葡萄糖基转移酶结构域,与其他植物中的糖基转移酶蛋白同源性较高。     

棉花EIN3/EIL家族基因序列分析及GhEIL3基因克隆

该研究以拟南芥AtEIN3基因为探针,从陆地棉TM-1全基因组测序数据库中筛选其同源序列,序列分析得到16条具有EIN3结构域的基因序列。对陆地棉EIN3/EIL家族基因的基因结构、系统进化、序列相似性及结构域分布情况进行分析,发现它们与拟南芥EIN3/EIL家族基因在N端具有较高相似度,其中15条基因序列包含5个保守结构,1条包含4个保守结构。在此基础上,采用RT-PCR方法从抗枯萎病的陆地棉品种‘中棉所12’中克隆得到一个新的EIN3/EIL家族基因,命名为GhEIL3(GenBank登录号为KY072936)。序列分析表明:GhEIL3基因开放阅读框长1 092bp,编码363个氨基酸,含有一个EIN3结构域。实时荧光定量PCR(qRT-PCR)结果显示,GhEIL3基因在枯萎病菌诱导后呈上调表达,诱导后1h其相对表达量达到最大值,推测GhEIL3基因可能参与棉花对枯萎病菌的防御反应。     

Production and characterization of thermostable cellulases from Streptomyces transformant T3-1

A total of 26 thermophilic isolates, selected from a compost of agricultural waste, which was mostly composed of vegetable, corncob and rice straw, were cultivated at 50 °C for further studies of thermostable cellulase production. The thermostable cellulase gene from the chromosomal DNA of actinomycetes isolate no. 10 was shotgun-cloned and transformed into Streptomyces sp. IAF 10-164. A transformant, T3-1, was found to be a good strain for the production of thermostable cellulases. Cultivation of T3-1 in modified Mandels–Reese broth containing 1% carboxymethylcellulose (CMC)-sodium salt and the optimal condition for microbial growth were studied. Batch cultivation in a flask revealed that CMCase and Avicelase production reached the maximum between the third to fifth day, whereas maximum -glucosidase production occurred on the ninth day. Microbial biomass increased from the first day to the fifth day and then decreased. The crude enzyme had the highest activity at 50 °C and at pH 6.5. The enzyme was shown to be a thermostable cellulase whose activities were stable at 50 °C for more than 7 days.     

Isolation and characterization of Schizosaccharomyces pombe mutants phenotypically similar to ras1-

Summary We isolated mutants of Schizosaccharomyces pombe which have deformed cell morphology, are deficient in conjugation and poor in sporulation. This phenotype is characteristic of the ras1 defective mutant previously identified. Tests of the mutants for allelism using cell fusion showed that they define five complementation groups, one of which is ras1 itself. The others are named ral1 through ral4 (ras like). Mutants in ral3 or ral4 conjugate at a very low frequency, while the others apparently do not conjugate at all. Plasmid clones complementing ral1, ral2 or ral3, which apparently carry the respective gene, were isolated from S. pombe genomic libraries. Multiple copies of either the ral2 or the ral3 gene could partially restore mating ability in ral1 ^–strains. Multiple copies of the ras1 gene could partially restore mating ability in ral1 ^–and ral2 ^–strains. These results suggest that the ral1, ral2 and ras1 genes may function in a common pathway in that order. The ral3 gene may influence this pathway. Analysis of these gene products will aid identification of factors which interact with Ras proteins.     

B-class MADS-box genes in trioecious papaya: two paleoAP3 paralogs, CpTM6-1 and CpTM6-2, and a PI ortholog CpPI

In the ABC model of flower development, B function organ-identity genes act in the second and third whorls of the flower to control petal and stamen identity. The trioecious papaya has male, female, and hermaphrodite flowers and is an ideal system for testing the B-class gene expression patterns in trioecious plants. We cloned papaya B-class genes, CpTM6-1, CpTM6-2, and CpPI, using MADS box gene specific degenerate primers followed by cDNA library screening and sequencing of positive clones. While phylogenetic analyses show that CpPI is the ortholog of the Arabidopsis gene PI, the CpTM6-1 and CpTM6-2 loci are representatives of the paralogous TM6 lineage that contain paleoAP3 motifs unlike the euAP3 gene observed in Arabidopsis. These two paralogs appeared to have originated from a tandem duplication occurred approximately 13.4 million year ago (mya) (bootstrap range 13.36 ± 2.42). In-situ hybridization and RT-PCR showed that the papaya B-class genes were highly expressed in young flowers across all floral organ primordia. As the flower organs developed, all three B-class genes were highly expressed in petals of all three-sex types and in stamens of hermaphrodite and male flowers. CpTM6-1 expressed at low levels in sepals and carpels, whereas CpTM6-2 expressed at a low level in sepals and at a high level in leaves. Our results showed that B-class gene homologs could function as predicted by the ABC model in trioecous flowers but differential expressions of CpTM6-1, and CpTM6-2, and CpPI suggested the diversification of their functions after the duplication events. Christine M. Ackerman, Qingyi Yu contributed equally to this work.     

青稞HvnRPS2基因克隆及其在条纹病胁迫下的表达分析

为探索NBS LRR类基因RPS2在青稞抗条纹病过程中的作用,该研究以抗条纹病青稞品种‘昆仑14号’和感病品种‘Z1141’为材料,参照转录组序列设计引物,克隆得到一个差异表达的青稞HvnRPS2基因,进行相应的生物信息学分析,并采用实时荧光定量PCR(qRT PCR)法分析HvnRPS2基因在条纹病侵染下不同抗性青稞品种的表达模式。结果表明：(1)HvnRPS2基因全长3 089 bp,无内含子,包含1个2 760 bp的开放阅读框,编码919个氨基酸,理论等电点为5.93,预测蛋白分子量为104.2 kD,其编码的蛋白为亲水性蛋白,二级结构主要由无规则卷曲和ɑ 螺旋组成。(2)蛋白质多序列比对及进化树分析表明,HvnRPS2含有高度保守的NB ARC和LRR结构域,属于NB ARC蛋白家族成员,与大麦HvRPS2和水稻OsRPS2亲缘关系最近。(3)qRT PCR分析显示,随着条纹病感病时间的延长,青稞HvnRPS2基因表达量呈先降低后升高再降低的模式;与正常叶片相比,感病叶片的HvnRPS2基因表达量显著下调,且感病品种表达量下调值显著低于抗病品种(P＜0.01)。研究认为,HvnRPS2在青稞抗条纹病过程中发挥重要的负调控作用。研究结果为进一步探究该基因在青稞抗条纹病中的调控机理奠定基础。     

Comparative Genomic Sequence Analysis of the FXR Gene Family: FMR1, FXR1, and FXR2

Mutations in the X-linked gene FMR1 cause fragile X syndrome, the leading cause of inherited mental retardation. Two autosomal paralogs of FMR1 have been identified, and are known as FXR1 and FXR2. Here we describe and compare the genomic structures of the mouse and human genes FMR1, FXR1, and FXR2. All three genes are very well conserved from mouse to human, with identical exon sizes for all but two FXR2 exons. In addition, the three genes share a conserved gene structure, suggesting they are derived from a common ancestral gene. As a first step towards exploring this hypothesis, we reexamined the Drosophila melanogaster gene Fmr1, and found it to have several of the same intron/exon junctions as the mammalian FXRs. Finally, we noted several regions of mouse/human homology in the noncoding portions of FMR1 and FXR1. Knowledge of the genomic structure and sequence of the FXR family of genes will facilitate further studies into the function of these proteins.     

The 14-3-3 Proteins: Gene,Gene Expression,and Function

14-3-3 Proteins were discovered by Moore and Perez in the soluble extract of bovine brain. These proteins are highly abundant in the brain. In this review 14-3-3 cDNA cloning, nucleotide sequence of 14-3-3 cDNA, the structure of 14-3-3 gene and 14-3-3 gene expression, in situ hybridization of 14-3-3 mRNA in the brain, the function and regulation of 14-3-3 protein, the binding of 14-3-3 protein to other proteins, the effects of 14-3-3 protein on the binding of a protein to other proteins, and the effect on protein kinase, etc., are concisely described. From the recent rapid development of proteom technology, markedly more target proteins of 14-3-3 protein should be discovered.     

蔗茅EfMYB1基因的克隆与表达分析

为了充分利用蔗茅(Erianthus fulvus)野生资源,挖掘其优良的抗性基因,丰富转基因甘蔗育种候选基因库,该研究结合蔗茅转录组数据,以蔗茅99 1无性系为试验材料,利用RT PCR技术克隆蔗茅MYB基因,并对其进行生物信息学分析及胁迫表达分析,以解析蔗茅的耐寒机理,为转基因甘蔗育种奠定理论基础。结果表明：(1)成功克隆得到一个蔗茅MYB基因,命名为EfMYB1基因(登录号ON586646)。(2)生物信息学分析表明,EfMYB1基因全长1 000 bp,ORF为759 bp,编码251个氨基酸;编码蛋白具有一个保守的SANT结构域,无跨膜结构和信号肽,有多个磷酸化位点;二级结构与三级结构主要以α螺旋和无规则卷曲为主;与南荻相似性最高,遗传距离最近。(3)qRT PCR分析结果发现,EfMYB1基因在蔗茅根和叶组织中的相对表达量随低温胁迫时间的持续而逐渐显著上调,并于胁迫72 h时达到最大值,而在茎中的表达则几乎没有变化;茉莉酸甲酯胁迫下,EfMYB1基因的相对表达量呈先升高后降低的趋势,且在处理6 h时达到最高值;脱落酸胁迫下EfMYB1基因的表达水平较0 h时极显著降低。研究认为,EfMYB1基因属于低温胁迫响应基因,可能参与蔗茅低温胁迫下的应答反应。     

Fine Mapping and in silico Isolation of the EUI1 Gene Controlling Upper Internode Elongation in Rice

Upper internode elongation in rice is an important agronomic trait. Well-known mutants with an elongated uppermost internode (eui) are important germplasms for developing unsheathed-panicle male-sterile lines in hybrid rice breeding. We finely mapped the eui1 gene and identified its candidate gene using in silico analysis based on previous research work and rice genomic sequence data. The rice eui1 gene was mapped to two overlapping BAC clones, OSJNBa0095J22 and OSJNBb0099O15, between the markers AC40 and AC46, that were 0.64 cM apart and spanned approximately 152 kb. A simple sequence repeat (SSR) marker AC41 that cosegregated with eui1 was located in an intron of a putative cytochrome P450-related gene. In silico analysis suggested that this encoded the cytochrome CYP714D1. Allelic sequencing confirmed that EUI1 corresponded to this P450 gene. A gamma ray-induced eui1 mutant carried a deletion in exon II of the EUI1 gene, and resulted in a frame-shift deletion that produced a truncated polypeptide. We conclude that the EUI1 gene controlling the upper internode elongation in rice is 9804 bp long, and comprises two exons and one intron. The length of the cDNA is 1931 bp containing a 1734 bp ORF, a 110 bp 5′-UTR and a 87 bp 3′-UTR. The ORF encodes an unknown 577 amino acid functional protein, that appears to be a member of the cytochrome P450 family. Hongli Ma, Shubiao Zhang: These authors contributed equally to this work     

Isolation,expression, and evolution of the gene encoding mitochondrial elongation factor Tu in Arabidopsis thaliana

We have characterized a second nuclear gene (tufM) in Arabidopsis thaliana that encodes a eubacterial-like protein synthesis elongation factor Tu (EF-Tu). This gene does not closely resemble the previously described Arabidopsis nuclear tufA gene, which encodes the plastid EF-Tu, and does not contain sequence elements found in all cyanobacterial and plastid tufA genes. However, the predicted amino acid sequence includes an N-terminal extension which resembles an organellar targeting sequence and shares three unique sequence elements with mitochondrial EF-Tu's, from Saccharomyces cerevisiae and Homo sapiens, suggesting that this gene encodes the Arabidopsis mitochondrial EF-Tu. Consistent with this interpretation, the gene is expressed at a higher level in flowers than in leaves. Phylogenetic analysis confirms the mitochondrial character of the sequence and indicates that the human, yeast, and Arabidopsis tufM genes have undergone considerably more sequence divergence than their cytoplasmic counterparts, perhaps reflecting a cross-compartmental acceleration of gene evolution for components of the mitochondrial translation apparatus. As previously observed for tufA, the tufM gene is present in one copy in Arabidopsis but in several copies in other species of crucifers.     

Seasonal changes of sperm storage and correlative structures in male and female soft-shelled turtles, Trionyx sinensis

Reproductive ducts of male and female soft-shelled turtles, Trionyx sinensis were examined throughout the year (March, May, September, December) using brightfield and electron microscopes (TEM and SEM), to determine the location and histomorphological characteristics of sperm storage structures as well as their changes at different phases of the seasonal reproductive cycle. Sperm stored in the epididymis were also examined. In the male, spermatogenesis is initiated in spring (May), and then the mature sperm are released in autumn as an episodic event. Spermatogenesis is inactive in winter. However, in this species, the epididymis contains sperm throughout the entire year. Sperm observed in the epididymis are intact and some structures are uniquely different from other reptiles, and is characterized by 35–40 concentric mitochondria with a dense core in the centre. Many glycogen granules are observed in the cytoplasm of the midpiece. However, the epithelial cell type of epididymal duct change in different seasons. The cells are fully developed with a highly secretory activity in September. The materials secreted from the epithelium might have the function as nourishment for the stored sperm. Sperm storage structures in the form of tubules are observed in the wall of the isthmus of the oviduct in hibernating females but are absent in the groups of May and September. These tubules develop either by folding or fusion of the oviductal mucosal folds and are lined by both ciliated and secretory cells. These tubules might provide a microenvironment for the sperm to enable its long-term storage. After being separated 4 months (December–March) from the male, sperm are observed in the tubules of the isthmus of the oviduct. The unique character of the sperm combined with the special sperm storage structures enable the sperm to maintain fertility and activity during their storage.     

续随子ElFAD2基因的序列及表达特性分析

为了研究油酸脱氢酶(FAD2)基因ElFAD2对续随子(Euphorbia lathyris L.)中不饱和脂肪酸合成的调控作用,该研究在续随子转录组数据的基础上经筛选获得ElFAD2基因序列,并对其序列及表达特性进行分析。序列分析结果显示,ElFAD2基因全长1 907 bp,ORF长1 152 bp,共编码383个氨基酸,包含有典型的脂肪酸去饱和酶结构域。续随子ElFAD2蛋白理论等电点为8.08,属于稳定蛋白,包含4个跨膜区和3个保守的组氨酸簇。基于FAD2的系统发育分析表明,续随子与同科植物乌桕(Triadica sebifera L.)的亲缘关系最近。荧光定量PCR分析发现,ElFAD2基因在不同器官中均有表达,且在花后15 d的种子中表达量最高,在叶与花后30 d及45 d种子中的表达量相当,而在根、茎、花中的表达量最低。该研究结果为深入探讨续随子ElFAD2基因的生物学功能提供了基础数据,也为解析续随子种子中脂肪酸合成的分子机制奠定了基础。     

小花草玉梅正常和自然变异植株的AP3-3基因研究

野生小花草玉梅(Anemone rivularis var.flore-minore)正常植株和花被片自然变异植株的外观形态差异很大,该研究以二者为材料,利用常规PCR和高效热不对称PCR(Hi-Tail PCR)技术从其正常和变异植株的基因组中各分离得到1个B类基因。序列分析证明,二者隶属于B类MADS-box基因AP3家族的旁系同源基因AP3-3分枝,分别命名为NArAP3-3(正常植株)和VArAP3-3(变异植株)。NArAP3-3基因全长3 795bp,VArAP3-3基因全长3 898bp,二者均含有1个666bp的开放阅读框(ORF),可编码221个氨基酸,具有典型的植物MADS-box基因结构,其编码肽链包含了MADS区、K区、Ⅰ区和C区。对比NArAP3-3和VArAP3-3基因的全长序列,发现VArAP3-3基因比NArAP3-3多了1段49bp的插入,且在ORF序列与NArAP3-3基因相比有4个碱基突变。对二者的全长序列、所编码的221个氨基酸及插入序列的生物信息学分析显示,二者在基因启动子、蛋白质基本性质、结构功能域、二级三级预测结构等方面均有差异,推测这些差异可能是花被片变异产生的原因之一。该研究结果为进一步探索其变异机制奠定了基础。