不同昆虫泛素延伸蛋白基因的生物信息学分析

采用生物信息学方法系统分析了甜菜夜蛾、菜粉蝶、烟夜蛾和黑腹果蝇泛素延伸蛋白(UBE)基因序列的遗传多样性、分子进化及其编码氨基酸序列的结构功能域和基序特点.结果显示,4种昆虫UBE基因序列的同源性较高(81.8%～99.7%),且遗传距离较近(0.003～0.199),均编码ubiquitin/L40 UBE.共检出8...     

Fibroblast growth factor receptors from liver vary in three structural domains.

Changes in heparin-binding fibroblast growth factor gene expression and receptor phenotype occur during liver regeneration and in hepatoma cells. The nucleotide sequence of complementary DNA predicts that three amino-terminal domain motifs, two juxtamembrane motifs, and two intracellular carboxyl-terminal domain motifs combine to form a minimum of 6 and potentially 12 homologous polypeptides that constitute the growth factor receptor family in a single human liver cell population. Amino-terminal variants consisted of two transmembrane molecules that contained three and two immunoglobulin-like disulfide loops, as well as a potential intracellular form of the receptor. The two intracellular juxtamembrane motifs differed in a potential serine-threonine kinase phosphorylation site. One carboxyl-terminal motif was a putative tyrosine kinase that contained potential tyrosine phosphorylation sites. The second carboxyl-terminal motif was probably not a tyrosine kinase and did not exhibit the same candidate carboxyl-terminal tyrosine phosphorylation sites.     

Cell cycle regulation of myosin-V by calcium/calmodulin-dependent protein kinase II

Organelle transport by myosin-V is down-regulated during mitosis, presumably by myosin-V phosphorylation. We used mass spectrometry phosphopeptide mapping to show that the tail of myosin-V was phosphorylated in mitotic Xenopus egg extract on a single serine residue localized in the carboxyl-terminal organelle-binding domain. Phosphorylation resulted in the release of the motor from the organelle. The phosphorylation site matched the consensus sequence of calcium/calmodulin-dependent protein kinase II (CaMKII), and inhibitors of CaMKII prevented myosin-V release. The modulation of cargo binding by phosphorylation is likely to represent a general mechanism regulating organelle transport by myosin-V.     

月季花瓣丝氨酸蛋白酶基因RhSep1的克隆及生物信息学分析

利用RT-PCR技术,从切花月季品种"Samantha"中克隆丝氨酸蛋白酶基因RhSep1。利用生物信息学技术对所得到的丝氨酸蛋白酶RhSep1序列进行结构与功能预测。结果表明:RhSep1基因全长2 442 bp,开放阅读框编码769个氨基酸,推定该丝氨酸蛋白酶分子质量为80.48 kD。通过NCBI和MEROPS肽酶数据库等对Rh-Sep1进行Protein Blast,发现RhSep1具有肽酶S8₃家族SA的典型结构域Petidase_S8₃（序列为Tyr-108-Leu-341）和PA_subtilisin_like的结构域（序列为Tyr-348-Ile-474）。预测RhSep1可能具有信号肽、明显疏水区和典型跨膜区,同时RhSep1氨基酸序列中存在较多蛋白激酶C和酪蛋白激酶Ⅱ磷酸化位点、豆蔻酰化位点。这些活性位点往往与蛋白的磷酸化、G蛋白相互作用等信号转导事件有关,RhSep1可能存在复杂的蛋白水平调控机制。     

Cloning and Bioinformatics Analysis of ZmERECTA-LIKE1 and Construction of Plant Expression Vector

Objective] This study was conducted to clone and analyze ERECTA-LIKE1 gene in Zea mays by PCR and bioinfor-matics methods and to construct plant expression vector pCambia3301-zmERECTA-LIKE1. [Method] zmERECTA-LIKE1 (zmERL1) gene was obtained using RT-PCR, and physical-chemical properties were analyzed by bioinformatics methods, including domains, transmembrane regions, N-Glycosylation potential sites phosphorylation sites, and etc. [Result] Bioinformatics results showed that zmERL1 gene was 2 169 bp, which encoded a protein consisting of 722 amino acids, 11 N-glycosylation potential sites and 42 kinase specific phosphorylation sites. According to CDD2.23 and TMHMM Server v. 2.0 software, there were leucine-rich repeats, a PKC domain and a transmembrane region in this protein. The theoretical pI and molecular weight of zmERL1 encoded protein was 6.20 and 79 184.8 using Compute PI/Mw tool. Furthermore, we constructed the plant expression vector pCambia3301-zmERECTA-LIKE1 by subcloning zmERL1 gene into pCambia3301 instead of GUS. [Conclusion] The results provide a theoretical basis for the application of zmERL1 gene in future study.     

Autophosphorylation of protein kinase C at three separated regions of its primary sequence

The major autophosphorylation sites of the rat beta II isozyme of protein kinase C were identified. The modified threonine and serine residues were found in the amino-terminal peptide, the carboxyl-terminal tail, and the hinge region between the regulatory lipid-binding domain and the catalytic kinase domain. Because this autophosphorylation follows an intrapeptide mechanism, extraordinary flexibility of the protein is necessary to phosphorylate the three regions. Comparison of the sequences surrounding the modified residues showed no obvious recognition motif nor any similarity to substrate phosphorylation sites, suggesting that proximity to the active site may be the primary criterion for their phosphorylation.     

Bora and the kinase Aurora a cooperatively activate the kinase Plk1 and control mitotic entry

A central question in the study of cell proliferation is, what controls cell-cycle transitions? Although the accumulation of mitotic cyclins drives the transition from the G2 phase to the M phase in embryonic cells, the trigger for mitotic entry in somatic cells remains unknown. We report that the synergistic action of Bora and the kinase Aurora A (Aur-A) controls the G2-M transition. Bora accumulates in the G2 phase and promotes Aur-A-mediated activation of Polo-like kinase 1 (Plk1), leading to the activation of cyclin-dependent kinase 1 and mitotic entry. Mechanistically, Bora interacts with Plk1 and controls the accessibility of its activation loop for phosphorylation and activation by Aur-A. Thus, Bora and Aur-A control mitotic entry, which provides a mechanism for one of the most important yet ill-defined events in the cell cycle.     

荞麦ARF基因家族的鉴定及生物信息学分析

生长素响应因子(auxin response factor, ARF)基因应答了生长素信号,在植物生长发育中具有重要的调控作用。以荞麦基因组数据库为基础,利用BlastP比对程序共鉴定了21个荞麦ARF基因,并对其基因结构、编码蛋白理化性质、保守结构域、保守基序、亚细胞定位、潜在磷酸化位点及系统进化关系进行了分析。基因结构分析表明,21个荞麦ARF基因均含有内含子,且不同基因间内含子数目存在较大差异。保守结构域分析显示,21个ARF蛋白均含有保守的B3和ARF结构域,部分ARF蛋白还含有Aux/IAA结构域。蛋白保守基序分析表明,21个ARF蛋白共有10个保守基序,基序长度在13~55个氨基酸之间。亚细胞定位分析表明,大多数ARF蛋白定位于细胞核,个别定位于叶绿体。潜在磷酸化位点分析显示,所有ARF蛋白均含有潜在的丝氨酸(Ser)、苏氨酸(Thr)和酪氨酸(Tyr)磷酸化位点,但各蛋白的不同磷酸化位点的数目差异较大。系统进化分析表明,21个ARF基因可以分为Ⅰ、Ⅱ、Ⅲ三个亚家族,其中,Ⅰ亚家族可以进一步分为Ⅰa和Ⅰb两个家族,Ⅱ亚家族可以进一步分为Ⅱa和Ⅱb两个家族。研究结果为进一步克隆荞麦ARF基因及深入研究它们在荞麦中的功能提供了参考。     

兰州大尾羊PPARG全长cDNA克隆及生物信息学分析

【目的】克隆兰州大尾羊过氧化物酶体增殖物激活受体（peroxisome proliferator-activated receptor gamma, PPARG）基因,分析其序列及编码蛋白的生物学特性,阐明PPARG基因在绵羊中的生物学作用,为生产应用提供理论依据。【方法】根据绵羊PPARG基因CDS序列设计特异性引物,利用RACE和RT-PCR技术克隆获得兰州大尾羊PPARG基因序列,结合生物信息学方法分析其生物学特性。【结果】克隆获得兰州大尾羊PPARG cDNA 序列全长1 774 bp（GenBank序列号：KF727439）,其CDS区片段长1 428 bp,编码475个氨基酸,编码区两侧翼分别具有5’-UTR 131 bp（1-131 nt）和3’-UTR 214 bp（1 560-1 774 nt）。预测兰州大尾羊PPARG蛋白分子量为54.40 kD,理论等电点为4.94。预测PPARG编码蛋白疏水性最大值为3.600,最小值为-2.744,为非跨膜的疏水性蛋白。亚细胞定位主要在细胞质（65.2%）和细胞核（21.7%）中,少量作用于细胞支架（4.3%）和过氧化物酶体（4.3%）,无信号肽,不属于分泌蛋白。预测其氨基酸序列有26个磷酸化位点,无糖基化位点,含有1个ZnF_C4结构域、1个HOLI结构域和1个LCR结构域,二级结构以随机卷曲为主。同源性分析显示兰州大尾羊PPARG核苷酸序列与山羊、野牛、水牛、绵羊、虎鲸、野猪和人类核苷酸序列间的同源性分别为99% 、98% 、97% 、99%、 94%、92%和90%,兰州大尾羊PPARG氨基酸序列与山羊、野牛、水牛、绵羊、虎鲸、野猪和人类核苷酸序列间的同源性分别为100% 、99.8% 、100% 、100%、 98.7%、98.5%和97.5%。系统发育树表明,兰州大尾羊与山羊、绵羊和水牛的进化水平更为接近,与鱼类、人类和鼠类较远。其基因第486位发生碱基转换（C←→T）,第828位发生碱基转换（C←→A）,但其所编码氨基酸不变。【结论】兰州大尾羊与其他物种PPARG在结构上相似性较高,说明该基因具有高度的保守性。推测PPARG蛋白大部分在游离核糖体上合成,其功能与过氧化物酶体有关,该预测结果符合其过氧化物酶体增殖物激活受体的身份。PPARG氨基酸序列有26个可以成为蛋白质激酶磷酸化的位点,某些位点被磷酸化后,可导致一系列肥胖相关基因的功能失调和表达变化, 如胰岛素增敏激素,脂联素( adiponectin)的表达减少。其序列包含的ZnF_C4锌指结构域具有与脂质结合的功能,HOLI即LBD配体结构域在激素信号转导过程中发挥重要作用,其中PPARG锌指结构域中的磷酸化位点Ser112,被MAPK磷酸化后,可以抑制PPARG同配体的结合,从而降低PPARG蛋白的活性,两个结构域均与成脂分化过程相关联。文章为进一步研究PPARG在成脂分化过程中的作用提供了参考。     

A retroviral oncogene, akt, encoding a serine-threonine kinase containing an SH2-like region.

The v-akt oncogene codes for a 105-kilodalton fusion phosphoprotein containing Gag sequences at its amino terminus. Sequence analysis of v-akt and biochemical characterization of its product revealed that it codes for a protein kinase C-related serine-threonine kinase whose cellular homolog is expressed in most tissues, with the highest amount found in thymus. Although Akt is a serine-threonine kinase, part of its regulatory region is similar to the Src homology-2 domain, a structural motif characteristic of cytoplasmic tyrosine kinases that functions in protein-protein interactions. This suggests that Akt may form a functional link between tyrosine and serine-threonine phosphorylation pathways.     

甘蔗钙依赖蛋白激酶基因克隆与序列分析

[目的]克隆甘蔗钙依赖蛋白激酶基因(ScCDPK1),为其功能解析和育种利用打下基础.[方法]根据甘蔗cDNA文库中的CDPK基因序列信息设计引物,利用RT-PCR克隆ScCDPK1基因,并采用在线生物信息学分析软件对其推导蛋白的理化性质、跨膜结构、信号肽及保守结构域等进行预测分析.[结果]克隆获得的ScCDPK1基因完整编码区大小1650 bp,编码549个氨基酸,相对分子量61.971 kD,等电点(pI)6.78,不稳定指数35.63.同源性和遗传进化树分析结果显示,ScCDPK1基因与小麦TaCPK7基因亲缘关系最近,同源性达88%;ScCDPK1蛋白与其他已知CDPK蛋白一致,具有CDPKs家族特有的4个保守区域(可变区、蛋白激酶区、自抑制区和钙离子结合区),其二级结构主要由α螺旋(42.80%)和无规则卷曲(32.97%)构成;蛋白功能分类预测结果显示,ScCDPK1蛋白是一种阳离子通道蛋白,可能参与植物胁迫应答、信号转导和翻译调控等生物反应.[结论]ScCDPK1基因编码的蛋白与其他已知CDPK蛋白一致,具有CDPKs家族特有的4个保守区域,是一种阳离子通道蛋白.     

Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex

The PDZ protein interaction domain of neuronal nitric oxide synthase (nNOS) can heterodimerize with the PDZ domains of postsynaptic density protein 95 and syntrophin through interactions that are not mediated by recognition of a typical carboxyl-terminal motif. The nNOS-syntrophin PDZ complex structure revealed that the domains interact in an unusual linear head-to-tail arrangement. The nNOS PDZ domain has two opposite interaction surfaces-one face has the canonical peptide binding groove, whereas the other has a beta-hairpin "finger." This nNOS beta finger docks in the syntrophin peptide binding groove, mimicking a peptide ligand, except that a sharp beta turn replaces the normally required carboxyl terminus. This structure explains how PDZ domains can participate in diverse interaction modes to assemble protein networks.     

Crystal structure of the malaria vaccine candidate apical membrane antigen 1

Apical membrane antigen 1 from Plasmodium is a leading malaria vaccine candidate. The protein is essential for host-cell invasion, but its molecular function is unknown. The crystal structure of the three domains comprising the ectoplasmic region of the antigen from P. vivax, solved at 1.8 angstrom resolution, shows that domains I and II belong to the PAN motif, which defines a superfamily of protein folds implicated in receptor binding. We also mapped the epitope of an invasion-inhibitory monoclonal antibody specific for the P. falciparum ortholog and modeled this to the structure. The location of the epitope and current knowledge on structure-function correlations for PAN domains together suggest a receptor-binding role during invasion in which domain II plays a critical part. These results are likely to aid vaccine and drug design.     

同安钮夜蛾核型多角体病毒pst I-G片段克隆及序列分析

 【目的】测定同安钮夜蛾核型多角体病毒（OpdiNPV）pst I-G 片断的序列,了解OpdiNPV的遗传结构和与其它昆虫病毒的进化关系。【方法】用pstⅠ酶切病毒基因组,电泳分离并回收pst I-G片段,连接到PUC18,转化入E.coli DH 5α,挑取阳性菌落测序。【结果】该片段长度为5 056 bp,有4个ORF,分别编码ODV-E66的C末端（EU 623602）,P87/VP80的C末端（EU 732665）,ODV-Ec43（EU617337）和Ac108（EU 732666）。ac108基因和odv-ec43起始密码子上游都有1个晚期启动子结构域TAAG,odv-ec43 基因起始密码子上游有2个早期转录起始元件CAGT;由odv-ec43推导的蛋白有2个跨膜螺旋、3个N-糖基化位点、1个N端酰基化位点、7个PKC磷酸化位点、1个酪氨酸激酶磷酸化位点和4个CKⅡ磷酸化位点;p87/vp80基因终止密码子下游有polyA信号。【结论】氨基酸序列同源分析和相似性分析显示Ac108、ODV-E66和 P87/VP80与其它昆虫病毒差异较大,ODV-Ec43的保守性较高。     

Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A

Biological responses to histone methylation critically depend on the faithful readout and transduction of the methyl-lysine signal by "effector" proteins, yet our understanding of methyl-lysine recognition has so far been limited to the study of histone binding by chromodomain and WD40-repeat proteins. The double tudor domain of JMJD2A, a Jmjc domain-containing histone demethylase, binds methylated histone H3-K4 and H4-K20. We found that the double tudor domain has an interdigitated structure, and the unusual fold is required for its ability to bind methylated histone tails. The cocrystal structure of the JMJD2A double tudor domain with a trimethylated H3-K4 peptide reveals that the trimethyl-K4 is bound in a cage of three aromatic residues, two of which are from the tudor-2 motif, whereas the binding specificity is determined by side-chain interactions involving amino acids from the tudor-1 motif. Our study provides mechanistic insights into recognition of methylated histone tails by tudor domains and reveals the structural intricacy of methyl-lysine recognition by two closely spaced effector domains.     

Cloning of an interleukin-3 receptor gene: a member of a distinct receptor gene family

Interleukin-3 (IL-3) binds to its receptor with high and low affinities, induces tyrosine phosphorylation, and promotes the proliferation and differentiation of hematopoietic cells. A binding component of the IL-3 receptor was cloned. Fibroblasts transfected with the complementary DNA bound IL-3 with a low affinity [dissociation constant (Kd) of 17.9 +/- 3.6 nM]. No consensus sequence for a tyrosine kinase was present in the cytoplasmic domain. Thus, additional components are required for a functional high affinity IL-3 receptor. A sequence comparison of the IL-3 receptor with other cytokine receptors (erythropoietin, IL-4, IL-6, and the beta chain IL-2 receptor) revealed a common motif of a distinct receptor gene family.     

Positive regulation of Itk PH domain function by soluble IP4

Pleckstrin homology (PH) domain-mediated protein recruitment to cellular membranes is of paramount importance for signal transduction. The recruitment of many PH domains is controlled through production and turnover of their membrane ligand, phosphatidylinositol 3,4,5-trisphosphate (PIP3). We show that phosphorylation of the second messenger inositol 1,4,5-trisphosphate (IP3) into inositol 1,3,4,5-tetrakisphosphate (IP4) establishes another mode of PH domain regulation through a soluble ligand. At physiological concentrations, IP4 promoted PH domain binding to PIP3. In primary mouse CD4+CD8+ thymocytes, this was required for full activation of the protein tyrosine kinase Itk after T cell receptor engagement. Our data suggest that IP4 establishes a feedback loop of phospholipase C-gamma1 activation through Itk that is essential for T cell development.     

不同花生品种B06基因的克隆与序列分析

Dof（DNA binding with one finger）转录因子是一类植物特有的、进化上高度保守的基因家族,对植物多方面的生理过程均发挥调控作用。根据Dof家族中的一个B06基因的cDNA保守序列设计引物,对8个品种花生的B06基因进行PCR扩增克隆相似基因,并测定序列。实验成功克隆出四粒红和073103的完整...