Beta-arrestin 2 regulates zebrafish development through the hedgehog signaling pathway

beta-arrestins are multifunctional proteins that act as scaffolds and transducers of intracellular signals from heptahelical transmembrane-spanning receptors (7TMR). Hedgehog (Hh) signaling, which uses the putative 7TMR, Smoothened, is established as a fundamental pathway in development, and unregulated Hh signaling is associated with certain malignancies. Here, we show that the functional knockdown of beta-arrestin 2 in zebrafish embryos recapitulates the many phenotypes of Hh pathway mutants. Expression of wild-type beta-arrestin 2, or constitutive activation of the Hh pathway downstream of Smoothened, rescues the phenotypes caused by beta-arrestin 2 deficiency. These results suggest that a functional interaction between beta-arrestin 2 and Smoothened may be critical to regulate Hh signaling in zebrafish development.     

Deconstructing the hedgehog pathway in development and disease

The Hedgehog (Hh) family of secreted signaling proteins is a master regulator of cell fate determination in metazoans, contributing to both pattern formation during embryonic development and postembryonic tissue homeostasis. In a universally used mode of action, graded distribution of Hh protein induces differential cell fate in a dose-dependent manner in cells that receive Hh. Though much of this pathway has been elucidated from genetically based studies in model organisms, such as Drosophila and mice, the importance of Hh-mediated signaling in humans is clearly evident from malformations and a broad range of cancers that arise when the pathway is corrupted.     

Functional genomic analysis of the Wnt-wingless signaling pathway

The Wnt-Wingless (Wg) pathway is one of a core set of evolutionarily conserved signaling pathways that regulates many aspects of metazoan development. Aberrant Wnt signaling has been linked to human disease. In the present study, we used a genomewide RNA interference (RNAi) screen in Drosophila cells to screen for regulators of the Wnt pathway. We identified 238 potential regulators, which include known pathway components, genes with functions not previously linked to this pathway, and genes with no previously assigned functions. Reciprocal-Best-Blast analyses reveal that 50% of the genes identified in the screen have human orthologs, of which approximately 18% are associated with human disease. Functional assays of selected genes from the cell-based screen in Drosophila, mammalian cells, and zebrafish embryos demonstrated that these genes have evolutionarily conserved functions in Wnt signaling. High-throughput RNAi screens in cultured cells, followed by functional analyses in model organisms, prove to be a rapid means of identifying regulators of signaling pathways implicated in development and disease.     

Skinny hedgehog, an acyltransferase required for palmitoylation and activity of the hedgehog signal

One of the most dominant influences in the patterning of multicellular embryos is exerted by the Hedgehog (Hh) family of secreted signaling proteins. Here, we identify a segment polarity gene in Drosophila melanogaster, skinny hedgehog (ski), and show that its product is required in Hh-expressing cells for production of appropriate signaling activity in embryos and in the imaginal precursors of adult tissues. The ski gene encodes an apparent acyltransferase, and we provide genetic and biochemical evidence that Hh proteins from ski mutant cells retain carboxyl-terminal cholesterol modification but lack amino-terminal palmitate modification. Our results suggest that ski encodes an enzyme that acts within the secretory pathway to catalyze amino-terminal palmitoylation of Hh, and further demonstrate that this lipid modification is required for the embryonic and larval patterning activities of the Hh signal.     

草菇VEGF信号通路中vv-SPK基因的结构与表达分析

VEGF通路是一条调控细胞增殖、分化、迁移、应激反应以及生存的信号通路。本研究从草菇基因组中获得1个在VEGF通路中编码SPK蛋白的基因,将其命名为vv-SPK,并对该基因进行结构分析,结果显示:基因vv-SPK全长1 996bp,包含11个内含子;ORF长为1 401bp,编码466个氨基酸。通过BLASTP比对显示,vv-SPK基因与纹缘盔孢伞、双色蜡蘑以及紫蜡蘑的相似度最高;经过荧光定量PCR验证后发现,SPK蛋白的基因表达量与菌柄的伸长有关。根据SPK在VEGF通路中参与的细胞增殖途径以及SPK蛋白本身的激酶特性,推测其对草菇菌柄生长过程的细胞分裂和伸长有显著的促进作用,且草菇中可能存在SPK激酶介导的促进细胞增殖、伸长的信号通路。     

Dishevelled 2 recruits beta-arrestin 2 to mediate Wnt5A-stimulated endocytosis of Frizzled 4

Wnt proteins, regulators of development in many organisms, bind to seven transmembrane-spanning (7TMS) receptors called frizzleds, thereby recruiting the cytoplasmic molecule dishevelled (Dvl) to the plasma membrane.Frizzled-mediated endocytosis of Wg (a Drosophila Wnt protein) and lysosomal degradation may regulate the formation of morphogen gradients. Endocytosis of Frizzled 4 (Fz4) in human embryonic kidney 293 cells was dependent on added Wnt5A protein and was accomplished by the multifunctional adaptor protein beta-arrestin 2 (betaarr2), which was recruited to Fz4 by binding to phosphorylated Dvl2. These findings provide a previously unrecognized mechanism for receptor recruitment of beta-arrestin and demonstrate that Dvl plays an important role in the endocytosis of frizzled, as well as in promoting signaling.     

The Hedgehog pathway promotes blood-brain barrier integrity and CNS immune quiescence

The blood-brain barrier (BBB) is composed of tightly bound endothelial cells (ECs) and perivascular astrocytes that regulate central nervous system (CNS) homeostasis. We showed that astrocytes secrete Sonic hedgehog and that BBB ECs express Hedgehog (Hh) receptors, which together promote BBB formation and integrity during embryonic development and adulthood. Using pharmacological inhibition and genetic inactivation of the Hh signaling pathway in ECs, we also demonstrated a critical role of the Hh pathway in promoting the immune quiescence of BBB ECs by decreasing the expression of proinflammatory mediators and the adhesion and migration of leukocytes, in vivo and in vitro. Overall, the Hh pathway provides a barrier-promoting effect and an endogenous anti-inflammatory balance to CNS-directed immune attacks, as occurs in multiple sclerosis.     

Signaling specificity by Frizzled receptors in Drosophila

Wnt-Frizzled (Fz) signaling pathways play recurring important roles during the development and homeostasis of vertebrates and invertebrates. Fz receptors can signal through beta-catenin-dependent and -independent pathways. In Drosophila, Fz and Fz2 are redundant receptors for Wg. In addition, Fz conveys signals through a distinct pathway to organize planar polarization of epithelial structures. We demonstrate that the cytoplasmic sequences of Fz2 and Fz preferentially activate the beta-catenin and planar polarity cascade, respectively. Both receptors activate either pathway, but with different efficiencies. Intrinsic differences in signaling efficiency in closely related receptors might be a general mechanism for generating signaling specificity in vivo.     

野生罗非鱼响应低温胁迫的脑组织转录组测序分析

【目的】比较低温胁迫下野生罗非鱼和养殖吉富罗非鱼的基因表达模式,揭示野生罗非鱼低温应答的特有分子调控机制,为后续开展野生罗非鱼耐冷亲本大范围筛选打下基础。【方法】挑选规格相近的野生罗非鱼和养殖吉富罗非鱼进行梯度降温试验,水温先以1℃/12 h的速度从26℃降至14℃,并保持288 h（12 d）,于26℃、20℃及14℃保持0、120和288 h等5个时间点分别解剖罗非鱼采集脑组织样品,构建cDNA文库后以Illumina HiSeq×Ten测序平台进行双端测序及比较转录组分析,并采用实时荧光定量PCR对具有重要功能的差异表达基因（DEGs）进行表达验证。【结果】野生罗非鱼在11℃时开始出现死亡个体,但在8℃时仍有50.0%的存活个体,说明野生罗非鱼较养殖吉富罗非鱼具有更强的低温耐受能力。在14℃的长时间低温胁迫过程中,养殖吉富罗非鱼脑组织中表达显著上调的差异表达基因数量约是野生罗非鱼的10倍,即养殖吉富罗非鱼的应激反应远比野生罗非鱼强烈。KEGG信号通路富集分析结果显示,养殖吉富罗非鱼和野生罗非鱼在14℃保持120和288 h的上调差异表达基因均富集到核糖体发生、内质网蛋白加工及剪接体信号等信号通路上,野生罗非鱼的上调差异表达基因还额外富集到核苷酸切除修复、N-糖基化生物合成和DNA复制信号等通路上。与养殖吉富罗非鱼相比,在野生罗非鱼中发现577个特有的差异表达基因,主要富集在NOD受体信号通路、凋亡和内吞等通路上,且表现为NOD受体信号通路被启动,而细胞凋亡受抑制。在野生罗非鱼中,参与NOD受体信号通路的关键功能基因（Nemo、NFκB、p38、JNK和IL-1β）在长时间低温胁迫中均维持在一个较高的表达水平,而内吞途径关键基因的表达上升倍数也明显高于养殖吉富罗非鱼。【结论】野生罗非鱼通过避免过度的应激反应和维持低水平代谢的细胞稳定以减轻低温胁迫对机体的损伤,并持续启动NOD受体信号通路及内吞途径以维持其免疫能力,而具有较养殖罗非鱼更强的低温耐受力。     

Genome-wide RNAi analysis of growth and viability in Drosophila cells

A crucial aim upon completion of whole genome sequences is the functional analysis of all predicted genes. We have applied a high-throughput RNA-interference (RNAi) screen of 19,470 double-stranded (ds) RNAs in cultured cells to characterize the function of nearly all (91%) predicted Drosophila genes in cell growth and viability. We found 438 dsRNAs that identified essential genes, among which 80% lacked mutant alleles. A quantitative assay of cell number was applied to identify genes of known and uncharacterized functions. In particular, we demonstrate a role for the homolog of a mammalian acute myeloid leukemia gene (AML1) in cell survival. Such a systematic screen for cell phenotypes, such as cell viability, can thus be effective in characterizing functionally related genes on a genome-wide scale.     

版纳微型猪近交系RNF4基因克隆、多组织qPCR表达及功能生物信息学分析

RNF4基因调节精细胞分化和增殖过程,文章以Gen Bank下载的猪及近缘物种RNF4 mRNA序列为参考序列,设计特异引物扩增版纳微型猪近交系(BMI)RNF4基因。应用qPCR分析15个重要组织mRNA表达谱,并对蛋白质序列作功能生物信息学分析,构建多物种系统进化树。研究获得BMI RNF4 573 bp编码区序列(Gen Bank登录号:KU705638,对应氨基酸登录号:AOC89056),编码190个氨基酸,蛋白质分子质量(Mw)为21.43 ku,等电点(pI)为6.95。多组织荧光定量表达分析表明RNF4基因在尿道球腺、睾丸、肝、肺中高水平表达;在其他11个组织中呈中低水平表达。功能生物信息学分析表明RNF4蛋白质存在1个保守结构域,无跨膜结构,无信号肽序列;N末端疏水,C末端疏水;有4类功能活性位点,位于细胞核概率为94.1%。系统进化分析表明,BMI与狗亲缘关系最近。结果为研究RNF4基因在猪精细胞分化和增殖方面作用奠定基础。     

油松JAZ基因家族特征及其与DELLA蛋白互作的功能域鉴定

  目的  对油松JAZ基因家族特征及其与赤霉素负调控因子DELLA蛋白互作的功能域深入分析，旨在为解析针叶树以JAZ-DELLA为核心模块、茉莉酸（JA）-赤霉素（GA）介导的生长/防御平衡策略奠定基础。  方法  以油松全基因组数据为基础，筛选鉴定油松全部的JAZ家族基因成员，并分析其基本特征；构建多物种JAZ基因家族系统发育进化树，解析油松JAZ基因家族在系统进化过程中的特点；利用酵母双杂交技术，明确油松中JAZ与DELLA蛋白互作的功能域。  结果  油松中共鉴定得到53个JAZ基因家族成员，均具有TIFY和Jas保守结构，而且在degron序列中进化出了更丰富的变异。多个油松JAZ基因家族成员启动子区域包含响应JA和GA的顺式作用元件，并与模式植物中多个JAZ蛋白有着较近的进化距离。进一步实验发现，油松中5个JAZ蛋白（TIFY4、TIFY11、TIFY16、TIFY25、TIFY59）的Jas结构域与油松DPL（DELLA-like）蛋白存在相互作用，明确了油松中Jas结构域是JAZ蛋白与DELLA蛋白互作的功能域。  结论  明确了油松JAZ基因家族的基本序列特征，确定了油松中JAZ与DELLA蛋白互作的Jas功能域，为针叶树JAZ基因家族及JA-GA信号转导通路的深入研究提供了重要依据。      

Four-jointed is a Golgi kinase that phosphorylates a subset of cadherin domains

The atypical cadherin Fat acts as a receptor for a signaling pathway that regulates growth, gene expression, and planar cell polarity. Genetic studies in Drosophila identified the four-jointed gene as a regulator of Fat signaling. We show that four-jointed encodes a protein kinase that phosphorylates serine or threonine residues within extracellular cadherin domains of Fat and its transmembrane ligand, Dachsous. Four-jointed functions in the Golgi and is the first molecularly defined kinase that phosphorylates protein domains destined to be extracellular. An acidic sequence motif (Asp-Asn-Glu) within Four-jointed was essential for its kinase activity in vitro and for its biological activity in vivo. Our results indicate that Four-jointed regulates Fat signaling by phosphorylating cadherin domains of Fat and Dachsous as they transit through the Golgi.     

Patched1 regulates hedgehog signaling at the primary cilium

Primary cilia are essential for transduction of the Hedgehog (Hh) signal in mammals. We investigated the role of primary cilia in regulation of Patched1 (Ptc1), the receptor for Sonic Hedgehog (Shh). Ptc1 localized to cilia and inhibited Smoothened (Smo) by preventing its accumulation within cilia. When Shh bound to Ptc1, Ptc1 left the cilia, leading to accumulation of Smo and activation of signaling. Thus, primary cilia sense Shh and transduce signals that play critical roles in development, carcinogenesis, and stem cell function.     

基于TMT蛋白组学及生物信息学分析牦牛抗冻差异蛋白

【目的】从蛋白水平阐明牦牛抗寒性能机理,并进一步从营养学角度提高其代谢性能,为牦牛有效抵御外界恶劣气候条件提供科学依据。【方法】应用TMT蛋白组学技术对寒冷季节（1月）和温暖季节（8月）的牦牛抗冻蛋白进行挖掘,并对鉴定到的牦牛抗冻蛋白进行亚细胞定位、结构域、GO功能富集、KEGG信号通路注释、蛋白相互作用等生物信息学分析。【结果】从牦牛耳组织中共鉴定获得21856个肽段（Peptide）,其中特有肽段（Unique peptide）序列为18452个,定量获得4519个蛋白,最终筛选出144个差异蛋白,其中上调蛋白89个、下调蛋白55个。144个牦牛抗冻差异蛋白亚细胞定位到7个条目上,分别是细胞核蛋白56个、细胞质蛋白51个、质膜蛋白24个、细胞外蛋白23个、线粒体蛋白18个、细胞骨架蛋白1个和溶酶体蛋白1个;共鉴定到194个结构域。GO功能富集分析结果显示,生物过程主要富集到细胞过程蛋白79个、代谢过程蛋白70个和生物调控蛋白42个等,分子功能主要富集到结合功能蛋白75个和催化活性蛋白64个等,细胞组分主要富集到细胞部分蛋白89个和细胞蛋白89个等。144个牦牛抗冻差异蛋白在KEGG数据库中注释到205条KEGG信号通路,主要涉及核糖体、氮代谢、胞质DNA感受、动物体内生热作用、氧化磷酸化、白细胞介素-17及钙离子信号等通路。牦牛抗冻差异蛋白相互作用网络分析发现L8IHE5的关联度最高,且冷诱导RNA结合蛋白（CIRP）和HSP70结合蛋白在蛋白相互作用网络中具有更多的相互作用关系。【结论】基于TMT蛋白组学对牦牛抗冻差异蛋白进行挖掘,结果鉴定获得144个抗冻差异蛋白（上调蛋白89个,下调蛋白55个）,其中CIRP和HSP70在冷应激条件下呈上调趋势,能促使牦牛肌体适应低温环境,可作为牦牛抗冻性育种的候选分子标记。     

大白公猪精浆外泌体miRNA表征鉴定及功能分析

【目的】精浆外泌体(Seminal plasma exosome,spEX)在精子成熟、凋亡、受精中起着至关重要的作用。本文旨在探究种公猪spEX miRNA表达及miRNA在精子成熟及功能维持过程中的潜在调控作用。【方法】提取大白公猪spEX并进行电镜分析、粒径分析、标志性蛋白表达分析和miRNA高通量测序。【结果】成功分离出spEX，利用miRNA测序共鉴定出329个spEX miRNA。对高表达miRNA进行靶基因预测和功能富集分析，结果表明spEX miRNA在射精、P53信号通路、前列腺癌、细胞对DNA损伤刺激的反应、负调控凋亡过程、顶体膜结合、受精等通路中均发挥了潜在调控作用。【结论】本研究为spEX miRNA在调控精子活力和精子受精作用方面提供基础数据，并为精液保存调控机制的研究提供参考。     

黄白双花口服液治疗犊牛腹泻的系统药理学分析

【目的】利用系统药理学构建黄白双花口服液治疗犊牛腹泻的活性化合物—靶点—通路—疾病相关蛋白的关系网络模型,阐述黄白双花口服液治疗犊牛腹泻的分子机制,为犊牛腹泻防治药物研发提供理论依据。【方法】根据口服利用度（OB）≥30%和类药性（DL）≥0.18,利用中药系统药理学数据库（TCMSP）检索黄白双花口服液中每味中药（黄连、白头翁、金银花、黄芩、地榆和乌梅）的活性化合物及与其相对应的作用靶点,导入Cytoscape绘图软件中建立活性化合物与其对应靶点的互作网络图;通过基因数据库（Gene Cards）检索犊牛腹泻的有关靶点基因,使用维恩图求取二者的交集,得到犊牛腹泻与黄白双花口服液共同的靶点基因组合,然后导入String数据库中以获得相关蛋白相互作用网络图;将黄白双花口服液作用于犊牛腹泻的靶点基因导入DAVID数据库中,分别进行GO功能富集分析和KEGG通路富集分析。【结果】从黄白双花口服液中筛选出43种活性化合物,分别对应131个相关靶点基因。黄白双花口服液与犊牛腹泻交集的蛋白质—蛋白质相互作用网络图包括128个节点及205条相互关系,其中丝氨酸/苏氨酸蛋白激酶1（AKT1）、白介素2（IL-2）、白介素6（IL-6）、白介素8（IL-8）、促分裂素原活化蛋白激酶1（MAPK1）及含半胱氨酸的天冬氨酸蛋白酶3（CASP3）的出现频率较高。利用DAVID数据库对黄白双花口服液与犊牛腹泻交集靶点的蛋白进行GO功能富集分析,最终富集到204条GO功能条目（FDR< 10-2）,其中细胞组成条目8条、分子功能条目12条、生物过程条目184条;黄白双花口服液治疗犊牛腹泻的相关蛋白主要富集于19条信号通路上（FDR< 10-2）。【结论】黄白双花口服液主要以黄连、白头翁、金银花、黄芩、地榆和乌梅中的槲皮素、β-谷甾醇、豆甾醇及山奈酚等活性化合物成分,通过ATK1、MAPK1、IL-2、IL-6和IL-8等靶点,经Toll样受体信号通路、NOD样受体信号通路、T细胞受体信号通路和B细胞受体信号通路等,发挥抗菌消炎、抑制细胞损伤及调节免疫力等作用,以达到治疗犊牛腹泻的目的。