瓠瓜KNOX基因家族全基因组鉴定及组织表达分析

【目的】 探明瓠瓜KNOX基因家族特征,在瓠瓜全基因组水平上对KNOX基因家族成员进行鉴定和分析,研究其组织表达模式。【方法】利用生物信息学方法,对瓠瓜KNOX家族基因成员进行鉴定、编码蛋白理化性质分析及家族成员结构域和保守基序分析,利用MEGA 5.05软件构建系统进化树,采用实时荧光定量PCR技术,分析KNOX基因在瓠瓜不同组织（根、茎、叶、花、果实）中的表达情况。【结果】鉴定到12个瓠瓜KNOX家族基因,这些基因分布在6条染色体上,且均定位于细胞核。大多数瓠瓜KNOX家族蛋白含有同源异型盒蛋白特有的4种结构域KNOX1、KNOX2、ELK 和Homeobox_KN。系统进化分析将瓠瓜KNOX基因分为KNOX Class Ⅰ和KNOX Class Ⅱ 2大类群,2个类群又可进一步分为5个分支,其中Class Ⅰ-C为瓠瓜特有的进化分支。KNOX基因启动子区有多个激素响应元件和植物生长相关元件。组织表达分析发现,瓠瓜KNOX基因具有不同的表达模式,KNOX Class Ⅰ类基因表达具有组织特异性,在根、茎和果实中表达量较高,在其余组织中表达量较低或不表达,其中Lsi04G014450在根和茎中表达量最高,Lsi11G006380在果实中表达量最高;KNOX Class Ⅱ类基因在所有组织中均有较高表达。【结论】瓠瓜KNOX基因家族有12个成员,分布于6条染色体上,在进化关系上可分为5组,具有瓠瓜特有的进化分支,在不同组织中的表达具有特异性。     

PKS-NRPS数据库的研究进展

非核糖体多肽合成酶(NRPS)和聚酮合成酶(PKS)是调控次级代谢物聚酮类物质和非核糖体多肽合成的关键酶。随着生物息学的快速发展,国外的NRPS-PKS数据库和预测软件不断推出。本文对几个重要NRPS和PKS领域的数据库与预测软件的研究做一综述     

Cloning and Sequence Analysis of Major Histocompatibility Complex Ⅰ Gene from Goose F1 of Fast-growth Lines

According to the multiple alignments identified major histocompatibility complex Ⅰ (MHC Ⅰ) gene conserved sequence registered in GenBank from the family ducks (Anatidae) anser waterfowl, a pairs of specific primers for the fragments of MHCⅠgene of goose F1 from fast-growth lines were designed and synthesized by Primer Premier 5.0. Using the genome DNA of goose F1 from fast-growth lines, the target gene fragment was obtained by PCR. To conduct sequencing of the fragments of MHCⅠgene of goose F1 from fast-growth lines and make sequence alignment and analysis of protein structure and function by bioinformatics, and research the characteristics of MHCⅠgene of goose F1 and the physicochemical properties of the protein. Bioinformatics was analyzed the nucleic acid data, deduced amino acid sequence and phylogenetic trees. The result of sequence analysis showed that the fragments of MHCⅠgene of goose F1 from fast-growth lines was 1036 bp in length, which coded 96 amino acids polyprotein. The homology were 93% and 83% with MHC Ⅰ gene and coding sequence of Wulong goose in NCBI respectively. There were 72 different bases sequence and 16 amino acids change. There also was higher homology with other poultry, and existed genetic relationship of Siji goose > chickens > ducks.The homology segment sequences corresponding to the fragments of MHCⅠ gene of goose F1 coded 96 amino acids protein, which molecular weight, PI, positively or negatively charged amino acid, estimated half-life, instability index, aliphatic index and average hydrophobicity were 11.342 ku, 5.32, 14, 17, 2.8 h, 34.92, 42.81, -1.066, respectively, and appeared 9 B cell epitopes, but contained no signal peptide. These results indicated that the protein for hydrophilic non-secreted proteins, had the high immunogenicity. In addition, The protein structure study indicated that alpha-helix, beta-sheet, beta-turn and random coil were 31.25%,16.67%, 14.58% and 37.50%, respectively. There existed amino terminal domain and carboxyl terminal domain in the tertiary structure. Therefore, MHC gene had significant difference between species and populations of individuals by the pathogen pressure in environment, and there were the interaction between polymorphism of MHC molecules and the diversity of antigenic peptide. MHC determined the differences of individual susceptibility to disease, and could be treated as a candidate gene for disease resistance.     

Expression and Bioinformatic Analysis of ADIPOQ Gene in Hanper Sheep

The aim of this study was to investigate the expression and biological characteristics of adiponectin (ADIPOQ) gene in longissimus dorsi muscle of Hanper sheep at different months of age.The ADIPOQ gene mRNA expression was detected in longissimus dorsi muscle of Hanper sheep at 3 different growth periods (1,7 and 13 months old) by Real-time quantitative PCR.The bioinformatics method was used to analyze the nucleotide and amino acid sequences of ADIPOQ gene,protein characteristics and network interaction protein.The results showed that ADIPOQ gene was expressed in longissimus dorsi muscle of Hanper sheep,which showed an increasing trend with the growth of the months age without significant difference (P>0.05).There was higher homology of ADIPOQ gene with Capra hircus (98.60%,99.00%) and Bos taurus (98.60%,87.00%) in nucleotide and amino acid sequences.The results of physical and chemical properties analysis showed that the molecular formula of ADIPOQ protein was C₁₁₇₂H₁₇₇₆N₃₁₄O₃₄₉S₅,the molecular mass was 26.00 ku,and the theoretical isoelectric point (pI) was 5.88,which suggested that the protein was acidic.The average value of ADIPOQ hydrophilic protein (GRAVY) was －0.403,which indicated that the protein was hydrophilic and didn’t belong to transmembrane protein.In addition,the signal peptide sequence was Met¹-Ala¹⁷,and the cleavage site was between Ala¹⁷ and Arg¹⁸.ADIPOQ existed collagen structure domain and C1Q conserved structure domain at position 45－101 and 101－237,respectively.The secondary structure mainly composed of random coil (66.95%).The construction of protein interaction network indicated that ADIPOQ might interact with ADIPOR1,ADIPOR2,CDH13 and LEP.The results provided a theoretical basis for further exploring the molecular biological functions of ADIPOQ gene in the process of muscle development in Hanper sheep.     

山羊ACSS2基因的克隆、序列分析及组织表达研究

本研究旨在对山羊乙酰辅酶A合成酶2（acetyl-CoA synthetase 2,ACSS2）基因进行克隆和生物信息学分析,并检测其在山羊不同泌乳时期乳腺组织中的表达量变化。以山羊乳腺组织RNA为模板,采用RT-PCR方法扩增并克隆山羊ACSS2基因完整CDS区序列,对测序结果进行生物信息学分析,并对ACSS2基因在山羊不同泌乳时期乳腺组织中的表达量进行分析。结果显示,山羊ACSS2基因CDS区序列长2 106 bp,编码701个氨基酸;山羊ACSS2基因与牛、马、人、犬、猪、小鼠和鸡的同源性分别为97.8%、92.0%、91.3%、91.3%、91.1%、88.1%和73.3%。蛋白理化性质分析结果表明,ACSS2蛋白分子质量为78.72 ku,理论等电点为6.03,属于酸性蛋白;跨膜结构和信号肽分析表明,ACSS2蛋白不含跨膜结构和信号肽;结构域分析表明,该蛋白含有1个乙酰辅酶A合成酶N端结构域。亚细胞定位分析结果表明,该蛋白主要分布在内质网（44.4%）、线粒体（33.3%）、细胞质（11.1%）和细胞核（11.1%）中。蛋白质结构预测发现ACSS2蛋白含有α-螺旋（29.10%）、延伸链（21.54%）、β-转角（9.84%）及无规则卷曲（39.52%）。实时荧光定量PCR分析结果表明,ACSS2基因在不同泌乳时期均有表达,其中在泌乳中期表达量最高,在干奶期表达量最低。本试验结果为进一步研究山羊ACSS2基因在脂质代谢过程中的功能及转录调控机制提供了参考。     

山羊溶酶体α-AMA基因的克隆、生物信息学及组织表达谱分析

本研究旨在对山羊溶酶体α-甘露糖苷酶(α-AMA)基因进行组织表达谱和生物信息学分析。参考牛α-AMA基因序列设计引物,采用PCR技术克隆山羊α-AMA基因序列,并利用荧光定量RT-PCR进行组织表达谱分析以及进行生物信息学预测。首次获得了山羊α-AMA基因,含有完整CDS编码区3 000bp,编码999个氨基酸,其中前50个氨基酸为信号肽序列。其编码区的核苷酸序列和预测氨基酸序列与牛的α-AMA相似性最高,分别为95.93%和94.79%。组织表达谱分析表明α-AMA在山羊各组织均不同程度的表达,其中在肺脏、肝脏、小脑表达量较高。生物信息学预测发现,α-AMA蛋白属于糖苷水解酶38家族成员,有2个保守的结构域,存在9个N-糖基化位点。SWISS-MODEL同源建模山羊α-AMA具有良好的可信度。本研究为探讨酶的作用机理及疯草解毒剂的研制提供了理论依据。     

鸡RNF165蛋白多克隆抗体制备及其生物信息学分析

【目的】制备鸡环指蛋白165(RNF165)多克隆抗体并对RNF165蛋白进行生物信息学分析,以期为研究鸡RNF165的生物学功能提供参考。【方法】以鸡胚成纤维细胞(DF-1)为试验材料,提取总RNA,反转录获得cDNA,通过PCR扩增RNF165基因,将其连接至pET-28a(+)质粒构建重组表达质粒pET-28a-RNF165。将测序正确的重组表达质粒转化大肠杆菌BL21感受态细胞进行诱导表达,将表达的融合蛋白纯化后按照制定的免疫程序免疫7周龄BALB/c雌鼠。第3次免疫7 d后,分离小鼠血清,用Western blotting检测鼠抗RNF165蛋白多克隆抗体的特异性,间接ELISA法测定其效价。使用在线生物信息学软件对RNF165蛋白理化性质、信号肽、磷酸化位点、亚细胞定位、跨膜结构、二级结构和保守结构域进行分析。【结果】成功扩增得到大小为1 068 bp的RNF165基因。成功构建原核表达载体pET-28a-RNF165,并诱导表达出约43 ku的RNF165蛋白。Western blotting结果显示,制备的鼠抗RNF165蛋白多克隆抗体能特异性识别DF-1细胞中过表达的...     

马乳脂肪球膜蛋白组鉴定及潜在功能分析

试验旨在研究马乳脂肪球膜（milk fat globule membrane,MFGM）蛋白组成及潜在的生物学功能。选取12匹5岁左右、平均体重为450~500 kg的健康纯血母马作为试验动物,主要饲喂干牧草,所有马匹饲养和管理条件均相同。将12份样品以每组4份进行混合,分离提取产后第60天马乳中MFGM蛋白,进行高分辨质谱仪鉴定和生物信息学分析。结果显示,马MFGM组分中共鉴定出310种表达蛋白,这些蛋白主要参与的生物过程为生物调节、刺激应答、定位、多细胞生物过程、运输、信号、细胞通讯、发育过程、细胞分化和免疫系统过程等;细胞成分主要为胞外区域、膜、囊泡、核仁和线粒体等;分子功能主要为催化活性、蛋白质结合、碳水化合物衍生物结合和小分子结合等。KEGG通路分析表明,MFGM蛋白主要参与血小板活化通路、内吞、脂肪酸生物合成和Ras信号通路等。马乳MFGM蛋白的蛋白质互作网络分析图中共包含215种蛋白质。本研究结果揭示了马乳MFGM蛋白质组的复杂性,为解析其营养和生物学功能提供了科学数据。     

东北虎γ-干扰素基因的克隆、生物信息学分析及其在毕赤酵母中的表达

本试验旨在通过克隆东北虎γ-干扰素(IFN-γ)基因,研究其分子特征并预测蛋白生物学功能,为后续研究干扰素抗病毒活性做前期准备。通过RT-PCR从ConA诱导过的东北虎血淋巴细胞中扩增东北虎IFN-γ基因并测序,应用生物信息学方法进行序列分析。结果表明:东北虎IFN-γ编码区由504个核苷酸组成,共编码167个氨基酸,蛋白相对分子质量为19.59 ku,等电点为9.03,所编码的蛋白为碱性亲水性蛋白,其中前23个氨基酸可能为信号肽,IFN-γ编码蛋白保守结构域为IFN-γ超家族,且存在跨膜结构,其中1-6位氨基酸为胞内区域,7-28位氨基酸为跨膜区域,29-167位氨基酸为胞外区域;IFN-γ编码蛋白二级结构主要以α-螺旋(58.08%)和无规则卷曲(33.53%)为主,存在5个潜在的B细胞抗原表位,3个潜在的N-糖基化位点;分子进化分析显示,东北虎IFN-γ与GenBank上发表的东北虎、非洲狮、金钱豹、美洲狮、猎豹、家猫、加拿大猞猁、野猪等的核苷酸相似性为80.4%~99.8%,氨基酸相似性为70.5%~100%,东北虎IFN-γ与非洲狮、金钱豹亲缘关系最近,美洲狮、猎豹、家猫、猞猁次之,野猪最远。通过合成改造后的东北虎IFN-γ基因,构建能表达IFN-γ蛋白的重组质粒pPIC9K-IFN-γ,将其导入高效表达系统-毕赤酵母中进行诱导表达,经SDS-PAGE分析,表达蛋白的分子量约17.8 ku,与预期大小相符,表明东北虎IFN-γ成功表达。