家蚕核多角体病毒p10基因的克隆和分子系统进化分析

根据GenBank中家蚕核多角体病毒T3株中p10基因的保守序列,克隆得到了8个不同地区的家蚕核多角体病毒的p10基因,并分别与GenBank中的NPVp10基因进行比对.结果发现p10基因都含有1个213 bp的开放阅读框(ORF)共编码70个氨基酸,8株P10蛋白间氨基酸序列相似性为95%~100%,相似性高.与GenBank中Ac-MNPV和BmNPV的P10蛋白相比,8株BmNPV P10蛋白都缺失了3个保守结构域中的C-端结构域,只含有2个保守结构域,即N-端卷曲螺旋和Pro丰富区.     

The LDL receptor gene: a mosaic of exons shared with different proteins

The multifunctional nature of coated pit receptors predicts that these proteins will contain multiple domains. To establish the genetic basis for these domains (LDL) receptor. This gene is more than 45 kilobases in length and contains 18 exons, most of which correlate with functional domains previously defined at the protein level. Thirteen of the 18 exons encode protein sequences that are homologous to sequences in other proteins: five of these exons encode a sequence similar to one in the C9 component of complement; three exons encode a sequence similar to a repeat sequence in the precursor for epidermal growth factor (EGF) and in three proteins of the blood clotting system (factor IX, factor X, and protein C); and five other exons encode nonrepeated sequences that are shared only with the EGF precursor. The LDL receptor appears to be a mosaic protein built up of exons shared with different proteins, and it therefore belongs to several supergene families.     

Potential metal-binding domains in nucleic acid binding proteins

A systematic search for sequences that potentially could form metal-binding domains in proteins has been performed. Five classes of proteins involved in nucleic acid binding or gene regulation were found to contain such sequences. These observations suggest numerous experiments aimed at determining whether metal-binding domains are present in these proteins and, if present, what roles such domains play in the processes of nucleic acid binding and gene regulation.     

The primary structure and heterogeneity of tau protein from mouse brain

Tau protein is a family of microtubule binding proteins, heterogeneous in molecular weight, that are induced during neurite outgrowth and are found prominently in neurofibrillary tangles in Alzheimer's disease. The predicted amino acid sequences of two forms of tau protein from mouse brain were determined from complementary DNA clones. These forms are identical in their amino-terminal sequences but differ in their carboxyl-terminal domains. Both proteins contain repeated sequences that may be tubulin binding sites. The sequence suggests that tau is an elongated molecule with no extensive alpha-helical or beta-sheet domains. These complementary DNAs should enable the study of various functional domains of tau and the study of tau expression in normal and pathological states.     

Structure and function of an essential component of the outer membrane protein assembly machine

Integral beta-barrel proteins are found in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. The machine that assembles these proteins contains an integral membrane protein, called YaeT in Escherichia coli, which has one or more polypeptide transport-associated (POTRA) domains. The crystal structure of a periplasmic fragment of YaeT reveals the POTRA domain fold and suggests a model for how POTRA domains can bind different peptide sequences, as required for a machine that handles numerous beta-barrel protein precursors. Analysis of POTRA domain deletions shows which are essential and provides a view of the spatial organization of this assembly machine.     

硝化还原假单胞菌SPQ03 PnSoxRS调控子的克隆和功能初步分析

从对百草枯具有高度抗性的硝化还原假单胞菌(Pseudomonas nitroreducens)菌株SPQ03中分离了PnSoxR和PnSoxS调控子.ScanProsite程序分析结果表明,SoxR氨基端含有一个MerR家族特有的DNA结合域,羧基端含有4个半胱氨酸残基,是MerR家族成员之一;SoxS是AraC家族成员,含有2个典型的AraC-HTH保守域;PnSoxR所编码的氨基酸与大肠杆菌SoxR的一致性为98%,而与同属的铜绿假单胞菌(Pseudomonas aeruginos)SoxR的一致性仅为56%,PnSoxR与大肠杆菌SoxS的一致性为100%,铜绿假单胞菌中没有发现SoxR基因存在.将PnSoxR和PnSoxS分别转化E.coli BL21,发现PnSoxS能赋予BL21百草枯(Paraquat)抗性.     

酿酒酵母分泌蛋白组的计算机分析

 结合计算机技术和生物信息学的方法，采用组合的信号肽分析软件SignalP v3.0、TargetP v1.01、Big-PI predictor和TMHMM v2.0对已公布的6 700个酿酒酵母（Saccaromyces cerevieiae）基因的N-端氨基酸序列进行信号肽分析，同时系统分析了信号肽的类型及结构。结果表明，在6 700个酿酒酵母蛋白中，163个为Sec-信号肽分泌蛋白，经Sec途径分泌。在163个分泌蛋白中，有47个的信号肽没有典型的N-区，仅有H-区和C-区，其余116个分泌蛋白的信号肽包含完整的3个区，即N-区、H-区和C-区。比较了酿酒酵母与白假丝酵母菌(Candida albicans)分泌蛋白信号肽的氨基酸组成顺序，表明酿酒酵母与白假丝酵母菌的信号肽的氨基酸组成和顺序差异很大，两者信号肽长度分布范围、氨基酸种类及其出现频率大体一致。在酿酒酵母分泌蛋白中出现了少数氨基酸组成完全一致的信号肽，为进一步确认具有相同信号肽的分泌蛋白是否具有同源性，分别采用BLAST 2 SEQUENECES 和CLUSTAL W 对具有相同信号肽的分泌蛋白进行了序列比对。结果表明具有相同信号肽的分泌蛋白同源性非常高，氨基酸组成也非常保守。由此可以推断，编码这些分泌蛋白的基因属于旁系同源基因（paralogous）。酿酒酵母作为一种模式生物，以其诸多的优点，被认为是表达真核外源蛋白的首选宿主。对酿酒酵母进行基因组水平的分泌蛋白及信号肽结构的分析，可更好地利用该宿主表达分泌型的外源蛋白研究提供参考信息。     

Computational Analysis of Signal Peptide-Dependent Secreted Proteins in Saccharomyces cerevisiae

Computer based software such as the SignalP v3.0, TargetP v1.01, big-PI predictor and TMHMM v2.0 were combined to predict the signal peptides, and the signal peptide-dependent secreted proteins among the 6 700 ORFs in genome of Saccharomyces cerevisiae. The results showed that 163 proteins were the secreted ones containing signal peptides, and they were secreted via Sec pathway. Among the 163 predicted secreted proteins, the signal peptides of 47 secreted proteins included only the H-domain and C-domain, without N-domain, but the signal peptides of other 116 secreted proteins included all the three domains. There were differences in the constitution of signal peptides between the secreted proteins of S. cerevisiae and of Candida albicans, but the length and amino acids types of their signal peptides were similar in general. Few of the same signal peptides occurred in the secreted proteins of S. cerevisiae genome, and the homology could be compared among the secreted proteins with the same signal peptides. The BLAST 2 SEQUENECES and CLUSTAL W were used to align the two protein sequences and multi-protein sequences, respectively. The alignment result indicated that homology of these sequences with the same signal peptide was very highly conservative in amino acid of complete gene. The effect of the signal peptides in S. cerevisia on expression of foreign eukaryotic secreted proteins is discussed in this paper.     

猪CatSperB和CatSperG基因的克隆、表达及生物信息学

【目的】揭示猪CatSperB和CatSperG基因的存在、蛋白的结构特征、进化关系及时空表达特性。【方法】利用电子和分子克隆技术鉴定猪CatSperB和CatSperG基因全长cDNA,并利用定性RT-PCR和荧光定量RT-PCR进行CatSperB和CatSperG基因的时空表达研究。【结果】①分别获得了3 508 bp CatSperB和3 715 bp CatSperG电子转录子,分别包含3 330和3 483 bp开放阅读框,并经TA克隆测序验证,其CDS序列与人、牛、马和狗等的CatSperB和CatSperG基因的序列相似性在80%以上;②CatSperB分子质量为125.79 kD,为稳定蛋白;CatSperG分子质量为133.40 kD,为不稳定蛋白;③CatSperB和CatSperG 都包含 7 个通道蛋白保守的跨膜结构域,CatSperG蛋白C端含一个超螺旋结构,而CatSperB蛋白无明显的超螺旋结构信号;猪CatSperB和CatSperG与牛、狗和马的CatSperB和CatSperG蛋白同源关系较近,与人和小鼠的同源关系较远;④RT-PCR分析表明,CatSperB和CatSperG基因主要在睾丸中表达,但CatSperB在其它组织也有表达信号;⑤CatSperB和CatSperG基因mRNA表达水平在猪性发育的重要阶段,精子发生（60日龄）、初情期（90日龄）和性成熟（150日龄）前后都有显著提高（P＜0.05）。【结论】获得了猪CatSperB和CatSperG基因的cDNA克隆及其一系列生物信息学参数,揭示了CatSperB和CatSperG蛋白含7个保守的跨膜结构域及不同物种间的进化关系,证实CatSperB和CatSperG基因主要在睾丸表达,且其mRNA表达变化与公猪的性发育相一致。     

黄牛、牦牛和犏牛b-Sycp2基因的克隆 与睾丸组织mRNA的表达水平

【目的】克隆黄牛、牦牛和犏牛Sycp2基因序列,了解牛Sycp2基因序列特征和组织表达特征,分析睾丸组织中Sycp2基因的表达水平。【方法】采用电子克隆和克隆测序技术获得黄牛、牦牛和犏牛Sycp2基因序列,利用生物信息学方法分析其序列特征;采用RT-PCR分析牛Sycp2基因的组织表达特征;采用real-time PCR技术检测黄牛、牦牛和犏牛睾丸组织Sycp2基因的表达水平。【结果】①黄牛、牦牛和犏牛Sycp2基因编码区序列全长均为4 365 bp,命名为b-Sycp2,编码蛋白含有1 454个氨基酸残基,并包含卷曲螺旋结构域等典型结构域;②b-Sycp2基因在睾丸组织中特异表达,黄牛和牦牛睾丸组织中b-Sycp2基因的表达水平显著高于犏牛（P＜0.05）。【结论】成功克隆了b-Sycp2基因,b-Sycp2基因为睾丸组织的特异表达基因,且黄牛和牦牛睾丸组织b-Sycp2基因表达水平显著高于犏牛。     

Reprogramming control of an allosteric signaling switch through modular recombination

Many eukaryotic signaling proteins are composed of simple modular binding domains, yet they can display sophisticated behaviors such as allosteric gating and multi-input signal integration, properties essential for complex cellular circuits. To understand how such behavior can emerge from combinations of simple domains, we engineered variants of the actin regulatory protein N-WASP (neuronal Wiskott-Aldrich syndrome protein) in which the "output" domain of N-WASP was recombined with heterologous autoinhibitory "input" domains. Synthetic switch proteins were created with diverse gating behaviors in response to nonphysiological inputs. Thus, this type of modular framework can facilitate the evolution or engineering of cellular signaling circuits.     

The DNA-binding properties of the major regulatory protein alpha 4 of herpes simplex viruses

The transition from the expression of alpha, the first set of five herpes simplex virus genes expressed after infection, to beta and gamma genes, expressed later in infection, requires the participation of infected cell protein 4 (alpha 4), the major viral regulatory protein. The alpha 4 protein is present in complexes formed by proteins extracted from infected cells and viral DNA fragments derived from promoter domains. This report shows that the alpha 4 protein forms specific complexes with DNA fragments derived from 5' transcribed noncoding domains of late (gamma 2) genes whose expression requires viral DNA synthesis as well as functional alpha 4 protein. Some of the DNA fragments to which alpha 4 binds do not contain homologs of the previously reported DNA binding site consensus sequence, suggesting that alpha 4 may recognize and interact with more than one type of DNA binding site. The alpha 4 proteins can bind to DNA directly. A posttranslationally modified form of the alpha 4 protein designated alpha 4c differs from the alpha 4a and alpha 4b forms with respect to its affinity for DNA fragments differing in the nucleotide sequences of the binding sites.     

意大利蜜蜂Ci蛋白的生物信息学分析

【目的】掌握意大利蜜蜂转录因子(Ci)的生物信息学并阐述其功能,为揭示Ci蛋白在意大利蜜蜂Hh信号通路中的功能和作用打下基础。【方法】从NCBI获取意大利蜜蜂Ci蛋白氨基酸序列,分别使用ProtParam预测其理化性质、SignalP-5.0预测信号肽、TMHMM-2.0预测跨膜结构,通过NetOGlyc 3.0、NetNGlyc 1.0、NetPhos 3.1、SUMOplot等进行O-糖基化位点、N-糖基化位点、磷酸化位点及苏木化位点预测,采用GOR4、SWISS-MODEL、CD-Search等预测意大利蜜蜂Ci蛋白高级结构,在多重序列比对分析的基础上利用MEGA 11.0构建系统发育进化树,并通过String数据库预测相互作用蛋白。【结果】意大利蜜蜂Ci蛋白存在2个亚型,分别是XP＿624136.4和XP＿006558245.2。其中,XP＿624136.4亚型的开放阅读(ORF)为4338 bp,编码1445个氨基酸残基,编码蛋白分子量为15.50 kD,理论等电点(pI)为8.39;XP＿006558245.2亚型的ORF为3873 bp,编码1290个氨基酸残基,编码蛋白...     

Cloning of Thymidine Kinase Gene of Duck Plague Virus Using Degenerate PCR

The DNA of duck plague virus （DPV） thymidine kinase （TK） gene was cloned and sequenced from a vaccine virus in the study. Degenerate oligonucleotide primers for the consensus site of herpesvirus UL24, TK, and glycoprotein H（gH） gene were used in the polymerase chain reaction （PCR） to amplify DNA product with 3 741-base-pairs （bp） in size. DNA sequence analysis revealed a 1 077-base-pairs （bp） open reading frame （ORF） encoding a 358 amino acid polypeptide homologous to herpesvirus TK proteins. The predicted TK protein shared 31.2, 41.3, 35.7, 37.4, and 28.4% identity with herpes simplex virus typel, equine herpesvirus type 4, Marek＇s disease virus 2, herpesvirus turkey, and infectious laryngotracheitis virus, respectively. Comparison of the amino acid sequences of other herpesvirus TK proteins showed that these proteins were not conserved on the whole, otherwise the portion of the TK proteins corresponding to the nucleotide binding domain and the nucleoside binding site were highly conserved among herpesvirus. Comparison with the amino acid sequences of the conserved nucleotide and nucleoside binding domains of other eleven herpesvirus TK proteins to the predicted DPV peptide confirmed its identity as the DPV TK protein.     

多杀性巴氏杆菌基因组分泌蛋白的预测分析

分泌蛋白对于细菌自身的生命活动以及在介导病原体与宿主之间相互作用的过程中发挥着重要的作用,深入研究分泌蛋白将有助于明确细菌的生命活动及与病原微生物互作的分子机制.利用多杀性巴氏杆菌(Pasteurella multocida)基因组学研究成果,结合信号肽分析软件SignalP v3.0、跨膜螺旋结构软件TMHMM v2.0、亚细胞器蛋白定位软件PSORTb和GPI-锚定位点软件GPI-SOM这4个软件,对多杀性巴氏杆菌2105个编码蛋白的ORF进行预测分析,最终获得了136个分泌蛋白.对其信号肽长度、氨基酸组成、相应ORF长度进行了统计.运用Blast P对其功能进行同源性分析,发现11个蛋白为多杀性巴氏杆菌所特有,这对多杀性巴氏杆菌的临床诊断具有一定的潜在应用价值.     

三七根差异基因表达序列标签生物信息学分析

本研究利用生物信息学方法,对从三七根抑制消减杂交cDNA文库中随机挑选的91个EST序列进行了分析。结果表明:91个克隆组装分析后有4个重叠群和83个单拷贝EST,代表了87个基因。已知功能的基因序列共58个,占66%,按基因功能分类为10类,其中大多基因与代谢途径和分泌途径有关。未知功能基因序列29个,占33%。对33个氨基酸序列可通读的EST进行跨膜结构和信号肽分析,结果表明:9个克隆有信号肽,其中3个克隆有跨膜结构,可能为膜蛋白,6个克隆可能为分泌蛋白。功能位点分析结果表明:大多数基因与胞外分泌,调节细胞凋亡和细胞周期,信号传导有关。功能结构域分析结果表明:除9个克隆没有预测到功能结构域外,其它克隆的结构域与信号传导,转录调控,电子传递,协迫,光合作用,蛋白折叠等有关。亚细胞定位大多数位于细胞质和细胞核。     

A G protein gamma subunit shares homology with ras proteins

Guanine nucleotide binding proteins (G proteins) that transduce signals from cell surface receptors to effector molecules are made up of three subunits, alpha, beta, and gamma. A complementary DNA clone that encodes a 71-amino acid protein was isolated from bovine brain; this protein contains peptide sequences that were derived from the purified gamma subunit of Gi and Go. The primary sequence of this G protein gamma subunit (G gamma) has 55 percent homology to the gamma subunit of transducin (T gamma) and also has homology to functional domains of mammalian ras proteins. The probe for isolating the clone was generated with the use of the polymerase chain reaction (PCR). The extent of divergence between T gamma and G gamma, the isolation of homologous PCR-generated fragments, and the differences between the predicted amino acid sequence of G gamma and that derived from the gamma subunit of Gi and Go indicate that gamma subunits are encoded by a family of genes.     

Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion

The atomic structures of two proteins in the histidine biosynthesis pathway consist of beta/alpha barrels with a twofold repeat pattern. It is likely that these proteins evolved by twofold gene duplication and gene fusion from a common half-barrel ancestor. These ancestral domains are not visible as independent domains in the extant proteins but can be inferred from a combination of sequence and structural analysis. The detection of subdomain structures may be useful in efforts to search genome sequences for functionally and structurally related proteins.