拟南芥中myo-肌醇-多磷酸合成与代谢及其信号

在酵母、真菌、动物和植物等真核生物中, 以myo-肌醇为基石通过不同位点的磷酸化形成各种myo-肌醇-多磷酸及其衍生物。过去10年的研究发现这些肌醇多磷酸参与了膜脂定向转运、蛋白结构稳定、离子通道调控、RNA转运以及DNA修复和染色质重塑等细胞生物学的基本进程。近些年在模式植物拟南芥(Arabidopsis thaliana)的研究中, 许多调控植物生长发育和环境胁迫应答的重要基因被发现, 并证实这些基因参与myo-肌醇-多磷酸的合成与代谢。该文概述了拟南芥中myo-肌醇-多磷酸合成与代谢的基因调控机理, 综述了不同肌醇多磷酸作为信号分子的功能, 提出肌醇多磷酸如同一类信息代码传递着植物细胞有序进程的基本指令。     

植物中棉子糖系列寡糖代谢及其调控关键酶研究进展

棉子糖系列寡糖代谢与植物生长发育、逆境胁迫、种子耐贮性及脱水耐性等关系密切.棉子糖系列寡糖的合成从棉子糖的合成开始,由半乳糖苷肌醇上的半乳糖基的转移依次生成棉子糖、水苏糖、毛蕊花糖等.寡糖代谢是一个复杂的调控体系,其中肌醇-1-磷酸合成酶、肌醇半乳糖苷合成酶、蔗糖合成酶、棉子糖合成酶、水苏糖合成酶和毛蕊花糖合成酶等参与了棉子糖系列寡糖的生物合成过程.本文对植物中棉子糖系列寡糖的代谢及其重要调控酶的特性、功能及分子生物学研究进展进行综述.     

植物萜类合成酶1-脱氧-D-木酮糖-5-磷酸还原异构酶的分子结构特征与功能预测分析

采用生物信息学的方法和工具对已在GenBank上注册的拟南芥、玉米、岩蔷薇、水稻、黄花蒿、亚麻等植物的萜类合成酶1-脱氧-D-木酮糖-5-磷酸还原异构酶的核酸及氨基酸序列进行分析,并对其组成成分、转运肽、跨膜拓朴结构域、疏水性/亲水性、蛋白质二级及三级结构、分子系统进化关系等进行预测和推断。结果表明：该类酶基因的全长包括5′、3′非翻译区和一个开放阅读框,无跨膜结构域,是一个具转运肽的亲水性蛋白,包括两个功能DXR结合motif及两个功能NADPH结合motif,α-螺旋和不规则卷曲是蛋白质二级结构最大量的结构元件,β-转角和β-折叠散布于整个蛋白质中,蛋白质的功能域在空间结构上折叠成“V”形,“V”形的两臂由N-端与C-端构成,“V”形的底部,是N 端臂与C-端臂的结合域。     

植物蔗糖磷酸合成酶的生物信息学分析

本文采用生物信息学的方法对已在GenBank上注册的拟南芥、紫苜蓿、黑麦草、绿竹、文心兰等植物的蔗糖磷酸合成酶基因的核苷酸序列以及推导的氨基酸序列、组成成分、导肽、跨膜拓朴结构、疏水性／亲水性、蛋白质二级结构及功能域等进行分析预测和推断。结果表明：这些植物的蔗糖磷酸合成酶不存在导肽,为位于细胞质中非跨膜的亲水性不稳定蛋白,α-螺旋和不规则卷曲是其蛋白质二级结构的主要结构元件,β-转角和延伸链散布于整个蛋白质中,包含三个功能结构域。     

植物萜类合成酶3-羟基-3-甲基戊二酰辅酶A还原酶的生物信息学分析

采用生物信息学的方法和工具对已在GenBank上注册的橡胶、烟草、辣椒、穿心莲等植物的萜类合成酶3-羟基-3-甲基戊二酰辅酶A还原酶的核酸及氨基酸序列进行分析,并对其组成成分、信号肽、跨膜拓朴结构域、疏水性/亲水性、蛋白质二级及三级结构、分子系统进化关系等进行预测和推断。结果表明该类酶基因的全长包括5′、3′非翻译区和一个开放阅读框,无信号肽,是一个跨膜的亲水性蛋白,包括两个功能HMG-CoA结合motif及两个功能NADPH结合motif,α-螺旋和不规则盘绕是蛋白质二级结构最大量的结构元件,β-转角和延伸链散布于整个蛋白质中,蛋白质的功能域在空间布局上折叠成“V”形,“V”形的两臂由螺旋状的N结构域和S结构域构成,中间部分由L结构域构成。     

垫状卷柏海藻糖-6-磷酸合成酶基因的克隆及功能分析

海藻糖-6-磷酸合成酶(Trehalose-6-phosphate synthse, TPS)是植物海藻糖合成途径的关键酶, 在旱生卷柏等复苏植物对逆境胁迫应答中起重要作用。文章以我国特有旱生植物垫状卷柏(Selaginella pulvinata)为材料, 采用同源扩增与RACE技术相结合的方法克隆了海藻糖-6-磷酸合成酶基因SpTPS1, cDNA全长3 223 bp, 包括一个2 790 bp的开放阅读框, 推导的氨基酸序列与模式物种的海藻糖-6-磷酸合成酶具有较高的序列相似性, 催化活性中心保守位点基本一致。酵母功能互补实验证明, 用SpTPS1基因开放阅读框转化的海藻糖合成酶基因突变(tps1△)酵母菌株, 可恢复在以葡萄糖作为唯一碳源培养基上的生长, 说明垫状卷柏海藻糖-6-磷酸合成酶基因SpTPS1的编码蛋白具有生物活性, 可应用于植物抗逆性的转基因改良。     

高等植物葡萄糖-6- 磷酸脱氢酶与6- 磷酸葡萄糖酸脱氢酶基因的不同进化起源

葡萄糖-6-磷酸脱氢酶与6-磷酸葡萄糖酸脱氢酶是植物戊糖磷酸途径中的两个关键酶。在克隆了水稻质体葡萄糖-6-磷酸脱氢酶基因OsG6PDH2和质体6-磷酸葡萄糖脱氢酶基因Os6PGDH2基础上,分析比较了水稻胞质和质体葡萄糖-6-磷酸脱氢酶基因和6-磷酸葡萄糖酸脱氢酶基因的基因结构、表达特性和进化地位。结合双子叶模式植物拟南芥两种酶基因的分析结果,认为高等植物葡萄糖-6-磷酸脱氢酶基因和6-磷酸葡萄糖酸脱氢酶基因在进化方式上截然不同,葡萄糖-6-磷酸脱氢酶的胞质基因与动物和真菌等真核生物具有共同的祖先;6-磷酸葡萄糖酸脱氢酶的胞质酶和质体酶基因都起源于原核生物的内共生。讨论了植物葡萄糖-6-磷酸脱氢酶与6-磷酸葡萄糖酸脱氢酶基因可能的进化模式,为高等植物及质体的进化起源提供了新的资料。     

高等植物葡萄糖-6-磷酸脱氢酶与6-磷酸葡萄糖酸脱氢酶基因的不同进化起源

葡萄糖-6-磷酸脱氢酶与6-磷酸葡萄糖酸脱氢酶是植物戊糖磷酸途径中的两个酶.在克隆了水稻质体葡萄糖-6-磷酸脱氢酶基因OsG6PDH2和质体6-磷酸葡萄糖脱氢酶基因Os6PGDH2基础上,分析比较了水稻胞质和质体葡萄糖-6-磷酸脱氢酶基因和6-磷酸葡萄糖酸脱氢酶基因的基因结构、表达特性和进化地位.结合双子叶模式植物拟南芥两种酶基因的分析结果,认为高等植物葡萄糖-6-磷酸脱氢酶基因和6-磷酸葡萄糖酸脱氢酶基因在进化方式上截然不同,葡萄糖-6-磷酸脱氢酶的胞质基因与动物和真菌等真核生物具有共同的祖先;6-磷酸葡萄糖酸脱氢酶的胞质酶和质体酶基因都起源于原核生物的内共生.讨论了植物葡萄糖-6-磷酸脱氢酶与6-磷酸葡萄糖酸脱氢酶基因可能的进化模式,为高等植物及质体的进化起源提供了新的资料.     

植物阿魏酸-5-羟化酶生物信息学分析

阿魏酸-5-羟化酶(F5H)是木质素生物合成的关键酶之一,它依赖于细胞色素P450催化阿魏酸在5位上发生羟基化反应。采用生物信息学的方法和工具对在GenBank上注册的拟南芥(Arabidopsis thaliana)、油菜(Brassica napus)、杨树(Populus trichocarpa)、番茄(Lycopersicon esculentum)、紫苜蓿(Medicago sativa)、喜树(Camptotheca acuminate)等植物的阿魏酸-5-羟化酶基因的核苷酸序列及推导的氨基酸序列进行分析,包括组成成分、氨基酸翻译后修饰、跨膜拓扑结构域、疏水性/亲水性、蛋白质二级功能结构域等进行分析预测和推断。结果表明,植物F5H是一个具有跨膜结构域的亲水性蛋白,存在于内质网等分泌途径中,α-螺旋和不规则卷曲是其二级结构的主要结构元件,具有细胞色素P450家族特征性结构域及保守功能域。     

植物水溶性蔗糖合成酶生物信息学分析初探

用生物信息学方法对已在GenBank上注册的黑麦草、绿竹、菜豆、马铃薯、颤杨等植物水溶性蔗糖合成酶基因的核苷酸序列以及推导的氨基酸序列、组成成分、氨基酸翻译后修饰、导肽、跨膜拓朴结构域、疏水性／亲水性、蛋白质二级结构以及功能结构域等进行分析预测和推断的结果表明,这些植物的水溶性蔗糖合成酶位于线粒体中,是非跨膜的亲水性蛋白,α-螺旋和不规则卷曲是其蛋白质二级结构的主要结构元件,β-转角和延伸链散布于整个蛋白质中,包含2个功能结构域,即蔗糖合成功能域和糖基化合物转移功能域。     

Purification of two chitinases from Rhizopus oligosporus and isolation and sequencing of the encoding genes.

Two chitinases were purified from Rhizopus oligosporus, a filamentous fungus belonging to the class Zygomycetes, and designated chitinase I and chitinase II. Their N-terminal amino acid sequences were determined, and two synthetic oligonucleotide probes corresponding to these amino acid sequences were synthesized. Southern blot analyses of the total genomic DNA from R. oligosporus with these oligonucleotides as probes indicated that one of the two genes encoding these two chitinases was contained in a 2.9-kb EcoRI fragment and in a 3.6-kb HindIII fragment and that the other one was contained in a 2.9-kb EcoRI fragment and in a 11.5-kb HindIII fragment. Two DNA fragments were isolated from the phage bank of R. oligosporus genomic DNA with the synthetic oligonucleotides as probes. The restriction enzyme analyses of these fragments coincided with the Southern blot analyses described above and the amino acid sequences deduced from their nucleotide sequences contained those identical to the determined N-terminal amino acid sequences of the purified chitinases, indicating that each of these fragments contained a gene encoding chitinase (designated chi 1 and chi 2, encoding chitinase I and II, respectively). The deduced amino acid sequences of these two genes had domain structures similar to that of the published sequence of chitinase of Saccharomyces cerevisiae, except that they had an additional C-terminal domain. Furthermore, there were significant differences between the molecular weights experimentally determined with the two purified enzymes and those deduced from the nucleotide sequences for both genes. Analysis of the N- and C-terminal amino acid sequences of both chitinases and comparison of them with the amino acid sequences deduced from the nucleotide sequences revealed posttranslational processing not only at the N-terminal signal sequences but also at the C-terminal domains. It is concluded that these chitinases are synthesized with pre- and prosequences in addition to the mature enzyme sequences and that the prosequences are located at the C terminal.     

1992—1994年HIV—1国际流行株和云南株膜蛋白V3区氨基酸共有序列比较

对１９９２～１９９４年间１６个云南ＨＩＶ１株膜蛋白基因Ｖ３区进行了ＤＮＡ序列测定,经计算机ＤＮＡＳＩＳ及ＰＲＯＳＩＳ软件进行同源性分析,得出其相应的氨基酸共有序列ＹＮＶ３和两组共有序列ＹＮＶ３Ａ和ＹＮＶ３Ｂ,计算了ＹＮＶ３中每个氨基酸的保守性。分别将ＹＮＶ３Ａ和ＹＮＶ３Ｂ与世界各地的ＨＩＶ１代表株的相应序列进行了同源性比较。结果表明,ＨＩＶ１云南株膜蛋白Ｖ３区氨基酸共有序列ＹＮＶ３中每个氨基酸的平均变异度为７．６６％。两组共有序列ＹＮＶ３Ａ和ＹＮＶ３Ｂ,分别与ＨＩＶ１美欧株及泰国流行株Ｂ亚群相应序列有较高同源性。这一结果提示,在进化上云南瑞丽ＨＩＶ１流行毒株间有非常密切的关系,在这一时期该地区的流行毒株以ＨＩＶ１美欧株、泰国株Ｂ亚群及其衍生株为主。     

2009年中国流行的甲型流感病毒（H1N1）血凝素特征分析

目的研究甲型流感病毒（H1N1）暴发流行以来中国各地甲型流感病毒血凝素（HA）的特征。方法搜索甲型流感病毒（H1N1）暴发流行以来中国各地报道的血凝素（HA）的氨基酸序列,比较当年不同时期血凝素（HA）的氨基酸序列的变化,并比较2009年报道的血凝素（HA）的氨基酸序列和2008年、2007年报道的血凝素（HA）的氨基酸序列作比较,以分析和前2年血凝素（HA）氨基酸序列相比所发生的变化。结果2009年中国各地甲型流感病毒（H1N1）的血凝素（HA）的氨基酸序列（人源）的同源性为99%-100%,但和2008年以及2007年的同源性非常低,分别为70%-77%和71%-90%。结论2009年暴发流行的甲型流感病毒（H1N1）的血凝素氨基酸序列较往年发生了很大程度的变异,这可能是今年甲型流感病毒（H1N1）暴发流行的主要原因。     

Molecular phylogenetic analysis of HIV-1 vif gene from Korean isolates

Phylogenetic studies of nef, pol, and env gene sequences of HIV-1 isolated from Koreans suggested the presence of a Korean clade in which Korean sequences are clustered to the exclusion of foreign sequences. We attempted to identify and characterize the Korean clade using all vif gene sequences isolated from Koreans registered in the NCBI GenBank database (n = 233). Most (77 %) of the Korean isolates belonged to the Korean clade as a large subcluster in subtype B, designated the Korean clade subtype B (KCB). KCB sequences were relatively homogenous compared to Korean subtype B sequences that did not belong to the KCB (non-Korean clade subtype B; NKCB). Comparison of amino acid frequencies of KCB and NKCB sequences revealed several positions where the amino acid frequencies were significantly different. These amino acid residues were critical in separating KCB from NKCB or from foreign sequences, since substitution of these amino acids in KCB with the NKCB amino acids relocated the KCB sequences to NKCB, and vice versa. Further analyses of KCB will help us to understand the origin and evolutionary history of KCB.     

来源于Aspergillus candidus的乳糖酶基因的克隆及序列分析

从一株产乳糖酶的亮白曲霉（Aspergillus candidus)中克隆到了乳糖酶基因组DNA及cDNA序列（EMBL AC－CESSION No.AJ431643),序列分析表明,乳糖酶基因组DNA序列长3458bp,其中含有8个内含子,cDNA编码区长3015bp,共编码1005个氨基酸,前19个氨基酸为信号肽序列,氨基酸序列中共含有11个潜在的糖基化位点。将此基因在不同来源的乳糖酶基因序列进行比较发现,该基因与绝大多数乳糖酶基因同源性较低。虽与米曲霉ATCC20423的乳糖酶序列同源性较高,但其在酶学性质上更优于后者,亮白曲霉的乳糖酶基因可能是一个具有更广阔的生产应用前景的新基因。     

GP37蛋白结构分析与昆虫病毒分子进化的关系

The gp37 gene from LsMNPV has been sequenced and the deduced amino acid sequence was compared with other GP37 amino acid sequences from 8 insect viruses. The maximum homology of amino acid sequences and the conserved structural regions were analyzed with PROSIS software. The relationship of evolution of 9 insect viruses was discussed and the evolutionary tree was drawned.     

Prediction of two- and three-amino-acid sequences of Citrobacter Freundii beta-lactamase from its amino acid composition

The repeated amino-acid sequences in Citrobacter Freundii beta-lactamase may be indispensable for its function, because such repetitions cannot be simply attributed to a chance. In order to fully explore the functional units in Citrobacter Freundii beta-lactamase, it may need to analyse all the amino acid pairs, triplets, etc. along Citrobacter Freundii beta-lactamase from one terminal to the other terminal, to count their frequencies and calculate their probabilities. The amino-acid sequence of Citrobacter Freundii beta-lactamase was counted according to two-, three- and four-amino-acid sequences. The counted frequency and probability were compared with the predicted frequency and probability. The amino acid sequences, which appear in Citrobacter Freundii beta-lactamase and can be predicted from its amino acid composition according to a purely random mechanism, should not be deliberately evolved and conserved. By contrast, the amino acid sequences, which appear in Citrobacter Freundii beta-lactamase but cannot be predicted from its amino acid composition according to a purely random mechanism, should be deliberately evolved and conversed. Accordingly 99 (26.053%) and 33 (8.684%) of 380 two-amino-acid sequences can be predicted by the frequency and probability according to a purely random mechanism. Some kinds of amino acid sequences, which absent in Citrobacter Freundii beta-lactamase and can be predicted from its amino acid composition according to a purely random mechanism, should not be deliberately excluded from Citrobacter Freundii beta-lactamase. By contrast, some kinds of amino acid sequences, which absent in Citrobacter Freundii beta-lactamase and cannot be predicted from its amino acid composition according to a purely random mechanism, should be deliberately excluded from Citrobacter Freundii beta-lactamase. Accordingly 89 (48.370%) and 41 (22.283%) of 184 kinds of absent two-amino-acid sequences can be predicted by the frequency and probability according to a purely random mechanism, and 7236 (99.848%) of 7247 kinds of absent three-amino-acid sequences can be predicted by the frequency according to a purely random mechanism. The amino acids, whose probabilities in following certain preceding amino acids can be predicted from Citrobacter Freundii beta-lactamase amino acid composition according to a purely random mechanism, should not be deliberately evolved and conversed, accordingly 2 (0.526%) of 380 counted first order Markov transition probabilities for the second amino acid in two-amino-acid sequences match the predicted conditional probabilities.     

Complete nucleotide sequences and comparison of the structural genes of two 2-haloalkanoic acid dehalogenases from Pseudomonas sp. strain CBS3.

The nucleotide sequences of two DNA segments from Pseudomonas sp. strain CBS3 that code for two different haloalkanoic acid halidohydrolases were determined. Two open reading frames with coding capacities of 227 amino acids (corresponding to a molecular mass of 25,401 Da) and 229 amino acids (corresponding to a molecular mass of 25,683 Da) were identified as structural genes of 2-haloalkanoic acid dehalogenases I (dehCI) and II (dehCII) by comparison with the N-terminal amino acid sequences of these enzymes. Comparison of the two sequences revealed 45% homology on the DNA level and 37.5% homology on the amino acid level. No homology with other known protein or nucleotide sequences was found.     

猪胸膜肺炎放线杆菌转铁结合蛋白基因（rbp8）分析及建模

为了深入研究猪胸膜肺炎放线杆菌（Actinobacillus pleuropneumonie,App）转铁结合蛋白基因（Transferrin BindingProtein8,脚）的生物学特性,采用生物信息学方法,对GenBank中的5株App的TbpB的核酸及其氨基酸序列进行比对,选取其中的中国湖北分离株（JL03）对其分子结构、理化性质及功能域、蛋白质二级和三级结构等重要参数进行了预测和分析,并在三级结构的基础上进行了同源建模。结果表明,不同APP菌株之间核酸序列相似性较大,而氨基酸序列存在较大差异,二级结构以延伸链和随机卷曲为主要构件,其空间结构与脑膜炎双球菌GNAl870蛋白相似性较高,以此为模板成功构建了三维结构分子模型,为TbpB基因功能的深入研究提供了线索和参考依据。     

Amino acid sequence of rat liver cathepsin L

The complete amino acid sequences of the heavy and light chains of rat liver cathepsin L (EC 3.4.22.15) were determined at the protein level. The heavy and light chains consisted of 175 and 44 amino acid residues, respectively, and their Mr values without glycosyl groups calculated from these sequences were 18941 and 5056, respectively. The amino acid sequence was also determined from the N-terminal sequences of the heavy and light chains, and the sequences of cleavage fragments of the heavy chain with lysylendopeptidase and cyanogen bromide. The fragments were aligned by comparison with the amino acid sequence deduced from the sequence of cDNA of rat preprocathepsin L. The sequence of rat liver cathepsin L determined at the protein level was identical with that deduced from the cDNA sequence except that in the heavy chain, residues 176-177 (Asp-Ser) were not present at the C-terminus and alanine was replaced by proline at residue 125. Asn-108 in the heavy chain is modified with carbohydrate.