水稻钙调蛋白基因的克隆及结构分析

钙调蛋白(Calmodulin)是生物细胞内一种重要的调控蛋白,通过其与靶酶的相互作用,控制细胞正常的生长和发育。我们以湖北光敏感核不育水稻cDNA第一条链为模板,参考大麦钙调蛋白基因序列合成5’端和3’端引物,利用多聚酶链式反应(PcR)合成了完整的水稻钙调蛋白cDNA,克隆并测定其序列。结果表明,光敏核不育水稻的钙调蛋白基因由450个桉苷酸组成,共编码148个氨基酸,且与迄今为止在植物领域里发表的大麦及苜蓿的钙调蛋白基因有很高的同源性。在核苷酸序列上与大麦有90％的同源性,与苜蓿有86％的同源性,其编码的148个氨基酸与大麦和苜蓿的差异分别只有1个。这是国际上第一次克隆水稻的钙调蛋白基因。     

玉米核糖体失活蛋白基因的克隆及序列分析

将提取的玉米RNA反转录成Cdna,以此为模板,合成特异性引物,应用多聚酶链式反应(PCR)技术扩增出目的片段。对PCR片段直接进行序列分析,测定并克隆玉米的核糖体失活蛋白(RIP)基因。序列分析表明,已测定的玉米RIP基因序列长为983bp,其中编码区长828bp,共编码有275个氨基酸和一个终止密码子,GC含量为58.3%。与已发表的序列相比较其核苷酸序列及推导的氨基酸序列的同源性分别为98.4%和97.4%。     

禾谷镰孢菌α-微管蛋白基因克隆及其与多菌灵抗药性关系分析

根据禾谷镰孢菌参考菌株NRRL310 84 (PH 1)的α- 微管蛋白基因核苷酸序列设计 4对引物 ,采用PCR方法克隆并测序了禾谷镰孢菌 (Fusariumgraminearum)对多菌灵 (MBC)不同敏感性表型的 6个中国菌株的α 微管蛋白基因全序列。DNA序列对照表明中国的 3个敏感菌株和 3个抗药菌株的α- 微管蛋白基因核苷酸序列同源性没有差异 ,多菌灵抗药性与α- 微管蛋白无关。该基因全长 1718bp ,含有 6个内元 ,编码 4 4 9aa ;与NRRL310 84的α- 微管蛋白基因核苷酸序列同源性为 99% ,存在 5个差异核苷酸 ,与其所编码的氨基酸序列同源性为 99 78% ;与其他 6种真菌α- 微管蛋白基因所编码的氨基酸序列同源性为 37%～ 86 %。     

小菜粉蝶颗粒体病毒颗粒体蛋白基因的序列测定及在大肠杆菌中的表达

根据颗粒体病毒颗粒体蛋白(Granulin)基因在其起始密码子上游的12个碱基高度保守序列(TATAAGGAATTT)以及大菜粉蝶颗粒体病毒(PbGV)的颗粒体蛋白基因的序列[1]设计引物,PCR扩增得到850bp左右大小的片段,核苷酸序列测定结果表明该病毒的granulin基因全长为855bp,起始密码位于第38～40位碱基,终止密码位于779～781位碱基,编码框序列全长为744;推测该基因编码一段由247个氨基酸组成的多肽,分子质量约为2.9178×104道尔顿.与其它颗粒体病毒颗粒体蛋白基因进行同源性比较,核苷酸同源性都在70%以上,氨基酸同源性都在75%以上,最高的为大菜粉蝶颗粒体病毒(PbGV),核苷酸同源性为97%,氨基酸同源性为98%.构建了重组表达载体pet-28a-Gran,IPTG诱导后经SDS-PAGE检测,表明获得了颗粒体蛋白基因在大肠杆菌BL21中的特异表达.     

脓肿分支枝杆菌embB基因耐乙胺丁醇的分析

目的 分析脓肿分支枝杆菌的embB基因,以探讨其耐乙胺丁醇的分子机制.方法 用16S rRNA基因序列分析法鉴定5株脓肿分枝杆菌临床株,测定乙胺丁醇对临床株及标准株( ATCC 19977)的最低抑菌浓度(MIC).PCR扩增embB基因的全序列,将所测序列进行生物信息学分析.结果 乙胺丁醇对5株脓肿分支杆菌标准株和临床株的MIC均为128μg/mL.,属高度耐药.从脓肿分支枝杆菌的标准株和临床株均扩增出约3200 bp片段,与GenBank中脓肿分支枝杆菌标准株的embB基因大小一致.5株临床株与标准株比较,其核苷酸序列存在9个点突变,在突变位点所编码的氨基酸序列中,仅第18位、87位、770位密码子编码与标准株不同的氨基酸.6株脓肿分支枝杆菌的embB基因与对EMB敏感的结核分支杆菌标准株(H37RV)的相应基因序列比较,第303-305位密码子的核苷酸序列存在差异,但仅第303、304位核苷酸编码的氨基酸序列不同,第306位密码子的核苷酸序列无差异.结论 脓肿分支杆菌对乙胺丁醇的耐药并非embB基因的突变所致,为embB基因天然存在结构的不同,属于天然耐药.结构的差异与第306位密码子无关,可能与第303、304密码子有关.     

小菜粉蝶颗粒体病毒颗粒体蛋白基因的序列测定及在大肠杆菌中的表达

根据颗粒体病毒颗粒体蛋白(Granulin)基因在其起始密码子上游的12个碱基高度保守序列(TATAAGGAATTT)以及大菜粉蝶颗粒体病毒(PbGV)的颗粒体蛋白基因的序列[1]设计引物,PCR扩增得到850bp左右大小的片段,核苷酸序列测定结果表明该病毒的granulin基因全长为855bp,起始密码位于第38~40位碱基,终止密码位于779~781位碱基,编码框序列全长为744;推测该基因编码一段由247个氨基酸组成的多肽,分子质量约为2.9178×104道尔顿。与其它颗粒体病毒颗粒体蛋白基因进行同源性比较,核苷酸同源性都在70%以上,氨基酸同源性都在75%以上,最高的为大菜粉蝶颗粒体病毒(PbGV),核苷酸同源性为97%,氨基酸同源性为98%。构建了重组表达载体pet-28a-Gran,IPTG诱导后经SDS-PAGE检测,表明获得了颗粒体蛋白基因在大肠杆菌BL21中的特异表达。     

粉拟青霉类枯草杆菌蛋白酶基因的cDNA克隆及其序列和蛋白质分析

粉拟青霉是一种常见的昆虫病原真菌,被广泛用于生物防治。根据GenBank中已登录的淡紫拟青霉,球孢白僵菌和金龟子绿僵菌的类枯草杆菌蛋白酶基因序列的同源性比较,以它们高度保守的核苷酸序列设计一对引物,采用RT-PCR和3’/5’-RACE相结合的方法,首次从粉拟青霉中克隆出完整的类枯草杆菌蛋白酶cDNA基因。其全序列为2060bp,该序列5’-端和3’-端的非编码序列长度分别为209bp和252bp,开放阅读框为1599bp,编码532个氨基酸,信号肽长度为16个氨基酸。成熟蛋白的氨基酸序列和金龟子绿僵菌小孢变种(CAB63913),玉米赤霉菌(EAA68914),金龟子绿僵菌蚱蜢变种(CAC95047)及柄孢壳(AAC03564)的同源性分别为69%、71%、68%和68%。成熟蛋白具有典型的丝氨酸蛋白酶活性位点,同时有5个半胱氨酸,3个潜在的N-糖基化位点和2个可能的O-糖基化位点。该基因在的密码子第三位碱基的使用上,显示出明显的对C的偏爱。     

猪肺炎支原体P46基因的突变及序列分析

目的:将猪肺炎支原体P46基因中编码Trp的密码子TGA突变为TGG,为P46蛋白的研究及猪肺炎支原体抗体检测方法的建立奠定基础.方法:参考GenBank登录的猪肺炎支原体(Mycoplasma hyopneumoniae Mhp)P46基因序列,利用Primer 5.0软件设计合成一对引物,对猪肺炎支原体强毒株F60 P46基因的编码区进行扩增,后又设计了三对突变引物,通过重叠延伸PCR(SOE-PCR)对猪肺炎支原体P46基因的三个位点进行定点突变.结果:得到的序列与GenBank中登录的P46基因的核苷酸及氨基酸序列进行序列比较,结果表明它们有较高的同源性.突变后测序结果表明已成功将猪肺炎支原体P46基因中编码Trp的密码子TGA突变为TGG.结论:已成功突变Mhp P46基因并且序列比较显示其与其它序列同源性较高     

易变山羊草抗禾谷孢囊线虫基因中核苷酸结合位点区(NBS)的克隆及序列分析

 大部分已克隆的植物抗病基因都包含有核苷酸结合位点区 (NBS)和富含亮氨酸的重复序列区 (LRR) .利用来自节节麦的抗禾谷孢囊线虫基因Cre3位点NBS区保守序列设计特异引物 ,从含有来自易变山羊草的抗禾谷孢囊线虫基因的小麦品系E 10的基因组中PCR扩增得到一条约 5 30bp的单一条带 .将扩增条带克隆和序列分析发现 ,该克隆 (Rccn4 )的编码区长 5 2 8bp ,含一个不完整的开放读码框 ,没有起始密码子、终止密码子和内含子结构 ,它编码一个 176个氨基酸残基的蛋白质 ,分子量为 2 0 4kD .Rccn4含有NBS LRR类抗病基因NBS区共有的保守模体I(V)LDD、T(T S)R、G(L S)PLA(A I L)、RCF(A L)Y ,并且与Cre3基因的NBS编码区核苷酸和氨基酸同源性分别为99 4 %和 98% .它是一个新的含NBS编码区核苷酸的抗禾谷孢囊线虫基因     

绞股蓝法呢基焦磷酸合酶基因的克隆及其序列分析

目的:克隆并分析绞股蓝法呢基焦磷酸合酶(FPS)基因的全长序列。方法:参照罗汉果法呢基焦磷酸合酶基因,设计扩增绞股蓝FPS基因的3′RACE引物,采用3'RACE和5'RACE法克隆绞股蓝FPS基因全长cDNA。结果:获得绞股蓝FPS基因全长cDNA序列共1288个核苷酸,包含一个1026核苷酸的开放读框,编码342个氨基酸残基,推断该蛋白的相对分子质量为3.94×104。NCBI Blast结果显示绞股蓝FPS基因编码蛋白的氨基酸序列与已知的植物FPS氨基酸序列的同源性为91%~74%,核酸序列的同源性为88%~78%。结论:克隆了绞股蓝FPS基因全长cDNA序列,为进一步研究绞股蓝FPS基因的表达及三萜皂苷合成通路关键酶分子的进化奠定了基础。     

Essential factors determining codon usage in ubiquitin genes

Summary Ubiquitin is ubiquitous in all eukaryotes and its amino acid sequence shows extreme conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences coding for 13 ubiquitin genes from 11 species reported so far have been compiled and analyzed. The G+C content of codon third base reveals a positive linear correlation with the genome G+C content of the corresponding species. The slope strongly suggests that the overall G+C content of codons of polyubiquitin genes clearly reflects the genome G+C content by AT/GC substitutions at the codon third position. The G+C content of ubiquitin codon third base also shows a positive linear correlation with the overall G+C content of coding regions of compiled genes, indicating the codon choices among synonymous codons reflect the average codon usage pattern of corresponding species. On the other hand, the monoubiquitin gene, which is different from the polyubiquitin gene in gene organization, gene expression, and function of the encoding protein, shows a different codon usage pattern compared with that of the polyubiquitin gene. From comparisons of the levels of synonymous substitutions among ubiquitin repeats and the homology of the amino acid sequence of the tail of monomeric ubiquitin genes, we propose that the molecular evolution of ubiquitin genes occurred as follows: Plural primitive ubiquitin sequences were dispersed on genome in ancestral eukaryotes. Some of them situated in a particular environment fused with the tail sequence to produce monomeric ubiquitin genes that were maintained across species. After divergence of species, polyubiquitin genes were formed by duplication of the other primitive ubiquitin sequences on different chromosomes. Differences in the environments in which ubiquitin genes are embedded reflect the differences in codon choice and in gene expression pattern between poly- and monomeric ubiquitin genes.     

3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR.

3-Nitropyrrole and 5-nitroindole have been assessed as universal bases in primers for dideoxy DNA sequencing and in the polymerase chain reaction (PCR). In contrast to a previous report, we have found that the introduction of more than one 3-nitropyrrole residue at dispersed positions into primers significantly reduced their efficiency in PCR and sequencing reactions. Primers containing 5-nitroindole at multiple dispersed positions were similarly affected; for both bases only a small number of substitutions were tolerated. In PCR experiments neither base, when incorporated into primers in codon third positions, was as effective as hypoxanthine, which was incorporated in six codon third positions in a 20mer oligomer. However, primers containing up to four consecutive 5-nitroindole substitutions performed well in both PCR and sequencing reactions. Consecutive 3-nitropyrrole substitutions were tolerated, but less well in comparable reactions.     

The Mitochondrial Genome of the Honeybee Apis Mellifera: Complete Sequence and Genome Organization

The complete sequence of honeybee (Apis mellifera) mitochondrial DNA is reported being 16,343 bp long in the strain sequenced. Relative to their positions in the Drosophila map, 11 of the tRNA genes are in altered positions, but the other genes and regions are in the same relative positions. Comparisons of the predicted protein sequences indicate that the honeybee mitochondrial genetic code is the same as that for Drosophila; but the anticodons of two tRNAs differ between these two insects. The base composition shows extreme bias, being 84.9% AT (cf. 78.6% in Drosophila yakuba). In protein-encoding genes, the AT bias is strongest at the third codon positions (which in some cases lack guanines altogether), and least in second codon positions. Multiple stepwise regression analysis of the predicted products of the protein-encoding genes shows a significant association between the numbers of occurrences of amino acids and %T in codon family, but not with the number of codons per codon family or other parameters associated with codon family base composition. Differences in amino acid abundances are apparent between the predicted Apis and Drosophila proteins, with a relative abundance in the Apis proteins of lysine and a relative deficiency of alanine. Drosophila alanine residues are as often replaced by serine as conserved in Apis. The differences in abundances between Drosophila and Apis are associated with %AT in the codon families, and the degree of divergence in amino acid composition between proteins correlates with the divergence in %AT at the second codon positions. Overall, transversions are about twice as abundant as transitions when comparing Drosophila and Apis protein-encoding genes, but this ratio varies between codon positions. Marked excesses of transitions over chance expectation are seen for the third positions of protein-coding genes and for the gene for the small subunit of ribosomal RNA. For the third codon positions the excess of transitions is adequately explained as due to the restriction of observable substitutions to transitions for conserved amino acids with two-codon families; the excess of transitions over expectation for the small ribosomal subunit suggests that the conservation of nucleotide size is favored by selection.     

海葵神经毒素基因的克隆和序列分析

根据已发现的海葵神经毒素蛋白的两端保守氨基酸序列 ,设计简并引物 .用RT PCR方法 ,从侧花海葵 (Anthopleurasp .)触手总RNA中分离出多个神经毒素新基因 .它们分别编码 3个长度都是 4 7个氨基酸的毒素蛋白 ,它们的氨基酸序列与海葵神经毒素C(Ap C)最为相似 .新基因的发现为进一步研究其生物活性及应用打下了基础 .     

Correlations between the compositional properties of human genes,codon usage,and amino acid composition of proteins

Summary We have analyzed the correlation that exists between the GC levels of third and first or second codon position for about 1400 human coding sequences. The linear relationship that was found indicates that the large differences in GC level of third codon positions of human genes are paralleled by smaller differences in GC levels of first and second codon positions. Whereas third codon position differences correspond to very large differences in codon usage within the human genome, the first and second codon position differences correspond to smaller, yet very remarkable, differences in the amino acid composition of encoded proteins. Because GC levels of codon positions are linearly correlated with the GC levels of the isochores harboring the corresponding genes, both codon usage and amino acid composition are different for proteins encoded by genes located in isochores of different GC levels. Furthermore, we have also shown that a linear relationship with a unity slope and a correlation coefficient of 0.77 exists between GC levels of introns and exons from the 238 human genes currently available for this analysis. Introns are, however, about 5% lower in GC, on average, than exons from the same genes.     

Comparative analysis of the base biases at the gene terminal portions in seven eukaryote genomes

Adenine nucleotides have been found to appear preferentially in the regions after the initiation codons or before the termination codons of bacterial genes. Our previous experiments showed that AAA and AAT, the two most frequent second codons in Escherichia coli, significantly enhance translation efficiency. To determine whether such a characteristic feature of base frequencies exists in eukaryote genes, we performed a comparative analysis of the base biases at the gene terminal portions using the proteomes of seven eukaryotes. Here we show that the base appearance at the codon third positions of gene terminal regions is highly biased in eukaryote genomes, although the codon third positions are almost free from amino acid preference. The bias changes depending on its position in a gene, and is characteristic of each species. We also found that bias is most outstanding at the second codon, the codon after the initiation codon. NCN is preferred in every genome; in particular, GCG is strongly favored in human and plant genes. The presence of the bias implies that the base sequences at the second codon affect translation efficiency in eukaryotes as well as bacteria.     

Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations

An ab initio model for gene prediction in prokaryotic genomes is proposed based on physicochemical characteristics of codons calculated from molecular dynamics (MD) simulations. The model requires a specification of three calculated quantities for each codon: the double-helical trinucleotide base pairing energy, the base pair stacking energy, and an index of the propensity of a codon for protein-nucleic acid interactions. The base pairing and stacking energies for each codon are obtained from recently reported MD simulations on all unique tetranucleotide steps, and the third parameter is assigned based on the conjugate rule previously proposed to account for the wobble hypothesis with respect to degeneracies in the genetic code. The third interaction propensity parameter values correlate well with ab initio MD calculated solvation energies and flexibility of codon sequences as well as codon usage in genes and amino acid composition frequencies in ∼175,000 protein sequences in the Swissprot database. Assignment of these three parameters for each codon enables the calculation of the magnitude and orientation of a cumulative three-dimensional vector for a DNA sequence of any length in each of the six genomic reading frames. Analysis of 372 genomes comprising ∼350,000 genes shows that the orientations of the gene and nongene vectors are well differentiated and make a clear distinction feasible between genic and nongenic sequences at a level equivalent to or better than currently available knowledge-based models trained on the basis of empirical data, presenting a strong support for the possibility of a unique and useful physicochemical characterization of DNA sequences from codons to genomes.     

应用PCR方法检测油菜菌核病菌对多菌灵的抗药性*

通过保守的寡核苷酸引物B1/B3扩增出油菜菌核病菌MBCHR和MBCS菌株的部分β-微管蛋白基因,结果发现编码的198位氨基酸由Glu(GAG)突变为Ala(GCG),表现高水平抗药性。根据MBCHR菌株的突变设计2个快速检测方法:第一种方法是根据MBCHR菌株197和198位密码子(GACGAG→GACGCG)形成ThaI酶切位点(3’CGCG 5’),将B1/B3的扩增产物874bp片段酶切成193bp和681bp片段,而MBCS菌株的PCR产物不被酶切;第二种方法用198位突变密码子作为3’末端碱基设计2个等位基因特异性寡核苷酸引物(ASO)用于“nested”PCR或直接从基因组DNA扩增。通过PCR扩增和ThaI酶切能直接检测油菜菌核病菌的MBCHR和MBCS菌株,所得结果与传统菌落直径法相吻合。     

DNA G+C content of the third codon position and codon usage biases of human genes

The human genome, as in other eukaryotes, has a wide heterogeneity in the DNA base composition. The evolutionary basis for this heterogeneity has been unknown. A previous study of the human genome (846 genes analyzed) has shown that, in the major range of the G+C content in the third codon position (0.25-0.75), biases from the Parity Rule 2 (PR2) among the synonymous codons of the four-codon amino acids are similar except in the highest G+C range (Sueoka, N., 1999. Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position. Gene 238, 53-58.). PR2 is an intra-strand rule where A=T and G=C are expected when there are no biases between the two complementary strands of DNA in mutation and selection rates (substitution rates). In this study, 14,026 human genes were analyzed. In addition, the third codon positions of two-codon amino acids were analyzed. New results show the following: (a) The G+C contents of the third codon position of human genes are scattered in the G+C range of 0.22-0.96 in the third codon position. (b) The PR2 biases are similar in the range of 0.25-0.75, whereas, in the high G+C range (0.75-0.96; 13% of the genes), the PR2-bias fingerprints are different from those of the major range. (c) Unlike the PR2 biases, the G+C contents of the third codon position for both four-codon and two-codon amino acids are all correlated almost perfectly with the G+C content of the third codon position over the total G+C ranges. These results support the notion that the directional mutation pressure, rather than the directional selection pressure, is mainly responsible for the heterogeneity of the G+C content of the third codon position.