牛RHOQ基因的电子克隆与生物信息学分析

利用电子克隆技术获得牛RHOQ基因cDNA序列,采用生物信息学方法对该基因及其编码蛋白的基本理化性质、疏水性、信号肽、二级结构和亚细胞定位等方面进行预测和分析。结果表明,牛RHOQ基因的cDNA序列全长1 517 bp,包含1个618 bp开放阅读框,编码205个氨基酸;其编码蛋白属疏水性蛋白,不存在信号肽及跨膜结构,定位于分泌系统囊泡;二级结构主要以无规则卷曲和α-螺旋为主。牛RHOQ基因编码蛋白可能具有生长因子功能,可能在神经再生和突触延伸过程中起重要作用。     

牛Pbx-1基因的电子克隆及生物信息学分析

新基因全长cDNA序列很难获得,但电子克隆却提供了基因克隆的一种策略.利用小鼠Pbx-1基因编码序列(NM_183355)为种子序列进行电子克隆获得牛Pbx-1基因完整编码序列.然后,用生物信息学方法分析了牛的Pbx-1基因的结构,密码子偏性和氨基酸的同源性等.结果表明:该基因cDNA全长1 754 bp,无内含子,最大开放阅读框1 305 bp.编码434个氨基酸.预测其编码的蛋白分子量为47 189.5 Da,与小鼠的同源性为81%.     

泥鳅MnSOD基因的电子克隆及序列分析

目的:电子克隆并分析泥鳅MnSOD基因.方法:通过电子克隆泥鳅MnSOD基因的开放阅读框,并对其氨基酸组成、功能结构域、系统进化、信号肽、二级结构、三级结构等信息进行预测分析.结果:通过电子克隆获得泥鳅MnSOD基因的cDNA.该基因的开放阅读框大小为675bp,编码224个氨基酸残基,推导的蛋白质分子量为25kDa,等电点约为8.41,其编码序列与其他物种相比非常保守,与鲤形目淡水鱼的MnSOD在进化上亲缘关系最近.其N端含转运肽,推测它定位于线粒体中.预测泥鳅MnSOD的二级结构及三级结构含有较多的不规则卷曲和α螺旋,其N端为两个长的反平行螺旋,C端则为含有拧成三股折叠片的α+β结构.结论:该研究为泥鳅进一步的分子生物学及抗氧化研究奠定了基础.     

玉米中一种新的蛋白激酶电子克隆与序列分析

目的：电子克隆玉米中一种新的蛋白激酶基因。方法：以拟南芥中一个蛋白激酶的氨基酸序列为探针,对玉米的EST数据库进行同源性检索和筛选并克隆。结果：序列分析显示该cDNA长1121bp,有一个450bp的开放阅读框,编码149个氨基酸,且具有保守苏氨酸/丝氨酸蛋白激酶结构域和TEY基元,说明所克隆的cDNA序列为玉米的MAPK全长cDNA。结论：所克隆的cDNA序列为玉米的MAPK全长cDNA。     

猪GATA-3基因的电子克隆、表达及其分子进化分析

基于猪的表达标签数据库电子克隆了猪的GATA-3基因,并通过RT-PCR验证了猪的GATA-3基因的核苷酸序列。测序结果显示猪的GATA-3基因的核苷酸长度由1,760bp个碱基组成,包括1,335bp的开放阅读框,编码产物为由444个氨基酸残基组成的多肽。通过半定量RT-PCR检测了GATA-3 mRNA在大白猪的各个组织的表达情况。GATA转录因子家族通常有2个Ⅳ型锌指蛋白结构,根据Ⅳ型锌指蛋白结构序列,使用Mega3．1软件构建了分子进化关系树。系统发育分析表明所有的脊椎动物的GATA转录因子都起源于共同的祖先,拓扑结构也表明进化过程中有多种事件发生,包括基因复制和Ⅳ型锌指蛋白结构域重组,根据所得数据有利于进一步了解GATA家族基因趋同和趋异的进化途径。     

高粱抗坏血酸过氧化物酶基因的电子克隆及序列分析

利用高粱EST数据库及电子克隆等技术克隆了高粱APX基因,其开放阅读框大小为753bp,编码250个氨基酸残基,推导的蛋白质分子量为27.1kDa,等电点约为5.135.它与C4植物玉米的胞质APX(ACG41151)在进化上的距离最短,亲缘关系最近.高粱APX无信号肽,是亲水性蛋白,推测它定位于细胞质中.第33-44氨基酸片段为其过氧化物酶活性区域,第155-165氨基酸片段则是其与亚铁血红素配基结合的区域.预测的二级结构及三级结构都表明高粱APX含有较多的不规则卷曲和α螺旋,三级结构上呈椭球体.     

Functional Analysis of Sesame Diacylglycerol Acyltransferase and Phospholipid: Diacylglycerol Acyltransferase Genes Using In Silico and In Vitro Approaches

Plant Molecular Biology Reporter - Sesamum indicum L. is one of the major oilseed crops of India. Sesame oil is stable with a good source of unsaturated fatty acids. To know the mechanism of oil...     

Mutational Analysis of the TYR and OCA2 Genes in Four Chinese Families with Oculocutaneous Albinism

Background

Oculocutaneous albinism (OCA) is an autosomal recessive disorder. The most common type OCA1 and OCA2 are caused by homozygous or compound heterozygous mutations in the tyrosinase gene (TYR) and OCA2 gene, respectively.

Objective

The purpose of this study was to evaluate the molecular basis of oculocutaneous albinism in four Chinese families.

Patients and Methods

Four non-consanguineous OCA families were included in the study. The TYR and OCA2 genes of all individuals were amplified by polymerase chain reaction (PCR), sequenced and compared with a reference database.

Results

Four patients with a diagnosis of oculocutaneous albinism, presented with milky skin, white or light brown hair and nystagmus. Genetic analyses demonstrated that patient A was compound heterozygous for c.1037-7T.A, c.1037-10_11delTT and c.1114delG mutations in the TYR gene; patient B was heterozygous for c.593C>T and c.1426A>G mutations in the OCA2 gene, patients C and D were compound heterozygous mutations in the TYR gene (c.549_550delGT and c.896G>A, c.832C>T and c.985T>C, respectively). The heterozygous c.549_550delGT and c.1114delG alleles in the TYR gene were two novel mutations. Interestingly, heterozygous members in these pedigrees who carried c.1114delG mutations in the TYR gene or c.1426A>G mutations in the OCA2 gene presented with blond or brown hair and pale skin, but no ocular disorders when they were born; the skin of these patients accumulated pigment over time and with sun exposure.

Conclusion

This study expands the mutation spectrum of oculocutaneous albinism. It is the first time, to the best of our knowledge, to report that c.549_550delGT and c.1114delG mutations in the TYR gene were associated with OCA. The two mutations (c.1114delG in the TYR gene and c.1426A>G in the OCA2 gene) may be responsible for partial clinical manifestations of OCA.     

黄瓜CsEXP 10基因的电子克隆及生物信息学分析

以黄瓜CsEXP10 cDNA片段为信息探针,利用电子克隆和序列拼接方法获得了1191bp的cDNA序列。应用生物信息学软件预测了该蛋白的理化性质、卷曲螺旋、疏水性、信号肽、跨膜结构、糖基位点、活性位点、亚细胞定位及二级和高级结构。结果表明：该蛋白是一个疏水性稳定蛋白,定位于细胞壁,含有4个α-螺旋,11个β-折叠,5个跨膜区域,10个糖基化位点,具有催化域和多糖结合域两个结构域。     

In Silico Analysis of Functional Single Nucleotide Polymorphisms in the Human TRIM22 Gene

Tripartite motif protein 22 (TRIM22) is an evolutionarily ancient protein that plays an integral role in the host innate immune response to viruses. The antiviral TRIM22 protein has been shown to inhibit the replication of a number of viruses, including HIV-1, hepatitis B, and influenza A. TRIM22 expression has also been associated with multiple sclerosis, cancer, and autoimmune disease. In this study, multiple in silico computational methods were used to identify non-synonymous or amino acid-changing SNPs (nsSNP) that are deleterious to TRIM22 structure and/or function. A sequence homology-based approach was adopted for screening nsSNPs in TRIM22, including six different in silico prediction algorithms and evolutionary conservation data from the ConSurf web server. In total, 14 high-risk nsSNPs were identified in TRIM22, most of which are located in a protein interaction module called the B30.2 domain. Additionally, 9 of the top high-risk nsSNPs altered the putative structure of TRIM22''s B30.2 domain, particularly in the surface-exposed v2 and v3 regions. These same regions are critical for retroviral restriction by the closely-related TRIM5α protein. A number of putative structural and functional residues, including several sites that undergo post-translational modification, were also identified in TRIM22. This study is the first extensive in silico analysis of the highly polymorphic TRIM22 gene and will be a valuable resource for future targeted mechanistic and population-based studies.     

In Silico Analysis of Usher Encoding Genes in Klebsiella pneumoniae and Characterization of Their Role in Adhesion and Colonization

Chaperone/usher (CU) assembly pathway is used by a wide range of Enterobacteriaceae to assemble adhesive surface structures called pili or fimbriae that play a role in bacteria-host cell interactions. In silico analysis revealed that the genome of Klebsiella pneumoniae LM21 harbors eight chromosomal CU loci belonging to γκп and ϭ clusters. Of these, only two correspond to previously described operons, namely type 1 and type 3-encoding operons. Isogenic usher deletion mutants of K. pneumoniae LM21 were constructed for each locus and their role in adhesion to animal (Intestine 407) and plant (Arabidopsis thaliana) cells, biofilm formation and murine intestinal colonization was investigated. Type 3 pili usher deleted mutant was impaired in all assays, whereas type 1 pili usher deleted mutant only showed attenuation in adhesion to plant cells and in intestinal colonization. The LM21ΔkpjC mutant was impaired in its capacity to adhere to Arabidopsis cells and to colonize the murine intestine, either alone or in co-inoculation experiments. Deletion of LM21kpgC induced a significant decrease in biofilm formation, in adhesion to animal cells and in colonization of the mice intestine. The LM21∆kpaC and LM21∆kpeC mutants were only attenuated in biofilm formation and the adhesion abilities to Arabidopsis cells, respectively. No clear in vitro or in vivo effect was observed for LM21∆kpbC and LM21∆kpdC mutants. The multiplicity of CU loci in K. pneumoniae genome and their specific adhesion pattern probably reflect the ability of the bacteria to adhere to different substrates in its diverse ecological niches.     

In Silico Analysis of Peptide Potential Biological Functions

Over the past decade, tools of omics technologies have generated a large amount of data in various repositories, which are of interest for meta-analysis today. Now, researchers in the field of proteomics and peptidomics focus not on sequencing, but on functions performed by molecules and metabolic interactions, in which the proteins or peptides participate. As a result of a single LC-MS/MS analysis, several thousand unique peptides can be identified, each of which may be bioactive. A classic technique for determining the peptide function is a direct experiment. Bioinformatics approaches as a preliminary analysis of potential biological functions are an important step and are able to significantly reduce time and cost of experimental verification. This article provides an overview of computational methods for predicting biological functions of peptides. Approaches based on machine learning, which are the most popular today, algorithms using structural, evolutionary, or statistical patterns, as well as methods based on molecular docking, are considered. Databases of bioactive peptides are reported, providing information necessary to construct new algorithms for predicting biological functions. Attention is paid to the characteristics of peptides, on the basis of which it is possible to draw conclusions about their bioactivity. In addition, the report provides a list of online services that may be used by researchers to analyze potential activities of peptides with which they work.