Immunochemical investigations on Bacteroides fragilis antigenic structure

Bacteroides fragilis strain 62/73 was studied. We demonstrated that formation of capsules is not a constant feature of cells of this strain. After chemical treatment we obtained six serologically active substances. The studied strain releases serologically active substances into the culture medium. We also found that endotoxin is the bacterial fraction according to which the strain may be classified to the appropriate serotype.     

Genomic structure of murine mitochondrial DNA polymerase-gamma

We have sequenced a genomic clone of the gene encoding the mouse mitochondrial DNA polymerase. The gene consists of 23 exons, which span approximately 13.2 kb, with exons ranging in size from 53 to 768 bp. All intron-exon boundaries conform to the GT-AG rule. By comparison with the human genomic sequence, we found remarkable conservation of the gene structure; the intron-exon borders are in almost identical locations for the 22 introns. The 5' upstream region contains approximately 300 bp of homology between the mouse and human sequences that presumably contain the promoter element. This region lacks any obvious TATA domain and is relatively GC rich, consistent with the housekeeping function of the mitochondrial DNA polymerase. Finally, within the 5' flanking region, both mouse and human genes have a region of 73 bp with high homology to the tRNA-Arg gene.     

Genomic structure of the human ezrin gene

The ERM proteins, ezrin, radixin, and moesin, act as linkers between the plasma membrane and actin cytoskeleton. They are involved in a variety of cellular functions, such as cell adhesion, migration, and the organization of cell surface structures, and are highly homologous, both in protein sequence and in functional activity, with merlin/schwannomin, a neurofibromatosis-2-associated tumor-suppressor protein. We report here the genomic structure and intron junction sequences of the human ezrin gene. Ezrin consists of 13 exons and spans approximately 24 kb genomic DNA. The coding parts of the exons range in size from 12 bp to 275 bp and the introns from 182 bp to 7 kb. The genomic structures of ezrin and moesin are highly conserved, suggesting their recent divergence. Radiation hybrid mapping has refined the location of ezrin to the interval between D6S442 and D6S281. Received: 1 June 1998 / Accepted: 25 August 1998     

Genomic DNA structure of two new horseradish-peroxidase-encoding genes

Genomic DNAs encoding the horseradish peroxidase (HRP) isozymes, prxC2 and prxC3, were cloned and sequenced. By comparing the sequences of the HRP isozyme-encoding genes, prxC1a and prxC1b and their cDNA [Fujiyama et al., Eur. J. Biochem. 173 (1988) 681-687], , it was concluded that prxC2 and prxC3 consisted of four exons and three introns as in the prxC1 gene family. The position of introns in coding regions were the same in all four prx genes. Genes prxC2 and prxC3 coded for 347 and 349 amino acid (aa) residues, respectively, including putative signal sequences at the N termini. In the flanking regions of both genes, putative promoters and polyadenylation signals were found. Nucleotide sequence homology in the coding region was 71% between prxC1a and prxC2, and 66% between prxC1a and prxC3. The aa sequence homologies in plant and microbial peroxidases were compared.     

Genomic structure of the human PLZF gene.

The human PLZF (promyelocytic leukaemia zinc finger) gene encodes a Krüppel-like zinc finger protein, which was identified via the reciprocal translocation t(11;17)(q23;q21) fusing it to the retinoic acid receptor alpha (RARalpha) gene in promyelocytic leukaemia. To determine its complete genomic organisation, we constructed a cosmid-map fully containing the hPLZF gene. The gene has seven exons, including a novel 5' untranslated exon, varying in size from 87 to 1358bp and spans at least 120kb. Flanking intronic sequences were identified and all splice acceptor and donor sites conformed to the gt/ag rule. Five polymorphic markers could be fine located in its vicinity. These data will facilitate mutation analysis of hPLZF in t(11;17) leukaemia cases, as well as assist mapping and loss-of-heterozygosity analysis. Here we have tested hPLZF as a possible candidate for the PGL1 locus involved in hereditary head and neck paragangliomas. However, mutation analysis revealed no aberration in 12 paraganglioma patients from different families.     

基因组SNP揭示少根根霉种群结构

少根根霉在自然界分布广泛,是重要的食品发酵菌,又是著名的机会致病菌,在形态和生化上多样性丰富,包括原变种、德氏变种和东京变种等3个分类学变种,原型、德氏型、东京型和鲁氏型等4个形态型,以及乳酸组和富马苹果酸组等2个生化组。DNA分子多样性更为丰富。但这些多样性之间缺乏系统的关联研究。本研究选择能代表以上多样性的67个菌株,通过全基因组重测序提取ITS、IGS rDNA和SNP多态性位点进行分子系统发育和群体结构分析,结果将少根根霉分为4个主要的系统发育分支,分支1和2是姐妹群关系,共同构成德氏变种,另外两个分支分别对应东京变种和原变种。鲁氏形态型多系,源自原变种和德氏变种。群体结构分析表明在少根根霉物种内,德氏变种首先分歧出来,然后东京变种和原变种发生分化,最后3个变种分化出各自的亚群;这些亚群表明少根根霉物种正沿着8个相互杂交的分子群体进行演化。本研究首次利用基因组范围的信息支持所有的生态群、分类学变种、形态型、生化组和系统发育分支仍然属于同一个物种,物种分化尚未完成,同时实现了对少根根霉多个DNA分子群体的解析并推导出其演化规律。     

Genomic structure of murine Rab11 family members

Rab11a, Rab11b, and Rab25 in mammals are thought to comprise a subfamily of Rab proteins, although Rab25 has two amino acid differences in its effector domain. We have isolated and characterized the genomic sequences of murine Rab11a and Rab25 and compared them with those of previously characterized mammalian Rab genes. The Rab11a gene spans 29 kb and Rab25 spans 9 kb. The genes have TATA-less promoters, but contain GC-rich areas in their upstream 5' regions. Both genes have 5 exons, with the introns containing characteristic repeats. Rab11a has an unusually long 8. 5-kb fourth intron. The Rab11a and Rab25 genes are localized to chromosomes 9C and 3E3/F1, respectively. The overall organization of the Rab11a, Rab11b, and Rab25 genes is similar, with homologous exon-intron boundaries, and differs markedly from those of Rab3A and Rab1A. These results confirm that Rab11A, Rab11b, and Rab25 represent a closely related gene family.     

Genomic structure predicts metabolite dynamics in microbial communities

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Genomic structure and expression of human guanosine monophosphate reductase

Summary In vitro translation in the rabbit reticulocyte system and transient expression in Cos7 cells were performed to characterize the protein encoded by a chromosome 6-linked human cDNA clone, whose nucleotide sequence is homologous to that of Escherichia coli guanosine monophosphate reductase (GMP reductase) cDNA. The molecular weight of the peptide produced by the cDNA was about 37,000 Dalton, and the protein produced in the Cos7 cells exhibited GMP reductase activity, substantiating that the cDNA is for human GMP reductase. The corresponding genomic clones were obtained from two human genomic libraries. The gene spans about 50 Kb and is composed of 9 exons, which encode 345 amino acid residues. Organization of exons and introns was established by DNA sequencing of each exon and splicing junctions. The gene contains two potential SpI binding sites within exon 1, and a functional atypical polyadenylation signal in exon 9.     

Genomic structure and alternative splicing of chicken angiopoietin-2

Angiopoietin-1 (Ang-1) prevents endothelial cell apoptosis and promotes blood vessel stability, while angiopoietin-2 (Ang-2), a natural antagonist of Ang-1, disrupts blood vessel structure and induces apoptosis. We have sequenced the chicken angiopoietin-2 gene that spans about 46 kb of DNA and is split in 9 exons by 8 introns. Alternative splicing of the gene gives rise to three different species of Ang-2 mRNAs: Ang-2A, Ang-2B, and Ang-2C. The three mRNA isoforms, also present in humans, codify for proteins with an identical fibrinogen-like C-terminal domain and a different coiled-coil N-terminal domain. Ang-2A and particularly Ang-2C are expressed in immature testis and regressed adult testis undergoing vascular remodeling, while their expression is barely detectable in quiescent adult testis. Conversely, Ang-2B is only detectable in adult testis. The new isoforms with truncated amino-terminal domains may modulate the Tie2 receptor during vascular angiogenesis and regression.     

Genomic diversity and geographical structure of the Pyrenean desman

The Pyrenean desman (Galemys pyrenaicus) is a small semi-aquatic mammal endemic to the Iberian Peninsula. The species has recently experienced a strong decline and some of its populations are severely threatened with extinction. To help in the preservation of this species, it is critical to understand its genetic structure and main evolutionary units, as these may have specific local adaptations and could be of great conservation value. Sequencing reduced representation libraries (ddRAD) from 26 specimens selected from across its entire range, we obtained around 45,000 loci per specimen and 1185 single nucleotide polymorphisms. Heterozygosity varied substantially among individuals from different areas. Interestingly, specimens from the southeastern Pyrenees had some of the lowest proportions of heterozygous positions inferred from genome-wide data in mammals so far. In addition, we estimated a tree reflecting genomic divergence, performed a principal component analysis, and carried out a Bayesian analysis of the population structure. Combined evidence supported the existence of five distinct genomic clusters largely coincident with the main mountain ranges where the species occurs, with few specimens presenting relevant admixture levels. There was good correspondence between these populations and the mitochondrial lineages detected in a previous study, yet substantial differences in some areas demonstrate the importance of performing genomic analysis to reveal the whole population history. Although the analysis of further specimens is necessary to better characterize the distribution of the different evolutionary units, the distinctive geographical structure of this species revealed by the genomic data should be considered in future conservation plans.     

Genomic structure of the human mitochondrial aldehyde dehydrogenase gene

We have isolated and characterized four overlapping clones from two cosmid human genomic libraries, which span about 90 kilobase pairs (kbp) and contain the entire human mitochondrial aldehyde dehydrogenase (ALDH2) gene. Restriction maps of the genomic clones were elucidated utilizing cDNA probes and specific oligonucleotide probes. The organization of exons and introns was established by DNA sequencing of each exon and splicing junctions. The ALDH2 gene is about 44 kbp in length and contains at least 13 exons which encode 517 amino acid residues. Except for the signal NH2-terminal peptide, which is absent in the mature enzyme, the amino acid sequence deduced from the exons coincided with the reported primary structure of human liver ALDH2 (J. Hempel, R. Kaiser, and H. J?rnvall, 1985, Eur. J. Biochem. 153: 13-28). Several introns contain Alu repetitive sequences. A TATA-like sequence (TTATAAAA) and a CAAT-like sequence (GTCATCAT) are located 473 and 515 bp, respectively, upstream from the translation initiation codon. Primer extension and S1 nuclease mapping were performed to characterize the 5'-region of the gene.     

新型冠状病毒基因组结构与蛋白功能

2019年12月以来,武汉市暴发新型冠状病毒肺炎(coronavirus disease 2019,COVID-19)疫情并迅速蔓延全国,2020年1月30日被世界卫生组织(World Health Organization,WHO)列为“国际关注的突发公共卫生事件”(public health emergency of international concern,PHEIC)。核酸序列分析证明COVID-19由新型冠状病毒(2019 novel coronavirus,2019-nCoV)引起。2019-nCoV为正链单链RNA病毒,基因组长约30 kb,两端为非编码区,中间为非结构蛋白编码区和结构蛋白编码区。非结构蛋白编码区主要包括开放读码框架(open reading frame,ORF)1a和ORF1b基因,编码16个非结构蛋白(non-structural proteins,NSP),即NSP1～16。结构蛋白编码区主要编码刺突(spike,S)蛋白、包膜(envelope,E)蛋白、膜(membrane,M)蛋白和核衣壳(nucleocapsid,N)蛋白。深入了解2019-nCoV基因组的结构和蛋白功能,将为2019-nCoV相关的病毒溯源、复制增殖、致病免疫、药物与疫苗研发以及当前疫情的防控提供有力的支撑。