中国微生物资源数据库细菌性状子库的数据结构与检索功能设计

提出了构建中国微生物资源数据库CDMR(China Database for Microbial Resources)的方案。该库包括微生物性状库、微生物产品的商品信息库、微生物名称库以及微生物名词库四个分库。本文详细介绍了细菌性状子库的数据结构与检索功能。     

蛋白骨架在随机肽库构建及靶分子筛选中的应用*

自然界有着丰富的蛋白骨架来源。选择适宜的蛋白骨架和展示、筛选方法,可构建基于合理蛋白骨架结构的优化限制性随机肽库。与非限制性随机肽库相比,可望获得针对靶分子具有新功能的蛋白结构或更高亲和力的配体分子。目前,骨架蛋白限制的随机肽库已在高效靶分子筛选、基础研究、临床诊断和医学治疗等方面显示出巨大的潜在应用价值。以S-S限制性骨架、抗体分子、锌指蛋白、Z结构域、FN3结构域等为主要代表,综合介绍了蛋白骨架的结构基础、分类、基于蛋白骨架的限制性随机肽库构建及近年来在靶分子筛选等方面的应用最新进展。     

微生物代谢产物库研究进展

微生物代谢物具有极大的化学结构多样性和复杂性,建立微生物代谢物库对发现新药有重要意义。对几种重要的微生物代谢物库及建库方法作一综述。     

植物芽库的研究进展

芽库即所有潜在的能进行营养繁殖的芽的集合。芽库和种子库一同构成了植物的繁殖库,在植被的维持和更新中占据着重要地位。根据最新研究进展,从以下几方面归纳了芽库的研究概况:1)芽库与种子库的区别与联系;2)芽库的分类;3)环境因子对芽库建成和动态的影响;4)模型(如矩阵模型、三角函数、马尔可夫(Markov)模型等)在芽库研究中的应用;5)芽库与地上植被的关系。将来应加强不同生态系统的芽库研究、芽库和种子库对地上植被更新的相对贡献以及芽库在植被恢复和重建中的应用。     

噬菌体抗体库技术及其在医学微生物学中应用

９０年代发展起来的噬菌体抗体库技术,可以不经过杂交瘤,甚至不经过免疫而直接用个体细胞从功能水平均建抗体库,并从同一库中筛选多种特异性抗体。这项技术在医学微生物学领域得到了应用,已在抗病毒等病原微生物人单克隆抗体的制备上表现出较大的优越性。     

用SELEX技术筛选核酸适配子的原理及应用

SELEX技术是一项新的体外筛选技术,它是用体外合成的、库容为10^14-15左右的随机寡核苷酸库与靶物质结合,通过数轮的筛选与扩增,筛选到靶物质的目的的DNA或RNA片段,在疾病的诊断与治疗方面起着重要的作用,为核心酸的结构和功能的研究,提供了一个有效的方法。     

插入突变在功能基因组学研究中的应用

插入突变库的构建是功能基因组学研究的一个重要内容,可为确定基因的功能提供最直接的证据。构建插入突变库的方法有T-DNA插入突变、转座子插入突变和质粒介导的插入突变。本文分别介绍三种方法的原理及其在功能基因组学研究中的应用和研究进展。     

噬菌体展示文库及其应用

近十几年来,噬菌体展示技术得到了迅速的发展。通过展示随机肽库可用来筛选与特殊靶分子相结合的配基;模拟非蛋白的配基;也可用作确定抗体表位的工具。展示蛋白;或其功能结构的文库为我们提供了分析结构与功能关系的体系,并能产生具有改变结合位点或新的催化活性的蛋白。展示短的抗原决定簇的融合噬菌体为开发新的疫苗提供了基础,而表达抗体片段的文库则提供了一种产生单克隆抗体的方法。     

水稻插入突变库构建研究进展

水稻是单子叶植物基因组研究的一种模式植物 ,其全基因组测序已经完成 ,在此基础上开展功能基因组的研究。水稻插入突变体库的建立是功能基因组研究的一个重要内容 ,在此基础上也能进行正向遗传学及反向遗传学的研究。水稻插入突变体库构建的方法有T DNA插入突变、Ac Ds系统插入突变、Tos1 7插入突变。分别介绍三种方法的原理及其在水稻突变体库构建中的应用和研究进展。     

农田土壤有机碳库大小及周转

对水稻土、早地潮土和红壤下土壤有机碳库的大小、分解速率和平均驻留时间进行了分析,根据有机碳周转时间的不同,可将土壤有机碳库划分为活性碳库、缓效性碳库和惰效性碳库3个库,其遵循三库一级动力学方程,根据土壤有机碳的分解变化,用此方程在SAS8.2软件上拟合出活性碳库、缓效性碳库的大小及其分解速率.结果表明,农田土壤各剖面的活性碳一般占土壤有机碳的0.6%～3.7%,平均驻留时间为4～45 d;缓效性碳库一般占土壤有机碳的37.7%～81.2%,平均驻留时间为5～24年;利用酸水解测得的惰效性碳一般占土壤有机碳的17.1%～48.1%.不同水型及不同母质下的水稻土中各碳库变化规律分别为：潴育型水稻土＞潜育型水稻土＞淹育型水稻土、第四纪红粘土＞第三纪红砂岩类.不同水稻土和旱地土壤中,活性碳库变化规律为水稻土＞旱地,而缓效性碳为旱地土壤＞水稻土,表明旱地土壤的固碳能力较水田强.     

Structure and antigenic properties of the tip-located P pilus proteins of uropathogenic Escherichia coli.

Pyelonephritogenic Escherichia coli frequently expresses pili which bind to Gal alpha (1-4)Gal receptors present on the uroepithelium. Binding of these pili is mediated by a pilus-associated adhesin, PapG, and not by the major subunit which constitutes the bulk of the pilus structure. The adhesin and two pilinlike proteins, PapE and PapF, are present in only a few copies each at the pilus tip. Surface exposure of both PapF and PapG is required to achieve receptor-specific binding. The nucleotide sequences for the genes encoding the tip-associated proteins PapE, PapF, and PapG were determined for two E. coli clones expressing P pili of serotypes F11 and F7(2) and compared with the corresponding sequences established for proteins of F13 pili. Specific antisera were used to study the cross-reactivity between the F13 tip proteins and the equivalent proteins in F11 and F7(2) pili. We present data showing that, like the major pilus subunit, PapE varies its structure and antigenic properties among pili of different serotypes. In contrast, the PapF protein was highly conserved, and PapF-specific antisera raised against serotype F13 cross-reacted with the PapF proteins of both F11 and F7(2) serotypes. The PapG adhesin protein from F11 and F7(2) pili differed by only five amino acids out of 316 residues. However, the F13 adhesin showed only 45% amino acid homology with the other two variants.     

Defective F pili and other characteristics of Flac and Hfr Escherichia coli mutants resistant to bacteriophage R17.

Mutants resistant to the donor-specific bacteriophage R17 were isolated from Hfr and Flac-containing strains of Escherichia coli K-12. Thirty-five mutants were examined for the presence of F pili by electron microscopy. The pilus morphology was studied, as were the abilities of the cells to retract their pili and to synthesize new pili. Measurements were made of the efficiency of the conjugal deoxyribonucleic acid transfer and of M13 and R17 phage infection. All mutants had noticeable defects in pilus production, structure, or function. Mutants were found which produced unusually long pili, displayed wide variations in the number of pili per cell, and were deficient in pilus retraction and synthesis. Evidence is presented that there may be two pathways of pilus retraction.     

Location of the antigenic determinants of conjugative F-like pili

The amino terminus of the pilin protein constitutes the major epitope of F-like conjugative pili studied to date (F, ColB2, R1-19, R100-1, and pED208). Anti-pED208 pilus antibodies were passed through a CNBr-Sepharose affinity column linked to bovine serum albumin which was conjugated to a synthetic peptide, AcP(1-12), containing the major epitope at the amino terminus of pED208 pilin. This allowed the separation of two classes of antibodies; one was specific for the amino terminus and bound to the column, while the other, which recognizes a second epitope on the pilus, did not bind to the column. In addition, antibodies were raised against two amino-terminal peptide-bovine serum albumin conjugates [AcP(1-8) and AcP(1-12)] to ensure a source of pure, high-titer antibodies directed against the amino terminus. The location of these antibodies on intact pili was assayed by immunoelectron microscopy with a protein A-gold technique. The amino terminus-specific antibodies did not bind to the sides of the pili but appeared to be associated with the pilus tip. In addition, these antibodies were found to bind to the vesicle-like structure at the base of the pilus. The anti-pilus antibodies not specific for the amino terminus (unbound immunoglobulin G) were found to bind to the sides of the pilus. Anti-F and anti-ColB2 pilus antibodies bound to the sides of F, ColB2, and R1-19 pili, which have only their secondary epitope in common. The carboxyl-terminal lysine of R1-19 pilin prevents the absorption of anti-F plus antiserum but not anti-ColB2 pilus antiserum to the sides of the pilus, presumably by interfering with the recognition of this secondary epitope.     

Function of the usher N-terminus in catalysing pilus assembly

The chaperone/usher (CU) pathway is a conserved bacterial secretion system that assembles adhesive fibres termed pili or fimbriae. Pilus biogenesis by the CU pathway requires a periplasmic chaperone and an outer membrane (OM) assembly platform termed the usher. The usher catalyses formation of subunit-subunit interactions to promote polymerization of the pilus fibre and provides the channel for fibre secretion. The mechanism by which the usher catalyses pilus assembly is not known. Using the P and type 1 pilus systems of uropathogenic Escherichia coli, we show that a conserved N-terminal disulphide region of the PapC and FimD ushers, as well as residue F4 of FimD, are required for the catalytic activity of the ushers. PapC disulphide loop mutants were able to bind PapDG chaperone-subunit complexes, but did not assemble PapG into pilus fibres. FimD disulphide loop and F4 mutants were able to bind chaperone-subunit complexes and initiate assembly of pilus fibres, but were defective for extending the pilus fibres, as measured using in vivo co-purification and in vitro pilus polymerization assays. These results suggest that the catalytic activity of PapC is required to initiate pilus biogenesis, whereas the catalytic activity of FimD is required for extension of the pilus fibre.     

Genetic complementation analysis of Escherichia coli type 1 somatic pilus mutants.

A genetic complementation analysis of 75 stable nonpiliated mutants of a type 1 piliated strain of Escherichia coli K-12, AW405, was performed. Strains containing pairs of pil mutations were constructed by the infectious transfer of an F101 plasmid containing one pil mutation into E. coli K-12 AW 405 containing another pil mutation. The presence or absence of type 1 pili on the merodiploid strains was determined by agglutination with type 1 pilus antiserum. All 75 mutants fell into one of four complementation groups. The pattern of complementation defined three cistrons involved in pilus formation, pilA, pilB, and pilC. The fourth complementation group was composed of a large number of mutants defective in both pilA and pilB functions.     

Interaction with type IV pili induces structural changes in the bacterial outer membrane secretin PilQ

Type IV pili are cell surface organelles found on many Gram-negative bacteria. They mediate a variety of functions, including adhesion, twitching motility, and competence for DNA uptake. The type IV pilus is a helical polymer of pilin protein subunits and is capable of rapid polymerization or depolymerization, generating large motor forces in the process. Here we show that a specific interaction between the outer membrane secretin PilQ and the type IV pilus fiber can be detected by far-Western analysis and sucrose density gradient centrifugation. Transmission electron microscopy of preparations of purified pili, to which the purified PilQ oligomer had been added, showed that PilQ was uniquely located at one end of the pilus fiber, effectively forming a "mallet-type" structure. Determination of the three-dimensional structure of the PilQ-type IV pilus complex at 26-angstroms resolution showed that the cavity within the protein complex was filled. Comparison with a previously determined structure of PilQ at 12-angstroms resolution indicated that binding of the pilus fiber induced a dissociation of the "cap" feature and lateral movement of the "arms" of the PilQ oligomer. The results demonstrate that the PilQ structure exhibits a dynamic response to the binding of its transported substrate and suggest that the secretin could play an active role in type IV pilus assembly as well as secretion.     

A study of resources of Fagopyrum (Polygonaceae) native to China

Morphology, taxonomy, reproductive biology, esterase isozyme patterns and chromosome number were studied in 16 accessions of cultivated and wild buckwheat native to Tibet, Sichuan, Guizhou and Yunnan. Among these are four established species: Fagopyrum esculentum, F tataricum, F. pleioramosum and F gracilipes. The first three species are diploid (2 n = 16) and the last one is tetraploid (2 n = 32). In addition to the above, three new species are described: F. zuogongense, F. megaspartanium and E pilus. There are clear differences in esterase isozyme patterns between these species. The zymographs of esterase isozyme of diploid F. megaspartanium (native to Sichuan) and F. pilus (native to Tibet) are similar to those of F. esculentum and F tataricum respectively. F. gracilipes , in the small achene group of the genus, has a zymograph of esterase isozyme that is very different from the species in the large-achene group. The diploid accessions of F. pilus and F. megaspartanium may be ancestors of cultivated buckwheat.     

Structural differences between the Streptococcus agalactiae housekeeping and pilus-specific sortases: SrtA and SrtC1

The assembly of pili on the cell wall of Gram-positive bacteria requires transpeptidase enzymes called sortases. In Streptococcus agalactiae, the PI-1 pilus island of strain 2603V/R encodes two pilus-specific sortases (SrtC1 and SrtC2) and three pilins (GBS80, GBS52 and GBS104). Although either pilus-specific sortase is sufficient for the polymerization of the major pilin, GBS80, incorporation of the minor pilins GBS52 and GBS104 into the pilus structure requires SrtC1 and SrtC2, respectively. The S. agalactiae housekeeping sortase, SrtA, whose gene is present at a different location and does not catalyze pilus polymerization, was shown to be involved in cell wall anchoring of pilus polymers. To understand the structural basis of sortases involved in such diverse functions, we determined the crystal structures of S. agalactiae SrtC1 and SrtA. Both enzymes are made of an eight-stranded beta-barrel core with variations in their active site architecture. SrtA exhibits a catalytic triad arrangement similar to that in Streptococcus pyogenes SrtA but different from that in Staphylococcus aureus SrtA. In contrast, the SrtC1 enzyme contains an N-terminal helical domain and a 'lid' in its putative active site, which is similar to that seen in Streptococcus pneumoniae pilus-specific sortases, although with subtle differences in positioning and composition. To understand the effect of such differences on substrate recognition, we have also determined the crystal structure of a SrtC1 mutant, in which the conserved DP(W/F/Y) motif was replaced with the sorting signal motif of GBS80, IPNTG. By comparing the structures of WT wild type SrtA and SrtC1 and the 'lid' mutant of SrtC1, we propose that structural elements within the active site and the lid may be important for defining the role of specific sortase in pili biogenesis.     

五个中国荞麦(Fagopyrum)种的核型分析

用去壁低渗法对甜荞 ( Fagopyrum esculentum)、苦荞 ( F.tataricum)、左贡野荞 ( F.zuogongense Q.F.Chen) ,大野荞 ( F.megaspartanium Q.F.Chen)及毛野荞 ( F.pilus Q.F.Chen)等大粒组荞麦种的根尖和茎尖有丝分裂染色体进行了观察 ,并对其茎尖有丝分裂染色体的核型进行了比较分析。结果表明 :这 5种荞麦在核型上类似 ,都有 2对随体染色体 ,而且都为对称核型。但它们彼此有一定的差异。甜荞、苦荞、大野荞、毛野荞及左贡野荞的核型公式分别为 1 2 m+4m( SAT)、1 2 m+4sm( SAT)、8m+4sm+4m( SAT)、1 2 m+2 m( SAT) +2 sm( SAT)及 2 4 m+4sm+4m( SAT)。     

Structural basis of typhoid: Salmonella typhi type IVb pilin (PilS) and cystic fibrosis transmembrane conductance regulator interaction

The type IVb pilus of the enteropathogenic bacteria Salmonella typhi is a major adhesion factor during the entry of this pathogen into gastrointestinal epithelial cells. Its target of adhesion is a stretch of 10 residues from the first extracellular domain of cystic fibrosis transmembrane conductance regulator (CFTR). The crystal structure of the N‐terminal 25 amino acid deleted S. typhi native PilS protein (ΔPilS), which makes the pilus, was determined at 1.9 Å resolution by the multiwavelength anomalous dispersion method. Also, the structure of the complex of ΔPilS and a target CFTR peptide, determined at 1.8 Å, confirms that residues 113–117 (NKEER) of CFTR are involved in binding with the pilin protein and gives us insight on the amino acids that are essential for binding. Furthermore, we have also explored the role of a conserved disulfide bridge in pilus formation. The subunit structure and assembly architecture are crucial for understanding pilus functions and designing suitable therapeutics against typhoid. Proteins 2009. © 2009 Wiley‐Liss, Inc.