Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli

Gram-negative bacteria, such as Escherichia coli, expel toxic chemicals through tripartite efflux pumps that span both the inner and outer membrane. The three parts are an inner membrane, substrate-binding transporter; a membrane fusion protein; and an outer-membrane-anchored channel. The fusion protein connects the transporter to the channel within the periplasmic space. A crystallographic model of this tripartite efflux complex has been unavailable because co-crystallization of the various components of the system has proven to be extremely difficult. We previously described the crystal structures of both the inner membrane transporter CusA and the membrane fusion protein CusB of the CusCBA efflux system of E. coli. Here we report the co-crystal structure of the CusBA efflux complex, showing that the transporter (or pump) CusA, which is present as a trimer, interacts with six CusB protomers and that the periplasmic domain of CusA is involved in these interactions. The six CusB molecules seem to form a continuous channel. The affinity of the CusA and CusB interaction was found to be in the micromolar range. Finally, we have predicted a three-dimensional structure for the trimeric CusC outer membrane channel and developed a model of the tripartite efflux assemblage. This CusC(3)-CusB(6)-CusA(3) model shows a 750-kilodalton efflux complex that spans the entire bacterial cell envelope and exports Cu I and Ag I ions.     

BHDPE/LDPE共混物在不同热压历史下的结晶行为

通过差示扫描量热法(DSC)和扫描电子显微镜(SEM)对双峰高密度聚乙烯(BHDPE/)低密度聚乙烯(LDPE)共混物在不同热压历史条件下的结晶行为和结晶形态进行了研究.实验结果表明,高压下的大分子链更易进行有序排列并形成较高完善度的晶体,当样品在不同的冷却方式下结晶,淬冷能大大促进共结晶的发生,在缓慢冷却条件下则不容易形成共晶.SEM拍摄的照片显示:不同热压历史条件下BHDPE/LDPE所形成的结晶形态完全各异.图7,表1,参13.     

纳豆激酶基因的克隆及其在大肠杆菌中的表达

纳豆激酶是一种良好的天然蛋白酶类溶栓物质。国内外许多学者对该酶进行了基因工程研究,但在克隆表达过程中出现了许多长短不同的基因片段。本研究通过原产日本的优质纳豆中分离鉴定出高产纳豆杆菌N07并提取该菌株的全基因组;通过PCR手段扩增出能编码纳豆激酶信号肽,前导肽和成熟肽的前纳豆激酶酶原基因NK1,以及能编码纳豆激酶成熟肽的纳豆激酶基因NK2,构建了纳豆激酶基因的表达载体pET30a-NK1和pET30a-NK2,转化E.coli BL21后在大肠杆菌中表达,并进行了活性分析。结果发现,纳豆激酶酶原基因片段NK1能成功表达出有活性的分泌型纳豆激酶;而纳豆激酶基因片段NK2的表达产物为无活性的包涵体。在对NK1和NK2的比较研究后可知,纳豆激酶酶原基因片段NK1能在大肠杆菌中很好的分泌表达,这将为纳豆激酶基因工程的深入研究奠定基础。     

Domain of E. coli DNA polymerase I showing sequence homology to T7 DNA polymerase

Escherichia coli contains three DNA polymerases that differ in their size, ability to interact with accessory proteins and biological function. Monomeric DNA polymerase I (Pol I) has a relative molecular mass (Mr) of 103,000 (103K) and is involved primarily in the repair of damaged DNA and the processing of Okazaki fragments; polymerase II is of Mr 120K, and polymerase III has a Mr of 140K, is responsible for the replication of the DNA chromosome and is just one of several proteins that are required for replication. DNA polymerases from bacteriophage as well as those of eukaryotic viral and cellular origin also differ with respect to their size and the number of associated proteins that are required for them to function in replication. However, the template-directed copying of DNA is identical in all cases. The crystal structure of the large proteolytic fragment of Pol I shows that it consists of two domains, the larger of which contains a deep crevice whose dimensions are such that it can bind duplex DNA. The T7 polymerase consists of two subunits, the 80K gene 5 protein and the host-encoded 12K thioredoxin of E. coli. We show here that there is an amino acid sequence homology between at least eight polypeptide segments that form the large cleft in the Klenow fragment and polypeptides in T7 DNA polymerase gene 5 protein, suggesting that this domain evolved from a common precursor. The parts of the Pol I and T7 DNA polymerase molecules that bind the DNA substrate appear to share common structural features, and these features may be shared by all of these varied DNA polymerases.     

A whole genome approach to in vivo DNA-protein interactions in E. coli.

The increasingly rapid pace at which genomic DNA sequences are being determined has created a need for more efficient techniques to determine which parts of these sequences are bound in vivo by the proteins controlling processes such as gene expression, DNA replication and chromosomal mechanics. Here we describe a whole-genome approach to identify and characterize such DNA sequences. The method uses endogenous or artificially introduced methylases to methylate all genomic targets except those protected in vivo by protein or non-protein factors interfering with methylase action. These protected targets remain unmethylated in purified genomic DNA and are identified using methylation-sensitive restriction endonucleases. When the method was applied to the Escherichia coli genome, 0.1% of the endogenous adenine methyl-transferase (Dam methylase) targets were found to be unmethylated. Five foreign methylases were examined by transfection. Database-matched DNA sequences flanking the in vivo-protected Dam sites all fell in the non-coding regions of seven E. coli operons (mtl, cdd, flh, gut, car, psp and fep). In the first four operons these DNA sequences closely matched the consensus sequence that binds to the cyclic AMP-receptor protein. The in vivo protection at the Dam site upstream of the car operon was correlated with a downregulation of car expression, as expected of a feedback repressor-binding model.     

Paenibacillus sp. K1 β-半乳糖苷酶基因的克隆及在大肠杆菌中的表达

从鲜牛奶中分离到1株产β-galactosidase的细菌,经16S rDNA序列比对鉴定为类芽孢菌Paenibacillus sp. K1。提取该菌株的染色体DNA,以pUC18（lac-）为载体,构建其DNA文库;在含有X-gal的LB平板上筛选该文库,得到6个蓝色菌落;对阳性克隆中插入的DNA片段序列测定,鉴定出1个编码全长为2028bp并携带有组成型启动子的β-半乳糖苷酶基因。将该基因导入大肠杆菌BL21（DE3）中,实现了β-半乳糖苷酶高效表达,其酶活为25.06U/mL,高于原始菌株的4.55U/mL,并进一步用亲和层析将该酶进行了纯化。     

An inducible DNA replication-cell division coupling mechanism in E. coli

Cell division is a tightly regulated periodic process. In steady-state cultures of Enterobacteriaceae, division takes place at a well defined cell mass and is strictly coordinated with DNA replication. In wild-type Escherichia coli the formation of cells lacking DNA is very rare, and interruptions of DNA replication arrest cell division. The molecular bases of this replication-division coupling have been elusive but several models have been proposed. It has been suggested, for example, that the termination of a round of DNA replication may trigger a key event required for cell division. A quite different model postulates the existence of a division inhibitor which prevents untimely division and whose synthesis is induced to high levels when DNA replication is perturbed. The work reported here establishes the existence of the latter type of replication-division coupling in E. coli, and shows that the sfiA gene product is an inducible component of this division inhibition mechanism which is synthesized at high levels after perturbations of DNA replication.     

Control of RNase E-mediated RNA degradation by 5'-terminal base pairing in E. coli.

Despite the variety of messenger RNA half-lives in bacteria (0.5-30 min in Escherichia coli) and their importance in controlling gene expression, their molecular basis remains obscure. The lifetime of an entire mRNA molecule can be determined by features near its 5' end, but no 5' exoribonuclease has been identified in any prokaryotic organism. A mutation that inactivates E. coli RNase E also increases the average lifetime of bulk E. coli mRNA and of many individual messages, suggesting that cleavage by this endonuclease may be the rate-determining step in the degradation of most mRNAs in E. coli. We have investigated the substrate preference of RNase E in E. coli by using variants of RNA I, a small untranslated RNA whose swift degradation in vivo is initiated by RNase E cleavage at an internal site. We report here that RNase E has an unprecedented substrate specificity for an endoribonuclease, as it preferentially cleaves RNAs that have several unpaired nucleotides at the 5' end. The sensitivity of RNase E to 5'-terminal base pairing may explain how determinants near the 5' end can control rates of mRNA decay in bacteria.     

粤北地区鸡致病性大肠杆菌蜂胶佐剂疫苗的免疫试验

从粤北地区分离到的鸡致病性大肠杆菌中选择6株优势致病性大肠杆菌菌株做为制苗菌种，制备制苗菌液，按相同比例混合灭活，加蜂胶乙醇浸液为佐剂制备多价菌苗．安全试验结果证实，该灭活菌苗对20日龄肉仔鸡安全，试验鸡元不良反应；在5～10℃保存12个月，疫苗物理性状稳定．免疫效力试验结果：疫苗保护率为100％；接种20日龄雏鸡O．5ml／只，血凝试验检测结果为接种多价蜂胶灭活疫苗的试验鸡在免疫后第二周可检测出抗体，抗体滴度均数为3．10log2；免疫后第四周达到最高峰，抗体滴度均数为3．60log2；免疫后第五周抗体滴度开始下降，抗体滴度均数为2．10log2，但抗体滴度仍高于对照组（1．25log2）．在大肠杆菌感染鸡场进行的多批区域试验结果表明，该多价灭活疫苗安全，具有良好的保护作用．     

Responses of plant rhizosphere to atmospheric CO2 enrichment

Plant root growth is generally stimulated under elevated CO2. This will bring more carbon to the below-ground through root death and exudate. This potential increase in below-ground carbon sink may lead to changes in long-term soil sequestration and relationship between host plants and symbions. On the other hand, changes in litter components due to the changes in plant chemical composition may also affect soil processes, such as litter decomposition, soil organic matter sequestration and hetero-nutritional bacteria activities. These issues are discussed.     

Crystal structure of a dUTPase.

The enzyme dUTPase catalyses the hydrolysis of dUTP and maintains a low intracellular concentration of dUTP so that uracil cannot be incorporated into DNA. dUTPase from Escherichia coli is strictly specific for its dUTP substrate, the active site discriminating between nucleotides with respect to the sugar moiety as well as the pyrimidine base. Here we report the three-dimensional structure of E. coli dUTPase determined by X-ray crystallography at a resolution of 1.9 A. The enzyme is a symmetrical trimer, and of the 152 amino acid residues in the subunit, the first 136 are visible in the crystal structure. The tertiary structure resembles a jelly-roll fold and does not show the 'classical' nucleotide-binding domain. In the quaternary structure there is a complex interaction between the subunits that may be important in catalysis. This possibility is supported by the location of conserved elements in the sequence.     

Intercellular adhesion molecule-1 is an endothelial cell adhesion receptor for Plasmodium falciparum

The primary event in the pathogenesis of severe malaria in Plasmodium falciparum infection is thought to be adherence of trophozoite- and schizont-infected erythrocytes to capillary endothelium, a process called sequestration. Identifying the endothelial molecules used as receptors is an essential step in understanding this disease process. Recent work implicates the membrane glycoprotein CD36 (platelet glycoprotein IV; refs 2-5) and the multi-functional glycoprotein thrombospondin as receptors. Although CD36 has a widespread distribution on microvascular endothelium, it may not be expressed on all capillary beds where sequestration occurs, especially in the brain. The role of thrombospondin in cell adhesion, in vitro or in vivo, is less certain. We have noticed that some parasites bind to human umbilical-vein endothelial cells independently of CD36 or thrombospondin. To screen for alternative receptors, we have developed a novel cell-adhesion assay using transfected COS cells, which confirms that CD36 is a cell-adhesion receptor. In addition, we find that an endothelial-binding line of P. falciparum binds to COS cells transfected with a complementary DNA encoding intercellular adhesion molecule-1. As this molecule is widely distributed on capillaries and is inducible, this finding may be relevant to the pathogenesis of severe malaria.     

湿地恢复对碳固存影响研究进展

湿地生态系统是地球的一种主要生态系统,其储存碳的功能对全球碳的循环和平衡机制具有重要作用,对全球气候变化研究具有重要影响。对于湿地碳固存的含义以及影响因素已有一定研究,但对不同湿地恢复方式对碳固存影响的研究较薄弱,而恢复湿地的固碳功能是湿地碳研究和保护的前提。本文基于文献调研,从湿地碳固存的含义、湿地恢复与其他自然因素对碳固存的影响、相关的研究技术与方法等方面综述了湿地恢复对碳固存影响研究进展,并分析了研究过程中存在的问题,提出相应的发展趋势,为湿地碳固存的保护与恢复提供科学参考。     

Multiple liquid crystal phases of DNA at high concentrations

DNA packaging in vivo is very tight, with volume concentrations approaching 70% w/v in sperm heads, virus capsids and bacterial nucleoids. The packaging mechanisms adopted may be related to the natural tendency of semi-rigid polymers to form liquid crystalline phases in concentrated solutions. We find that DNA forms at least three distinct liquid crystalline phases at concentrations comparable to those in vivo, with phase transitions occurring over relatively narrow ranges of DNA concentration. A weakly birefringent, dynamic, 'precholesteric' mesophase with microscopic textures intermediate between those of a nematic and a true cholesteric phase forms at the lowest concentrations required for phase separation. At slightly higher DNA concentrations, a second mesophase forms which is a strongly birefringent, well-ordered cholesteric phase with a concentration-dependent pitch varying from 2 to 10 micron. At the highest DNA concentrations, a phase forms which is two-dimensionally ordered and resembles smectic phases of thermotropic liquid crystals observed with small molecules.     

Responses of plant rhizosphere to atmospheric CO2 enrichment

Plant root growth is generally stimulated under elevated CO₂. This will bring more carbon to the below-ground through root death and exudate. This potential increase in below-ground carbon sink may lead to changes in long-term soil sequestration and relationship between host plants and symbions. On the other hand, changes in litter components due to the changes in plant chemical composition may also affect soil processes, such as litter decomposition, soil organic matter sequestration and hetero-nutritional bacteria activities. These issues are discussed.     

The human CST complex is a terminator of telomerase activity

The lengths of human telomeres, which protect chromosome ends from degradation and end fusions, are crucial determinants of cell lifespan. During embryogenesis and in cancer, the telomerase enzyme counteracts telomeric DNA shortening. As shown in cancer cells, human telomerase binds the shelterin component TPP1 at telomeres during the S phase of the cell cycle, and adds ~60 nucleotides in a single round of extension, after which telomerase is turned off by unknown mechanisms. Here we show that the human CST (CTC1, STN1 and TEN1) complex, previously implicated in telomere protection and DNA metabolism, inhibits telomerase activity through primer sequestration and physical interaction with the protection of telomeres 1 (POT1)–TPP1 telomerase processivity factor. CST competes with POT1–TPP1 for telomeric DNA, and CST–telomeric-DNA binding increases during late S/G2 phase only on telomerase action, coinciding with telomerase shut-off. Depletion of CST allows excessive telomerase activity, promoting telomere elongation. We propose that through binding of the telomerase-extended telomere, CST limits telomerase action at individual telomeres to approximately one binding and extension event per cell cycle. Our findings define the sequence of events that occur to first enable and then terminate telomerase-mediated telomere elongation.     

Inducible repair of oxidative DNA damage in Escherichia coli

Hydrogen peroxide is lethal to many cell types, including the bacterium Escherichia coli. Peroxides yield transient radical species that can damage DNA and cause mutations. Such partially reduced oxygen species are occasionally released during cellular respiration and are generated by lethal and mutagenic ionizing radiation. Because cells live in an environment where the threat of oxidative DNA damage is continual, cellular mechanisms may have evolved to avoid and repair this damage. Enzymes are known which evidently perform these functions. We report here that resistance to hydrogen peroxide toxicity can be induced in E. coli, that this novel induction is specific and occurs, in part, at the level of DNA repair.     

Plasmids from Staphylococcus aureus replicate in yeast Saccharomyces cerevisiae

It is known that some plasmids, such as RP4, can replicate in many Gram-negative bacteria. Certain small Staphylococcus aureus plasmids have an even broader host range, being able to replicate in not only phylogenetically distant Gram-positive bacteria such as Bacillus subtilis or Streptococcus pneumoniae, but also in the Gram-negative bacterium Escherichia coli. Here we have examined whether these plasmids can also replicate in a lower eukaryote, the yeast Saccharomyces cerevisiae. For this purpose we constructed hybrids between a S. aureus plasmid pC194 and an E. coli plasmid YIp5, which carries a ura-3 gene easy to select for in yeast but cannot replicate in this host. We found that the hybrids transformed yeast with high efficiency (as did hybrids between YIp5 and three other S. aureus plasmids); were maintained extrachromosomally in yeast; and were not modified during residence in yeast. We conclude from this evidence that S. aureus plasmids can replicate in yeast, which raises the questions of whether the replication signals used by prokaryotes and eukaryotes are similar, and how far up the phylogenetic tree the organisms still able to be hosts to S. aureus plasmids may be.