Multienzyme systems of DNA replication

Replication is accomplished by multienzyme systems whose operations are usefully considered in respect to three stages of the process: initiation, elongation, anid termination. 1) Initiation entails synthesis of a short RNA fragment that serves as primer for the elongation step of DNA synthesis. This stage, probed by SS phage DNA templates, reveals three distinctive and highly specific systems in E. coli. The Ml3 DNA utilizes RNA polymerase in a manner that may reflect how plasmid elements are replicated in the cell. The ?X174 DNA does not rely on RNA-polymerase, but requires instead five distinctive proteins which may belong to an apparatus for initiating a host chromosome replication cycle at the origin. The G4 DNA, also independent of RNA polymerase, needs simply the dnaG protein for its distinctive initiation and may thus resemble the system that initiates the replication fragments at the nascent growing fork. In each case it is essential that in vitro the DNA-unwinding protein coat the viral DNA and influence its structure. 2) Elongation is achieved in every case by the multisubunit, holoenzyme form of DNA polymerase III. Copolymerase III, which is an enzyme subunit, and adenosine triphosphate are required to form a proper complex with the primer template but appear dispensable for the ensuing chain growth by DNA polymerase (33). 3) Termination requires excision of the RNA priming fragment, filling of gaps and sealing of interruptions to produce a covalently intact phosphodiester backbone. DNA polymerase I has the capacity for excision and gapfilling and DNA ligase is required for sealing. What once appeared to be a simple DNA polymerase-mediated conversion of a single-strand to a duplex circle (34) is now seen as a complex series of events in which diverse multienzyme systems function. Annoyance with the difficulties in resolving and reconstituting these systems is tempered by the conviction that these are the very systems used ,by the cell in replicating its chromosome and extrachromosomal elements. Thus, understanding of the regulation of replication events in the cell, their localization at membrane surfaces and integration with cell division, and their coordination with phage DNA maturation and particle assembly will all be advanced by knowledge of the components of the replicative machinery.     

Disulfide bond engineered into T4 lysozyme: stabilization of the protein toward thermal inactivation

By recombinant DNA techniques, a disulfide bond was introduced at a specific site in T4 lysozyme, a disulfide-free enzyme. This derivative retained full enzymatic activity and was more stable toward thermal inactivation than the wild-type protein. The derivative, T4 lysozyme (Ile3----Cys), was prepared by substituting a Cys codon for an Ile codon at position 3 in the cloned lysozyme gene by means of oligonucleotide-dependent, site-directed mutagenesis. The new gene was expressed in Escherichia coli under control of the (trp-lac) hybrid tac promoter, and the protein was purified. Mild oxidation generated a disulfide bond between the new Cys3 and Cys97, one of the two unpaired cysteines of the native molecule. Oxidized T4 lysozyme (Ile3----Cys) exhibited specific activity identical to that of the wild-type enzyme when measured at 20 degrees C in a cell-clearing assay. The cross-linked protein was more stable than the wild type during incubation at elevated temperatures as determined by recovered enzymatic activity at 20 degrees C.     

Ultraviolet damage to bacteria and bacteriophage at low temperatures

The survival of Escherichia coli B/r WP2 (tryptophan-requiring) from ultraviolet irradiation when suspended in 0.067M phosphate buffer (pH 7) has been studied over the temperature range 22 degrees to -269 degrees C. In unfrozen suspensions there was no appreciable change in sensitivity between 22 degrees and -10 degrees C. The sensitivity in the presence of ice progressively increased by a factor of 7 when the temperature was lowered to -79 degrees C. Between -79 degrees and -196 degrees C the sensitivity decreased to less than four times the sensitivity at 22 degrees C and was not appreciably different at -269 degrees C. Evidence from experiments with bacteriophage T1 and E. coli WP2 HCR(-) (a strain unable to excise thymine dimers) indicates that a new, qualitatively different lesion, less amenable to repair, may replace the thymine dimer in E. coli irradiated at -79 degrees C.     

海栖热袍菌极端耐热木聚糖酶B的提纯

克隆并在大肠杆菌中表达的海栖热袍菌的 xyn B基因 ,其表达产物木聚糖酶 B的 C 末端带有 6×His标签 ,研究了这种基因重组酶的提纯方法。通过对粗酶提取液的热变性处理 ,Ni NTA亲和柱层析和离子柱层析 ,最终得到了电泳纯的木聚糖酶 B,提纯倍数 4 4.4 ,得率 11。SDS PAGE法测定木聚糖酶 B的相对分子质量为 4 2 ku,与理论推算值 4 2 333u相吻合     

对香豆酰辅酶A酯生物合成及纯化方法

木质素是绿色植物生长发育所需的重要化合物之一。肉桂酰辅酶A还原酶(CCR)是在木质素合成过程中,催化苯丙烷类合成途径第1步的关键酶。本文以其底物之一——对香豆酰辅酶A酯为例,以现有的辅酶A酯合成纯化的文献报道为参考,介绍经过整合改进并不断试验而得到的CCR底物的合成与纯化方法。从大肠杆菌中提取出来的重组酶4-香豆酸辅酶A连接酶(4CL)用于合成CCR底物,这比从植物组织中提取更易获得。提纯后的4CL可以在-80 ℃下保存3、4个月。4CL反应后的产物在2个不同梯度下通过C18反相柱进一步纯化,并用高效液相色谱仪监测。在整个纯化过程中,所有用于装载对香豆酸和对香豆酰辅酶A酯的容器都用锡箔纸完全包裹起来。最后提纯出来的产物用质谱和核磁共振检测。检测的结果表明,提纯出来的辅酶A酯单一性非常好。      

SQR基因在大肠杆菌和乳酸菌中的表达

为了研究硫化物-醌氧化还原酶(SQR)基因的乳酸菌表达载体pMG36e-SQR-Myc的构建及其在大肠杆菌DH5a和乳酸菌MG1363中的表达,通过限制性内切酶酶切大肠杆菌-乳酸菌穿梭表达载体pMG36e与目的片段SQR-Myc,回收纯化并用T4连接酶进行连接,连接产物通过KCM法转化到大肠杆菌DH5a中,提取所得到阳性大肠杆菌菌株质粒pMG36e-SQR-Myc进行双酶切鉴定与普通PCR鉴定;并通过电转化将重组质粒导入乳酸菌MG1363中,采用SDS-PAGE电泳和Western-blotting检测SQR蛋白质在其中的表达情况。结果显示,SQR乳酸菌重组表达载体pMG36e-SQR-Myc被成功构建,目的蛋白质SQR在大肠杆菌和乳酸菌MG1363中被成功检测到。因此,乳酸菌MG1363可以用来表达硫化物-醌氧化还原酶(SQR)。     

Parallel stranded DNA

A series of four hairpin deoxyoligonucleotides was synthesized with a four-nucleotide central loop (either C or G) flanked by the complementary sequences d(T)10 and d(A)10. Two of the molecules contain either a 3'-p-3' or 5'-p-5' linkage in the loop, so that the strands in the stem have the same, that is, parallel (ps) polarity. The pair of reference oligonucleotides have normal phosphodiester linkages throughout and antiparallel (aps) stem regions. All the molecules adopt a duplex helical structure in that (i) the electrophoretic mobilities in polyacrylamide gels of the ps and aps oligomers are similar. (ii) The ps hairpins are substrates for T4 polynucleotide kinase, T4 DNA ligase, and Escherichia coli exonuclease III. (iii) Salt-dependent thermal transitions are observed for all hairpins, but the ps molecules denature 10 degrees C lower than the corresponding aps oligomers. (iv) The ultraviolet absorption and circular dichroism spectra are indicative of a base-paired duplex in the stems of the ps hairpins but differ systematically from those of the aps counterparts. (v) The bis-benzimidazole drug Hoechst-33258, which binds in the minor groove of B-DNA, exhibits very little fluorescence in the presence of the ps hairpins but a normal, enhanced emission with the aps oligonucleotides. In contrast, the intercalator ethidium bromide forms a strongly fluorescent complex with all hairpins, the intensity of which is even higher for the ps species. (vi) The pattern of chemical methylation is the same for both the ps and aps hairpins. The combined results are consistent with the prediction from force field analysis of a parallel stranded right-handed helical form of d(A)n.d(T)n with a secondary structure involving reverse Watson-Crick base pairs and a stability not significantly different from that of the B-DNA double helix. Models of the various hairpins optimized with force field calculations are described.     

RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites

Mutations affecting the BRCT domains of the breast cancer-associated tumor suppressor BRCA1 disrupt the recruitment of this protein to DNA double-strand breaks (DSBs). The molecular structures at DSBs recognized by BRCA1 are presently unknown. We report the interaction of the BRCA1 BRCT domain with RAP80, a ubiquitin-binding protein. RAP80 targets a complex containing the BRCA1-BARD1 (BRCA1-associated ring domain protein 1) E3 ligase and the deubiquitinating enzyme (DUB) BRCC36 to MDC1-gammaH2AX-dependent lysine(6)- and lysine(63)-linked ubiquitin polymers at DSBs. These events are required for cell cycle checkpoint and repair responses to ionizing radiation, implicating ubiquitin chain recognition and turnover in the BRCA1-mediated repair of DSBs.     

The structural basis of ribozyme-catalyzed RNA assembly

Life originated, according to the RNA World hypothesis, from self-replicating ribozymes that catalyzed ligation of RNA fragments. We have solved the 2.6 angstrom crystal structure of a ligase ribozyme that catalyzes regiospecific formation of a 5' to 3' phosphodiester bond between the 5'-triphosphate and the 3'-hydroxyl termini of two RNA fragments. Invariant residues form tertiary contacts that stabilize a flexible stem of the ribozyme at the ligation site, where an essential magnesium ion coordinates three phosphates. The structure of the active site permits us to suggest how transition-state stabilization and a general base may catalyze the ligation reaction required for prebiotic RNA assembly.     

大肠杆菌k88ac菌毛蛋白亚基因的克隆、表达及亲和层析纯化

利用PCR技术,从E.coli C83902中扩增出不含信号肽序列的K88ac菌毛蛋白亚基基因片段,将其克隆到表达载体pQE-30中,构建了原核表达载体pQE30-K88ac,并转入E.coli XL1-Blue中。经IPTG诱导后,由T5启动子调控表达了氨基端带6个连续组氨酸残基的以包涵体形式存在的K88ac蛋白,在变性条件下对目的蛋白进行纯化,并获得了高纯度的融合蛋白。     

HTLV-I trans-activator protein, tax, is a trans-repressor of the human beta-polymerase gene

Human T cell leukemia virus type I (HTLV-I) is the etiological agent for adult T cell leukemia (ATL). The HTLV-I trans-activator protein Tax can activate the expression of its own long terminal repeat (LTR) and many cellular and viral genes. Tax down-regulated the expression of human beta-polymerase (hu beta-pol), a cellular enzyme involved in host cell DNA repair. This finding suggests a possible correlation between HTLV-I infection and host chromosomal damage, which is often seen in ATL cells.     

Mutants of bovine pancreatic trypsin inhibitor lacking cysteines 14 and 38 can fold properly

It is a generally accepted principle of biology that a protein's primary sequence is the main determinant of its tertiary structure. However, the mechanism by which a protein proceeds from an unfolded, disordered state to a folded, relatively well-ordered, native conformation is obscure. Studies have been initiated to examine the "genetics" of protein folding, with mutants of bovine pancreatic trypsin inhibitor (BPTI) being used to explore the nature of the specific intramolecular interactions that direct this process. Previous work with BPTI chemically modified at cysteines 14 and 38 indicated that transient disulfide bond formation by these residues contributed to efficient folding at 25 degrees C. In the present work, mutants of BPTI in which these cysteines were replaced by alanines or threonines were made and the mutant proteins were produced by a heterologous Escherichia coli expression system. At 25 degrees C in vitro, the refolding behavior of these mutants was characterized by a pronounced lag. However, when expressed at 37 degrees C in E. coli, or when refolded at 37 degrees or 52 degrees C in vitro, the mutant proteins folded readily into the native conformation, albeit at a rate somewhat slower than that exhibited by wild-type BPTI. These results indicate that, at physiological temperatures, BPTI lacking cysteines 14 and 38 can refold quantitatively.     

5'-Deoxyribose phosphate lyase activity of human DNA polymerase iota in vitro

DNA polymerase iota (pol iota) is one of several recently discovered DNA polymerases in mammalian cells whose function is unknown. We report here that human pol iota has an intrinsic 5'-deoxyribose phosphate (dRP) lyase activity. In reactions reconstituted with uracil-DNA glycosylase (UDG), apurinic/apyrimidinic (AP) endonuclease and DNA ligase I, pol iota can use its dRP lyase and polymerase activities to repair G*U and A*U pairs in DNA. These data and three distinct catalytic properties of pol iota implicate it in specialized forms of base excision repair (BER).     

Mycobacterial Ku and ligase proteins constitute a two-component NHEJ repair machine

In mammalian cells, repair of DNA double-strand breaks (DSBs) by nonhomologous end-joining (NHEJ) is critical for genome stability. Although the end-bridging and ligation steps of NHEJ have been reconstituted in vitro, little is known about the end-processing reactions that occur before ligation. Recently, functionally homologous end-bridging and ligation activities have been identified in prokarya. Consistent with its homology to polymerases and nucleases, we demonstrate that DNA ligase D from Mycobacterium tuberculosis (Mt-Lig) possesses a unique variety of nucleotidyl transferase activities, including gap-filling polymerase, terminal transferase, and primase, and is also a 3' to 5' exonuclease. These enzyme activities allow the Mt-Ku and Mt-Lig proteins to join incompatible DSB ends in vitro, as well as to reconstitute NHEJ in vivo in yeast. These results demonstrate that prokaryotic Ku and ligase form a bona fide NHEJ system that encodes all the recognition, processing, and ligation activities required for DSB repair.     

General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme

Many protein enzymes use general acid-base catalysis as a way to increase reaction rates. The amino acid histidine is optimized for this function because it has a pK(a) (where K(a) is the acid dissociation constant) near physiological pH. The RNA enzyme (ribozyme) from hepatitis delta virus catalyzes self-cleavage of a phosphodiester bond. Reactivity-pH profiles in monovalent or divalent cations, as well as distance to the leaving-group oxygen, implicate cytosine 75 (C75) of the ribozyme as the general acid and ribozyme-bound hydrated metal hydroxide as the general base in the self-cleavage reaction. Moreover, C75 has a pK(a) perturbed to neutrality, making it "histidine-like." Anticooperative interaction is observed between protonated C75 and a metal ion, which serves to modulate the pK(a) of C75. General acid-base catalysis expands the catalytic repertoire of RNA and may provide improved rate acceleration.     

A bacterial inhibitor of host programmed cell death defenses is an E3 ubiquitin ligase

The Pseudomonas syringae protein AvrPtoB is translocated into plant cells, where it inhibits immunity-associated programmed cell death (PCD). The structure of a C-terminal domain of AvrPtoB that is essential for anti-PCD activity reveals an unexpected homology to the U-box and RING-finger components of eukaryotic E3 ubiquitin ligases, and we show that AvrPtoB has ubiquitin ligase activity. Mutation of conserved residues involved in the binding of E2 ubiquitin-conjugating enzymes abolishes this activity in vitro, as well as anti-PCD activity in tomato leaves, which dramatically decreases virulence. These results show that Pseudomonas syringae uses a mimic of host E3 ubiquitin ligases to inactivate plant defenses.     

肇东盐单胞菌中胞苷酸激酶基因cmk的克隆与功能分析

为探究一株中度嗜盐菌-肇东盐单胞菌(Halomonas zhaodongensis)NEAU-ST10-25T的耐盐碱机制,采用基因文库筛选方法从该菌株获得一个重组质粒p UC-LYS1。该质粒可恢复大肠杆菌(Escherichia coli)Na+/H+逆向转运蛋白缺陷株KNabc在含有0.2 mol·L-1Na Cl的LBK培养基上生长。序列分析显示,重组质粒p UC-LYS1中外源DNA片段由1个N端截短的ORF1、三个完整的ORF(ORF2-4)以及1个C端截短的ORF5组成。其中,ORF4与伸长盐单胞菌(Halomonas enlongata)中1个推测的胞苷酸激酶(Cytidylate kinase,CMK)同源性最高(86%)。为便于区分与其同源物,编码ORF4的基因cmk来自肇东盐单胞菌(Halomonas zhaodongensis)被定名为Hz_cmk。Hz_CMK也与包括已被鉴定来自大肠杆菌(E.coli)的Ec_CMK等其他同源物具有较高同源性。为进一步鉴定Hz_cmk是否编码胞苷酸激酶,通过PCR扩增分别将Hz_cmk和大肠杆菌(E.coli)的同源基因Ec_cmk(作为正对照)构建至原核表达载体p ET19,转化到大肠杆菌(E.coli)C41(DE3)感受态细胞中诱导表达。SDS-PAGE表明其以可溶形式存在。酶学分析表明Hz_CMK与Ec_CMK均具有较高胞苷酸激酶活性。为国内外首次中度嗜盐菌的胞苷酸激酶基因功能鉴定。     

pGEX-4T-1-cMC4R原核表达载体的构建与表达

[目的]构建犬MC4R基因编码区的融合表达载体并在大肠杆菌中诱导表达融合蛋白。[方法]以Beagle犬基因组DNA为模板,经PCR技术扩增目的片段,利用LP Recco PCR克隆技术将目的片段直接重组到原核表达载体pGEX-4T-1上,转化到E.coliDH5α,筛选阳性克隆,BamHI、XhoI酶切鉴定,DNA测序检测插入序列的正确性。将测序正确的重组表达质粒pGEX-4T-1-cMC4R转化到E.co-liBL21内,经IPTG诱导后,利用SDS-PAGE检测犬MC4R蛋白的表达。[结果]成功构建重组表达质粒pGEX-4T-1-cMC4R,经DNA测序证实插入序列与设计基本一致,只有777位碱基T变成了C,这是由于犬MC4R编码区存在的多态性引起,对表达的犬MC4R蛋白序列无影响。大肠杆菌诱导后表达出犬MC4R融合性蛋白。[结论]成功构建犬MC4R原核表达载体,此重组体能在E.coliBL21内表达犬MC4R融合蛋白,为进一步获取犬MC4R的单克隆抗体奠定物质基础,也为研究犬MC4R蛋白的结构和生理功能提供帮助。     

细菌过氧化氢酶基因的克隆方法研究

[目的]研究细菌过氧化酶基因的克隆方法。[方法]培养扩增E.coli W3110,提取其基因组DNA,采用限制性内切酶Sau3A I对其进行部分酶切,分离纯化1.5 kb以上的DNA片段。将经BamH I酶切的大肠杆菌质粒pUC18与经Sau3A I部分酶切的不同片段用T4连接酶进行连接,并转化大肠杆菌DH5α。通过BHI-单宁酸培养介质,筛选出含有活性过氧化氢酶基因的重组子。[结果]经酶切和PCR鉴定,证实所克隆的过氧化氢酶基因是正确的,与理论相符。[结论]该研究结果为快速简便地克隆筛选活性细菌过氧化氢酶基因奠定了基础。