Protein Dynamics Control the Progression and Efficiency of the Catalytic Reaction Cycle of the Escherichia coli DNA-Repair Enzyme AlkB

A central goal of enzymology is to understand the physicochemical mechanisms that enable proteins to catalyze complex chemical reactions with high efficiency. Recent methodological advances enable the contribution of protein dynamics to enzyme efficiency to be explored more deeply. Here, we utilize enzymological and biophysical studies, including NMR measurements of conformational dynamics, to develop a quantitative mechanistic scheme for the DNA repair enzyme AlkB. Like other iron/2-oxoglutarate-dependent dioxygenases, AlkB employs a two-step mechanism in which oxidation of 2-oxoglutarate generates a highly reactive enzyme-bound oxyferryl intermediate that, in the case of AlkB, slowly hydroxylates an alkylated nucleobase. Our results demonstrate that a microsecond-to-millisecond time scale conformational transition facilitates the proper sequential order of substrate binding to AlkB. Mutations altering the dynamics of this transition allow generation of the oxyferryl intermediate but promote its premature quenching by solvent, which uncouples 2-oxoglutarate turnover from nucleobase oxidation. Therefore, efficient catalysis by AlkB depends upon the dynamics of a specific conformational transition, establishing another paradigm for the control of enzyme function by protein dynamics.     

Kinetic studies of Escherichia coli AlkB using a new fluorescence-based assay for DNA demethylation

The Escherichia coli AlkB protein catalyzes the direct reversal of alkylation damage to DNA; primarily 1-methyladenine (1mA) and 3-methylcytosine (3mC) lesions created by endogenous or environmental alkylating agents. AlkB is a member of the non-heme iron (II) α-ketoglutarate-dependent dioxygenase superfamily, which removes the alkyl group through oxidation eliminating a methyl group as formaldehyde. We have developed a fluorescence-based assay for the dealkylation activity of this family of enzymes. It uses formaldehyde dehydrogenase to convert formaldehyde to formic acid and monitors the creation of an NADH analog using fluorescence. This assay is a great improvement over the existing assays for DNA demethylation in that it is continuous, rapid and does not require radioactively labeled material. It may also be used to study other demethylation reactions including demethylation of histones. We used it to determine the kinetic constants for AlkB and found them to be somewhat different than previously reported values. The results show that AlkB demethylates 1mA and 3mC with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart.     

胆固醇氧化酶基因的克隆及在E.coli中的表达

根据NCBI中报道的BrevibacteriumsterolicumATCC21387胆固醇氧化酶基因序列,采用PCR方法以Brevibacteriumsp.DGCDC-82的基因组为模板,扩增得到了编码胆固醇氧化酶的基因,该基因与来源于BrevibacteriumsterolicumATCC21387的胆固醇氧化酶基因(choB)同源性为98%。将得到的基因定向克隆到pET28a载体中,转化至含有编码argU和proL基因的大肠杆菌BL21-CodonPlus(DE3)-RP中表达。经过IPTG诱导后,经SDS-PAGE检测在约55kD处有一蛋白表达条带,目的蛋白表达量约占总蛋白的16%,经测定酶活为340U/L。     

IL-17在黏附侵袭性大肠杆菌感染小鼠结肠过程中的作用机制研究

目的:评价IL-17在黏附侵袭性大肠杆菌感染小鼠结肠过程中的作用及其可能机制。方法:选择野生型及IL-17基因敲除的SPF级C57BL/6小鼠并随机分成4组,分别给予不同的处理:(1)野生小鼠+单纯蒸馏水灌胃处理组;(2)野生小鼠+E.coli LF82(1×109/CFU/只)灌胃10天处理组;(3)IL-17敲除小鼠+单纯蒸馏水灌胃处理组;(4)IL-17敲除小鼠+E.coli LF82灌胃10天处理组。从以下5个方面评价各组小鼠的炎症反应和IL-17水平:(1)组织病理评分评估炎症反应严重程度;(2)透射电镜下观察结肠上皮细胞的超微结构;(3)免疫组织化学检测结肠分泌的IL-17;(4)PCR检测小鼠结肠中IL-17m RNA表达;(5)ELISA检测结肠组织中IL-17的含量。结果:定植了E.coli LF82的IL-17敲除小鼠肠道炎症程度和超微结构损伤较野生型小鼠更加严重(P0.05)。与未经E.coli LF82处理组相比,定植了E.coli LF82的野生小鼠肠道中IL-17m RNA和IL-17含量明显升高(P0.05)。结论:IL-17在E.coli LF82在黏附侵袭结肠粘膜过程中的保护作用,IL-17是针对AIEC菌株E.coli LF82免疫的重要效应物,而结肠局部分泌增加的IL-17会改善感染的结果。     

DNA aptamers for as analytical tools for the quantitative analysis of DNA-dealkylating enzymes

The AlkB family of oxygenases catalyze the removal of alkyl groups from nucleic acid substrates in an iron and 2-oxoglutarate-dependent manner and have roles including in DNA repair. To understand the biological functions of these DNA-dealkylating enzymes it is desirable to measure their expression levels in vitro and in vivo in complex biological matrixes. Quantitative analyses of the enzymes require affinity probes capable of binding AlkB family members selectively and with high affinity. Here we report that DNA aptamers can serve as efficient affinity probes for quantitative detection of such enzymes in vitro. Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) was applied as a general tool for: (i) selection of DNA aptamers, (ii) characterization of binding parameters for the aptamers, and (iii) quantitative detection of the target in an aptamer-based affinity analysis. The selected aptamers have a range of K_d values between 20 and 240 nM. The aptamers enabled accurate quantitative analysis of AlkB even in the presence of the Escherichia coli cell lysate. Aptamers can likely be developed for other nucleic acid repair enzymes. They may also be developed for use in in vitro and potentially in vivo studies of known nucleic acid-modifying enzymes including for functional analysis.     

Structural studies of the O-antigenic polysaccharides from the enteroaggregative Escherichia coli strain 87/D2 and international type strains from E. coli O128

The O-antigen of the lipopolysaccharide (LPS) from the enteroaggregative Escherichia coli strain 87/D2 has been determined by component analysis together with NMR spectroscopy. The polysaccharide has pentasaccharide repeating units in which all the residues have the galacto-configuration. The repeating unit of the O-antigen, elucidated using the O-deacylated LPS, is branched with the following structure: Analysis of the 1H NMR spectrum of the LPS revealed O-acetyl groups (approximately 0.7 per repeating unit) distributed over two positions. Subsequent analysis showed that the galactose residue carries acetyl groups at either O-3 or O-4 in a ratio of approximately 2:1. The international reference strain from E. coli O128ab was investigated and the repeating unit of the O-antigens has the following structure: Analysis of the 1H NMR spectrum of the LPS revealed O-acetyl groups (approximately one per repeating unit) distributed over two positions. The integrals of the resonances for the O-acetyl groups indicated similarities between the O-antigen from E. coli O128ab and that of E. coli strain 87/D2, whereas the O-acetyl substitution pattern in the E. coli O128ac O-antigen differed slightly. Enzyme immunoassay using specific anti-E. coli O128ab and anti-E. coli O128ac rabbit sera confirmed the results.     

小鼠pdd87基因在大肠杆菌中的表达与纯化

利用PCR和基因重组技术构建了三个小鼠pdd87基因的原核表达质粒：表达全长cDNA的pET-28a-pdd87质粒;表达PDD87C端404个氨基酸的pET-28a-pdd87-404质粒;表达全长cDNA的pMXB10-pdd87质粒。经IPTG诱导后三种质粒都得到表达。pET-28a-pdd87质粒和pET-28a-pdd87-404质粒表达的蛋白经His6亲和层析纯化后分别获得了带His标签的PDD87蛋白和含C端404个氨基酸的蛋白。pMXB10-pdd87质粒表达的蛋白经几丁质柱亲和层析纯化后获得了纯的PDD87蛋白。     

Comparative evaluation of Escherichia coli strains as markers for the study of bacteriophages

The count of coliphages in polluted waters was found to be dependent on many experimental factors. The host-strain used for their enumeration is among the most important. In this paper we report a comparative investigation on the variability of counts of coliphages in sewage as a result of variations in host-strains of Escherichia coli and in methodologies. Two methods were used for enumerating them: the M.P.N. and the direct count. E. coli C, B1, Hfr and E36 consistently produced more plaques than any other host tested.     

Escherichia coli relA strains as hosts for amplification of pBR322 plasmid DNA

Abstract We have proposed that guanosine tetraphosphate produced in Escherichia coli cells subjected to an isoleucine limitation inhibits pBR322 DNA replication [1]. In E. coli relA which cannot synthesize guanosine tetraphosphate (ppGpp) upon amino acid limitation pBR322 DNA is amplified after arginine starvation. The yield of plasmid DNA amplified either by chloramphenicol (Cm) or by arginine limitation is compared. The plasmid yield per cell is equal in amino acid-starved cells and in cells treated with Cm. To increase the plasmid content per ml of cell suspension the growth medium was supplemented with increasing amounts of nutrients. Plasmid DNA can be isolated in large quantities by this procedure. This simple method can be used for the enrichment of pBR325 DNA which cannot be amplified by Cm treatment. Our results indicate that E. coli relA strains might be suitable hosts for the amplification of pBR322 and related plasmids in E. coli .     

Genetic studies of the ribosomal proteins in Escherichia coli. 3. Compositions of ribosomal proteins in various strains of Escherichia coli

Summary The comparative chromatographic investigations into the ribosomal proteins of various strains of E. coli have demonstrated that most of the strains including three strains of E. coli subsp. communior had ribosomes with the same protein compositions (C-type). The ribosomes from strain B are different from the C-type ribosomes in having the specific 30-4 (B) component in place of 30-4 (B-type), while those from strains K 12 may be distinguished from the type-C ribosomes by the presence of the specific 30-7 (K) component in place of 30-7 (K-type) or, in addition to 30-7 (K), the presence of 30-9 (W3637) in place of 30-9 (K-3637 type). Two strains, IAM 1132 and IAM 1182, have R-type ribosomes, in which at least six 50s proteins and four 30s protein components are distinct from the corresponding protein components in the C-type ribosomes.     

Evaluation of Escherichia coli K-12 343/113 and derived strains for microbial mutagenicity assays

Several characteristics of the E. coli K-12 mutagenicity tester strains 343/113 and 343/120 have been investigated for their effects on induced mutagenesis using the arg56 and nad113 genes, and resistance to valine. We found, as have earlier authors, that the nad113 marker is relatively specific for detecting frameshift-inducing mutagens and relatively insensitive to agents that cause point mutations. In contrast, both the Arg and Val markers are primarily specific for reversion (or mutation) induction by point mutagens. In all cases tested, the Arg and Val markers respond to mutagens in a qualitatively similar manner. We have enhanced the sensitivity of this tester system to a wide variety of mutagens by permeabilization of the tester cell population using Tris-EDTA treatment. This treatment prior to mutagen exposure enables the detection of mutagenicity of several compounds that are weakly mutagenic or nonmutagenic in untreated cells. We have also increased the mutagenicity of some chemicals by preincubating with rat-liver S9 at pH values other than 7.4. For diethylnitrosamine, for instance, maximal induction occurred at pH 6.5, and for benzo[a]pyrene, maximal induction was at pH 6.8.     

Aqueous two-phase polymer systems as tools for the study of a recombinant surface-expressed Escherichia coli hemagglutinin.

The surface expression of an integral membrane hemagglutinin, HRA1, cloned from Escherichia coli O9: H10:K99 in heterologous E. coli strains was studied by utilizing a variety of polyethylene glycol-dextran and dextran-Ficoll aqueous two-phase polymer systems. Bacteria containing plasmids that encoded the hemagglutinin were found to partition differently from both the host bacteria lacking the plasmid and the original hemagglutinating strain in several of these systems. By using molecular biological techniques, the origin of the partition difference was unambiguously correlated to the expression of HRA1, providing evidence independent of the agglutination phenotype that the protein was accessible to the surrounding milieu. It was demonstrated by using bacterial partition in charge-sensitive systems that the agglutination event was not likely to be due to the presence of a nonspecific positively charged surface protein, as HRA1-expressing clones showed no less affinity for the relatively positive polyethylene glycol-rich upper phase than did control bacteria. This work demonstrates the utility of aqueous polymer two-phase systems for the study of surface-expressed recombinant proteins, due to the sensitivity of the systems and the presence of excellent controls (the host bacteria before plasmid introduction). In cloning and expression studies of surface-associated proteins, two-phase aqueous polymer systems could be used as an alternative to antibody production for the monitoring of surface expression, and these systems may give valuable information on the surface exposure of the protein.     

Escherichia coli K12 relA strains as safe hosts for expression of recombinant DNA

Most Escherichia coli K12 strains survive for a relatively long time outside the laboratory. Under the same conditions the isoallelic E. coli K12 relA mutants die faster because they lack the stringent response. The killing rate is increased by using a plasmid-encoded suicide system consisting of the phage T7 lysozyme gene driven by the E. coli alkaline phosphatase gene promoter (phoA). Cells containing this system were rapidly and effectively killed as soon as phosphate was made limiting. The combination of the chromosomal relA mutation and a conditional suicide system of this type provides an effective means of biological containment for recombinant E. coli strains.