DNA binding and antigenic specifications of DNA gyrase.

Complexes of DNA gyrase and minichromosomal DNA containing the origin of replication of Escherichia coli (oriC) can be formed without metabolic energy and visualised by electron microscopy. The A subunit, part of the A2B2-DNA gyrase complex is the binding protein. Various binding sites are scattered around the minichromosomal DNA including oriC. The minimal origin contains the only prominent and reproducible binding site. Binding to this site is suppressed by oxolinic acid and the ATP analogue beta-y-imido ATP. If gyrase isolated from the gram-positive bacterium Bacillus subtilis is used no binding to oriC is seen. This observation is consistent with antigenic differences between the A subunits of the two microorganisms. The binding to oriC might reflect a requirement for DNA gyrase during the initiation of DNA replication.     

Avian retrovirus pp32 DNA binding protein. Preferential binding to the promoter region of long terminal repeat DNA

The avian retrovirus pp32 protein possesses DNA endonuclease activity and unique DNA binding properties. An improved purification procedure was developed for pp32, resulting in a severalfold increase in the yield of this virion protein. By use of the nitrocellulose filter binding assay, the protein retains approximately 2-fold more supercoiled (form I) DNA molecules than equivalent linear duplex DNA molecules. Single-stranded DNA is only slightly preferred over double-stranded DNA for pp32 binding. The pp32 DNA binding sites on form I pBR322 DNA which contained an insert of avian retrovirus long terminal repeat (LTR) DNA were determined. A preformed protein-DNA complex was digested with one of several different multicut restriction enzymes and filtered through nitrocellulose filters. Fragments containing viral LTR DNA sequences and plasmid DNA containing promoter sequences for the ampicillin and tetracycline genes, sequences for the "left-end" inverted repeat of transposon 3, and sequences encompassing the carboxyl terminus of the beta-lactamase gene were preferentially retained on the filter by pp32. Partial mapping of pp32 DNA binding sites on LTR DNA was accomplished by generation of deletions in LTR DNA sequences. The pp32 protein preferentially bound viral DNA fragments which contain the viral promoter (TATTTAA) and the adjacent "R" repeat sequences. Computer analysis revealed that three of the four plasmid DNA fragments retained by pp32 contained LTR DNA promoter-like sequences (one mismatch only) which were part of statistically significant and thermodynamically stable hairpin structures.     

从耐药产气肠杆菌中首次发现DNA旋转酶A亚单位基因gyrA新的变异型

目的 全面了解2株耐药产气肠杆菌对β-内酰胺类、氨基糖苷类、喹诺酮类的耐药机制.方法 2株耐药产气肠杆菌:zjm001株和zjm002株,分离自2012年3月一家三级甲等医院住院患者送检的血液标本,做gyrA和parC基因扩增、测序、GenBank比对确认菌种,再用PCR法分析39种β-内酰胺类药物获得性耐药基因、14种氨基糖苷类药物获得性耐药基因、7种喹诺酮类耐药相关基因、11种可移动遗传元件标记.结果 zjm001株的β-内酰胺类耐药基因检出CTX-M-3,氨基糖苷类耐药基因检出ant(3”)-Ⅰ,喹诺酮类耐药基因检出gyrA突变,可移动遗传元件检出int Ⅰ 1、ISEcp1、IS26、IS903;zjm002株的β-内酰胺类耐药基因检出ACT-1、CMY-2,喹诺酮类耐药基因检出gyrA突变.2株耐药产气肠杆菌的gyrA基因序列均为新变异型,GenBank登录号分别为:JX268598,JX273641.结论 2株耐药产气肠杆菌的耐药基因与耐药表型相符.在耐药产气肠杆菌中发现DNA旋转酶A亚单位基因gyrA新变异型是国内首次报道.     

Nonspecific induction of beta-lactamase in Enterobacter cloacae

Induction of beta-lactamase was monitored in a strain of Enterobacter cloacae exhibiting high resistance to most beta-lactam antibiotics. Large amounts of the enzyme were induced not only in the presence of beta-lactams, but also in the presence of other bicyclic molecules such as folic acid, thiamin, tryptophan or haemin. Moreover, complex media (such as Trypticase soy broth and Schaedler's broth) and various body fluids (serum, pleural fluid and cerebrospinal fluid) also possessed considerable induction potency. Neither 'specific' induction (by beta-lactams) nor 'non-specific' induction (by other bicyclic compounds) could be augmented by addition of exogenous cAMP. These findings indicate that inducible beta-lactamases deserve more attention, above all with respect to the development of resistance against third-generation cephalosporins.     

Nucleotide binding to DNA gyrase causes loss of DNA wrap

DNA gyrase negatively supercoils DNA in a reaction coupled to the binding and hydrolysis of ATP. Limited supercoiling can be achieved in the presence of the non-hydrolysable ATP analogue, 5'-adenylyl beta,gamma-imidodiphosphate (ADPNP). In order to negatively supercoil DNA, gyrase must wrap a length of DNA around itself in a positive sense. In previous work, the effect of ADPNP on the gyrase-DNA interaction has been assessed but has produced conflicting results; the aim of this work was to resolve this conflict. We have probed the wrapping of DNA around gyrase in the presence and in the absence of ADPNP using direct observation by atomic force microscopy (AFM). We confirm that gyrase indeed generates a significant curvature in DNA in the absence of nucleotide and we show that the addition of ADPNP leads to a complete loss of wrap. These results have been corroborated using a DNA relaxation assay involving topoisomerase I. We have re-analysed previous hydroxyl-radical footprinting and crystallography data, and highlight the fact that the gyrase-DNA complex is surprisingly asymmetric in the absence of nucleotide but is symmetric in the presence of ADPNP. We suggest a revised model for the conformation of DNA bound to the enzyme that is fully consistent with these AFM data, in which a closed loop of DNA is stabilised by the enzyme in the absence of ADPNP and is lost in the presence of nucleotide.     

Characterization of quercetin binding site on DNA gyrase

Gyrases are DNA topology modifying enzymes present only in prokaryotes which makes them an attractive target for antibacterial drugs. Quercetin, one of the most abundant natural flavonoids, inhibits supercoiling activity of bacterial gyrase and induces DNA cleavage. It has been generally assumed that the mechanism of flavonoid inhibition is based on interaction with DNA. We show that quercetin binds to the 24 kDa fragment of gyrase B of Escherichia coli with a K(D) value of 15 microM and inhibits ATPase activity of gyrase B. Its binding site overlaps with ATP binding pocket and could be competitively replaced by either ATP or novobiocin. The structural model of quercetin-gyrase complex was prepared, based on the close similarity with ATP and quercetin binding sites of the src family tyrosine kinase Hck. We propose that quercetin inhibits gyrases through two different mechanisms based either on interaction with DNA or with ATP binding site of gyrase.     

The influence of DNA gyrase on the transcription of linear DNA in vitro

To determine the mode of disulphide bond formation in conotoxin GI, a tridecapeptide amide with 4 Cys residues, all 3 of its peptides having different modes of disulphide-bond formation were synthesized by solution procedure using selectively removable protective groups at the Cys residues. After deprotection with HF, one pair of acetamidomethyl groups was left unremoved, and then two sets of disulphide bonds were formed selectively. The toxic potency in mice of one product was comparable with that reported for native conotoxin GI and was almost 10-fold as high as that of the other two products. The toxicity of the native toxin reportedly is not regenerated upon reduction and reoxidation, but this study showed that the most toxic product was the most readily formed one.