Stabilization of Compact Spermidine Nucleoids fromEscherichia coliunder Crowded Conditions: Implications forin VivoNucleoid Structure

Nucleoids fromEscherichia coliwere isolated in the presence of spermidine at low salt concentrations. The nucleoids denature at relatively low temperatures or salt concentrations, yielding broad slowly sedimenting zones and/or macroscopic aggregates upon sucrose gradient centrifugation. Denaturation is accompanied by a loss of a characteristically compact shape as visualized by light and electron microscopy. Addition of polyethylene glycol or dextran prevents these changes, extending the range of stability of the isolated nucleoids to temperatures and ionic conditions like those which commonly occurin vivo.The effects of the polymers are consistent with stabilization by macromolecular crowding. Enzymatic digestion of the nucleoid DNA primarily releases three small proteins (H-NS, FIS, and HU) and RNA polymerase, as well as residual lysozyme from the cell lysis procedure. If isolated nucleoids are extracted with elevated salt concentrations under crowded, stabilized conditions, two of the proteins (HU and lysozyme) are efficiently removed and the compact form of the nucleoids is retained. These extracted nucleoids maintain their compact form upon reisolation into the initial uncrowded low-salt medium, indicating that HU, the most common “histone-like” protein ofE. coli,is not a necessary component for maintaining compaction in these preparations.     

Isolation, Overexpression, and Biochemical Characterization of the Two Isoforms of Glutamic Acid Decarboxylase fromEscherichia coli

Escherichia coliglutamic acid decarboxylase is a pyridoxal phosphate-dependent enzyme that catalyzes the α-decarboxylation of glutamate to yield 4-aminobutyrate and CO₂. TheE. colichromosome contains two genes encoding for this enzyme,gadAandgadB,which map at distinctloci.Their protein products differ in only five amino acid residues, four of which are located in the N-terminal region (Smithet al.,1992,J. Bacteriol.174, 5820–5826). Herein, we report the sequences of the twogadgenes, including their regulatory regions. Both genes were separately cloned into the vector pQE60, for overexpression under the control of thelacpromoter. In this way, we have succeded in separately expressing large quantities of each pure isoform. The two isoforms were characterized biochemically and all evidence, including that from analysis of the complex pre-steady-state kinetic behavior of the enzymes, indicates that the functional properties of the two isoenzymes are identical.     

Essential sulfhydryl group of malic enzyme fromEscherichia coli

The activity of malic enzyme fromEscherichia coli was unaffected by the monovalent cations Na⁺ or Li⁺ at 10 mM. At 100 mM, Li⁺ or Na⁺ inhibited the enzyme activity by 88% and 83%, respectively. However, the enzyme activity was stimulated by 40–80-fold with 10 mM K⁺, Rb⁺, Cs⁺, or NH ₄ ⁺ . Less stimulation was observed with 100 mM of these stimulating cations. The stimulatory effect was lost after the enzyme was dialyzed against Tris-Cl buffer, but was regained after incubating the dialyzed enzyme with dithiothreitol. The regenerated enzyme was inactivated by 5,5-dithiobis(2-nitrobenzoic acid). The resulting inactive thionitrobenzoyl enzyme could be regenerated to the active thiol-enzyme by eithiothreitol or converted to the inactive thiocyanoylated enzyme by KCN. The thiocyanoylated enzyme was insensitive to K⁺ stimulation, which suggested the essentiality of the sulfhydryl groups of theE. coli malic enzyme.     

Large scale purification and refolding of HIV-1 protease fromEscherichia coli inclusion bodies

The protease encoded by the human immunodeficiency virus type 1 (HIV-1) was engineered inEscherichia coli as a construct in which the natural 99-residue polypeptide was preceded by an NH₂-terminal methionine initiator. Inclusion bodies harboring the recombinant HIV-I protease were dissolved in 50% acetic acid and the solution was subjected to gel filtration on a column of Sephadex G-75. The protein, eluted in the second of two peaks, migrated in SDS-PAGE as a single sharp band ofM _r 10,000. The purified HIV-1 protease was refolded into an active enzyme by diluting a solution of the protein in 50% acetic acid with 25 volumes of buffer atpH 5.5. This method of purification, which has also been applied to the purification of HIV-2 protease, provides a single-step procedure to produce 100 mg quantities of fully active enzyme.     

Determination of the disulfide bond pairings in human tissue factor pathway inhibitor purified fromEscherichia coli

The disulfide bond assignments of human alanyl tissue factor pathway inhibitor purified fromEscherichia coli have been determined. This inhibitor of the extrinsic blood coagulation pathway possesses three Kunitz-type inhibitor domains, each containing three disulfide bonds. The disulfide bond pairings in domains 1 and 3 were determined by amino acid sequencing and mass spectrometry of peptides derived from a thermolysin digest. However, thermolysin digestion did not cleave any peptide bonds within domain 2. The disulfide bond pairings in domain 2 were determined by isolating it from the thermolysin treatment and subsequently cleaving it with pepsin and trypsin into peptides which yielded the three disulfide bond pairings in this domain. These results demonstrate that the disulfide pairings in each of the three domains of human tissue factor pathway inhibitor purified fromEscherichia coli are homologous to each other and also to those in bovine pancreatic trypsin inhibitor.     

The carboxy-terminal region of haemolysin 2001 is required for secretion of the toxin fromEscherichia coli

Summary As a first step in the detailed analysis of the mechanism of secretion of haemolysin, we sought to identify sequences or domains within haemolysin A (HlyA) that are essential for its secretion. For this purpose we examined the properties of a deletion and Tn5 insertions into the region of theHlyA gene encoding the C-terminal part of the protein, since both of these are relatively simple to generate. We showed that removal of 27 amino acids from the C-terminus of HlyA is sufficient to inhibit secretion drastically, although the residual polypeptide is still haemolytically active. Cellular fractionation studies showed that haemolytic activity does not accumulate in large amounts within the periplasmic space during normal secretion. More significantly, activity does not appear to accumulate within this compartment when the export functionshlyB andhlyD are removed. These results are consistent with a mechanism in which interaction of the C-terminus of HlyA with the secretion machinery, located in the inner membrane, is followed by direct transfer of haemolysin to the medium.     

Isolation and Characterization of Mitochondrial Nucleoids from the Yeast Pichia jadinii

Mitochondrial (mt) nucleoids were isolated with a high degreeof purity from the yeast Pichia jadinii, in which the mitochondrialDNA (mtDNA) is linear. Field-inversion gel electrophoresis (FIGE)revealed that significant amounts of mtDNA could be isolatedintact, as linear molecules of 41 kbp, from the isolated mt-nucleoids.Fifteen different proteins were detected in the mt-nucleoidfraction and, eight of these proteins bound to DNA. The patternsof mt-nucleoid proteins and of the DNA-binding proteins aftergel electrophoresis in the presence of SDS were somewhat differentfrom those of such proteins from Saccharomyces cerevisiae. Thecorresponding proteins isolated from the mt-nucleoids of fourother species of yeast in the genera Pichia and Williopsis alsodiffered from one another in terms of electrophoretic mobilityin the presence of SDS. In immunoblotting experiments, antibodiesthat had been raised against the 67-kDa protein of mt-nucleoidsfrom S. cerevisiae and the YMN-1 monoclonal antibody that isspecific for a 48-kDa protein in the mt-nucleoids from S. cerevisiaedid not recognize any proteins in the mt-nucleoids from Pichiajadinii and four other species of yeast. The results suggestthe considerable diversity of the proteins in the mt-nucleoidsof yeasts. (Received March 28, 1996; Accepted June 19, 1996)     

Isolation and genetic mapping of Escherichia coli aminopeptidase mutants

Summary Many mutant strains devoid of aminopeptidase activity have been isolated in Escherichia coli. All of them produce cross-reacting material when tested against specific antiaminopeptidase antibody. The map position of the locus specifying this enzyme has been determined by three conjugations and two P₁ mediated transduction experiments. By analogy with Salmonella typhimurium this locus has been called pepN (Miller, 1975). Mutations in pepN are jointly transduced with fabA and pyrD at high frequency. These data and conjugation results suggest a location between 20.5 and 22.5 minutes on E. coli genetic map.     

Identification of Two New Proteins in Spermidine Nucleoids Isolated from Escherichia coli

The Escherichia coli nucleoid contains DNA in a condensed but functional form. Analysis of proteins released from isolated spermidine nucleoids after treatment with DNase I reveals significant amounts of two proteins not previously detected in wild-type E. coli. Partial amino-terminal sequencing has identified them as the products of rdgC and yejK. These proteins are strongly conserved in gram-negative bacteria, suggesting that they have important cellular roles.     

Isolation and characterization of spontaneous srl-recA deletion mutants in Escherichia coli K-12

Summary A method was developed for the isolation of spontaneous mutants of Escherichia coli K-12 with deletions extending from the srl operon to the adjacent recA gene. The srl-recA deletion mutants were extremely sensitive to DNA-damaging agents; unable to support growth of the feckless red gam mutant bio11; and recombination-deficient in transduction and in conjugation. They therefore resembled recA point mutants such as recA13. The existence of these recA deletion mutants shows that the recA gene is not essential for viability.     

Biosynthesis and Characterization of 4-Fluorotryptophan-Labeled Escherichia coli Arginyl-tRNA Synthetase

Escherichia coli 4-fluorotryptophan-substituted arginyl-tRNA synthetase was biosynthetically prepared and purified from a tryptophan auxotroph which could overproduce this enzyme. A method was developed to separate 4-fluorotryptophan from tryptophan and to determine accurately their contents in the 4-fluorotryptophan-containing proteins. It was confirmed that more than 95% of the tryptophan residues in the purified 4-fluorotryptophan-substituted arginyl-tRNA synthetase were replaced by 4-fluorotryptophan. Studies on the effect of the 4-fluorotryptophan replacement on properties of the enzyme showed that, when compared with the native enzyme, both the specific activity and the first-order rate constant of the fluorinated enzyme decreased by approximately 20% with just slightly higher K _m values. CD studies, however, did not reveal any difference between the secondary structure of the native and fluorinated enzymes. In addition, thermal unfolding studies showed that the 4-fluorotryptophan replacement did not significantly affect the thermal stability of the enzyme. We may conclude that the substitution of 4-fluorotryptophan in arginyl-tRNA synthetase had no substantial effect on the structure and function of the enzyme. Finally, a preliminary study of ¹⁹F nuclear magnetic resonance spectroscopy of the fluorinated enzyme has shown promising prospect for further investigation of its structure and function with NMR.     

肥胖基因的分离及其在大肠杆菌中的表达

利用PCR技术自外周血白细胞染色体DNA中扩增获取了肥胖基因(ob基因)的外显子2和3序列.经过拼接,获得了全长的ob基因编码序列. 测序结果表明,获得的序列与文献报道完全一致.利用PCR技术扩增出成熟蛋白的编码序列,克隆至表达载体pBV220中获得了表达菌株,并对表达产物进行了初步纯化,为进一步研究ob基因产物的功能与应用奠定了基础.     

产NDM-5大肠埃希菌的鉴定及特征分析

对分离自血液标本的1株碳青霉烯类耐药大肠埃希菌(Escherichia coli)SCNJ06进行特征分析,以期为临床耐药菌株感染的防治提供理论参考。采用全基因组测序以及生物信息学分析,该菌株属于序列型167(ST167),含有11种耐药基因,分别是rmtB、aph(3″)-Ib、aph(6)-Id、bla_(NDM-5)、bla_(TEM-1B)、bla_(CTX-M-55)、fosA3、floR、sul2、tet(A)和mdf(A)。其中,bla_(NDM-5)位于IncX3型质粒pNDM5_SCNJ06上,mdf(A)位于染色体上,其余耐药基因位于IncFII型质粒prmtB_SCNJ06上。接合试验显示,pNDM5_SCNJ06和prmtB_SCNJ06均能够发生接合转移。应加强抗菌药物临床应用管理和医院感染防控措施,重视细菌耐药监测工作。     

Isolation and properties of Tn10 insertions in the rac locus of Escherichia coli

Summary Two Tn10 insertions that are in the rac locus of the chromosome of Escherichia coli have been isolated and characterized. These insertions are located at min 29.7 and min 30.0. The insertions are stable when an F123 rac::Tn10 episome is transferred to an F^- rac ⁺ recipient, but they are lost at a high frequency when transferred to an F^- rac ^- recipient. This latter condition has been previously, demonstrated to cause the excision of the rac locus. The Tn10 insertions are also lost at a high frequency when strains containing them are lysogenized with reverse. If the lysogens that have lost the Tn10 insertion are subsequently cured of reverse, the cells no longer contain sequences homologous with rac locus DNA. These strains were rac ^- when tested for recombination activation (Low 1973), and this procedure consequently provides a simple means to make isogenic rac ^- and rac ^- strains.     

Isolation of the mini insertions IS6 and IS7 of E. coli

Summary The mini IS elements IS6 and IS7 have been detected in constitutive gal ⁺ revertants of galOP-308::IS2 (I), in which the expression of the gal operon is turned off by IS2 in orientation I. Both, IS6 and IS7, are integrated into IS2 proximal to the gal structural genes. IS6 is 115 base pairs long and causes 50% constitutive expression of the gal genes. IS7 is only 65 base pairs long and the gal operon is expressed 20% constitutively compared to the gal ⁺ wild type operon. Both IS6 and IS7 are excised frequently, in the absence of selective pressure. These findings are discussed with respect to the evolution of gene expression.