bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of Long-Range Interaction in Lithium-Ion Battery Electrodes
Authors: Mistry Aashutosh , Juarez-Robles Daniel , Stein Malcolm , Smith Kandler , Mukherjee Partha P.
Published: November 2016

The lithium-ion battery (LIB) electrode represents a complex porous composite, consisting of multiple phases including active material (AM), conductive additive, and polymeric binder. This study proposes a mesoscale model to probe the effects of the cathode composition, e.g., the ratio of active material, conductive additive, and binder content, on the electrochemical properties and performance. The results reveal a complex nonmonotonic behavior in the effective electrical conductivity as the amount of conductive additive is increased. Insufficient electronic conductivity of the electrode limits the cell operation to lower currents. Once sufficient electron conduction (i.e., percolation) is achieved, the rate performance can be a strong function of ion-blockage effect and pore phase transport resistance. Even for the same porosity, different arrangements of the solid phases may lead to notable difference in the cell performance, which highlights the need for accurate microstructural characterization and composite electrode preparation strategies.
Simulation of cryogenic silicon etching under SF6/O2/Ar plasma discharge
Authors: Haidar Yehya , Rhallabi Ahmed , Pateau Amand , Mokrani Arezki , Taher Fadia , Roqueta Fabrice , Boufnichel Mohamed
Published: November 2016

An etching simulator is developed to study the two-dimensional (2D) silicon etch profile evolution under SF6/O2 inductively coupled plasma discharge. The simulator is composed of three modules: plasma kinetic module, sheath module, and etching module. With this approach, the authors can predict the 2D etch profile evolution versus reactor parameters. Simulation results from the sheath model show that the shape of the bimodal ion energy distribution function for each incident angle depends on the ion mass. It is all the larger that the ion mass is low. As shown in the experiment, the simulation results reveal that the atomic oxygen plays an important role in the passivation process along the side-wall. Indeed, the simulation results show the decrease of the undercut when the %O2 increases. This improves the etching anisotropy. However, the decrease in the etch rate is observed for a high %O2. Moreover, for a moderate direct current (DC) bias (some 10 V), a low variation of the silicon etch profile versus DC bias is observed. The moderate ion energy only allows removing of the passivation layer on the surface bottom. The etching process is mainly controlled by the chemical etching under fluorine flux.
Comparative study of resists and lithographic tools using the Lumped Parameter Model
Authors: Fallica Roberto , Kirchner Robert , Ekinci Yasin , Mailly Dominique
Published: November 2016

A comparison of the performance of high resolution lithographic tools is presented here. The authors use extreme ultraviolet interference lithography, electron beam lithography, and He ion beam lithography tools on two different resists that are processed under the same conditions. The dose-to-clear and the lithographic contrast are determined experimentally and are used to compare the relative efficiency of each tool. The results are compared to previous studies and interpreted in the light of each tool-specific secondary electron yield. In addition, the patterning performance is studied by exposing dense lines/spaces patterns, and the relation between critical dimension and exposure dose is discussed. Finally, the lumped parameter model is employed in order to quantitatively estimate the critical dimension of lines/spaces, using each tool specific aerial image. Our implementation is then validated by fitting the model to the experimental data from interference lithography exposures and extracting the resist contrast.
Complete Genome Sequences of Porcine Epidemic Diarrhea Virus Strains JSLS-1/2015 and JS-2/2015 Isolated from China
Authors: Tao Jie , Li Benqiang , Zhang Chunling , Liu Huili
Published: November 2016

Two porcine epidemic diarrhea virus (PEDV) strains, JSLS-1/2015 and JS-2/2015, were isolated from piglets with watery diarrhea in South China. Two genomic sequences were highly homologous to the attenuated DR13 strain. Furthermore, JSLS-1/2015 contains a 24-amino-acid deletion in open reading frame 1b, which was first reported in PEDV isolates.
Complete Genome Sequence of an Extensively Drug-Resistant Shewanella xiamenensis Strain Isolated from Algerian Hospital Effluents
Authors: Yousfi Khadidja , Touati Abdelaziz , Bekal Sadjia
Published: November 2016

In this study, we present the first complete genome of an extensively drug-resistant strain of
Shewanella xiamenensis
, collected from hospital effluents in Algeria. This genome includes the chromosome and a large new plasmid harboring several drug-resistance genes.
Complete Genome Sequence of Brevibacterium linens SMQ-1335
Authors: de Melo Alessandra G. , Labrie Simon J. , Dumaresq Jeannot , Roberts Richard J. , Tremblay Denise M. , Moineau Sylvain
Published: November 2016

Brevibacterium linens
is one of the main bacteria found in the smear of surface-ripened cheeses. The genome of the industrial strain SMQ-1335 was sequenced using PacBio. It has 4,209,935 bp, a 62.6% G+C content, 3,848 open reading frames, and 61 structural RNAs. A new type I restriction-modification system was identified.
Complete Genome Sequence of NEB 5-alpha, a Derivative of Escherichia coli K-12 DH5α
Authors: Anton Brian P. , Raleigh Elisabeth A.
Published: November 2016

Escherichia coli
K-12 DH5α is one of the most popular and widely available laboratory strains, but, surprisingly, no complete genome sequence has been publicly available. Here, we report the complete, finished sequence of NEB 5-alpha (DH5α
fhuA2
). It should serve as a useful reference for researchers working with DH5α.
Complete Genome Sequence of Human Coronavirus OC43 Isolated from Mexico
Authors: Taboada B. T. , Isa P. , Espinoza M. A. , Aponte F. E. , Arias-Ortiz M. A. , Monge-Martínez J. , Rodríguez-Vázquez R. , Díaz-Hernández F. , Zárate-Vidal F. , Wong-Chew R. M. , Firo-Reyes V. , del Río-Almendárez C. N. , Gaitán-Meza J. , Villaseñor-Sierra A. , Martínez-Aguilar G. , García-Borjas M. , Noyola D. E. , Pérez-Gónzalez L. F. , López S. , Santos-Preciado J. I. , Arias C. F.
Published: November 2016

We report the complete genome sequence of the first Mexican human coronavirus (HCoV) OC43, obtained by new-generation sequencing and a metagenomic approach, isolated from a child hospitalized with pneumonia. The genome is closely related to the other OC43 genome sequences available, ranging from 99.8% to 98.2% nucleotide sequence identity.
Draft Genome Sequence of
Cupriavidus
UYMMa02A, a Novel Beta-Rhizobium Species
Authors: Iriarte Andrés , Platero Raúl , Romero Valeria , Fabiano Elena , Sotelo-Silveira José R.
Published: November 2016

We present the draft genome of
Cupriavidus
UYMMa02A, a rhizobium strain isolated from root nodules of
Mimosa magentea
. The assembly has approximately 8.1 million bp with an average G+C of 64.1%. Symbiotic and metal-resistance genes were identified. The study of this genome will contribute to the understanding of rhizobial evolution.
Draft Genome Sequence of the Soil Isolate Lysinibacillus fusiformis M5, a Potential Hypoxanthine Producer
Authors: Gallegos-Monterrosa Ramses , Maróti Gergely , Bálint Balázs , Kovács Ákos T.
Published: November 2016

Lysinibacillus fusiformis
strain M5 is a potential hypoxanthine producer that was isolated from clay soil. Here, we present the draft genome sequence that was annotated in order to facilitate future studies of
L. fusiformis
M5.
Draft Genome Sequence of an Extended-Spectrum-β-Lactamase-Positive Hypervirulent Klebsiella pneumoniae Strain with Novel Sequence Type 2318 Isolated from a Neonate
Authors: Shankar Chaitra , Santhanam Sridhar , Kumar Manish , Gupta Vijay , Devanga Ragupathi Naveen Kumar , Veeraraghavan Balaji
Published: November 2016

Antimicrobial resistance among hypervirulent
Klebsiella pneumoniae
is increasingly reported. Here, we report the draft genome sequence of a hypervirulent
K. pneumoniae
strain isolated from a neonate with sepsis belonging to novel sequence type 2318 (ST2318).
Complete Genome Sequence of a Phycodnavirus, Heterosigma akashiwo Virus Strain 53
Authors: Ogura Yoshitoshi , Hayashi Tetsuya , Ueki Shoko
Published: November 2016

We report the complete genome sequence of
Heterosigma akashiwo
virus strain 53. The virus is a member of the
Phycodnaviridae
, one of the families regarded as giant double-stranded DNA viruses. The 274,793-bp genome contained 246 protein-coding and 3 tRNA-coding sequences.
Genome Sequence of a Subgenotype 1a Bovine Viral Diarrhea Virus in China
Authors: Gao Shandian , Du Junzheng , Tian Zhancheng , Xing Shanshan , Luo Jianxun , Liu Guangyuan , Chang Huiyun , Yin Hong
Published: November 2016

A bovine viral diarrhea virus (BVDV), GS5, of the BVDV-1a subgenotype was isolated from dairy cattle in Gansu Province, northwest China. Its near-full-length genome was determined to be closely related to an early Belgian BVDV-1a strain, WAX-N, but the relatedness to domestic strains is relatively low, indicating that different genetic evolution occurred between the viral strains in cattle in China.
Identification of a divergent M protein gene and an M protein-related gene family in Streptococcus pyogenes serotype 49
Authors: Haanes E J , Cleary P P
Published: November 2016

The antigenically variant M protein of Streptococcus pyogenes enhances virulence by promoting resistance to phagocytosis. The serum opacity factor (OF), produced by a subset of M serotypes, is also antigenically variant, and its antigenic variability exactly parallels that of M protein. OF-positive and OF-negative streptococci are also phenotypically distinguishable by a number of other criteria. In order to study the differences between OF-positive and OF-negative streptococci, we cloned and sequenced the type 49 M protein gene (emm49), the first to be cloned from an OF-positive strain. This gene showed evolutionary divergence from the OF-negative M protein genes studied previously. Furthermore, emm49 was part of a gene family, in contrast to the single-copy nature of previously characterized M protein genes.
Nutritional regulation of yeast delta-9 fatty acid desaturase activity
Authors: Bossie M A , Martin C E
Published: November 2016

The addition of unsaturated fatty acids to cultures of Saccharomyces cerevisiae significantly altered the microsomal lipid composition. Supplementation with either of the naturally occurring palmitoleic (16:1) or oleic (18:1) acids caused increased levels in membrane phospholipids and reduced levels of the complementary acid. Growth in the presence of equimolar quantities of 16:1 and 18:1 acids, however, produced a fatty acid composition similar to that found in unsupplemented cell membranes. Linoleic acid (18:2) was not found in S. cerevisiae grown under normal conditions. It was preferentially internalized and incorporated into microsomes, however, at levels exceeding 50% of the total fatty acid species. This resulted in an almost total loss of 16:1 and a reduction of 18:1 to 25% of its normal level. The delta-9 fatty acid desaturase, a microsomal enzyme that forms 16:1 and 18:1 from saturated acyl coenzyme A precursors, was affected by the presence of exogenous fatty acids. Enzyme activity toward the 16:0 coenzyme A substrate was elevated in microsomes from saturated-fatty-acid-supplemented cultures and sharply repressed following the addition of unsaturated fatty acids, including 18:2. Northern (RNA blot) and slot-blot analyses of mRNA encoded by the OLE1 gene, which appears to be the structural gene for the delta-9 desaturase, indicated that it was sharply reduced in unsaturated-fatty-acid-fed cells. These data suggest that a significant part of the regulation involves modulation of available transcripts.
Proteus mirabilis urease: nucleotide sequence determination and comparison with jack bean urease
Authors: Jones B D , Mobley H L
Published: November 2016

Proteus mirabilis, a common cause of urinary tract infection, produces a potent urease that hydrolyzes urea to NH3 and CO2, initiating kidney stone formation. Urease genes, which were localized to a 7.6-kilobase-pair region of DNA, were sequenced by using the dideoxy method. Six open reading frames were found within a region of 4,952 base pairs which were predicted to encode polypeptides of 31.0 (ureD), 11.0 (ureA), 12.2 (ureB), 61.0 (ureC), 17.9 (ureE), and 23.0 (ureF) kilodaltons (kDa). Each open reading frame was preceded by a ribosome-binding site, with the exception of ureE. Putative promoterlike sequences were identified upstream of ureD, ureA, and ureF. Possible termination sites were found downstream of ureD, ureC, and ureF. Structural subunits of the enzyme were encoded by ureA, ureB, and ureC and were translated from a single transcript in the order of 11.0, 12.2, and 61.0 kDa. When the deduced amino acid sequences of the P. mirabilis urease subunits were compared with the amino acid sequence of the jack bean urease, significant amino acid similarity was observed (58% exact matches; 73% exact plus conservative replacements). The 11.0-kDa polypeptide aligned with the N-terminal residues of the plant enzyme, the 12.2-kDa polypeptide lined up with internal residues, and the 61.0-kDa polypeptide matched with the C-terminal residues, suggesting an evolutionary relationship of the urease genes of jack bean and P. mirabilis.
Methyl-directed repair of frameshift heteroduplexes in cell extracts from Escherichia coli
Authors: Learn B A , Grafstrom R H
Published: November 2016

The methyl-directed DNA repair efficiency of a series of M13mp9 frameshift heteroduplexes 1, 2, or 3 unpaired bases was determined by using an in vitro DNA mismatch repair assay. Repair of hemimethylated frameshift heteroduplexes in vitro was directed to the unmethylated strand; was dependent on MutH, MutL, and MutS; and was equally efficient on base insertions and deletions. However, fully methylated frameshift heteroduplexes were resistant to repair, while totally unmethylated substrates were repaired with no strand bias. Hemimethylated 1-, 2-, or 3-base insertion and deletion heteroduplexes were repaired by the methyl-directed mismatch repair pathway as efficiently as the G.T mismatch. These results are consistent with earlier in vivo studies and demonstrate the involvement of methyl-directed DNA repair in the efficient prevention of frameshift mutations.
Formate auxotroph of Methanobacterium thermoautotrophicum Marburg
Authors: Tanner R S , McInerney M J , Nagle D P
Published: November 2016

A formate-requiring auxotroph of Methanobacterium thermoautotrophicum Marburg was isolated after hydroxylamine mutagenesis and bacitracin selection. The requirement for formate is unique and specific; combined pools of other volatile fatty acids, amino acids, vitamins, and nitrogen bases did not substitute for formate. Compared with those of the wild type, cell extracts of the formate auxotroph were deficient in formate dehydrogenase activity, but cells of all of the strains examined catalyzed a formate-carbon dioxide exchange activity. All of the strains examined took up a small amount (200 to 260 mumol/liter) of formate (3 mM) added to medium. The results of the study of this novel auxotroph indicate a role for formate in biosynthetic reactions in this methanogen. Moreover, because methanogenesis from H2-CO2 is not impaired in the mutant, free formate is not an intermediate in the reduction of CO2 to CH4.
Differential expression of gap and pgk genes within the gap operon of Zymomonas mobilis
Authors: Eddy C K , Mejia J P , Conway T , Ingram L O
Published: November 2016

In Zymomonas mobilis, the genes encoding glyceraldehyde-3-phosphate dehydrogenase (GAP) and phosphoglycerate kinase (PGK) are encoded in an operon that is transcribed from tandem promoters. The promoter-proximal gap gene is expressed at six- to ninefold higher levels than the pgk gene from chromosomal genes and from multiple copies of plasmid-borne genes. Two dominant transcripts were identified. The smaller, most abundant transcript contained primarily the gap message, whereas the larger, less abundant message contained both genes. The ratio of message levels for gap and pgk was calculated to be 5:1 and is sufficient to account for the observed differences in levels of GAP and PGK. The differences in message abundance are proposed to result from either transcriptional attenuation or preferential degradation of the 3' region encoding pgk. Increases in gene dosage were accompanied by one-third the expected increase in enzymatic activity on the basis of estimates of copy number, consistent with the presence of a limiting, positive regulatory factor. However, GAP and PGK expressions were not reduced from the chromosome in recombinants that contained multiple copies of the gap operon with inactive genes.
envM genes of Salmonella typhimurium and Escherichia coli
Authors: Turnowsky F , Fuchs K , Jeschek C , Högenauer G
Published: November 2016

Conjugation and bacteriophage P1 transduction experiments in Escherichia coli showed that resistance to the antibacterial compound diazaborine is caused by an allelic form of the envM gene. The envM gene from Salmonella typhimurium was cloned and sequenced. It codes for a 27,765-dalton protein. The plasmids carrying this DNA complemented a conditionally lethal envM mutant of E. coli. Recombinant plasmids containing gene envM from a diazaborine-resistant S. typhimurium strain conferred the drug resistance phenotype to susceptible E. coli cells. A guanine-to-adenine exchange in the envM gene changing a Gly codon to a Ser codon was shown to be responsible for the resistance character. Upstream of envM a small gene coding for a 10,445-dalton protein was identified. Incubating a temperature-sensitive E. coli envM mutant at the nonpermissive temperature caused effects on the cells similar to those caused by treatment with diazaborine, i.e., inhibition of fatty acid, phospholipid, and lipopolysaccharide biosynthesis, induction of a 28,000-dalton inner membrane protein, and change in the ratio of the porins OmpC and OmpF.
Characterization of the precursor of Serratia marcescens serine protease and COOH-terminal processing of the precursor during its excretion through the outer membrane of Escherichia coli
Authors: Miyazaki H , Yanagida N , Horinouchi S , Beppu T
Published: November 2016

The Serratia marcescens serine protease, which is directed by the gene encoding a precursor composed of a typical NH2-terminal signal sequence, a mature enzyme domain, and a large COOH-terminal domain, was excreted through the outer membrane of Escherichia coli. The precursor, with the expected molecular size (110 kilodaltons), was detected in an insoluble form in the periplasmic space of E. coli cells after induction with isopropyl-beta-D-thiogalactopyranoside of the expression of the gene under the control of the tac promoter. Upon membrane fractionation of the disrupted cells by sucrose density gradient centrifugation, the precursor was recovered from a fraction slightly heavier than the outer membrane fraction but not from the inner membrane fraction. Conversion of the precursor into the mature form, which was accompanied by its excretion into the medium, was observed even in the absence of de novo protein synthesis caused by the addition of chloramphenicol. The mutated gene product lacking all of the COOH-terminal domain was localized in the periplasmic space only and was not excreted into the medium. Additional mutant genes were generated by site-directed mutagenesis to test the role of some amino acids in the excretion of this protease in E. coli. The mutant protein with no protease activity because of the change of the catalytic residue Ser-341 to Thr was still excreted into the medium but with abnormal processing. Both self-processing and host-dependent processing of the precursor seem to be involved in the excretion of the mature enzyme. Replacement of the four Cys residues, two in the mature enzyme and two in the COOH-terminal domain, with Ser in different combinations caused a distinct or complete loss of excretion, suggesting that a certain conformation possibly formed via disulfide bonding was important for the excretion of the S. marcescens protease.
Nucleotide sequences of the tolA and tolB genes and localization of their products, components of a multistep translocation system in Escherichia coli
Authors: Levengood S K , Webster R E
Published: November 2016

Various mutations in the tolQRAB gene cluster of Escherichia coli render the bacteria tolerant to high concentrations of the E, A, or K colicins as well as tolerant to infection by the single-stranded filamentous bacteriophage. The nucleotide sequence of a 2.8-kilobase fragment containing the tolA and tolB genes was determined. This sequence predicts TolA to be a 421-amino-acid protein of molecular mass 44,190 daltons. Studies using minicells show it to be associated with the inner membrane, presumably via a 21-amino-acid hydrophobic sequence between residues 13 and 35. The remaining 387 residues on the carboxyl side of this region are located in the periplasm. Within this region of TolA is a 230-residue portion that is predicted to form a very long helical segment. This region is rich in alanine, lysine, and glutamic and aspartic acids. The TolB protein is predicted to contain 431 amino acids. Localization studies using minicells show two proteins encoded by this open reading frame. The larger protein of 47.5 kilodaltons appears to be associated with the membrane fractions. The smaller protein is 43 kilodaltons in size and is found with the periplasmic components of the cell.
Introduction of transposon Tn916 DNA into Haemophilus influenzae and Haemophilus parainfluenzae
Authors: Kauc L , Goodgal S H
Published: November 2016

Enterococcus (Streptococcus) faecalis transposon Tn916 was introduced into Haemophilus influenzae Rd and Haemophilus parainfluenzae by transformation and demonstrated to transpose efficiently. Haemophilus transformants resistant to tetracycline were observed at a frequency of approximately 3 x 10(2) to 5 x 10(3)/micrograms of either pAM120 (pGL101::Tn916) or pAM180 (pAM81::Tn916) plasmid DNAs, which are incapable of autonomous replication in this host. Restriction enzyme analysis and Southern blot hybridization revealed that (i) Tn916 integrates into many different sites in the H. influenzae and H. parainfluenzae genomes; (ii) only the 16.4-kilobase-pair Tn916 DNA integrates, and no vector DNA was detected; and (iii) the Tetr phenotype was stable in the absence of selective pressure. Second-generation Tn916 transformants occurred at the high frequency of chromosomal markers and retained their original chromosomal locations. Similar results were obtained with H. influenzae Rd BC200 rec-1 as the recipient strain, which suggests host rec functions are not required in Tn916 integrative transposition. Transposition with Tn916 is an important procedure for mutagenesis of Haemophilus species.
Cloning of the crystalline cell wall protein gene of Bacillus licheniformis NM 105
Authors: Tang M , Owens K , Pietri R , Zhu X R , McVeigh R , Ghosh B K
Published: November 2016

A protein with a tetragonal pattern, defined as RS protein, was found on the wall surface of an alkaline phosphatase secretion-deficient mutant (NM 105) of Bacillus licheniformis 749/C. The protein was present on the wall surface of the exponential-growth-phase cells, but at the stationary growth phase it was overproduced and hypersecreted. This protein was precipitated to homogeneity from the culture fluid by 80% ammonium sulfate saturation and chilled acetone. The molecular mass of the protein was 98 kilodaltons, and it had a single subunit in a sodium dodecyl sulfate gel. Specific anti-RS antibody was generated in rabbits and used to immunolabel the RS protein on the cells at different growth phases. In early-exponential-growth-phase cells, the outside surface of the wall, the cytoplasm, and the inside surface of the cytoplasmic membrane were labeled. In stationary-growth-phase cells, the cytoplasm was poorly labeled, but the labeling on the outside surface of the wall was high. AB. licheniformis NM 105 gene library was made by using the lambda phage EMBL3. The RS protein expression from this gene library was detected by a modified autoradiographic procedure. One of the amplified RS protein-positive plaques (4213-1) containing recombinant DNA was chosen, and the restriction map of this DNA was prepared. The RS protein expressed in Escherichia coli NM 539 infected with 4213-1 recombinant phage had a lower molecular mass than the purified authentic RS protein. The 4.5-kilobase-pair (kbp) SalI-EcoRI fragment of the recombinant DNA was cloned in the shuttle plasmid pMK4 to construct pMK462, which was expressed in B. subtilis MI112 and produced the RS protein identical in molecular mass to the purified authentic RS protein. The RS protein expression was also demonstrated in cryosections of transformed E. coli and B. subtilis cells by immunoelectron microscopy. The 1.2-kbp SalI-HindIII and 1.8-kbp HindIII-HindIII recombinant DNA restriction enzyme fragments, respectively, from the right of the restriction map produced anti-RS antibody cross-reacting proteins. The expression of the 1.2-kbp SalI-HindIII DNA fragment cloned in pUC8 could be induced with isopropyl-beta-D-thiogalactopyranoside. The 1.8-kbp DNA restriction fragment hybridized with both the chromosomal DNA of strain NM 105 and the recombinant phage 4213-1 DNA. The RS gene expression was finally demonstrated in transformed E. coli 539 cells by in situ hybridization of frozen thin sections with the 1.8-kbp HindIII biotin-dATP probe and immunolabeling these with anti-biotin immunoglobulin G and protein A-gold.
Cyclic diguanylic acid and cellulose synthesis in Agrobacterium tumefaciens
Authors: Amikam D , Benziman M
Published: November 2016

The occurrence of the novel regulatory nucleotide bis(3',5')-cyclic diguanylic acid (c-di-GMP) and its relation to cellulose biogenesis in the plant pathogen Agrobacterium tumefaciens was studied. c-di-GMP was detected in acid extracts of 32P-labeled cells grown in various media, and an enzyme responsible for its formation from GTP was found to be present in cell-free preparations. Cellulose synthesis in vivo was quantitatively assessed with [14C]glucose as a tracer. The organism produced cellulose during growth in the absence of plant cells, and this capacity was retained in resting cells. Synthesis of a cellulosic product from UDP-glucose in vitro with membrane preparations was markedly stimulated by c-di-GMP and its precursor GTP and was further enhanced by Ca2+. The calcium effect was attributed to inhibition of a c-di-GMP-degrading enzyme shown to be present in the cellulose synthase-containing membranes.
Binding to collagen by Yersinia enterocolitica and Yersinia pseudotuberculosis: evidence for yopA-mediated and chromosomally encoded mechanisms
Authors: Emödy L , Heesemann J , Wolf-Watz H , Skurnik M , Kapperud G , O'Toole P , Wadström T
Published: November 2016

Binding of Yersinia enterocolitica and Yersinia pseudotuberculosis strains to type I, II, and IV collagens has been studied. Wild-type strains which harbored the 40- to 50-megadalton virulence plasmid specifically bound all three types of collagen. Curing of the virulence plasmid or Tn5 insertion in the yopA gene encoding the temperature-inducible outer membrane protein YOP1 abolished the binding of all three collagen types to Y. enterocolitica and type I and II collagens to Y. pseudotuberculosis. Full binding capacity was restored by introduction of the yopA gene into nonbinding Yersinia strains. Binding of type I, II, and IV collagens was expressed in Escherichia coli constructs harboring the yopA gene of either Y. enterocolitica or Y. pseudotuberculosis. The interaction of bacterial cells with type I collagen could be blocked by nonradiolabeled native collagens or denatured collagen but not with other serum and connective-tissue proteins. Unlabeled collagen could not displace bound radiolabeled collagen. The binding was inhibited by YOP1-specific polyclonal antibodies, in contrast to normal rabbit serum. The interaction was rapid and was quite resistant to heat treatment, to proteolytic enzymes, to various pHs in both acidic and alkaline ranges, and to the chaotropic agent urea. We propose that this newly identified interaction may be involved both in the first steps of the pathogenesis and in the complications of Yersinia infections affecting connective tissue.
Substitution of a pentalenolactone-sensitive glyceraldehyde-3-phosphate dehydrogenase by a genetically distinct resistant isoform accompanies pentalenolactone production in Streptomyces arenae
Authors: Fröhlich K U , Wiedmann M , Lottspeich F , Mecke D
Published: November 2016

Pentalenolactone (PL), an antibiotic produced by Streptomyces arenae, is a potent inhibitor of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The producer strain contains different isoforms of GAPDH: a PL-sensitive enzyme on nonproduction media and a PL-insensitive enzyme on production media. After induction of PL synthesis, the sensitive GAPDH disappears parallel to the disappearance of its activity, as shown by Western (immunoblot) hybridization. The two isoenzymes exhibit little immunological cross-reactivity and differ in size, amino acid composition, and several amino acid residues of their amino termini. Two different types of plasmids from a S. arenae genomic library, named pBRPLR1 and pBRPLR2, were cloned in Escherichia coli by selection for enhanced PL resistance. Both contain a GAPDH structural gene. Plasmid pBRPLR1 increases E. coli PL tolerance 7-fold, and plasmid pBRPLR2 increases it 30-fold. GAPDH from pBRPLR1 transformants shows biphasic PL inactivation kinetics. These cells contain PL-sensitive GAPDH from both E. coli and S. arenae. GAPDH from pBRPLR2 transformants tolerates higher PL concentrations than either E. coli or S. arenae PL-sensitive GAPDH but is less resistant than S. arenae PL-insensitive GAPDH. Nondenaturing polyacrylamide electrophoresis showed this GAPDH to be a hybrid of E. coli and S. arenae PL-insensitive GAPDH. The hybrid enzyme could be purified to homogeneity. Induction of the lacZ promoter of pUC subclones of both GAPDH genes had only a small effect on raising the level of intracellular GAPDH.
Chromosome map of the thermophilic archaebacterium Thermococcus celer
Authors: Noll K M
Published: November 2016

A physical map for the chromosome of the thermophilic archaebacterium Thermococcus celer Vu13 has been constructed. Thirty-four restriction endonucleases were tested for their ability to generate large restriction fragments from the chromosome of T. celer. Of these, the enzymes NheI, SpeI, and XbaI yielded the fewest fragments when analyzed by pulsed-field electrophoresis. NheI and SpeI each gave 5 fragments, while XbaI gave 12. The size of the T. celer chromosome was determined from the sum of the apparent sizes of restriction fragments derived from single and double digests by using these enzymes and was found to be 1,890 +/- 27 kilobase pairs. Partial and complete digests allowed the order of all but three small (less than 15 kilobase pairs) fragments to be deduced. These three fragments were assigned positions by using hybridization probes derived from these restriction fragments. The positions of the other fragments were confirmed by using hybridization probes derived in the same manner. The positions of the 5S, 16S, and 23S rRNA genes as well as the 7S RNA gene were located on this map by using cloned portions of these genes as hybridization probes. The 5S rRNA gene was localized 48 to 196 kilobases from the 5' end of the 16S gene. The 7S RNA gene was localized 190 to 504 kilobases from the 3' end of the 23S gene. These analyses demonstrated that the chromosome of T. celer is a single, circular DNA molecule. This is the first such demonstration of the structure of an archaebacterial chromosome.
In vitro reconstitution of a hexagonal array with a surface layer protein synthesized by Bacillus subtilis harboring the surface layer protein gene from Bacillus brevis 47
Authors: Tsuboi A , Uchihi R , Engelhardt H , Hattori H , Shimizu S , Tsukagoshi N , Udaka S
Published: November 2016

Bacillus brevis 47 contains two surface layer proteins, termed the outer wall protein and the middle wall protein (MWP), which form a hexagonal array in the cell wall. Introduction of the MWP structural gene into Bacillus subtilis by using a low-copy-number plasmid led to the synthesis of an immunoreactive polypeptide with a molecular mass almost the same as that of the MWP synthesized by B. brevis 47. Biochemical analysis indicated that most of the MWP synthesized by B. subtilis was localized in the cytoplasmic fraction. This was further confirmed by using immunogold electron microscopy. The amino-terminal amino acid sequence of the MWP purified from the cytoplasm of B. subtilis indicated that the MWP was precursor with a signal peptide of 23 amino acid residues to the amino terminus of the mature protein. The precursor of the MWP possessed the ability to reassemble in vitro on the B. brevis 47 peptidoglycan layer, resulting in the formation of almost the same hexagonal arrays as with the mature MWP purified from B. brevis 47, judging from images averaged at a resolution of about 2.5 nm. Furthermore, a center-to-center distance of the hexagonal lattice on the envelope reconstituted by using the precursor MWP was calibrated as 18.3 nm, which was almost identical to the value of 17.8 nm obtained with the mature protein.
Nucleotide sequence and insertional inactivation of a Bacillus subtilis gene that affects cell division, sporulation, and temperature sensitivity
Authors: Beall B , Lutkenhaus J
Published: November 2016

Located at 135 degrees on the Bacillus subtilis genetic map are several genes suspected to be involved in cell division and sporulation. Previously isolated mutations mapping at 135 degrees include the tms-12 mutation and mutations in the B. subtilis homologs of the Escherichia coli cell division genes ftsA and ftsZ. Previously, we cloned and sequenced the B. subtilis ftsA and ftsZ genes that are present on an 11-kilobase-pair EcoRI fragment and found that the gene products and organization of these two genes are conserved between the two bacterial species. We have since found that the mutation in the temperature-sensitive filamenting tms-12 mutant maps upstream of the ftsA gene on the same 11-kilobase-pair EcoRI fragment in a gene we designated dds. Sequence analysis of the dds gene and four other open reading frames upstream of ftsA revealed no significant homology to other known genes. It was found that the dds gene is not absolutely essential for viability since the dds gene could be insertionally inactivated. The dds null mutants grew slowly, were filamentous, and exhibited a reduced level of sporulation. Additionally, these mutants were extremely temperature sensitive and were unable to form colonies at 37 degrees C. Another insertion, which resulted in the elimination of 103 C-terminal residues, resulted in a temperature-sensitive phenotype less severe than that in the dds null mutant and similar to that in the known tms-12 mutant. The tms-12 mutation was cloned and sequenced, revealing a nonsense codon that was predicted to result in an amber fragment that was about 65% of the wild-type size (elimination of 93 C-terminal residues).
Peptidoglycan-associated polypeptides of Mycobacterium tuberculosis
Authors: Hirschfield G R , McNeil M , Brennan P J
Published: November 2016

Important protein-based immunoreactivities have long been associated with the cell wall core of mycobacteria. In order to explore the molecular basis of such activities, purified cell walls of Mycobacterium tuberculosis were extracted with sodium dodecyl sulfate to produce an insoluble residue composed of the mycolylarabinogalactan-peptidoglycan complex and about 2% of unextractable protein. Treatment of the product from an avirulent strain of M. tuberculosis with trifluoromethanesulfonic acid released a single polypeptide with a molecular size of 23 kilodaltons, accounting for all of the insoluble cell wall protein. Extensive purification and then analysis of the 23-kilodalton protein demonstrated the absence of diaminopimelic acid, muramic acid, or other peptidoglycan components, pointing to either a novel linkage between protein and peptidoglycan or a noncovalent but tenacious association. The released 23-kilodalton protein showed amino acid homology and other similarities to the outer membrane protein OmpF of Escherichia coli. Although a similar product was released in small quantities from cell walls of the virulent M. tuberculosis Erdman and H37Rv by lysozyme treatment, the cell walls of virulent bacilli were dominated by the presence of poly-alpha-L-glutamine, accounting for as much as 10% of their weight. The poly-alpha-L-glutamine was successfully separated from the cell wall proper, demonstrating again the absence of a covalent association between peptidoglycan and the polymer. The antigenicity of these products is demonstrated, and their roles vis-a-vis analogous polypeptides from other bacteria in immunogenicity, pathogenicity, and bacterial physiology are discussed.
Isolation and characterization of a novel extracellular metalloprotease from Bacillus subtilis
Authors: Rufo G A , Sullivan B J , Sloma A , Pero J
Published: November 2016

We have isolated and characterized two minor extracellular proteases from culture supernatants of a strain of Bacillus subtilis containing deletion mutations of the genes for the extracellular proteases subtilisin (apr) and neutral protease (npr) and a minor extracellular protease (epr) as well as intracellular serine protease-I (isp-1). Characterization studies have revealed that one of these enzymes is the previously described protease bacillopeptidase F. The second enzyme, the subject of this report, is a novel metalloprotease, which we designate Mpr. Mpr is a unique metalloprotease that has been purified to apparent homogeneity by using both conventional and high-performance liquid chromatography procedures. Mpr has a molecular mass of approximately 28 kilodaltons on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and a basic isoelectric point of 8.7. The enzyme showed maximal activity against azocoll at pH 7.5 and 50 degrees C. Mpr was inhibited by dithiothreitol and a combination of beta-mercaptoethanol and EDTA. Activity was moderately inhibited by beta-mercaptoethanol and EDTA alone as well as by cysteine and citrate and only marginally by phosphoramidon 1,10-phenanthroline and N-[N-(L-3-trans-carboxyoxiran-2-carbonyl)-L-leucyl]-agmatine. Mpr was not inhibited by phenylmethylsulfonyl fluoride. In addition, Mpr showed esterolytic but not collagenolytic activities. Our studies suggest that Mpr is a secreted metalloprotease containing cysteine residues that are required for maximal activity.
Analysis of protein localization by use of gene fusions with complementary properties
Authors: Manoil C
Published: November 2016

This report describes a new transposon designed to facilitate the combined use of beta-galactosidase and alkaline phosphatase gene fusions in the analysis of protein localization. The transposon, called TnlacZ, is a Tn5 derivative that permits the generation of gene fusions encoding hybrid proteins carrying beta-galactosidase at their C termini. In tests with plasmids, TnlacZ insertions that led to high cellular beta-galactosidase activity were restricted to sequences encoding either cytoplasmic proteins or cytoplasmic segments of a membrane protein. The fusion characteristics of TnlacZ are thus complementary to those of TnphoA, a transposon able to generate alkaline phosphatase fusions whose high-activity insertion sites generally correspond to periplasmic sequences. The structure of TnlacZ allows the conversion of a TnlacZ fusion into the corresponding TnphoA fusion (and vice versa) through recombination or in vitro manipulation in a process called fusion switching. Fusion switching was used to generate the following two types of fusions with unusual properties: a low-specific-activity beta-galactosidase-alkaline phosphatase gene fusion and two toxic periplasmic-domain serine chemoreceptor-beta-galactosidase gene fusions. The generation of both beta-galactosidase and alkaline phosphatase fusions at exactly the same site in a protein permits a comparison of the two enzyme activities in evaluating the subcellular location of the site, such as in studies of membrane protein topology. In addition, fusion switching makes it possible to generate gene fusions whose properties should facilitate the isolation of mutants defective in the export or membrane anchoring of different cell envelope proteins.
Expression of the Escherichia coli K5 capsular antigen: immunoelectron microscopic and biochemical studies with recombinant E. coli
Authors: Kröncke K D , Boulnois G , Roberts I , Bitter-Suermann D , Golecki J R , Jann B , Jann K
Published: November 2016

The capsular K5 polysaccharide, a representative of group II capsular antigens of Escherichia coli, has been cloned previously, and three gene regions responsible for polymerization and surface expression have been defined (I. S. Roberts, R. Mountford, R. Hodge, K. B. Jann, and G. J. Boulnois, J. Bacteriol. 170:1305-1310, 1988). In this report, we describe the immunoelectron microscopic analysis of recombinant bacteria expressing the K5 antigen and of mutants defective in either region 1 or region 3 gene functions, as well as the biochemical analysis of the K5 capsular polysaccharide. Whereas the K5 clone expressed the K5 polysaccharide as a well-developed capsule in about 25% of its population, no capsule was observed in whole mount preparations and ultrathin sections of the expression mutants. Immunogold labeling of sections from the region 3 mutant revealed the capsular K5 polysaccharide in the cytoplasm. With the region 1 mutant, the capsular polysaccharide appeared associated with the cell membrane, and, unlike the region 3 mutant polysaccharide, the capsular polysaccharide could be detected in the periplasm after plasmolysis of the bacteria. Polysaccharides were isolated from the homogenized mutants with cetyltrimethylammonium bromide. The polysaccharide from the region 1 mutant had the same size as that isolated from the capsule of the original K5 clone, and both polysaccharides were substituted with phosphatidic acid. The polysaccharide from the region 3 mutant was smaller and was not substituted with phosphatidic acid. These results prompt us to postulate that gene region 3 products are involved in the translocation of the capsular polysaccharide across the cytoplasmic membrane and that region 1 directs the transport of the lipid-substituted capsular polysaccharide through the periplasm and across the outer membrane.
Chemotaxis in Escherichia coli proceeds efficiently from different initial tumble frequencies
Authors: Weis R M , Koshland D E
Published: November 2016

The relationships between the level of tumbling, tumble frequency, and chemotactic ability were tested by constructing two Escherichia coli strains with the same signaling apparatus but with different adapted levels of tumbling, above and below the level of wild-type E. coli. This was achieved by introducing two different aspartate receptor genes into E. coli: a wild-type (wt-tars) and a mutant (m-tars) Salmonella typhimurium receptor gene. These cells were compared with each other and with wild-type E. coli (containing the wild-type E. coli aspartate receptor gene, wt-tare). It was found that in spite of the differences in the adapted levels of tumbling, the three strains had essentially equal response times and chemotactic ability toward aspartate. This shows that the absolute level of the tumbling can be varied without impairing chemotaxis if the signal processing system is normal. It also appears that a largely smooth-swimming mutant may undergo chemotaxis by increasing tumbling frequency in negative gradients.
Localization of enterobacterial common antigen immunoreactivity in the ribosomal cytoplasm of Escherichia coli cells cryosubstituted and embedded at low temperature
Authors: Acker G , Kammerer C
Published: November 2016

The application of two on-section immunogold labeling techniques, the Lowicryl K4M (progressive lowering of temperature) procedure and the cryosection technique of Tokuyasu, in a previous work to study the topology of enterobacterial common antigen (ECA) biosynthesis revealed the presence of label on the outer membrane and in areas associated with the inner side of the cytoplasmic membrane. However, labeling was also observed in the ribosomal cytoplasm. The question of whether the cytoplasmic label was a result of ECA displacement during the more slowly acting aldehyde fixation or whether cytoplasmic ECA precursors are true constituents of the ribosomal cytoplasm could not be resolved from these results. In the study described here, cells of the same Escherichia coli F470 strain were reinvestigated by comparison of the progressive lowering of temperature and improved cryosubstitution-low-temperature embedment techniques. The latter procedure, applied directly to nonpretreated and noncentrifuged cells, led to superior ultrastructural preservation of the cytoplasmic organization, with little opportunity for cytoplasmic antigen displacement after the primary cryofixation step; the label distribution obtained supports the conclusion that N-acetylmannosaminuronic acid (ManNAcA)-containing ECA precursors are real constituents of the ribosomal cytoplasm. Results from tunicamycin inhibition studies of ECA biogenesis in the E. coli mutant 2465 suggested that even the ECA precursor UDP-ManNAcA alone or a chemically unidentified product(s) generated from accumulated ManNAcA residues may react with the monoclonal antibody used, leading to weak but clearly positive cytoplasmic labeling. The relatively intense labeling obtained with cells grown in the absence of the drug can be explained by the reactivity of further ManNAcA-containing ECA precursors with the monoclonal antibody used.
Variations in the carbohydrate regions of Bordetella pertussis lipopolysaccharides: electrophoretic, serological, and structural features
Authors: Caroff M , Chaby R , Karibian D , Perry J , Deprun C , Szabó L
Published: November 2016

Structural and immunological differences between the two components that are usually present in unequal quantities in Bordetella pertussis endotoxin preparations and are visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis have been studied by using strains 1414, A100, and 134, all in phase I. According to analyses by both sodium dodecyl sulfate-polyacrylamide gel electrophoresis and thin-layer chromatography, the minor (8%) component of the endotoxin of strain 1414 (endotoxin 1414) appeared to be the predominating component of endotoxins A100 and 134. The masses of the carbohydrate chains isolated from endotoxin A100 and from the major component of endotoxin 1414 were 1,649 and 2,311 atomic mass units, respectively, as determined by 252Cf plasma desorption mass spectrometry. Comparison of the 1H nuclear magnetic resonance spectra of these chains established that four N-acetyl groups, an N-methyl group, and a 6-deoxy function, which characterize the nonreducing, distal trisaccharide of the glycose chain of strain 1414, were absent from that of strain A100. The antigenicity of endotoxin 1414, as measured by enzyme-linked immunosorbent assay, was higher than that of endotoxin A100, but fell below it when the glycose chain of endotoxin 1414 was deprived of seven sugars by treatment with nitrous acid. This observation suggests that at least three (distal, proximal, and intermediate) regions of the glycose chain of endotoxin 1414 carry antigenic determinants. One of these, located in the distal trisaccharide, is absent from both endotoxins A100 and 134.