bluuebunny/crossref_metadata_2025_split huggingface dataset:
Localization of theEscherichia coliRNA Polymerase β′ Subunit Residue Phosphorylated by Bacteriophage T7 Kinase Gp0.7
Authors: Severinova Elena , Severinov Konstantin 
Published: May 2006

ABSTRACTDuring bacteriophage T7 infection, theEscherichia coliRNA polymerase β′ subunit is phosphorylated by the phage-encoded kinase Gp0.7. Here, we used proteolytic degradation and mutational analysis to localize the phosphorylation site to a single amino acid, Thr1068, in the evolutionarily hypervariable segment of β′. Using a phosphomimetic substitution of Thr1068, we show that phosphorylation of β′ leads to increased ρ-dependent transcription termination, which may help to switch from host to viral RNA polymerase transcription during phage development.
Multiple
groESL
Operons Are Not Key Targets of RpoH1 and RpoH2 in
Sinorhizobium meliloti
Authors: Bittner Alycia N. , Oke Valerie 
Published: May 2006

ABSTRACT

Among the rhizobia that establish nitrogen-fixing nodules on the roots of host plants, many contain multiple copies of genes encoding the sigma factor RpoH and the chaperone GroEL/GroES. In
Sinorhizobium meliloti
there are two
rpoH
genes, four
groESL
operons, and one
groEL
gene.
rpoH1
mutants are defective for growth at high temperature and form ineffective nodules,
rpoH1 rpoH2
double mutants are unable to form nodules, and
groESL1
mutants form ineffective nodules. To explore the roles of RpoH1 and RpoH2, we identified mutants that suppress both the growth and nodulation defects. These mutants do not suppress the nitrogen fixation defect. This implies that the functions of RpoH1 during growth and RpoH1/RpoH2 during the initiation of symbiosis are similar but that there is a different function of RpoH1 needed later during symbiosis. We showed that, unlike in
Escherichia coli
, overexpression of
groESL
is not sufficient to bypass any of the RpoH defects. Under free-living conditions, we determined that RpoH2 does not control expression of the
groE
genes, and RpoH1 only controls expression of
groESL5
. Finally, we completed the series of
groE
mutants by constructing
groESL3
and
groEL4
mutants and demonstrated that they do not display symbiotic defects. Therefore, the only
groESL
operon required by itself for symbiosis is
groESL1
. Taken together, these results suggest that GroEL/GroES production alone cannot explain the requirements for RpoH1 and RpoH2 in
S. meliloti
and that there must be other crucial targets.
Studies of the CobA-Type ATP:Co(I)rrinoid Adenosyltransferase Enzyme ofMethanosarcina mazeiStrain Gö1
Authors: Buan Nicole R. , Rehfeld Kimberly , Escalante-Semerena Jorge C. 
Published: May 2006

ABSTRACTAlthough methanogenic archaea use B12extensively as a methyl carrier for methanogenesis, little is known about B12metabolism in these prokaryotes or any other archaea. To improve our understanding of how B12metabolism differs between bacteria and archaea, the gene encoding the ATP:co(I)rrinoid adenosyltransferase inMethanosarcina mazeistrain Gö1 (open reading frame MM3138, referred to ascobAMmhere) was cloned and used to restore coenzyme B12synthesis in aSalmonella entericastrain lacking the housekeeping CobA enzyme.cobAMmprotein was purified and its initial biochemical analysis performed. In vitro, the activity is enhanced 2.5-fold by the addition of Ca2+ions, but the activity was not enhanced by Mg2+and, unlike theS. entericaCobA enzyme, it was >50% inhibited by Mn2+. The CobAMmenzyme had aKmATPof 3 μM and aKmHOCblof 1 μM. Unlike theS. entericaenzyme, CobAMmused cobalamin (Cbl) as a substrate better than cobinamide (Cbi; a Cbl precursor); the β phosphate of ATP was required for binding to the enzyme. A striking difference between CobASeand CobAMmwas the use of ADP as a substrate by CobAMm, suggesting an important role for the γ phosphate of ATP in binding. The results from31P-nuclear magnetic resonance spectroscopy experiments showed that triphosphate (PPPi) is the reaction by-product; no cleavage of PPPiwas observed, and the enzyme was only slightly inhibited by pyrophosphate (PPi). The data suggested substantial variations in ATP binding and probably corrinoid binding between CobASeand CobAMmenzymes.
In Vitro Biofilm Formation of Commensal and PathogenicEscherichia coliStrains: Impact of Environmental and Genetic Factors
Authors: Reisner Andreas , Krogfelt Karen A. , Klein Bjarke M. , Zechner Ellen L. , Molin Søren 
Published: May 2006

ABSTRACTOur understanding ofEscherichia colibiofilm formation in vitro is based on studies of laboratory K-12 strains grown in standard media. However, pathogenicE. coliisolates differ substantially in their genetic repertoire fromE. coliK-12 and are subject to heterogeneous environmental conditions. In this study, in vitro biofilm formation of 331 nondomesticatedE. colistrains isolated from healthy (n= 105) and diarrhea-afflicted children (n= 68), bacteremia patients (n= 90), and male patients with urinary tract infections (n= 68) was monitored using a variety of growth conditions and compared to in vitro biofilm formation of prototypic pathogenic and laboratory strains. Our results revealed remarkable variation among the capacities of diverseE. coliisolates to form biofilms in vitro. Notably, we could not identify an association of increased biofilm formation in vitro with a specific strain collection that represented pathogenicE. colistrains. Instead, analysis of biofilm data revealed a significant dependence on growth medium composition (P< 0.05). Poor correlation between biofilm formation in the various media suggests that diverseE. coliisolates respond very differently to changing environmental conditions. The data demonstrate that prevalence and expression of three factors known to strongly promote biofilm formation inE. coliK-12 (F-like conjugative pili, aggregative adherence fimbriae, and curli) cannot adequately account for the increased biofilm formation of nondomesticatedE. coliisolates in vitro. This study highlights the complexity of genetic and environmental effectors of the biofilm phenotype within the speciesE. coli.
Structural and Functional Analysis of Rv3214 from
Mycobacterium tuberculosis
, a Protein with Conflicting Functional Annotations, Leads to Its Characterization as a Phosphatase
Authors: Watkins Harriet A. , Baker Edward N. 
Published: May 2006

ABSTRACT

The availability of complete genome sequences has highlighted the problems of functional annotation of the many gene products that have only limited sequence similarity with proteins of known function. The predicted protein encoded by open reading frame Rv3214 from the
Mycobacterium tuberculosis
H37Rv genome was originally annotated as EntD through sequence similarity with the
Escherichia coli
EntD, a 4′-phosphopantetheinyl transferase implicated in siderophore biosynthesis. An alternative annotation, based on slightly higher sequence identity, grouped Rv3214 with proteins of the cofactor-dependent phosphoglycerate mutase (dPGM) family. The crystal structure of this protein has been solved by single-wavelength anomalous dispersion methods and refined at 2.07-Å resolution (R = 0.229; R
free
= 0.245). The protein is dimeric, with a monomer fold corresponding to the classical dPGM α/β structure, albeit with some variations. Closer comparisons of structure and sequence indicate that it most closely corresponds with a broad-spectrum phosphatase subfamily within the dPGM superfamily. This functional annotation has been confirmed by biochemical assays which show negligible mutase activity but acid phosphatase activity with a pH optimum of 5.4 and suggests that Rv3214 may be important for mycobacterial phosphate metabolism in vivo. Despite its weak sequence similarity with the 4′-phosphopantetheinyl transferases (EntD homologues), there is little evidence to support this function.
Role of Conserved Amino Acids in the Catalytic Activity of
Escherichia coli
Primase
Authors: Rodina Anna , Godson G. Nigel 
Published: May 2006

ABSTRACT

The role of conserved amino acid residues in the polymerase domain of
Escherichia coli
primase has been studied by mutagenesis. We demonstrate that each of the conserved amino acids Arg146, Arg221, Tyr230, Gly266, and Asp311 is involved in the process of catalysis. Residues Glu265 and Asp309 are also critical because a substitution of each amino acid irreversibly destroys the catalytic activity. Two K229A and M268A mutant primase proteins synthesize only 2-nucleotide products in de novo synthesis reactions under standard conditions. Y267A mutant primase protein synthesizes both full-size and 2-nucleotide RNA, but with no intermediate-size products. From these data we discuss the significant step of the 2-nucleotide primer RNA synthesis by
E. coli
primase and the role of amino acids Lys229, Tyr267, and Met268 in primase complex stability.
Application of Comparative Phylogenomics To Study the Evolution ofYersinia enterocoliticaand To Identify Genetic Differences Relating to Pathogenicity
Authors: Howard Sarah L. , Gaunt Michael W. , Hinds Jason , Witney Adam A. , Stabler Richard , Wren Brendan W. 
Published: May 2006

ABSTRACTYersinia enterocolitica, an important cause of human gastroenteritis generally caused by the consumption of livestock, has traditionally been categorized into three groups with respect to pathogenicity, i.e., nonpathogenic (biotype 1A), low pathogenicity (biotypes 2 to 5), and highly pathogenic (biotype 1B). However, genetic differences that explain variation in pathogenesis and whether different biotypes are associated with specific nonhuman hosts are largely unknown. In this study, we applied comparative phylogenomics (whole-genome comparisons of microbes with DNA microarrays combined with Bayesian phylogenies) to investigate a diverse collection of 94 strains ofY. enterocoliticaconsisting of 35 human, 35 pig, 15 sheep, and 9 cattle isolates from nonpathogenic, low-pathogenicity, and highly pathogenic biotypes. Analysis confirmed three distinct statistically supported clusters composed of a nonpathogenic clade, a low-pathogenicity clade, and a highly pathogenic clade. Genetic differences revealed 125 predicted coding sequences (CDSs) present in all highly pathogenic strains but absent from the other clades. These included several previously uncharacterized CDSs that may encode novel virulence determinants including a hemolysin, a metalloprotease, and a type III secretion effector protein. Additionally, 27 CDSs were identified which were present in all 47 low-pathogenicity strains andY. enterocolitica8081 but absent from all nonpathogenic 1A isolates. Analysis of the core gene set forY. enterocoliticarevealed that 20.8% of the genes were shared by all of the strains, confirming this species as highly heterogeneous, adding to the case for the existence of three subspecies ofY. enterocolitica. Further analysis revealed thatY. enterocoliticadoes not cluster according to source (host).
Role of the Fur Regulon in Iron Transport in
Bacillus subtilis
Authors: Ollinger Juliane , Song Kyung-Bok , Antelmann Haike , Hecker Michael , Helmann John D. 
Published: May 2006

ABSTRACT

The
Bacillus subtilis
ferric uptake regulator (Fur) protein mediates the iron-dependent repression of at least 20 operons encoding ∼40 genes. We investigated the physiological roles of Fur-regulated genes by the construction of null mutations in 14 transcription units known or predicted to function in siderophore biosynthesis or iron uptake. We demonstrate that
ywbLMN
, encoding an elemental iron uptake system orthologous to the copper oxidase-dependent Fe(III) uptake system of
Saccharomyces cerevisiae
, is essential for growth in low iron minimal medium lacking citric acid. 2,3-Dihydroxybenzoyl-glycine (Itoic acid), the siderophore precursor produced by laboratory strains of
B. subtilis
, is of secondary importance. In the presence of citrate, the YfmCDEF ABC transporter is required for optimal growth.
B. subtilis
is unable to grow in minimal medium containing the iron chelator EDDHA unless the ability to synthesize the intact bacillibactin siderophore is restored (by the introduction of a functional
sfp
gene) or exogenous siderophores are provided. Utilization of the catecholate siderophores bacillibactin and enterobactin requires the FeuABC importer and the YusV ATPase. Utilization of hydroxamate siderophores requires the FhuBGC ABC transporter together with the FhuD (ferrichrome) or YxeB (ferrioxamine) substrate-binding proteins. Growth with schizokinen or arthrobactin is at least partially dependent on the YfhA YfiYZ importer and the YusV ATPase. We have also investigated the effects of a
fur
mutation on the proteome and documented the derepression of 11 Fur-regulated proteins, including a newly identified thioredoxin reductase homolog, YcgT.
Chemotaxis Is Required for Virulence and Competitive Fitness of the Bacterial Wilt Pathogen
Ralstonia solanacearum
Authors: Yao Jian , Allen Caitilyn 
Published: May 2006

ABSTRACT

Ralstonia solanacearum
, a soilborne plant pathogen of considerable economic importance, invades host plant roots from the soil. Qualitative and quantitative chemotaxis assays revealed that this bacterium is specifically attracted to diverse amino acids and organic acids, and especially to root exudates from the host plant tomato. Exudates from rice, a nonhost plant, were less attractive. Eight different strains from this heterogeneous species complex varied significantly in their attraction to a panel of carbohydrate stimuli, raising the possibility that chemotactic responses may be differentially selected traits that confer adaptation to various hosts or ecological conditions. Previous studies found that an aflagellate mutant lacking swimming motility is significantly reduced in virulence, but the role of directed motility mediated by the chemotaxis system was not known. Two site-directed
R. solanacearum
mutants lacking either CheA or CheW, which are core chemotaxis signal transduction proteins, were completely nonchemotactic but retained normal swimming motility. In biologically realistic soil soak virulence assays on tomato plants, both nonchemotactic mutants had significantly reduced virulence indistinguishable from that of a nonmotile mutant, demonstrating that directed motility, not simply random motion, is required for full virulence. In contrast, nontactic strains were as virulent as the wild-type strain was when bacteria were introduced directly into the plant stem through a cut petiole, indicating that taxis makes its contribution to virulence in the early stages of host invasion and colonization. When inoculated individually by soaking the soil, both nontactic mutants reached the same population sizes as the wild type did in the stems of tomato plants just beginning to wilt. However, when tomato plants were coinoculated with a 1:1 mixture of a nontactic mutant and its wild-type parent, the wild-type strain outcompeted both nontactic mutants by 100-fold. Together, these results indicate that chemotaxis is an important trait for virulence and pathogenic fitness in this plant pathogen.
Epidemiology, Risk Factors, and Prognosis of
Candida parapsilosis
Bloodstream Infections: Case-Control Population-Based Surveillance Study of Patients in Barcelona, Spain, from 2002 to 2003
Authors: Almirante Benito , Rodríguez Dolors , Cuenca-Estrella Manuel , Almela Manel , Sanchez Ferran , Ayats Josefina , Alonso-Tarres Carles , Rodriguez-Tudela Juan L. , Pahissa Albert ,   the Barcelona Candidemia Project Study Group
Published: May 2006

ABSTRACT

Candida parapsilosis
has emerged as an important yeast species causing fungemia. We describe the incidence and epidemiology of
C. parapsilosis
fungemia. Data from active population-based surveillance in Barcelona, Spain, from January 2002 to December 2003 were analyzed. We focused on 78 episodes of
C. parapsilosis
fungemia, and we compared them with 175
Candida albicans
controls.
C. parapsilosis
accounted for 23% of all fungemias. The annual incidences were 1 episode per 10
5
patients, 1.2 episodes per 10
4
discharges, and 1.7 episodes per 10
5
patient days. All isolates but one (99%) were fluconazole susceptible. Seventy-two isolates (92%) were inpatient candidemias. Forty-two episodes (51%) were considered catheter-related fungemia, 35 (45%) were considered primary fungemia, and 3 (4%) were considered secondary fungemia. Risk factors for candidemia were vascular catheterization (97%), prior antibiotic therapy (91%), parenteral nutrition (54%), prior surgery (46%), prior immunosuppressive therapy (38%), malignancy (27%), prior antifungal infection (26%), transplant recipient (16%), neutropenia (12%), and prior colonization (11%). Multivariate analysis of the differential characteristics showed that the factors that independently predicted the presence of
C. parapsilosis
fungemia were neonate patients (odds ratio [OR], 7.5; 95% confidence interval [CI], 2.1 to 26.8;
P
= 0.002), transplant recipients (OR, 9.2; 95% CI, 1.9 to 43.3;
P
= 0.005), patients with a history of prior antifungal therapy (OR, 5.4; 95% CI, 1.8 to 15.9;
P
= 0.002), and patients who received parenteral nutrition (OR, 2.2; 95% CI, 1.09 to 4.6;
P
= 0.028). The overall mortality rate was lower than that associated with
C. albicans
candidemia (23% versus 43%;
P
< 0.01). In summary,
C. parapsilosis
was responsible for 23% of all candidemias and was more frequent in neonates, in transplant recipients, and in patients who received parenteral nutrition or previous antifungal therapy, mainly fluconazole. The mortality rate was lower than that associated with
C. albicans
fungemia.
Kinetics of the addition of acids to olefins with and without boron fluoride catalysis
Authors: Latrèmouille G. A. , Eastham A. M. 
Published: May 2006

Isobutene reacts readily with excess trifluoroacetic acid in ethylene dichloride solution at ordinary temperatures to give t-butyl trifluoroacetate. The rate of the reaction is given, within the range of the experiments, by the expression d[ester]/dt = k[acid]2[olefin], and the apparent activation energy is about 6 kcal/mole. The rate of addition is markedly dependent on the strength of the reacting acid and is drastically reduced in the presence of mildly basic materials, such as dioxane. The boron fluoride catalyzed addition of acetic acid to 2-butene can be considered to follow a similar rate law, i.e. d[ester]/dt = k[acid·BF3]2[olefin], but only if some assumptions are made about the position of the equilibrium [Formula: see text]since only the 1:1 complex is reactive.
The crystal and molecular structure of thioformaldehyde trimer
Authors: Fleming J. E. , Lynton H. 
Published: May 2006

Crystals of thioformaldehyde trimer, (CH2S)3 are orthorhombic, space group Pmn21 with a = 7.697 Å [Formula: see text], b = 7.067 Å [Formula: see text], c = 5.323 Å [Formula: see text]. There are two molecules in the unit cell with sulfur and carbon atoms in positions (4b) and (2a). The atomic parameters for sulfur and carbon have been determined from a three-dimensional analysis using observed and calculated differential syntheses with isotropic temperature factors. No absorption corrections were applied to the intensity data and no attempt has been made to establish the hydrogen positions. The final discrepancy index is R = 0.093. The molecule has the chair configuration and shows no significant difference between the lengths of any S—C bonds. The mean S—C bond distance is 1.818 Å and the standard deviation of the mean is 0.003 Å. This value is in good agreement with the commonly accepted value of 1.817 ± 0.005 Å for the S—C paraffinic bond.
Mass-spectrometric investigation of reaction of oxygen atoms with methane
Authors: Wong Edgar L. , Potter Andrew E. 
Published: May 2006

A mass-spectrometric stirred-reactor technique was used to study the reaction of atomic oxygen with methane with low concentrations of molecular oxygen. An overall rate constant for oxygen-atom disappearance due to added methane was obtained for the temperature range 375 to 576°K. This rate constant was 4 × 1014 exp (− 10 000/RT) cm3 mole−1 s−1 and was compared with a previous rate constant for this reaction that had been measured in the presence of a large excess of molecular oxygen. This comparison showed that the presence of an excess of molecular oxygen produced a considerable increase in oxygen-atom consumption at low temperatures, but only a small increase at high temperatures. From product analyses, the stoichiometry of the reaction could be approximately represented by [Formula: see text]From the reaction stoichiometry and the rate constant for the oxygen-atom disappearance, the rate constant for methane disappearance was calculated to be 1 × 1014 exp (− 10 000/RT) cm3 mole−1 s−1. The presence of excess molecular oxygen has very little effect on this rate constant, contrary to the result found for the disappearance of atomic oxygen.
Absolute rate constants for hydrocarbon autoxidation. VI. Alkyl aromatic and olefinic hydrocarbons
Authors: Howard J. A. , Ingold K. U. 
Published: May 2006

Absolute rate constants have been measured for the autoxidation of a large number of hydrocarbons at 30 °C. The chain-propagating and chain-terminating rate constants depend on the structure of the hydrocarbon and also on the structure of the chain-carrying peroxy radical. With certain notable exceptions which are mainly due to steric hindrance, the rate constants for hydrogen-atom abstraction increase in the order primary < secondary < tertiary; and, for compounds losing a secondary hydrogen atom, the rate constants increase in the order unactivated < acyclic activated by a single π-electron system < cyclic activated by a single Π-system < acyclic activated by two π-systems < cyclic activated by two π-systems. The rate constants for chain termination by the self-reaction of two peroxy radicals generally increase in the order tertiary peroxy radicals < acyclic allylic secondary  [Formula: see text] cyclic secondary  [Formula: see text] acyclic benzylic secondary < primary peroxy radicals < hydroperoxy radicals.
Mercury-photosensitized reactions in the presence of CO: decomposition of ethylenimine
Authors: Jones A. , Lossing F. P. 
Published: May 2006

The effect of CO addition on a number of Hg(3P1) photosensitized decompositions, under conditions of incomplete quenching, has been investigated. Compounds having large quenching cross sections (i.e. those presumably decomposing through formation of triplet excited states) have enhanced rates of decomposition in the presence of CO. Those having small cross sections (i.e. those for which the primary interaction is presumably the direct attack of Hg(3P1) atom on a C—H bond) show no enhancement. This difference in behavior, which is interpreted in terms of activation by a HgCO* complex, suggests that CO addition under the appropriate conditions can be used to decide whether or not certain decomposition products aries from an electronically excited precursor. For example, the effect of CO on the sensitized decomposition of ethylenimine indicates that the major dissociation process to form C2H4and the NH radical proceeds by way of an electronically excited precursor, while a minor process (5%) to form[Formula: see text] radical and a H-atom does not. Some results on the sensitized decomposition of formaldehyde are also discussed.