bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cadmium Toxicity in Glutathione Mutants ofEscherichia coli
Authors: Helbig Kerstin , Grosse Cornelia , Nies Dietrich H. 
Published: June 2008

ABSTRACTThe higher affinity of Cd2+for sulfur compounds than for nitrogen and oxygen led to the theoretical consideration that cadmium toxicity should result mainly from the binding of Cd2+to sulfide, thiol groups, and sulfur-rich complex compounds rather than from Cd2+replacement of transition-metal cations from nitrogen- or oxygen-rich biological compounds. This hypothesis was tested by usingEscherichia colifor a global transcriptome analysis of cells synthesizing glutathione (GSH; wild type), γ-glutamylcysteine (ΔgshBmutant), or neither of the two cellular thiols (ΔgshAmutant). The resulting data, some of which were validated by quantitative reverse transcription-PCR, were sorted using the KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology system, which groups genes hierarchically with respect to the cellular functions of their respective products. The main difference among the three strains concerned tryptophan biosynthesis, which was up-regulated in wild-type cells upon cadmium shock and strongly up-regulated in ΔgshAcells but repressed in ΔgshBcells containing γ-glutamylcysteine instead of GSH. Overall, however, all threeE. colistrains responded to cadmium shock similarly, with the up-regulation of genes involved in protein, disulfide bond, and oxidative damage repair; cysteine and iron-sulfur cluster biosynthesis; the production of proteins containing sensitive iron-sulfur clusters; the storage of iron; and the detoxification of Cd2+by efflux. General energy conservation pathways and iron uptake were down-regulated. These findings indicated that the toxic action of Cd2+indeed results from the binding of the metal cation to sulfur, lending support to the hypothesis tested.
Global Regulation by (p)ppGpp and CodY inStreptococcus mutans
Authors: Lemos José A. , Nascimento Marcelle M. , Lin Vanessa K. , Abranches Jacqueline , Burne Robert A. 
Published: June 2008

ABSTRACTThe RelA, RelP, and RelQ enzymes are responsible for the production of the alarmone (p)ppGpp inStreptococcus mutans. A strain lacking all three synthetases (ΔrelAPQ) does not grow in minimal medium lacking the branched-chain amino acids (BCAA) leucine or valine but grows well if isoleucine is also omitted. Here, we investigated whether there was a correlation between growth in the absence of leucine and valine with (p)ppGpp pools and the activation of CodY. By using a combination of single, double, and triple mutants lacking the (p)ppGpp synthetase enzymes, we demonstrated that the ability to grow in the absence of leucine or valine required basal levels of (p)ppGpp production by RelP and RelQ. The introduction of acodYmutation into the ΔrelAPQstrain fully restored growth in medium lacking leucine or valine, revealing that the growth-defective phenotype of ΔrelAPQwas directly linked to CodY. Lowering GTP levels through the addition of decoyinine did not alleviate CodY repression or affect the expression of genes involved in BCAA biosynthesis, suggesting thatS. mutansCodY is not activated by GTP. The results of phenotypic studies revealed that thecodYmutant had a reduced capacity to form biofilms and that its growth was more sensitive to low pH, showing a role for CodY in two key virulence properties ofS. mutans. Microarray results revealed the extent of the CodY regulon. Notably, the identification of putative CodY-binding boxes upstream of genes that were downregulated in thecodYmutant indicates that CodY may also function as a transcriptional activator inS. mutans.
Virulence Gene Expression Is Independent of ResDE-Regulated Respiration Control inBacillus anthracis
Authors: Wilson Adam C. , Hoch James A. , Perego Marta 
Published: June 2008

ABSTRACTThe ResDE two-component system regulates the synthesis of several components of the aerobic and anaerobic respiratory pathways in bacilli. The ResD response regulator transcription factor has been implicated in the regulation of virulence factors in a number of gram-positive species, includingBacillus anthracis. The precise deletions ofresDandresEinB. anthracisthat retained the classical respiratory phenotypes did not affect the expression of the gene for the protective antigen of the anthrax toxin,pagA, or that of the toxin regulator,atxA. The results indicate that the loss of ResDE-controlled respiratory capacity does not affect the synthesis of anthrax toxin.
Relative Quantitative Comparisons of the Extracellular Protein Profiles ofStaphylococcus aureusUAMS-1 and ItssarA,agr, andsarA agrRegulatory Mutants Using One-Dimensional Polyacrylamide Gel Electrophoresis and Nanocapillary Liquid Chromatography Coupled with Tandem Mass Spectrometry
Authors: Jones Richard C. , Deck Joanna , Edmondson Ricky D. , Hart Mark E. 
Published: June 2008

ABSTRACTOne-dimensional polyacrylamide gel electrophoresis followed by nanocapillary liquid chromatography coupled with mass spectrometry was used to analyze proteins isolated fromStaphylococcus aureusUAMS-1 after 3, 6, 12, and 24 h of in vitro growth. Protein abundance was determined using a quantitative value termed normalized peptide number, and overall, proteins known to be associated with the cell wall were more abundant early on in growth, while proteins known to be secreted into the surrounding milieu were more abundant late in growth. In addition, proteins from spent media and cell lysates of strain UAMS-1 and its isogenicsarA,agr, andsarA agrregulatory mutant strains during exponential growth were identified, and their relative abundances were compared. Extracellular proteins known to be regulated by the global regulatorssarAandagrdisplayed protein levels in accordance with what is known regarding the effects of these regulators. For example, cysteine protease (SspB), endopeptidase (SspA), staphopain (ScpA), and aureolysin (Aur) were higher in abundance in thesarAandsarA agrmutants than in strain UAMS-1. The immunoglobulin G (IgG)-binding protein (Sbi), immunodominant staphylococcal antigen A (IsaA), IgG-binding protein A (Spa), and the heme-iron-binding protein (IsdA) were most abundant in theagrmutant background. Proteins whose abundance was decreased in thesarAmutant included fibrinogen-binding protein (Fib [Efb]), IsaA, lipase 1 and 2, and two proteins identified as putative leukocidin F and S subunits of the two-component leukotoxin family. Collectively, this approach identified 1,263 proteins (matches of two peptides or more) and provided a convenient and reliable way of identifying proteins and comparing their relative abundances.
Burkholderia pseudomallei,B. thailandensis, andB. ambifariaProduce 4-Hydroxy-2-Alkylquinoline Analogues with a Methyl Group at the 3 Position That Is Required for Quorum-Sensing Regulation
Authors: Vial Ludovic , Lépine François , Milot Sylvain , Groleau Marie-Christine , Dekimpe Valérie , Woods Donald E. , Déziel Eric 
Published: June 2008

ABSTRACT4-Hydroxy-2-alkylquinolines (HAQs), especially 3,4-dihydroxy-2-heptylquinoline (Pseudomonasquinolone signal) and its precursor, 4-hydroxy-2-heptylquinoline, are attracting much attention, mainly because of their role as signaling molecules inPseudomonas aeruginosa. ThepqsABCDEoperon is centrally involved in their biosynthesis. The presence of a homologous operon inBurkholderia pseudomalleiandB. thailandensiswas recently reported. Thus, we have investigated the abilities of 11Burkholderiaspecies to produce HAQ-like molecules by liquid chromatography/mass spectrometry. We have identified 29 different HAQ derivatives produced by the only threeBurkholderiaspecies where apqsABCDEhomologue was found among available sequencedBurkholderiaspecies genomes, includingB. ambifaria, a member of theBurkholderia cepaciacomplex. In contrast with those ofP. aeruginosa,BurkholderiaHAQs typically bear a methyl group, hence their designation as 4-hydroxy-3-methyl-2-alkylquinolines (HMAQs). We identified three families of HMAQs with a saturated or unsaturated alkyl chain at the 2′ position, in contrast with the 1′ position ofP. aeruginosa, including one with anN-oxide group. Furthermore, the operon in these species contains two more genes downstream of thepqsEhomologue, resulting in thehmqABCDEFGoperon. While the inactivation ofhmqAinhibits the production of HMAQs, the methylation of the quinoline ring requires a putative methyltransferase encoded byhmqG. Interestingly,hmqAorhmqGmutations increase the production of acyl homoserine lactones and, consequently, phenotypes under the control of quorum sensing inB. ambifaria: antifungal activity, siderophore production, and proteolytic activity. These results indicate that only HAQs bearing a methyl group (HMAQs) are involved in quorum-sensing regulation.
Anaerobic Degradation of
p
-Ethylphenol by “
Aromatoleum aromaticum
” Strain EbN1: Pathway, Regulation, and Involved Proteins
Authors: Wöhlbrand Lars , Wilkes Heinz , Halder Thomas , Rabus Ralf 
Published: June 2008

ABSTRACT

The denitrifying “
Aromatoleum aromaticum
” strain EbN1 was demonstrated to utilize
p
-ethylphenol under anoxic conditions and was suggested to employ a degradation pathway which is reminiscent of known anaerobic ethylbenzene degradation in the same bacterium: initial hydroxylation of
p
-ethylphenol to 1-(4-hydroxyphenyl)-ethanol followed by dehydrogenation to
p
-hydroxyacetophenone. Possibly, subsequent carboxylation and thiolytic cleavage yield
p
-hydroxybenzoyl-coenzyme A (CoA), which is channeled into the central benzoyl-CoA pathway. Substrate-specific formation of three of the four proposed intermediates was confirmed by gas chromatographic-mass spectrometric analysis and also by applying deuterated
p
-ethylphenol. Proteins suggested to be involved in this degradation pathway are encoded in a single large operon-like structure (∼15 kb). Among them are a
p
-cresol methylhydroxylase-like protein (PchCF), two predicted alcohol dehydrogenases (ChnA and EbA309), a biotin-dependent carboxylase (XccABC), and a thiolase (TioL). Proteomic analysis (two-dimensional difference gel electrophoresis) revealed their specific and coordinated upregulation in cells adapted to anaerobic growth with
p
-ethylphenol and
p
-hydroxyacetophenone (e.g., PchF up to 29-fold). Coregulated proteins of currently unknown function (e.g., EbA329) are possibly involved in
p
-ethylphenol- and
p
-hydroxyacetophenone-specific solvent stress responses and related to other aromatic solvent-induced proteins of strain EbN1.
Effects of pH and Temperature on the Composition of Polar Lipids in
Thermoplasma acidophilum
HO-62
Authors: Shimada Haruo , Nemoto Naoki , Shida Yasuo , Oshima Tairo , Yamagishi Akihiko 
Published: June 2008

ABSTRACT

Thermoplasma acidophilum
HO-62 was grown at different pHs and temperatures, and its polar lipid compositions were determined. Although the number of cyclopentane rings in the caldarchaeol moiety increased when
T. acidophilum
was cultured at high temperature, the number decreased at low pHs. Glycolipids, phosphoglycolipids, and phospholipids were analyzed by high-performance liquid chromatography with an evaporative light-scattering detector. The amount of caldarchaeol with more than two sugar units on one side increased under low-pH and high-temperature conditions. The amounts of glycolipids increased and those of phosphoglycolipids decreased under these conditions. The proton permeability of the liposomes obtained from the phosphoglycolipids that contained two or more sugar units was lower than that of the liposomes obtained from the phosphoglycolipids that contained one sugar unit. From these results, we propose the hypothesis that
T. acidophilum
adapts to low pHs and high temperatures by extending sugar chains on their cell surfaces, as well as by varying the number of cyclopentane rings.
Identification of a Putative Acetyltransferase Gene, MMP0350, Which Affects Proper Assembly of both Flagella and Pili in the ArchaeonMethanococcus maripaludis
Authors: VanDyke David J. , Wu John , Ng Sandy Y. M. , Kanbe Masaomi , Chaban Bonnie , Aizawa Shin-Ichi , Jarrell Ken F. 
Published: June 2008

ABSTRACTGlycosylation is a posttranslational modification utilized in all three domains of life. Compared to eukaryotic and bacterial systems, knowledge of the archaeal processes involved in glycosylation is limited. Recently,Methanococcus voltaeflagellin proteins were found to have an N-linked trisaccharide necessary for proper flagellum assembly. Current analysis by mass spectrometry ofMethanococcus maripaludisflagellin proteins also indicated the attachment of an N-glycan containing acetylated sugars. To identify genes involved in sugar biosynthesis inM. maripaludis, a putative acetyltransferase was targeted for in-frame deletion. Deletion of this gene (MMP0350) resulted in a flagellin molecular mass shift to a size comparable to that expected for underglycosylated or completely nonglycoslyated flagellins, as determined by immunoblotting. Assembled flagellar filaments were not observed by electron microscopy. Interestingly, the deletion also resulted in defective pilus anchoring. Mutant cells with a deletion of MMP0350 had very few, if any, pili attached to the cell surface compared to a nonflagellated but piliated strain. However, pili were obtained from culture supernatants of this strain, indicating that the defect was not in pilus assembly but in stable attachment to the cell surface. Complementation of MMP0350 on a plasmid restored pilus attachment, but it was unable to restore flagellation, likely because the mutant ceased to make detectable flagellin. These findings represent the first report of a biosynthetic gene involved in flagellin glycosylation in archaea. Also, it is the first gene to be associated with pili, linking flagellum and pilus structure and assembly through posttranslational modifications.
TheBradyrhizobium japonicumIrr Protein Is a Transcriptional Repressor with High-Affinity DNA-Binding Activity
Authors: Sangwan Indu , Small Sandra K. , O'Brian Mark R. 
Published: June 2008

ABSTRACTThe Irr protein is a global regulator of iron homeostasis inBradyrhizobium japonicum, and a subset of genes within the Irr regulon are negatively controlled under iron limitation. However, repressor function, high-affinity DNA binding in vitro, or promoter occupancy in vivo of Irr for a negatively regulated gene has not been demonstrated. Here, we show that the blr7895 and bll6680 genes are negatively regulated by Irr as determined by derepression of transcript levels in iron-limited cells of anirrmutant strain. Electrophoretic gel mobility shift analysis showed that a component in extracts of wild-type cells grown under iron limitation bound the iron control elements (ICE) within the promoters of blr7895 and bll6680 identified previously (G. Rudolph, G. Semini, F. Hauser, A. Lindemann, M. Friberg, H. Hennecke, and H. M. Fischer, J. Bacteriol. 188:733-744, 2006). Binding was not observed with extracts of cells from the parent strain grown under high iron conditions or with those from anirrmutant. Furthermore, gel mobility supershift experiments identified Irr as a component of the binding complex. Purified recombinant Irr bound to ICE DNA with high affinity in the presence of divalent metal, withKdvalues of 7 to 19 nM, consistent with a physiological role for Irr as a transcriptional regulator. In addition, in vitro transcription initiated from the blr7895 promoter was inhibited by Irr. Whole-cell cross-linking and immunoprecipitation experiments showed that Irr occupies the promoters of blr7895 and bll6680 in vivo in an iron-dependent manner. The findings demonstrate that Irr is a transcriptional repressor that binds DNA with high affinity.
Autoregulation of AbsB (RNase III) Expression in
Streptomyces coelicolor
by Endoribonucleolytic Cleavage of
absB
Operon Transcripts
Authors: Xu Weijing , Huang Jianqiang , Cohen Stanley N. 
Published: June 2008

ABSTRACT

The
Streptomyces coelicolor absB
gene encodes an RNase III family endoribonuclease and is normally essential for antibiotic biosynthesis. Here we report that AbsB controls its own expression by sequentially and site specifically cleaving stem-loop segments of its polycistronic transcript. Our results demonstrate a ribonucleolytic regulatory role for AbsB in vivo.
Genome Sequence of the Chemolithoautotrophic Bacterium
Oligotropha carboxidovorans
OM5
T
Authors: Paul Debarati , Bridges Susan , Burgess Shane C. , Dandass Yoginder , Lawrence Mark L. 
Published: June 2008

ABSTRACT

Oligotropha carboxidovorans
OM5
T
(DSM 1227, ATCC 49405) is a chemolithoautotrophic bacterium with the capability to utilize carbon monoxide, carbon dioxide, and hydrogen. It is also capable of heterotrophic growth under appropriate environmental conditions. Here we report the annotated genome sequence of the circular chromosome of this organism.
Identification of Genes Involved in Inversion of Stereochemistry of a C-12 Hydroxyl Group in the Catabolism of Cholic Acid by
Comamonas testosteroni
TA441
Authors: Horinouchi Masae , Hayashi Toshiaki , Koshino Hiroyuki , Malon Michal , Yamamoto Takako , Kudo Toshiaki 
Published: June 2008

ABSTRACT

Comamonas testosteroni
TA441 degrades steroids such as testosterone via aromatization of the A ring, followed by
meta
-cleavage of the ring. In the DNA region upstream of the
meta
-cleavage enzyme gene
tesB
, two genes required during cholic acid degradation for the inversion of an α-oriented hydroxyl group on C-12 were identified. A dehydrogenase, SteA, converts 7α,12α-dihydroxyandrosta-1,4-diene-3,17-dione to 7α-hydroxyandrosta-1,4-diene-3,12,17-trione, and a hydrogenase, SteB, converts the latter to 7α,12β-dihydroxyandrosta-1,4-diene-3,17-dione. Both enzymes are members of the short-chain dehydrogenase/reductase superfamily. The transformation of 7α,12α-dihydroxyandrosta-1,4-diene-3,17-dione to 7α,12β-dihydroxyandrosta-1,4-diene-3,17-dione is carried out far more effectively when both SteA and SteB are involved together. These two enzymes are encoded by two adjacent genes and are presumed to be expressed together. Inversion of the hydroxyl group at C-12 is indispensable for the subsequent effective B-ring cleavage of the androstane compound. In addition to the compounds already mentioned, 12α-hydroxyandrosta-1,4,6-triene-3,17-dione and 12β-hydroxyandrosta-1,4,6-triene-3,17-dione were identified as minor intermediate compounds in cholic acid degradation by
C. testosteroni
TA441.
Vo2requirement at different displayed power outputs on five cycle ergometer models: a preliminary study
Authors: Guiraud T , Léger L , Long A , Thébault N , Tremblay J , Passelergue P 
Published: June 2008

Background and aimsThe validity of five brands of cycle ergometers was evaluated by the comparison of the Vo2requirements at different displayed power.Methods and resultsFive physically active men performed a continuous incremental exercise test on five ergometers (Ergomeca, Lifecycle, Monark, Polar S710 and CompuTrainer). The latter was also compared with a standard dynamometer in order to associate Vo2values with the real power. Every test started with a 5-min warm-up on the same cycle ergometer (Ergomeca) at 100 W to make sure that the Vo2differences do not come from Vo2measurement error. Only last minute steady-state Vo2values of each 2-min stage were used for the Vo2–watt curve. Large differences (5– 10 ml kg−1min−1) at the same displayed power indicate inaccuracy of displayed power output (PO). Using corrected power values from the dynamometer revealed that for the same Vo2the CompuTrainer underestimates PO by ∼30 W between 100 and 300 W, whereas the Lifecycle overestimate it by 3–53 W from 100 to 300 W. The Monark and Polar S710 underestimate PO by 15 W and the Ergomeca by ∼5 W.ConclusionInaccuracies between −10% and 18% in displayed PO of various cycle ergometers question their interchangeability.
Analysing the protective potential of padded soccer goalkeeper shorts
Authors: Schmitt K U , Nusser M , Derler S , Boesiger P 
Published: June 2008

ObjectiveIn this study, the potential of currently available padded soccer goalkeeper shorts to prevent hip injuries sustained in side jumps was investigated.DesignWithin the scope of this study, a survey among professional and amateur goalkeepers, trainers and the medical staff was performed. In addition, commercially available shorts were impact-tested using an artificial hip model. The results were compared with requirements established for hip protectors for elderly.ResultsThe results of the survey found that contusions and abrasions were observed most often for all players. Fractures and arthritis were only reported by amateur players, whereas bursitis was more frequently observed by professional players. Amateurs have a significantly higher risk of injury than professional players, and the higher injury risk during training is significantly higher compared with the injury risk during a match. No difference of the injury risk was found between goalkeepers wearing padded shorts and those who did not.Impact tests indicated a wide range of performance of the currently available products. The padded shorts generally reduce impact forces, but mostly perform poorly. Only shorts that were made of visco-elastic foam fulfilled the basic requirements requested for hip protectors for elderly.ConclusionsThe quality of most of the currently available goalkeeper shorts needs to be improved to effectively prevent hip injury sustained in side jumps.
Ad libitum adjustments to fluid intake during cool environmental conditions maintain hydration status during a 3-day mountain bike race
Authors: Rose S , Peters-Futre E M 
Published: June 2008

ObjectiveIn this study, the hydration status of amateur cyclists who voluntarily adjusted their fluid intake to environmental conditions during a 3-day, 248-km mountain bike (MTB) race was assessed.DesignProspective observational field study.SettingSani2C MTB Race, KwaZulu-Natal, South Africa, 2006.Participants18 randomly selected amateur, male MTB cyclists.Main outcome measuresReported usual fluid intake, environmental conditions, voluntary fluid intake, urine voided, changes in body mass, serum osmolality (SO), sodium concentration [Na+] and urinary specific gravity (Usg) during each stage (S).ResultsDry bulb temperature (adjusted for windchill) ranged from 6° to 21.4°C during S1, S2 and S3. While 77.8% (n = 14) of subjects reported a usual intake of >750 ml h−1in previous MTB events, mean (SE) fluid intake in this race ranged from 341 (32) ml h−1during S1 to 551 (56) ml h−1during S3. Changes in mean body mass ranged between −0.99% and −2.02% during the three stages. Mean SO and serum [Na+] ranged between 292 (0.73) mOsm kg−1and 298 mOsm kg−1and 137 (0.35) mEq and 140 (0.42) mEq, respectively, during the 3-day period, while Usg remained ≤1.025.ConclusionAd libitum fluid intake during the 2006 Sani2C MTB Race, which took place in unexpectedly cold environmental conditions, was substantially lower than the usual reported fluid intake of subjects. Changes in body mass, SO, serum [Na+] and Usg were not clinically significant, indicating that an adequate hydration status was maintained during the multiday MTB cycle race.